{"id":3925,"date":"2017-06-08T10:26:21","date_gmt":"2017-06-08T10:26:21","guid":{"rendered":"http:\/\/acgt.cs.tau.ac.il\/?page_id=3925"},"modified":"2023-01-23T14:02:30","modified_gmt":"2023-01-23T14:02:30","slug":"previous-years-publications","status":"publish","type":"page","link":"https:\/\/acgt.cs.tau.ac.il\/?page_id=3925","title":{"rendered":"Previous years"},"content":{"rendered":"<h1>Publications<\/h1>\n<h2>Previous years<\/h2>\n<p>\t<a href=\"https:\/\/acgt.cs.tau.ac.il\/?page_id=3922\" target=\"_self\" role=\"button\" rel=\"noopener\"><br \/>\n\t\t\t\tGo to latest publications<br \/>\n\t\t\t<\/a><br \/>\n\t<form autocomplete=\"off\" name=\"wpv-filter-3714\" action=\"\/index.php?rest_route=%2Fwp%2Fv2%2Fpages%2F3925&#038;wpv_view_count=3714\" method=\"get\" class=\"wpv-filter-form js-wpv-filter-form js-wpv-filter-form-3714 js-wpv-form-full js-wpv-dps-enabled js-wpv-ajax-results-enabled\" data-viewnumber=\"3714\" data-viewid=\"3714\" 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class=\"panel-heading\">\n    <h3 class=\"panel-title\">Filter by year \/ search by key words<\/h3>\n  <\/div> \n  <div class=\"panel-body\"> \n    <div class=\"row\"> \n <form role=\"form\">\n  <div class=\"abc-checkbox\">\n<ul class=\"categorychecklist form-no-clear\"><li id=\"publication-year-198\"><label for=\"in-publication-year-198\" class=\"selectit\"><input type=\"checkbox\" id=\"in-publication-year-198\" class=\"js-wpv-filter-trigger\" name=\"wpv-publication-year[]\" value=\"1993\" \/> 1993<\/label><\/li>\n<li id=\"publication-year-197\"><label for=\"in-publication-year-197\" class=\"selectit\"><input type=\"checkbox\" id=\"in-publication-year-197\" class=\"js-wpv-filter-trigger\" name=\"wpv-publication-year[]\" value=\"1994\" \/> 1994<\/label><\/li>\n<li id=\"publication-year-196\"><label for=\"in-publication-year-196\" class=\"selectit\"><input type=\"checkbox\" id=\"in-publication-year-196\" class=\"js-wpv-filter-trigger\" name=\"wpv-publication-year[]\" value=\"1995\" \/> 1995<\/label><\/li>\n<li id=\"publication-year-195\"><label for=\"in-publication-year-195\" class=\"selectit\"><input type=\"checkbox\" id=\"in-publication-year-195\" class=\"js-wpv-filter-trigger\" name=\"wpv-publication-year[]\" value=\"1996\" \/> 1996<\/label><\/li>\n<li id=\"publication-year-194\"><label for=\"in-publication-year-194\" class=\"selectit\"><input type=\"checkbox\" id=\"in-publication-year-194\" class=\"js-wpv-filter-trigger\" name=\"wpv-publication-year[]\" value=\"1997\" \/> 1997<\/label><\/li>\n<li id=\"publication-year-193\"><label for=\"in-publication-year-193\" class=\"selectit\"><input type=\"checkbox\" id=\"in-publication-year-193\" class=\"js-wpv-filter-trigger\" name=\"wpv-publication-year[]\" value=\"1998\" \/> 1998<\/label><\/li>\n<li id=\"publication-year-192\"><label for=\"in-publication-year-192\" class=\"selectit\"><input type=\"checkbox\" id=\"in-publication-year-192\" class=\"js-wpv-filter-trigger\" name=\"wpv-publication-year[]\" value=\"1999\" \/> 1999<\/label><\/li>\n<li id=\"publication-year-191\"><label for=\"in-publication-year-191\" class=\"selectit\"><input type=\"checkbox\" id=\"in-publication-year-191\" class=\"js-wpv-filter-trigger\" name=\"wpv-publication-year[]\" value=\"2000\" \/> 2000<\/label><\/li>\n<li id=\"publication-year-190\"><label for=\"in-publication-year-190\" class=\"selectit\"><input type=\"checkbox\" id=\"in-publication-year-190\" class=\"js-wpv-filter-trigger\" name=\"wpv-publication-year[]\" value=\"2001\" \/> 2001<\/label><\/li>\n<li id=\"publication-year-189\"><label for=\"in-publication-year-189\" class=\"selectit\"><input type=\"checkbox\" id=\"in-publication-year-189\" class=\"js-wpv-filter-trigger\" name=\"wpv-publication-year[]\" value=\"2002\" \/> 2002<\/label><\/li>\n<li id=\"publication-year-188\" class=\"popular-category\"><label for=\"in-publication-year-188\" class=\"selectit\"><input type=\"checkbox\" id=\"in-publication-year-188\" class=\"js-wpv-filter-trigger\" name=\"wpv-publication-year[]\" value=\"2003\" \/> 2003<\/label><\/li>\n<li id=\"publication-year-187\" class=\"popular-category\"><label for=\"in-publication-year-187\" class=\"selectit\"><input type=\"checkbox\" id=\"in-publication-year-187\" class=\"js-wpv-filter-trigger\" name=\"wpv-publication-year[]\" value=\"2004\" \/> 2004<\/label><\/li>\n<li id=\"publication-year-186\" class=\"popular-category\"><label for=\"in-publication-year-186\" class=\"selectit\"><input type=\"checkbox\" id=\"in-publication-year-186\" class=\"js-wpv-filter-trigger\" name=\"wpv-publication-year[]\" value=\"2005\" \/> 2005<\/label><\/li>\n<li id=\"publication-year-185\" class=\"popular-category\"><label for=\"in-publication-year-185\" class=\"selectit\"><input type=\"checkbox\" id=\"in-publication-year-185\" class=\"js-wpv-filter-trigger\" name=\"wpv-publication-year[]\" value=\"2006\" \/> 2006<\/label><\/li>\n<li id=\"publication-year-184\" class=\"popular-category\"><label for=\"in-publication-year-184\" class=\"selectit\"><input type=\"checkbox\" id=\"in-publication-year-184\" class=\"js-wpv-filter-trigger\" name=\"wpv-publication-year[]\" value=\"2007\" \/> 2007<\/label><\/li>\n<li id=\"publication-year-183\" class=\"popular-category\"><label for=\"in-publication-year-183\" class=\"selectit\"><input type=\"checkbox\" id=\"in-publication-year-183\" class=\"js-wpv-filter-trigger\" name=\"wpv-publication-year[]\" value=\"2008\" \/> 2008<\/label><\/li>\n<li id=\"publication-year-182\" class=\"popular-category\"><label for=\"in-publication-year-182\" class=\"selectit\"><input type=\"checkbox\" id=\"in-publication-year-182\" class=\"js-wpv-filter-trigger\" name=\"wpv-publication-year[]\" value=\"2009\" \/> 2009<\/label><\/li>\n<li id=\"publication-year-181\" class=\"popular-category\"><label for=\"in-publication-year-181\" class=\"selectit\"><input type=\"checkbox\" id=\"in-publication-year-181\" class=\"js-wpv-filter-trigger\" name=\"wpv-publication-year[]\" value=\"2010\" \/> 2010<\/label><\/li>\n<li id=\"publication-year-180\"><label for=\"in-publication-year-180\" class=\"selectit\"><input type=\"checkbox\" id=\"in-publication-year-180\" class=\"js-wpv-filter-trigger\" name=\"wpv-publication-year[]\" value=\"2011\" \/> 2011<\/label><\/li>\n<li id=\"publication-year-179\"><label for=\"in-publication-year-179\" class=\"selectit\"><input type=\"checkbox\" id=\"in-publication-year-179\" class=\"js-wpv-filter-trigger\" name=\"wpv-publication-year[]\" value=\"2012\" \/> 2012<\/label><\/li>\n<li id=\"publication-year-178\"><label for=\"in-publication-year-178\" class=\"selectit\"><input type=\"checkbox\" id=\"in-publication-year-178\" class=\"js-wpv-filter-trigger\" name=\"wpv-publication-year[]\" value=\"2013\" \/> 2013<\/label><\/li>\n<li id=\"publication-year-177\"><label for=\"in-publication-year-177\" class=\"selectit\"><input type=\"checkbox\" id=\"in-publication-year-177\" class=\"js-wpv-filter-trigger\" name=\"wpv-publication-year[]\" value=\"2014\" \/> 2014<\/label><\/li>\n<li id=\"publication-year-176\"><label for=\"in-publication-year-176\" class=\"selectit\"><input type=\"checkbox\" id=\"in-publication-year-176\" class=\"js-wpv-filter-trigger\" name=\"wpv-publication-year[]\" value=\"2015\" \/> 2015<\/label><\/li>\n<li id=\"publication-year-175\" class=\"popular-category\"><label for=\"in-publication-year-175\" class=\"selectit\"><input type=\"checkbox\" id=\"in-publication-year-175\" class=\"js-wpv-filter-trigger\" name=\"wpv-publication-year[]\" value=\"2016\" \/> 2016<\/label><\/li>\n<li id=\"publication-year-174\" class=\"popular-category\"><label for=\"in-publication-year-174\" class=\"selectit\"><input type=\"checkbox\" id=\"in-publication-year-174\" class=\"js-wpv-filter-trigger\" name=\"wpv-publication-year[]\" value=\"2017\" \/> 2017<\/label><\/li>\n<li id=\"publication-year-222\"><label for=\"in-publication-year-222\" class=\"selectit\"><input type=\"checkbox\" id=\"in-publication-year-222\" class=\"js-wpv-filter-trigger\" name=\"wpv-publication-year[]\" value=\"2018\" \/> 2018<\/label><\/li>\n<li id=\"publication-year-230\"><label for=\"in-publication-year-230\" class=\"selectit\"><input type=\"checkbox\" id=\"in-publication-year-230\" class=\"js-wpv-filter-trigger\" name=\"wpv-publication-year[]\" value=\"2019\" \/> 2019<\/label><\/li>\n<li id=\"publication-year-285\"><label for=\"in-publication-year-285\" class=\"selectit\"><input type=\"checkbox\" id=\"in-publication-year-285\" class=\"js-wpv-filter-trigger\" name=\"wpv-publication-year[]\" value=\"2020\" \/> 2020<\/label><\/li>\n<li id=\"publication-year-286\"><label for=\"in-publication-year-286\" class=\"selectit\"><input type=\"checkbox\" id=\"in-publication-year-286\" class=\"js-wpv-filter-trigger\" name=\"wpv-publication-year[]\" value=\"2021\" \/> 2021<\/label><\/li>\n<li id=\"publication-year-287\"><label for=\"in-publication-year-287\" class=\"selectit\"><input type=\"checkbox\" id=\"in-publication-year-287\" class=\"js-wpv-filter-trigger\" name=\"wpv-publication-year[]\" value=\"2022\" \/> 2022<\/label><\/li>\n<li id=\"publication-year-288\"><label for=\"in-publication-year-288\" class=\"selectit\"><input type=\"checkbox\" id=\"in-publication-year-288\" class=\"js-wpv-filter-trigger\" name=\"wpv-publication-year[]\" value=\"2023\" \/> 2023<\/label><\/li>\n<li id=\"publication-year-292\"><label for=\"in-publication-year-292\" class=\"selectit\"><input type=\"checkbox\" id=\"in-publication-year-292\" class=\"js-wpv-filter-trigger\" name=\"wpv-publication-year[]\" value=\"2024\" \/> 2024<\/label><\/li>\n<li id=\"publication-year-298\"><label for=\"in-publication-year-298\" class=\"selectit\"><input type=\"checkbox\" id=\"in-publication-year-298\" class=\"js-wpv-filter-trigger\" name=\"wpv-publication-year[]\" value=\"2025\" \/> 2025<\/label><\/li>\n<li id=\"publication-year-304\"><label for=\"in-publication-year-304\" class=\"selectit\"><input type=\"checkbox\" id=\"in-publication-year-304\" class=\"js-wpv-filter-trigger\" name=\"wpv-publication-year[]\" value=\"2026\" \/> 2026<\/label><\/li>\n<\/ul> \n       \n  <\/div>\n<\/form>\n    <div class=\"row\">\n      <div class=\"col-xs-5 col-sm-7 col-md-4\">\n     <input type=\"text\" name=\"wpv_post_search\"  class=\"js-wpv-filter-trigger-delayed faculty-search\" style=\"faculty-search-style\" \/>\n      <\/div>\n      <div class=\"col-xs-2 col-sm-3 col-md-2\">\n        <input type=\"submit\" class=\"btn btn-default wpv-submit-trigger js-wpv-submit-trigger\" name=\"wpv_filter_submit\" value=\"Search\" \/>\n      <\/div>\n      \n        <div class=\"col-xs-2 col-sm-1 col-md-2\">\n         <button type=\"button\" class=\"btn btn-default wpv-reset-trigger js-wpv-reset-trigger\" style=\"all-button\">Reset<\/button><\/div>\n            \n          <div class=\"col-xs-4 col-sm-1 col-md-4\">\n  <div style=\"display:none\" class=\"js-wpv-dps-spinner\"><button class=\"btn btn-default\"><span class=\"glyphicon glyphicon-refresh 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data-permalink=\"\/index.php?rest_route=%2Fwp%2Fv2%2Fpages%2F3925&#038;wpv_view_count=3714\">\n\n\t\n\t\n\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/molecular_systems_biology-wpcf_80x100.jpg\" title=\"molecular_systems_biology\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Transcription factor family-specific DNA shape readout revealed by quantitative specificity models<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Yaron_910.full.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>L. Yang, Y. Orenstein, A. Jolma, Y. Yin, J. Taipale, R. Shamir and R. Rohs.<\/h4>\n     <a href=\"http:\/\/msb.embopress.org\/content\/13\/2\/910\"><em>Molecular Systems Biology, 13, 910, DOI 10.15252\/msb.20167238 (2017).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2019\/04\/bioinformatics_June_2015-wpcf_80x100.png\" title=\"bioinformatics_June_2015.png\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Improving the performance of minimizers and winnowing schemes<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2019\/04\/David_Pellow_btx235-1.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>G. Marcais, D. Pellow, D. Bork, Y. Orenstein, R. Shamir, C. Kingsford.<\/h4>\n     <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/28881970 \"><em>Bioinformatics, 15; 33(14): i110\u2013i117 (2017). <\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/oncogene_2017-wpcf_80x100.jpg\" title=\"oncogene_2017\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Utilizing somatic mutation data from numerous studies for cancer research: proof of concept and applications<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Didi_onc2016489a.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>D. Amar, S. Izraeli and R. Shamir.<\/h4>\n     <a href=\"http:\/\/www.nature.com\/onc\/journal\/vaop\/ncurrent\/full\/onc2016489a.html\"><em>Oncogene, doi:10.1038\/onc.2016.489 (2017).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/07\/bioinformatics-j-1-wpcf_80x100.jpg\" title=\"bioinformatics-j-1.jpg\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Recycler: an algorithm for detecting plasmids from de novo assembly graphs<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/029926.full.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>R. Rozov, A. Kav Brown, D. Bogumil, E. Halperin, I. Mizrahi, R. Shamir.<\/h4>\n     <a href=\"http:\/\/biorxiv.org\/content\/early\/2016\/02\/07\/029926\"><em>Bioinformatics, 10.1093\/bioinformatics\/btw651, 2016.<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Com_Bio-wpcf_80x100.jpg\" title=\"Com_Bio\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Sorting by cuts, joins and duplications<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/cmb_2E2016_2E0045.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>R. Zeira, R. Shamir.<\/h4>\n     <a href=\"http:\/\/link.springer.com\/chapter\/10.1007\/978-3-319-19929-0_34\"><em>Journal of Computational Biology Vol 23 No 0. pp 1-11 (2016).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/frontiers_in_genetics-wpcf_80x100.jpg\" title=\"frontiers_in_genetics\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Dissecting the effect of genetic variation on the hepatic expression of drug disposition genes across the collaborative cross mouse strains<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/fgene-07-00172.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>A. Nachshon, H. J. Abu-Toamih Atamni, R. Sheikh-Hamed, A. Dorman, R. Mott, J. C. Dohm, H. Lehrach, M. Sultan, R. Shamir, S. Sauer, H. Himmelbauer, F. A. Iraqi, I. Gat-Viks.<\/h4>\n     <a href=\"http:\/\/journal.frontiersin.org\/article\/10.3389\/fgene.2016.00172\/full?&#038;utm_source=Email_to_authors_&#038;utm_medium=Email&#038;utm_content=T1_11.5e1_author&#038;utm_campaign=Email_publication&#038;field=&#038;journalName=Frontiers_in_Genetics&#038;id=214342\"><em>Frontiers in Genetics Vol 7, Article 172, doi: 10.3389\/fgene.2016.00172 (2016).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Scientific_Reports-wpcf_80x100.jpg\" title=\"Scientific_Reports\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>SELMAP - SELEX affinity landscape MAPping of transcription factor binding sites using integrated microfluidics<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Yaron_scientific_reports_srep33351.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>D. Chen, Y. Orenstein, R. Golodnitsky, M. Pellach, D. Avrahami, C. Wachtel, A. Ovadia-Shochat, H. Shir-Shapira, A. Kedmi, T. Juven-Gershon, R. Shamir, D. Gerber.<\/h4>\n     <a href=\"http:\/\/www.nature.com\/articles\/srep33351\"><em>Scientific Reports 6, 33351; doi: 10.1038\/srep33351, 2016.<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/LNCS2016_algorithms-in-bioinformatics-wpcf_80x100.jpg\" title=\"LNCS2016_algorithms-in-bioinformatics\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Copy-Number Evolution Problems: Complexity and Algorithms<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Ron_Z_WABI_full_paper_with_appendix.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>M. El-Kebir, B. Raphael, R. Shamir, R. Sharan, S. Zaccaria, M. Zehavi, R. Zeira.<\/h4>\n     <a href=\"http:\/\/link.springer.com\/chapter\/10.1007\/978-3-319-43681-4_11\"><em>Proceedings of WABI 2016, Aarhus, Denmark, August, 2016, LNCS, 9838 pp. 137-149 (2016).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/LNCS2016_algorithms-in-bioinformatics-wpcf_80x100.jpg\" title=\"LNCS2016_algorithms-in-bioinformatics\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Compact universal k-mer hitting sets<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/David_P_compact_universal_k-mer_hitting_sets.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Y. Orenstein, D. Pellow, G. Marcais, R. Shamir, C. Kingsford.<\/h4>\n     <a href=\"http:\/\/link.springer.com\/chapter\/10.1007\/978-3-319-43681-4_21\"><em>Proceedings of WABI 2016, Aarhus, Denmark, August, 2016, LNCS, 9838 pp. 257--268 (2016).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/briefings_functional_genomics-wpcf_80x100.gif\" title=\"briefings_functional_genomics\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Modeling protein-DNA binding via high throughput in vitro technologies<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Yaron_Orenstein_bfgp.elw030.full.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Y. Orenstein, R. Shamir.<\/h4>\n     <a href=\"http:\/\/bfg.oxfordjournals.org\/cgi\/content\/full\/elw030?ijkey=IocabZNxUZIziHp&#038;keytype=ref\"><em>Briefings in Functional Genomics, doi: 10.1093\/bfgp\/elw030 (2016).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/PLOS_ONE-wpcf_80x87.jpg\" title=\"PLOS_ONE\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>RichMind: a tool for improved inference from large-scale neuroimaging results<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Adi_journal.pone.0159643.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>A. Maron-Katz, D. Amar, E. Ben-Simon, T. Hendler, R. Shamir.<\/h4>\n     <a href=\"http:\/\/journals.plos.org\/plosone\/article?id=10.1371%2Fjournal.pone.0159643\"><em>PLoS One, DOI:10.1371\/journal.pone.0159643 (2016).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Breast_Cancer_Research-wpcf_80x100.jpg\" title=\"Breast_Cancer_Research\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Expression and methylation signatures partition Luminal-A breast tumors into distinct prognostic subgroups<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Dvir_breast_cancer_research_Article_724.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>D. Netanely, A. Avraham, A. Ben-Baruch, E. Evron, R. Shamir<\/h4>\n     <a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC4936004\/\"><em>Breast Cancer Research, 18:74,DOI 10.1186\/s13058-016-0724-2 (2016). Erratum<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/lipics_Dagstuhl-wpcf_80x100.png\" title=\"lipics_Dagstuhl\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>A linear-time algorithm for the Copy Number Transformation Problem<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/RonZ_LIPIcs-CPM-2016-16.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>R. Shamir, M. Zehavi, R. Zeira<\/h4>\n     <a href=\"http:\/\/drops.dagstuhl.de\/opus\/volltexte\/2016\/6078\/\"><em>Proc. 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016), R. Grossi and M. Lewenstein (Editors), Dagstuhl, Germany, LIPIcs, vol. 54, pp. 16:1\u00d016:13.<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Genome_Research_April_2016-wpcf_80x100.jpg\" title=\"Genome_Research_April_2016\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Enhancer methylation dynamics contribute to cancer plasticity and patient mortality<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Rachel_Bell_gr.197194.115.full.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>R. E. Bell, T. Golan, D. Sheinboim, H. Malcov, D. Amar, A. Salamon, T. Liron, S. Gelfman, Y. Gabet, R. Shamir and C. Levy.<\/h4>\n     <a href=\"http:\/\/genome.cshlp.org\/content\/early\/2016\/04\/06\/gr.197194.115.abstract\"><em>Genome Research, 26 ( 5 ) pp. 601 - 611.<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Scientific_Reports-wpcf_80x100.jpg\" title=\"Scientific_Reports\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>A large-scale perspective on stress-induced alterations in resting-state networks<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Adi_srep21503.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>A. Maron-Katz, S. Vaisvaser, T. Lin, T. Hendler, R. Shamir.<\/h4>\n     <a href=\"http:\/\/www.nature.com\/articles\/srep21503\"><em>Scientific Reports, 6, Article number: 21503, doi:10.1038\/srep21503 (2016).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/cellular_molecular-wpcf_80x100.jpg\" title=\"cellular_molecular\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Evidence of TAF1 dysfunction in peripheral models of X-linked dystonia-parkinsonism.<\/h3>\n  <h4>A. Domingo, D. Amar, K. Gr\u009ftz, L. Lee, R. Rosales, N. Br\u009fggemann, R. D. Jamora, E. Cutiongco dela-Paz, K. Lohmann, R. Shamir, C. Klein, A. Westenberger.<\/h4>\n     <a href=\"http:\/\/link.springer.com\/article\/10.1007%2Fs00018-016-2159-4\"><em>Cellular and Molecular Life Sciences , DOI 10.1007\/s00018-016-2159-4 (2016).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/NAR_December2015-wpcf_80x100.gif\" title=\"NAR_December2015\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Integrated microfluidic approach for quantitative high-throughput measurements of transcription factor binding affinities.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/nar.gkv1327.full.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Y. Glick, Y. Orenstein, D. Chen, D. Avrahami, T. Zor, R. Shamir R, D. Gerber<\/h4>\n     <a href=\"http:\/\/nar.oxfordjournals.org\/content\/early\/2015\/12\/03\/nar.gkv1327.full\"><em>Nucl. Acids Res, doi: 10.1093\/nar\/gkv1327.<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/NAR_July2015-wpcf_80x100.jpg\" title=\"NAR_July2015\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Integrated analysis of numerous heterogeneous gene expression profiles for detecting robust disease-specific biomarkers and proposing drug targets<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Amar_7779.full.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>D. Amar, T. Hait, S. Izraeli and R. Shamir.<\/h4>\n     <a href=\"http:\/\/nar.oxfordjournals.org\/content\/43\/16\/7779\"><em>Nucleic Acids Research , 43 (16): 7779-7789, 2015.<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Transcription-wpcf_80x100.jpg\" title=\"Transcription\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>ElemeNT: a computational tool for detecting core promoter elements<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/ElemeNT_wFunding.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>A. Sloutskin, Y. M. Danino, Y. Zehavi, Y. Orenstein, T. Doniger, R. Shamir, T. Juven-Gershon<\/h4>\n     <a href=\"http:\/\/dx.doi.org\/10.1080\/21541264.2015.1067286\"><em>Transcription , 6:3, 41-50, 2015.<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/lncs-wpcf_80x100.jpg\" title=\"lncs\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Sorting by cuts, joins and and whole chromosome duplications<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/RonZeira_SCJD.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>R. Zeira and R. Shamir<\/h4>\n     <a href=\"http:\/\/link.springer.com\/chapter\/10.1007\/978-3-319-19929-0_34\"><em>Proceedings of CPM 2015, Ischia Island, Italy, June 2015. (F. Cicalese, E. Porat, U. Vaccaro, editors) LNCS , Vol 9133, pp 396-409, 2015.<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/BioRxiv-wpcf_80x100.jpg\" title=\"BioRxiv\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>HTS-IBIS: fast and accurate inference of binding site motifs from HT-SELEX data<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Yaron_bioRxiv_022277.full.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Y. Orenstein and R. Shamir<\/h4>\n     <a href=\"http:\/\/dx.doi.org\/10.1101\/022277\"><em>BioRxiv , doi.org\/10.1101\/022277, 2015.<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/development_July15-wpcf_80x100.gif\" title=\"development_July15\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>MicroRNAs of the RPE are essential for RPE differentiation and photoreceptor maturation<\/h3>\n  <h4>R. Ohana, B. Weiman-Kelman, S. Raviv, E. Tamm, M. Pasmanik-Chor, A. Rinon, D. Netanely, R. Shamir, AS.Salomon, R. Ashery-Padan.<\/h4>\n     <a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/26062936\"><em>Development , Jun 10. doi: 10.1242\/dev.121533, 2015.<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/bioinformatics_June_2015-wpcf_80x100.png\" title=\"bioinformatics_June_2015\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>A hierarchical Bayesian model for flexible module discovery in three-way time-series data<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/i17.full.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>D. Amar, D. Yekutieli, A. Maron-Katz, T. Hendler and R. Shamir.<\/h4>\n     <a href=\"http:\/\/bioinformatics.oxfordjournals.org\/cgi\/content\/full\/btv228?ijkey=QDbwBOVrh9sCKlW&#038;keytype=ref\"><em>Bioinformatics , 31 (12): i17-i26, ISMB\/ECCB 2015, proceedings paper, doi: 10.1093\/bioinformatics\/btv228, 2015.<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/physiologia_plantarum-wpcf_80x100.gif\" title=\"physiologia_plantarum\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>The MORPH-R web server and software tool for predicting missing genes in biological pathways<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Amar_et_al-2015-Physiologia_Plantarum.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>D. Amar, I. Frades, T. Diels, D. Zaltzman, N. Ghatan, P. E. Hedley, E. Alexandersson, O. Tzfadia and R. Shamir<\/h4>\n     <a href=\"http:\/\/onlinelibrary.wiley.com\/enhanced\/doi\/10.1111\/ppl.12326\/\"><em>Physiologia_Plantarum , doi:10.1111\/ppl.12326, 2015.<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/BMC_plant_biology-wpcf_80x56.png\" title=\"BMC_plant_biology\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Evaluation and integration of functional annotation pipelines for newly sequenced organisms: the potato genome as a test case.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Amar_BMC_Plant_Biology.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>D. Amar, I. Frades, A. Danek, T. Goldberg , S.K. Sharma, P.E. Hedley, E. Proux-Wera, E. Andreasson, R. Shamir, O. Tzfadia, E. Alexandersson.<\/h4>\n     <a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/25476999\"><em>BMC Plant Biology , 5;14(1):329, 2014.<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Gene_Developments-wpcf_80x100.gif\" title=\"Gene_Developments\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Drosophila TRF2 is a preferential core promoter regulator.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Genes_Dev-2014-Kedmi-gad.245670.114.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>A. Kedmi, Y. Zehavi, Y. Glick, Y. Orenstein, D. Ideses, C. Wachtel, T. Doniger, H. Waldman Ben-Asher, N. Muster, J. Thompson, S. Anderson, D. Avrahami, J. R. Yates III, R. Shamir, D. Gerber and T. Juven-Gershon<\/h4>\n     <a href=\"http:\/\/genesdev.cshlp.org\/content\/28\/19\/2163.abstract\"><em>Genes and Development, 28 (19) pp. 2163 - 2174, 2014.<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/BMC_bioinformatics-wpcf_80x100.gif\" title=\"BMC_bioinformatics\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Fast lossless compression via cascading Bloom filters.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Roye_1471-2105-15-S9-S7.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>R. Rozov, R. Shamir, E. Halperin<\/h4>\n     <a href=\"http:\/\/www.biomedcentral.com\/1471-2105\/15\/S9\/S7\"><em>BMC Bioinformatics, 15(Suppl 9):S7, 2014.<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/frontiers_in_genetics-wpcf_80x100.jpg\" title=\"frontiers_in_genetics\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Examination of Exhaustive Cloning Attempts Reveals that C. elegans piRNAs, Transposons, and Repeat Sequences are Efficiently Cloned in Yeast, but not in Bacteria.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/103032_Rechavi_ProvisionalPDF.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>O. Sagy, R. Shamir and O. Rechavi<\/h4>\n     <a href=\"http:\/\/journal.frontiersin.org\/Journal\/10.3389\/fgene.2014.00275\/abstract\"><em>Frontiers in Genetics, 5:275, doi: 10.3389\/fgene.2014.00275.<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/NAR_cover_July2014-wpcf_80x100.gif\" title=\"NAR_cover_July2014\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Functional gene groups are concentrated within chromosomes, among chromosomes and in the nuclear space of the human genome.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Annelyse_nar.gku667.full.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>A. Th\u008evenin, L. Ein-Dor, M. Ozery-Flato and R. Shamir<\/h4>\n     <a href=\"http:\/\/nar.oxfordjournals.org\/content\/early\/2014\/07\/22\/nar.gku667.long\"><em>Nucleic Acids Research, doi: 10.1093\/nar\/gku667.<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Science_Signaling-wpcf_80x100.jpg\" title=\"Science_Signaling\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Parallel Profiling of the Transcriptome, Cistrome, and Epigenome in the Cellular Response to Ionizing Radiation.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Rashi-Elkeles-et-al-2014.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>S. Rashi-Elkeles, H.J. Warnatz, R. Elkon, A. Kupershtein, Y. Chobod, A. Paz, V. Amstislavskiy, M. Sultan, H. Safer, W. Nietfeld, H. Lehrach, R. Shamir, M.L. Yaspo and Y. Shiloh.<\/h4>\n    <em>Science Signaling<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/NAR_Feb14-wpcf_80x100.png\" title=\"NAR_Feb14\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>A comparative analysis of transcription factor binding models learned from PBM, HT-SELEX and ChIP data.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Yaron_nar.gku117.full.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Y. Orenstein and R. Shamir<\/h4>\n     <a href=\"http:\/\/nar.oxfordjournals.org\/content\/early\/2014\/02\/05\/nar.gku117.full?keytype=ref&#038;ijkey=rRfrgyCUMSQrvJw\"><em>Nucleic Acids Research doi: 10.1093\/nar\/gku117, 2014.<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/NAR_Feb14-wpcf_80x100.png\" title=\"NAR_Feb14\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Constructing module maps for integrated analysis of heterogeneous biological networks.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Didi_nar.gku102.full.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>D. Amar and R. Shamir<\/h4>\n     <a href=\"http:\/\/nar.oxfordjournals.org\/content\/early\/2014\/02\/03\/nar.gku102.full?keytype=ref&#038;ijkey=Rp4NIFsKlw8AreK\"><em>Nucleic Acids Research doi:10.1093\/nar\/gku102, 2014.<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Plos_Genetics-wpcf_80x100.png\" title=\"Plos_Genetics\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Environmental stresses disrupt telomere length homeostasis.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/pgen.1003721.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>G.H. Romano, Y. Harar, T. Yehuda, A. Podhorzer, L. Rubinstein, R. Shamir, A. Gottlieb, Y. Silberberg, D. Pe\u00d5er, E. Ruppin, R. Sharan, M. Kupiec<\/h4>\n     <a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/24039592\"><em>PLoS Genetics,9(9):e1003721. doi: 10.1371\/journal.pgen.1003721. Epub 2013.<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Journal_Investigative_Dermatology-wpcf_80x100.jpg\" title=\"Journal_Investigative_Dermatology\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Transcription Factor\/microRNA Axis Blocks Melanoma Invasion Program by miR-211 Targeting NUAK1.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/TranscriptionSep13.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>R.E. Bell, M. Khaled, D. Netanely, S. Schubert, T. Golan, A. Buxbaum, M. M. Janas, B. Postolsky, M.S. Goldberg, R. Shamir, C. Levy<\/h4>\n     <a href=\"http:\/\/www.nature.com\/jid\/journal\/vaop\/naam\/abs\/jid2013340a.html\"><em>Journal of Investigative Dermatology, doi: 10.1038\/jid.2013.340, 2013.<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Bioinformatics-Jan13-wpcf_80x100.gif\" title=\"Bioinformatics-Jan13\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Design of shortest double-stranded DNA sequences covering all k-mers with applications to protein-binding microarrays and synthetic enhancers.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Yaron_i71.full.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Y. Orenstein, and R. Shamir<\/h4>\n     <a href=\"http:\/\/bioinformatics.oxfordjournals.org\/content\/29\/13\/i71.full\"><em>Bioinformatics, Vol. 29 ISMB\/ECCB, i71-i79, 2013.<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Com_Bio-wpcf_80x100.jpg\" title=\"Com_Bio\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>RAP: Accurate and fast motif finding based on protein binding microarray data.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Yaron_published_version.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Y. Orenstein, E. Mick and R. Shamir<\/h4>\n     <a href=\"http:\/\/online.liebertpub.com\/doi\/abs\/10.1089\/cmb.2012.0253\"><em>Journal of Computational Biology, Vol. 20, No. 5: 375-382 , 2013.<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/PLOS-Computational-Biology-1-wpcf_80x100.jpg\" title=\"PLOS Computational Biology\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Dissection of Regulatory Networks that Are Altered in Disease via Differential Co-expression.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/journal.pcbi.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>D. Amar, H. Safer, R. Shamir<\/h4>\n     <a href=\"http:\/\/www.plosone.org\/article\/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002955\"><em>PLOS Computational Biology, Vol. 9, No. 3. e1002955, 2013.<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Nature_Biotechnology-wpcf_80x100.jpg\" title=\"Nature_Biotechnology\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Evaluation of methods for modeling transcription factor sequence specificity.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Yaron_nbt.2486.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>M.T. Weirauch, A. Cote, R. Norel, M. Annala, Y. Zhao, T.R. Riley, J. Saez-Rodriguez, T. Cokelaer, A. Vedenko, S. Talukder, DREAM5 Consortium (including Y. Orenstein, C. Linhart, R. Shamir), H.J. Bussemaker, Q.D. Morris, M.L. Bulyk, G. Stolovitzky & T.R. Hughes.<\/h4>\n     <a href=\"http:\/\/www.nature.com\/nbt\/journal\/vaop\/ncurrent\/full\/nbt.2486.html\"><em>Nature Biotechnology,31(2):126-34, 2013.<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Bioinformatics-Jan13-wpcf_80x100.gif\" title=\"Bioinformatics-Jan13\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Systematic Inference of Highways of Horizontal Gene Transfer in Prokaryotes.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/bioinformatics.btt021.full.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>M.S. Bansal, G. Banay, T.J. Harlow, J.P. Gogarten, R. Shamir.<\/h4>\n     <a href=\"http:\/\/bioinformatics.oxfordjournals.org\/content\/early\/2013\/01\/17\/bioinformatics.btt021.abstract?keytype=ref&#038;ijkey=EDa5bU5pSIYzYzi\"><em>Bioinformatics, 29 ( 5 ) pp. 571 - 579, 2013.<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Plant_Cell-wpcf_80x100.jpg\" title=\"Plant_Cell\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>The MORPH Algorithm: Ranking Candidate Genes for Membership in Arabidopsis and Tomato Pathways.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/morph.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>O. Tzfadia, D. Amar, L.M.T. Bradbury, E.T. Wurtzel, and R. Shamir.<\/h4>\n     <a href=\"http:\/\/www.plantcell.org\/content\/early\/2012\/11\/29\/tpc.112.104513.full.pdf+html\"><em>The Plant Cell, 24(11):4389-406, 2012.<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/PLOS_ONE-wpcf_80x87.jpg\" title=\"PLOS_ONE\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Assessment of algorithms for inferring positional weight matrix motifs of transcription factor binding sites using protein binding microarray data.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/journal.pone.0046145.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Y. Orenstein, C. Linhart , R. Shamir.<\/h4>\n     <a href=\"http:\/\/www.plosone.org\/article\/info%3Adoi%2F10.1371%2Fjournal.pone.0046145\"><em>PLoS ONE, 7 (9) e46145, 2012.<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Nature_Methods-wpcf_80x100.jpg\" title=\"Nature_Methods\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Wisdom of crowds for robust gene network inference.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/nmeth.2016.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>D. Marbach, J. C. Costello, R. Kueffner, N. Vega, R. J. Prill, D. M. Camacho, K. R. Allison, the DREAM5 Consortium (including G. Karlebach, R. Shamir), M. Kellis, J. J. Collins G. Stolovitzky.<\/h4>\n     <a href=\"http:\/\/www.nature.com\/nmeth\/journal\/vaop\/ncurrent\/full\/nmeth.2016.html\"><em>Nature Methods, 9(8):796-804, 2012.<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Com_Bio-wpcf_80x100.jpg\" title=\"Com_Bio\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Network-Induced Classification Kernels for Gene Expression Profile Analysis.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/nick-jcb12.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>O. Lavi, G. Dror, and R. Shamir.<\/h4>\n     <a href=\"http:\/\/online.liebertpub.com\/doi\/abs\/10.1089\/cmb.2012.0065\"><em>Journal of Computational Biology, 19(6), 694-709, 2012.<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/BMC_bioinformatics-wpcf_80x100.gif\" title=\"BMC_bioinformatics\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>MGMR: leveraging RNA-Seq population data to optimize expression estimation.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/MGMR.BMC_Bioinformatics.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>R. Rozov, E. Halperin and R. Shamir.<\/h4>\n     <a href=\"http:\/\/www.biomedcentral.com\/1471-2105\/13\/S6\/S2\"><em>BMC Bioinformatics, Proceedings of the Second Annual RECOMB Satellite Workshop on Massively Parallel Sequencing (RECOMB-seq 2012), 13(Suppl 6):S2, 2012.<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/PLOS_ONE-wpcf_80x87.jpg\" title=\"PLOS_ONE\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Transcriptional and Proteomic Analysis of the Aspergillus fumigatus DprtT Protease-Deficient Mutant.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Hagag-PlosOne-2012.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>S.Hagag, P. Kubitschek-Barreira, G. W. P. Neves, D. Amar, W. Nierman, I. Shalit, R. Shamir, L. Lopes-Bezerra, N. Osherov.<\/h4>\n     <a href=\"http:\/\/www.plosone.org\/article\/info%3Adoi%2F10.1371%2Fjournal.pone.0033604\"><em>PLoS ONE, Volume 7, Issue 4, e33604, 2012.<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/GR_Jan12-wpcf_80x100.gif\" title=\"GR_Jan12\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>A novel candidate cis-regulatory motif pair in the promoters of germline and oogenesis genes in C. elegans.<\/h3><span style=\"float: right;\"><a href=\"http:\/\/genome.cshlp.org\/content\/early\/2011\/09\/19\/gr.115626.110\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>C. Linhart, Y. Halperin, A. Darom, S. Kidron, L. Broday and R. Shamir.<\/h4>\n     <a href=\"http:\/\/genome.cshlp.org\/content\/early\/2011\/09\/19\/gr.115626.110.abstract4\"><em>Genome Research, 22(1):76-83, 2012.<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Com_Bio-wpcf_80x100.jpg\" title=\"Com_Bio\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Constructing logical models of gene regulatory networks by integrating transcription factor-DNA interactions with expression data: an entropy based approach.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Modent.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>G. Karlebach and R. Shamir.<\/h4>\n    <em>Journal of Computational Biology<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/PLOS_ONE-wpcf_80x87.jpg\" title=\"PLOS_ONE\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>A Point Mutation in Translation Initiation Factor eIF2B Leads to Function- and Time-Specific Changes in Brain Gene Expression.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/point-mutation-plos-one-2011.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>L. Marom, I. Ulitsky, Y. Cabilly, R. Shamir, O. Elroy-Stein.<\/h4>\n     <a href=\"http:\/\/www.plosone.org\/article\/info%3Adoi%2F10.1371%2Fjournal.pone.0026992\"><em>PLoS ONE, 6, 269920, 2011.<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/bfb-cover-wpcf_80x100.jpg\" title=\"bfb-cover\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Bioinformatics for Biologists.<\/h3>\n  <h4>P. Pevzner and R. Shamir, editors .<\/h4>\n     <a href=\"http:\/\/www.amazon.com\/Bioinformatics-Biologists-Pavel-Pevzner\/dp\/1107648874\"><em>Textbook. Cambridge University Press, UK, 2011.<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/JDA-wpcf_80x100.gif\" title=\"JDA\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>An O(n3\/2\u00c3log(n)) algorithm for sorting by reciprocal translocations.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/discrete-algorithms-9-ozery-flato.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>M. Ozery-Flato, R. Shamir.<\/h4>\n     <a href=\"http:\/\/www.sciencedirect.com\/science\/article\/pii\/S1570866711000463\"><em>Journal of Discrete Algorithms, Volume 9, Issue 4, Pages 344-357(2011),<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/MolOncology-wpcf_80x100.jpg\" title=\"MolOncology\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Transcriptional Modulation Induced By Ionizing Radiation: P53 Remains A Central Player.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Rashi-Elkeles-et-al.2011.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>S.Rashi-Elkeles, R. Elkona, S. Shavit, Y. Lerenthal, C. Linhart, A. Kupershtein, N. Amariglio, G. Rechavi, R. Shamir and Y. Shiloh.<\/h4>\n     <a href=\"http:\/\/dx.doi.org\/10.1016\/j.molonc.2011.06.004\"><em>Molecular Oncology, 5, 336-348, 2011<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/GenomeBiology2011-wpcf_80x100.jpg\" title=\"GenomeBiology2011\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Large-scale analysis of chromosomal aberrations in cancer karyotypes reveals two distinct paths to aneuploidy.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Large-scale-analysis-GB.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Ozery-Flato M, Linhart C, Trakhtenbrot L, Izraeli S, Shamir R.<\/h4>\n     <a href=\"http:\/\/genomebiology.com\/2011\/12\/6\/R61\"><em>Genome Biology, 29;12(6):R61, 2011<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Com_Bio-wpcf_80x100.jpg\" title=\"Com_Bio\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Selected papers from the 2nd RECOMB satellite meeting on Bioinformatics Education (RECOMB-BE).<\/h3>\n  <h4>P. A. Pevzner, R. Shamir, editors.<\/h4>\n    <em>Journal of Computational Biology<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/164-wpcf_80x100.jpg\" title=\"TCBB_July-Sept.indd\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>A note on the fixed parameter tractability of the gene-duplication problem.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/FPT_2011.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Bansal, M.S. and Shamir, R.<\/h4>\n     <a href=\"http:\/\/www.scopus.com\/record\/display.url?eid=2-s2.0-79952845540&#038;origin=SingleRecordEmailAlert&#038;txGid=WO2jtIronDCuAE-4bz3vKuh%3a19\"><em>IEEE\/ACM Transactions on Computational Biology and Bioinformatics, 8 (3), art. no. 5557848, pp. 848-850, 2011<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/PLOS_ONE-wpcf_80x87.jpg\" title=\"PLOS_ONE\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Integration of Transcriptomics, Proteomics, and MicroRNA Analyses Reveals Novel MicroRNA Regulation of Targets in the Mammalian Inner Ear.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Elkan-Miller_2011.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>T. Elkan-Miller, I. Ulitsky, R. Hertzano, A. Rudnicki, A. A. Dror, D. R. Lenz, R. Elkon, M. Irmler, J. Beckers, R. Shamir, K.B. Avraham.<\/h4>\n     <a href=\"http:\/\/www.plosone.org\/article\/info%3Adoi%2F10.1371%2Fjournal.pone.0018195\"><em>PLoS One, Volume 6,Issue 4, e18195, 2011<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/PLOS_ONE-wpcf_80x87.jpg\" title=\"PLOS_ONE\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>PrtT-Regulated Proteins Secreted by Aspergillus fumigatus Activate MAPK Signaling in Exposed A549 Lung Cells Leading to Necrotic Cell Death.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/sharon-et-al-PLOS1-2011.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>H. Sharon, D. Amar, E. Levdansky, G. Mircus, Y. Shadkchan, R. Shamir, N. Osherov.<\/h4>\n     <a href=\"http:\/\/www.plosone.org\/article\/info%3Adoi%2F10.1371%2Fjournal.pone.0017509\"><em>PLoS One, Volume 6, Issue 3, e17509, 2011<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/CELLSTEMCELL-wpcf_80x100.gif\" title=\"CELLSTEMCELL\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Dynamic Changes in the Copy Number of Pluripotency and Cell Proliferation Genes in Human ESCs and iPSCs during Reprogramming and Time in Culture.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/PIIS1934.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>L.C. Laurent, I.Ulitsky, I.Slavin, H. Tran, A. Schork, R. Morey, C. Lynch, J.V. Harness, S. Lee, M.J. Barrero, S. Ku, M. Martynova, R. Semechkin, V. Galat, J. Gottesfeld, J.C. Izpisua Belmonte, C. Murry, H. S. Keirstead, H.-S. Park, U. Schmidt, A.L. Laslett, F.-J. Muller, C. M. Nievergelt, R. Shamir and J. F. Loring.<\/h4>\n     <a href=\"http:\/\/www.cell.com\/cell-stem-cell\/abstract\/S1934-5909(10)00698-3\"><em>Cell Stem Cell, doi: 10.1016\/j.stem.2010.12.003,2011.<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/NAR.png\" title=\"NAR\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>SPIKE: a database of highly curated human signaling pathways.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/D793.full.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>A. Paz, Z. Brownstein, Y. Ber, S. Bialik, E. David, D. Sagir, I. Ulitsky, R. Elkon, A. Kimchi, K. B. Avraham, Y. Shiloh and R. Shamir.<\/h4>\n     <a href=\"http:\/\/nar.oxfordjournals.org\/content\/early\/2010\/11\/19\/nar.gkq1167.abstract\"><em>Nucleic Acids Research, Vol. 39, Database issue D793-D799, 2011.<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/lncs-wpcf_80x100.jpg\" title=\"lncs\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Detecting Highways of Horizontal Gene Transfer.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Highways_RCG10.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Mukul S. Bansal, J. Peter Gogarten, and Ron Shamir.<\/h4>\n     <a href=\"http:\/\/recombcg.uottawa.ca\/recombcg2010\/\"><em>8th Annual RECOMB Comparative Genomics Workshop (RECOMB-CG 2010), LNCS, 6398: 109-120 (2010).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/PLOS_ONE-wpcf_80x87.jpg\" title=\"PLOS_ONE\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>DEGAS: De Novo Discovery of Dysregulated Pathways in Human Diseases.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/journal.pone.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Igor Ulitsky, Akshay Krishnamurthy, Richard M. Karp, Ron Shamir.<\/h4>\n     <a href=\"http:\/\/www.plosone.org\/article\/info%3Adoi%2F10.1371%2Fjournal.pone.0013367\"><em>PLoS One , 5 (10) e13367 (2010).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/lncs-wpcf_80x100.jpg\" title=\"lncs\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>PAKDD Data Mining Competition 2009: New Ways of Using Known Methods.<\/h3>\n  <h4>Chaim Linhart, Guy Harari, Sharon Abramovich and Altina Buchris.<\/h4>\n     <a href=\"http:\/\/www.springerlink.com\/content\/u50t0p6l6k77502v\/\"><em>Lecture Notes in Computer Science, Volume 5669\/2010, 99-105, DOI: 10.1007\/978-3-642-14640-4_7 (2010).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Com_Bio-wpcf_80x100.jpg\" title=\"Com_Bio\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>A Faster Algorithm for Simultaneous Alignment and Folding of RNA.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/cofolding1.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Ziv-Ukelson M, Gat-Viks I, Wexler Y, Shamir R.<\/h4>\n     <a href=\"http:\/\/www.biomedsearch.com\/nih\/Faster-Algorithm-Simultaneous-Alignment-Folding\/20649420.html\"><em>Journal of Computational Biology,17(8):1051-65,2010.<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/NAR.png\" title=\"NAR\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Towards computational prediction of microRNA function and activity.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Ulitsky.e160.full.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>I. Ulitsky, L. C. Laurent and R. Shamir.<\/h4>\n     <a href=\"http:\/\/nar.oxfordjournals.org\/cgi\/content\/abstract\/gkq570\"><em>Nucleic Acids Research, 38 (15): e160. pp 1-13 (2010).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/NSMB-wpcf_80x100.jpg\" title=\"NSMB\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>A plasma-membrane E-MAP reveals links of the eisosome with sphingolipid metabolism and endosomal trafficking.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/nsmb.1829.July10.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>P.S. Aguilar, F. Fr\u009ahlich, M. Rehman, M. Shales, I. Ulitsky, A. Olivera-Couto, H. Braberg, R. Shamir, P. Walter, M. Mann, C.S. Ejsing, N.J. Krogan, T.C. Walther.<\/h4>\n     <a href=\"http:\/\/www.nature.com\/nsmb\/journal\/v17\/n7\/abs\/nsmb.1829.html\"><em>Nature Structural and Molecular Biology , Vol. 17 no. 7, pp 901-909(2010).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Com_Bio-wpcf_80x100.jpg\" title=\"Com_Bio\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Topology-free querying of protein interaction networks.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/cmb.2009.0170.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Bruckner, S., H\u009fffner, F., Karp, R.M., Shamir, R., Sharan, R.<\/h4>\n     <a href=\"http:\/\/www.liebertonline.com\/doi\/abs\/10.1089\/cmb.2009.0170\"><em>Journal of Computational Biology , 17 (3), pp. 237-252 (2010).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/BMC_systems_biology-wpcf_80x100.gif\" title=\"BMC_systems_biology\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Minimally perturbing a gene regulatory network to avoid a disease phenotype: the glioma network as a test case.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/minimally_perturbing.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>G. Karlebach, R. Shamir .<\/h4>\n     <a href=\"http:\/\/www.biomedcentral.com\/1752-0509\/4\/15\"><em>BMC Systems Biology , 4:15 doi:10.1186\/1752-0509-4-15(2010).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/IJC-wpcf_80x100.gif\" title=\"IJC\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Ras inhibits ER Stress in Human Cancer Cells with Amplified Myc.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Ras_inhibits_IJC.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>S. Yaari-Stark, M. Shaked, Y. Nevo-Caspi, J. Jacob-Hircsh, R. Shamir, G. Rechavi, Y. Kloog.<\/h4>\n     <a href=\"http:\/\/www3.interscience.wiley.com\/cgi-bin\/fulltext\/123206961\/PDFSTART\"><em>International Journal of Cancer , Vol 126, 2268--2281 (2010).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/CIS-wpcf_73x100.jpg\" title=\"CIS\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Special issues dedicated to Michael Waterman on the occasion of his 67th birthday.<\/h3>\n  <h4>S. Istrail, P. Pevzner, R. Shamir. F. Sun, guest editors.<\/h4>\n     <a href=\"http:\/\/projecteuclid.org\/DPubS?service=UI&#038;version=1.0&#038;verb=Display&#038;page=toc&#038;handle=euclid.cis\/1264171153\"><em>Communication in Information and Systems , Vol 9 3-4 (2009), Vol 10 1-2 (2010).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/MSB-wpcf_80x100.jpg\" title=\"MSB\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Different sets of QTLs influence fitness variation in yeast.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/qtls_in_yeast.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>G. H. Romano, Y. Gurvich, O. Lavi, I. Ulitsky, R. Shamir, M. Kupiec.<\/h4>\n     <a href=\"http:\/\/www.nature.com\/msb\/journal\/v6\/n1\/full\/msb20101.html\"><em>Molecular Systems Biology 6:346, doi:10.1038\/msb.2010.1, 2010 .<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/natprot-wpcf_80x100.gif\" title=\"natprot\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Expander: from expression microarrays to networks and functions.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/prot2009.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>I. Ulitsky, A. Maron-Katz, S. Shavit, D. Sagir, C. Linhart, R. Elkon, A. Tanay, R. Sharan, Y. Shiloh, R. Shamir.<\/h4>\n     <a href=\"http:\/\/www.nature.com\/nprot\/journal\/v5\/n2\/full\/nprot.2009.230.html\"><em>Nature Protocols Vol 5, pp 303 - 322, 2010 .<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/plos.jpg\" title=\"plos\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Understanding gene sequence variation in the context of transcription regulation in yeast.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/journal.pgen.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>I. Gat-Viks, R. Meller, M. Kupiec, R. Shamir.<\/h4>\n     <a href=\"http:\/\/www.plosgenetics.org\/doi\/pgen.1000800\"><em>PLoS Genetics , Vol. 6 No. 1 e1000800 (2010).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/GenomeBiology.png\" title=\"GenomeBiology\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Towards accurate imputation of quantitative genetic interactions.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/gb.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>I. Ulitsky, N.J. Krogan and R. Shamir.<\/h4>\n     <a href=\"http:\/\/genomebiology.com\/2009\/10\/12\/R140\"><em>Genome Biology , Volume 10:R140 2009 .<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/abi_cover-wpcf_80x100.jpg\" title=\"abi_cover\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Assessing the Quality of Whole Genome Alignments in Bacteria.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/AssessingGenomeBacteria.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>F. Swidan, R. Shamir.<\/h4>\n     <a href=\"http:\/\/www.hindawi.com\/journals\/abi\/2009\/749027.html\"><em>Advances in Bioinformatics , Volume 2009, Article ID 749027, 8 pages doi:10.1155\/2009\/749027 (2009).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Com_Bio-wpcf_80x100.jpg\" title=\"Com_Bio\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Sorting Cancer Karyotypes by Elementary Operations.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/elementary.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>M. Ozery-Flato, R. Shamir.<\/h4>\n     <a href=\"http:\/\/www.liebertonline.com\/doi\/abs\/10.1089\/cmb.2009.0083\"><em>Journal of Computational Biology Vol. 16. no. 10, pp. 1445 - 1460, October 2009.<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/AAAS-wpcf_80x100.jpg\" title=\"AAAS\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Computing Has Changed Biology - Biology Education Must Catch Up.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/be-science.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>P. Pevzner, R. Shamir.<\/h4>\n     <a href=\"http:\/\/www.sciencemag.org\/cgi\/content\/short\/325\/5940\/541\"><em>Education Forum in Science Vol. 325. no. 5940, pp. 541 - 542 (31 July 2009).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/PLOS_ONE-wpcf_80x87.jpg\" title=\"PLOS_ONE\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>SlimPLS: a method for feature selection in gene expression-based disease classification.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/SlimPLS.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>M. Gutkin, G. Dror, R. Shamir.<\/h4>\n     <a href=\"http:\/\/dx.plos.org\/10.1371\/journal.pone.0006416\"><em>PLoS One Vol. 4 No. 7 e6416 (2009) .<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/IWPEC-wpcf_67x100.jpg\" title=\"IWPEC\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>A faster fixed-parameter approach to drawing binary tanglegrams.<\/h3>\n  <h4>S. Bocker, F. H\u009fffner, A. Truss, and M. Wahlstrom.<\/h4>\n     <a href=\"http:\/\/faculty.cs.tamu.edu\/chen\/iwpec2009\/index.html\"><em>In Proceedings of the 4th International Workshop on Parameterized and Exact Computation,(IWPEC '09) Copenhagen,Denmark,September 2009 Lecture Notes in Computer Science, Springer.<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/NAR.png\" title=\"NAR\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Torque: topology-free querying of protein interaction networks<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/torque_NAR.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>S. Bruckner, F. H\u009fffner, R. M. Karp, R. Shamir, R. Sharan.<\/h4>\n     <a href=\"http:\/\/nar.oxfordjournals.org\/content\/37\/suppl_2\/W106.full\"><em>Nucleic Acids Research doi: 10.1093\/nar\/gkp474.<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/CIS-wpcf_73x100.jpg\" title=\"CIS\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Increasing the Power of Association Studies by Imputation-based Sparse Tag SNP Selection<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/davidovich.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>O. Davidovich, G. Kimmel, E. Halperin, R. Shamir.<\/h4>\n     <a href=\"https:\/\/acgt.cs.tau.ac.il\/papers\/STAMPA2.pdf\"><em>Communications in Information and Systems 9 (3) 269-282 (2009)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/bioinformatics.png\" title=\"bioinformatics\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Identifying functional modules using expression profiles and confidence-scored protein interactions<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/cezanne.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>I. Ulitsky and R. Shamir.<\/h4>\n     <a href=\"http:\/\/bioinformatics.oxfordjournals.org\/cgi\/content\/abstract\/btp118\"><em>Bioinformatics Vol. 25 no. 9 pages 1158-1164 (2009) .<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/lncs-wpcf_80x100.jpg\" title=\"lncs\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Topology-free querying of protein interaction networks<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/torque_RECOMB.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>S. Bruckner, F. H\u009fffner, R. M. Karp, R. Shamir, R. Sharan.<\/h4>\n     <a href=\"http:\/\/www.springer.com\/computer\/computational+biology+and+bioinformatics\/book\/978-3-642-02007-0\"><em>Proceedings of RECOMB 2009 LNCS 5541 74-89,<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/jcss-wpcf_80x100.gif\" title=\"jcss\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Faster Pattern Matching with Character Classes using Prime Number Encoding<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/pmcc_JCSS_rev.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>C. Linhart and R. Shamir.<\/h4>\n     <a href=\"http:\/\/dx.doi.org\/10.1016\/j.jcss.2008.08.005\"><em>Journal of Computers and System Sciences , 75, 155--162 (2009).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/NAR.png\" title=\"NAR\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Allegro: Analyzing expression and sequence in concert to discover regulatory programs<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/allegro.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Y. Halperin, C. Linhart, I. Ulitsky and R. Shamir.<\/h4>\n     <a href=\"http:\/\/nar.oxfordjournals.org\/cgi\/content\/abstract\/gkn1064\"><em>Nucleic Acids Research 37:5, 1566-1579.<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/IPL.png\" title=\"IPL\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Matching with don't-cares and a small number of mismatches<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/wmkm_IPL_final.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>C. Linhart and R. Shamir.<\/h4>\n     <a href=\"http:\/\/dx.doi.org\/10.1016\/j.ipl.2008.10.016\"><em>Information Processing Letters Volume 109, Number 5, p. 273-277 (2009).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/lncs-wpcf_80x100.jpg\" title=\"lncs\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Sorting cancer karyotypes by elementary operations<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/elementary_gr.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>M. Ozery-Flato and R. Shamir.<\/h4>\n     <a href=\"http:\/\/www.springer.com\/computer\/computational+biology+and+bioinformatics\/book\/978-3-540-87988-6?cm_mmc=NBA-_-Oct-08_FRANCE_2503826-_-product-_-978-3-540-87988-6\"><em>Proceedings of the 6th RECOMB Satellite Workshop on Comparative Genomics 2008, LNCS Vol. 5267 pp. 211-225 (2008).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/lncs-wpcf_80x100.jpg\" title=\"lncs\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>A faster algorithm for RNA co-folding<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/cofolding.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>M. Ziv-Ukelson, I. Gat-Viks, Y. Wexler and R. Shamir.<\/h4>\n    <em>Proc. Algorithms in Bioinformatics, Keith A. Crandall and Jens Lagergren (Eds.)<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/nrm.png\" title=\"nrm\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Modeling and Analysis of Regulatory Networks<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/nrm2503.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>G. Karlebach and R. Shamir.<\/h4>\n     <a href=\"http:\/\/www.nature.com\/nrm\/journal\/vaop\/ncurrent\/abs\/nrm2503.html\"><em>Nature Reviews Molecular Cell Biology, Vol. 9 771--780 doi:10.1038\/nrm2503 (2008)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/scm_nature-wpcf_80x100.png\" title=\"scm_nature\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Regulatory networks define phenotypic classes of human stem cell lines.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/nature.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>F.J. Mueller, D. Kostka, L. Laurent, I. Ulitsky, R. Williams, C. Lu, M.S. Rao, R. Shamir, P.H. Schwartz, N.O. Schmidt and J.F. Loring.<\/h4>\n     <a href=\"http:\/\/www.nature.com\/nature\/journal\/v455\/n7211\/full\/nature07213.html\"><em>Nature. Vol. 455 No. 7211 p. 401-405 (2008)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/csb08-wpcf_80x100.gif\" title=\"csb08\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Detecting pathways transcriptionally correlated with clinical parameters<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/clipar-csb08.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>I. Ulitsky and R. Shamir<\/h4>\n     <a href=\"http:\/\/csb2008.org\/csb2008papers\/066Ulitsky.pdf\"><em>Proc. 7th Annual International Conference on Computational Systems Bioinformatics (CSB 08) pp. 249--258, Imperial College Press, London, UK (2008)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/JCB-wpcf_80x100.jpg\" title=\"JCB\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Sorting Genomes with Centromeres by Translocations<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/legal_jcb.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>M. Ozery-Flato and R. Shamir<\/h4>\n     <a href=\"http:\/\/www.liebertonline.com\/doi\/abs\/10.1089\/cmb.2007.0136\"><em>Journal of Computational Biology (2008) Vol. 15 No. 7<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/MSB-wpcf_80x100.jpg\" title=\"MSB\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>From E-MAPs to module maps: dissecting quantitative genetic interactions using physical interactions<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/emap.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>I. Ulitsky, T. Shlomi, M. Kupiec and R. Shamir<\/h4>\n     <a href=\"http:\/\/www.nature.com\/msb\/journal\/v4\/n1\/full\/msb200842.html\"><em>Molecular Systems Biology (2008) Vol. 4 doi:10.1038\/msb.2008.42<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/genome_research_v18_n7-wpcf_80x100.gif\" title=\"genome_research_v18_n7\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Transcription factor and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/amadeus.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>C. Linhart, Y. Halperin and R. Shamir<\/h4>\n     <a href=\"http:\/\/www.genome.org\/cgi\/content\/short\/18\/7\/1180\"><em>Genome Research (2008) Vol. 18 No. 7 1180-1189<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/StemCells.jpg\" title=\"StemCells\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Comprehensive MicroRNA Profiling Reveals a Unique Human Embryonic Stem Cell Signature Dominated by a Single Seed Sequence<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/scmirna.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>L.C. Laurent, J. Chen, I. Ulitsky, F.J. Mueller, C. Lu, R. Shamir, J.B. Fan and J.F. Loring<\/h4>\n     <a href=\"http:\/\/stemcells.alphamedpress.org\/cgi\/reprint\/2007-1081v1.pdf\"><em>Stem Cells doi: 10.1634\/stemcells.2007-1081<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/lncs-wpcf_80x100.jpg\" title=\"lncs\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Detecting Disease-Specific Dysregulated Pathways Via Analysis of Clinical Expression Profiles<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/clean.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>I. Ulitsky, R.M. Karp and R. Shamir<\/h4>\n     <a href=\"http:\/\/dx.doi.org\/10.1007\/978-3-540-78839-3_30\"><em>Proc. RECOMB 2008, pp. 347--359, LNBI 4955, Springer, Berlin, (2008).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/BMC-wpcf_80x100.jpg\" title=\"BMC\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>SPIKE - a database, visualization and analysis tool of cellular signaling pathways<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/spike.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>R. Elkon, R. Vesterman, N. Amit, I. Ulitsky, I. Zohar, M. Weisz, G. Mass, N. Orlev, G. Sternberg, R. Blekhman, J. Assa, Y. Shiloh and R.Shamir<\/h4>\n     <a href=\"http:\/\/www.biomedcentral.com\/1471-2105\/9\/110\"><em>BMC Bioinformatics (2008) Vol. 9 No. 11<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/tcbb-wpcf_80x100.jpg\" title=\"tcbb\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Computational Problems in Perfect Phylogeny Haplotyping: Typing without Calling the Allele<\/h3>\n  <h4>T. Barzuza, J.S. Beckmann, R. Shamir and I. Pe'er<\/h4>\n     <a href=\"http:\/\/csdl2.computer.org\/persagen\/DLAbsToc.jsp?resourcePath=\/dl\/trans\/tb\/&#038;toc=comp\/trans\/tb\/2008\/01\/ttb200801toc.xml&#038;DOI=10.1109\/TCBB.2007.1063\"><em>IEEE Transactions on Computational Biology and Bioinformatics (2008) Vol. 5 No. 1 101-9<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/plos.jpg\" title=\"plos\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Evolution and Selection in Yeast Promoters: Analyzing the Combined Effect of Diverse Transcription Factor Binding Sites<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/regcode-ploscb08.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>D. Raijman, R. Shamir and A. Tanay<\/h4>\n     <a href=\"http:\/\/www.ploscompbiol.org\/article\/info:doi\/10.1371\/journal.pcbi.0040007\"><em>PLoS Computational Biology (2008) Vol. 4 No. 1<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/GenomeBiology.png\" title=\"GenomeBiology\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>MetaReg: A platform for modeling, analysis and visualization of biological systems using large-scale experimental data<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/metarega.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>I. Ulitsky, I. Gat-Viks and R. Shamir<\/h4>\n     <a href=\"http:\/\/genomebiology.com\/2008\/9\/1\/R1\"><em>Genome Biology (2008) Vol. 9 No. R1<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/lncs-wpcf_80x100.jpg\" title=\"lncs\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>On the frequency of genome rearrangement events in cancer karyotypes<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/cancerGR_11b_report-1.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>M. Ozery-Flato and R. Shamir.<\/h4>\n     <a href=\"http:\/\/casb.ucsd.edu\/recombccb07\/index.php\"><em>Proc. RECOMB satellite on Computational Cancer Biology, 2007<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/IBD.png\" title=\"IBD\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Pediatric Onset Crohn's Disease is Characterized by Age and Genotype- Related Colonic Susceptibility<\/h3>\n  <h4>A. Levine, S. Kugathasan, A. Vito, V. Biank, E. Leshinsky-Silver, O. Davidovich, G. Kimmel, R. Shamir, P. Orazio, U. Broeckel, S. Cucchiara.<\/h4>\n     <a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/17763471\"><em>Inflammatory Bowel Disease (2007) Vol. 13 No. 12 1509-15<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/BMC_genomics.png\" title=\"BMC_genomics\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Functional genomic delineation of TLR-induced transcriptional networks<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/tlr.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>R. Elkon, C. Linhart, Y. Halperin, Y. Shiloh and R. Shamir<\/h4>\n     <a href=\"http:\/\/www.biomedcentral.com\/1471-2164\/8\/394\/abstract\"><em>BMC Genomics (2007) Vol. 8 No. 394<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/AJHG_v81_n5-wpcf_80x100.gif\" title=\"AJHG_v81_n5\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>A randomization test for controlling population stratification in whole-genome association studies<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/pop_strat.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>G. Kimmel, M.I. Jordan, E. Halperin, R. Shamir and R.M. Karp RM<\/h4>\n     <a href=\"http:\/\/www.journals.uchicago.edu\/AJHG\/journal\/issues\/v81n5\/44924\/44924.web.pdf\"><em>American Journal of Human Genetics (2007) , Vol. 81 No. 5, 895-905 (2007)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/PCRPrimerDesign-wpcf_80x100.png\" title=\"PCRPrimerDesign\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Degenerate Primer Design: Theoretical Analysis and the HYDEN program<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/dpd_chapter.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>C. Linhart and R. Shamir.<\/h4>\n     <a href=\"http:\/\/www.amazon.ca\/PCR-Primer-Design-Anton-Yuryev\/dp\/158829725X\"><em>PCR primer design, A. Yuryev, editor. The Methods in Molecular Biology series, Humana Press (2007)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/amjg-wpcf_80x100.png\" title=\"amjg\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Risk factors for perianal Crohn's disease: the role of genotype, phenotype, and ethnicity.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/crohn2.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>A. Karban, M. Itay, O. Davidovich, E. Leshinsky-Silver G. Kimmel, H. Fidder, R. Shamir, M. Waterman, R. Eliakim and A. Levine<\/h4>\n     <a href=\"http:\/\/www.blackwell-synergy.com\/doi\/abs\/10.1111\/j.1572-0241.2007.01277.x\"><em>The American Journal of Gastroenterology, Vol 102, No. 8 1702-8 (2007)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/jcss-wpcf_80x100.gif\" title=\"jcss\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Third special issue on Computational Biology<\/h3>\n  <h4>R. M. Karp, M. Li, P. Pevzner, R. Shamir, Guest editors.<\/h4>\n     <a href=\"http:\/\/www.sciencedirect.com\/science\/journal\/00220000\"><em>Journal of Computers and System Sciences Vol. 73, No. 7 (2007)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/MSB-wpcf_80x100.jpg\" title=\"MSB\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Pathway redundancy and protein essentiality revealed in the Saccharomyces cerevisiae interaction networks<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/gi.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>I. Ulitsky and R. Shamir<\/h4>\n     <a href=\"http:\/\/www.nature.com\/msb\/journal\/v3\/n1\/full\/msb4100144.html\"><em>Molecular Systems Biology, Vol. 3, No. 88 (2007)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/lncs-wpcf_80x100.jpg\" title=\"lncs\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Rearrangements in genomes with centromeres part I: translocations<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/legal.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>M. Ozery-Flato and R. Shamir.<\/h4>\n    <em>Proc. RECOMB<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/MSB-wpcf_80x100.jpg\" title=\"MSB\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Network-based prediction of protein function<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/funcnetrev.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>R. Sharan, I. Ulitsky and R. Shamir<\/h4>\n     <a href=\"http:\/\/www.nature.com\/msb\/journal\/v3\/n1\/full\/msb4100129.html\"><em>Molecular Systems Biology, Vol. 3, No. 88 (2007)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/int_journal_of_colorectal_disease-wpcf_80x100.jpg\" title=\"int_journal_of_colorectal_disease\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Lack of association of the 3'-UTR polymorphism in the NFKBIA gene with Crohn's disease in an Israeli cohort<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/crohn.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>E. Leshinsky-Silver, A. Karban, S. Cohen, M. Fridlander, O. Davidowich, G. Kimmel, R. Shamir and A. Levine<\/h4>\n     <a href=\"http:\/\/www.springerlink.com\/content\/955113108200u0l0\/\"><em>International Journal of Colorectal Disease (2007)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/JCB-wpcf_80x100.jpg\" title=\"JCB\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Sorting by reciprocal translocations via reversals theory<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/trans_jcb.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>M. Ozery-Flato and R. Shamir<\/h4>\n     <a href=\"http:\/\/www.liebertonline.com\/toc\/cmb\/14\/4\"><em>Journal of Computational Biology , Vol. 14 No. 4 (2007)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/nature_genetics_v39_n3-wpcf_80x100.gif\" title=\"nature_genetics_v39_n3\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>A genome-wide analysis in Saccharomyces cerevisiae demonstrates the influence of chromatin modifiers on transcription<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/cofactors.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>I. Steinfeld, R. Shamir and M. Kupiec<\/h4>\n     <a href=\"http:\/\/www.nature.com\/ng\/journal\/v39\/n3\/full\/ng1965.html\"><em>Nature Genetics, Vol. 39, No. 3 (2007) .<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/discrete_applied_mathematics-wpcf_80x100.gif\" title=\"discrete_applied_mathematics\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Fifth Special Issue in the Computational Molecular Biology Series<\/h3>\n  <h4>S. Istrail, P. Pevzner, R. Shamir, Editors<\/h4>\n     <a href=\"http:\/\/www.sciencedirect.com\/science?_ob=PublicationURL&#038;_cdi=5629&#038;_pubType=J&#038;_auth=y&#038;_acct=C000005078&#038;_version=1&#038;_urlVersion=0&#038;_userid=48161&#038;md5=984da94171b3c630c666b3b64c4907b2\"><em>Discrete Applied Mathematics, Vol. 155, No. 6-7 (2007)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/genome_research_v17_n3-wpcf_80x100.gif\" title=\"genome_research_v17_n3\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Refinement and expansion of signaling pathways: The osmotic response network in yeast<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/biometareg.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>I. Gat-Viks and R. Shamir<\/h4>\n     <a href=\"http:\/\/www.genome.org\/cgi\/reprint\/gr.5750507v1\"><em>Genome Research, Vol. 17, No. 3 (2007)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/BMC-wpcf_80x100.jpg\" title=\"BMC\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>GEVALT: An integrated software tool for genotype analysis<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/gevalt.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>O. Davidovich, G. Kimmel and R. Shamir<\/h4>\n     <a href=\"http:\/\/www.biomedcentral.com\/1471-2105\/8\/36\/abstract\"><em>BMC Bioinformatics, Vol. 8, No. 36 (2007)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/BMC-wpcf_80x100.jpg\" title=\"BMC\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Identification of functional modules using network topology and high-throughput data<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/matisse.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>I. Ulitsky and R. Shamir<\/h4>\n     <a href=\"http:\/\/www.biomedcentral.com\/1752-0509\/1\/8\"><em>BMC Systems Biology, Vol. 1, No. 8 (2007)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/BMC-wpcf_80x100.jpg\" title=\"BMC\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Assessing the number of ancestral alternatively spliced exons in the human genome<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/noaase.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>R. Sorek, G. Dror and R. Shamir<\/h4>\n     <a href=\"http:\/\/www.biomedcentral.com\/1471-2164\/7\/273\"><em>BMC Genomics, Vol. 7, pp. 273 (2006)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/lncs-wpcf_80x100.jpg\" title=\"lncs\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Sorting by translocations via reversals theory<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/srt_recomb_sat.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>M. Ozery-Flato and R. Shamir<\/h4>\n    <em>Proc. 4th RECOMB Satellite on Comparative Genomics, Lecture Notes in Computer Science<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/PNAS_v103_n35-wpcf_80x100.gif\" title=\"PNAS_v103_n35\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Quantification of protein half-lives in the budding yeast proteome<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/protdeg.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>A. Belle, A. Tanay, L. Bitincka, R. Shamir and E.K. O'Shea<\/h4>\n     <a href=\"http:\/\/www.pnas.org\/cgi\/content\/full\/103\/35\/13004\"><em>Proc. National Academy of Science USA, Vol. 103, No. 35, pp. 13004-13009 (2006)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/int_journal_of_cancer_v119_n3-wpcf_80x100.gif\" title=\"int_journal_of_cancer_v119_n3\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>E2F1 identified by promoter and biochemical analysis as a central target of glioblastoma cell-cycle arrest in response to RAS inhbibition<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/e2f1.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>R. Blum, I. Nakdimon, R. Elkon, R. Shamir, G. Rechavi and Y. Kloog<\/h4>\n     <a href=\"http:\/\/www3.interscience.wiley.com\/cgi-bin\/abstract\/112466044\/ABSTRACT\"><em>International Journal of Cancer, Vol. 119, No. 3, pp. 527-538 (2006)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/AJHG_v79_n3-wpcf_80x100.gif\" title=\"AJHG_v79_n3\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>A Fast Method for Computing High-Significance Disease Association in Large Population-Based Studies<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/rat-ajhg.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>G. Kimmel and R. Shamir<\/h4>\n     <a href=\"http:\/\/www.journals.uchicago.edu\/AJHG\/journal\/issues\/v79n3\/43735\/43735.web.pdf\"><em>American Journal of Human Genetics, Vol. 79, pp. 481-492 (2006)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/lncs-wpcf_80x100.jpg\" title=\"lncs\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>An O(n3\/2\u00c3log(n)) algorithm for sorting by reciprocal translocations<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/srt_cpm06.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>M. Ozery-Flato and R. Shamir<\/h4>\n    <em>Proc. of CPM<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/JCB-wpcf_80x100.jpg\" title=\"JCB\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>A probabilistic methodology for integrating knowledge and experiments on biological networks<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/FGN_JCB.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>I. Gat-Viks, A. Tanay, D. Raijman and R. Shamir<\/h4>\n     <a href=\"http:\/\/www.liebertonline.com\/doi\/abs\/10.1089\/cmb.2006.13.165\"><em>Journal of Computational Biology 2006 Mar;13(2):165-81<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/european_journal_of_cancer-wpcf_80x100.gif\" title=\"european_journal_of_cancer\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>RAD51 haplotypes and breast cancer risk in Jewish non-Ashkenazi high risk women<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/rad51hap.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>I. Gal, G. Kimmel, R. Gershoni-Baruch, M. Z. Papa, E. Dagan, R. Shamir, E. Friedman<\/h4>\n     <a href=\"http:\/\/www.sciencedirect.com\/science?_ob=MImg&#038;_imagekey=B6T68-4JRVFT0-8-1&#038;_cdi=5024&#038;_user=48161&#038;_orig=browse&#038;_coverDate=05%2F31%2F2006&#038;_sk=999579991&#038;view=c&#038;wchp=dGLzVzz-zSkzS&#038;md5=100ae44bfd51ee8e3c3fca5cea634f3c&#038;ie=\/sdarticle.pdf\"><em>European Journal of Cancer 42(8) pp. 1129-34 (2006)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/BJC-wpcf_80x100.gif\" title=\"BJC\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>ATM haplotypes and breast cancer risk in Jewish high risk women<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/atmhap.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>M. Koren, G. Kimmel, E. Ben-Asher, I. Gal, M. Z. Papa, J. S. Beckman, D. Lancet, R. Shamir, E. Friedman<\/h4>\n    <em>British Journal of Cancer<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/handbook_of_comp_mol_biol-wpcf_80x100.jpg\" title=\"handbook_of_comp_mol_biol\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Biclustering Algorithms: A Survey<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/bicrev_bioinfo.ps\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Amos Tanay, Roded Sharan and Ron Shamir<\/h4>\n     <a href=\"http:\/\/www.amazon.com\/Handbook-Computational-Molecular-Computer-Information\/dp\/1584884061\"><em>Handbook of Computational Molecular Biology , S. Aluru, editor, pp. 26-1 - 26-17, Chapman and Hall \/ CRC Press (2006)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/information_and_computation-wpcf_80x100.gif\" title=\"information_and_computation\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>A simpler and faster 1.5-approximation algorithm for sorting by transpositions<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/transpositions-IC06.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>T. Hartman and R. Shamir<\/h4>\n     <a href=\"http:\/\/www.sciencedirect.com\/science?_ob=MImg&#038;_imagekey=B6WGK-4HR72DJ-1-2&#038;_cdi=6825&#038;_user=10&#038;_orig=browse&#038;_coverDate=02%2F28%2F2006&#038;_sk=997959997&#038;view=c&#038;wchp=dGLzVzz-zSkzk&#038;md5=ec8b51b4806f3781d8869c71bcbbfdf8&#038;ie=\/sdarticle.pdf\"><em>Information and Computation 204 (2) 275-290 (2006)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/oncogene-wpcf_80x100.jpg\" title=\"oncogene\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Parallel induction of ATM-dependent pro- and anti-apoptotic signals in response to ionizing radiation in murine lymphoid tissue<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/atm-lymph.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>S. Rashi-Elkeles, R. Elkon, N. Weizman, C. Linhart, N. Amariglio, G. Sternberg, G. Rechavi, A. Barzilai, R. Shamir, Y. Shiloh<\/h4>\n     <a href=\"http:\/\/www.nature.com\/onc\/journal\/v25\/n10\/pdf\/1209189a.pdf\"><em>Oncogene 25, 1584-1592 (2006)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Deciphering Transcriptional Regulatory Elements That Encode Specific Cell-Cycle Phasing by Comparative Genomics Analysis<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/hcc2.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>C. Linhart, R. Elkon, Y. Shiloh, and R. Shamir<\/h4>\n     <a href=\"http:\/\/www.landesbioscience.com\/journals\/cc\/abstract.php?id=2173&#038;PHPSESSID=b50624c53e8fa0c4d071603a5261813c\"><em>Cell Cycle Vol. 4(12), pp. 1788-1797 Dec 2005<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>EXPANDER: an integrative suite for microarray data analysis<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/expander2.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>R. Shamir, A. Maron-Katz, A. Tanay, C. Linhart, I. Steinfeld, R.Sharan, Y. Shiloh, R. Elkon<\/h4>\n     <a href=\"http:\/\/www.biomedcentral.com\/1471-2105\/6\/232\/abstract\"><em>BMC Bioinformatics 6:232 (2005)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>A catalog of stability-associated sequence elements in 3~R UTRs of yeast mRNAs<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/3utr-Genome-Biology-05.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>R. Shalgi, M. Lapidot, R. Shamir, Y. Pilpel<\/h4>\n     <a href=\"http:\/\/genomebiology.com\/2005\/6\/10\/R86\"><em>Genome Biology 6:R86 (2005) (website)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Tag SNP Selection in Genotype Data for Maximizing SNP Prediction Accuracy<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/stampa-ISMB05.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>E. Halperin, G. Kimmel, R. Shamir.<\/h4>\n     <a href=\"http:\/\/bioinformatics.oxfordjournals.org\/cgi\/reprint\/21\/suppl_1\/i195\"><em>Proc. of ISMB 2005; Bioinformatics Vol. 21 Suppl. 1 pp. i195-i203 (2005)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Typing without calling the allele: a strategy for inferring SNP haplotypes<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/xpph-EJHG.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>T. Barzuza, J. S. Beckmann, R. Shamir and I. Pe'er<\/h4>\n     <a href=\"http:\/\/www.nature.com\/ejhg\/journal\/v13\/n8\/pdf\/5201440a.pdf\"><em>European Journal of Human Genetics Vol. 13, pp. 898-901 (2005)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Conservation and evolvability in regulatory networks: The evolution of ribosomal regulation in yeast<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/cisprof-PNAS.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>A. Tanay, A. Regev, R. Shamir<\/h4>\n     <a href=\"http:\/\/www.pnas.org\/cgi\/content\/abstract\/102\/20\/7203\"><em>Proc. National Academy of Science USA Vol. 102 No. 20, pp. 7203-7208 (2005)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Factor graph network models for biological systems<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/FGN_Recomb05.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>I. Gat-Viks, A. Tanay, D. Raijman, R. Shamir<\/h4>\n    <em>Proc. of RECOMB<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Dissection of a DNA damage-induced transcriptional network using a combination of microarrays, RNAi and computational promoter analysis<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/rnai.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>R. Elkon, S. Rashi-Elkeles, Y. Lerenthal, C. Linhart, T. Tenne, N. Amariglio, G. Rechavi, R. Shamir, Y. Shiloh<\/h4>\n     <a href=\"http:\/\/genomebiology.com\/2005\/6\/5\/R43\"><em>Genome Biology 6: R43 (2005)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>2nd special issue of JCSS on Computational Biology<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>R. M. Karp, M. Li, P. Pevzner, R. Shamir, guest editors<\/h4>\n     <a href=\"http:\/\/www.sciencedirect.com\/science?_ob=IssueURL&#038;_tockey=%23TOC%236864%232005%23999299996%23589782%23FLP%23Volume_70,_Issue_3,_Pages_283-431_(May_2005)%2BMSpecial_Issue_on_Bioinformatics_II%2BMEdited_by_R._Karp,_M._Li,_P._Pevzner,_R._Shamir&#038;_auth=y&#038;view=c&#038;_acct=C000050221&#038;_version=1&#038;_urlVersion=0&#038;_userid=10&#038;md5=a80c0464a40b612e146a8e1f3ad7ced8\"><em>Journal of Computers and System Sciences Volume 70, No. 3, May 2005<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Identification of Protein Complexes by Comparative Analysis of Yeast and Bacterial Protein Interaction Data<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/cpi-jcb.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>R. Sharan, T. Ideker, B. Kelley, R. Shamir, R. M. Karp<\/h4>\n     <a href=\"http:\/\/www.liebertonline.com\/doi\/abs\/10.1089\/cmb.2005.12.835\"><em>Journal of Computational Biology Volume 12, pp. 835-846, 2005<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>A Block-Free Hidden Markov Model for Genotypes and Its Application to Disease Association<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/hint.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>G. Kimmel and R. Shamir<\/h4>\n     <a href=\"http:\/\/www.liebertonline.com\/doi\/pdf\/10.1089\/cmb.2005.12.1243\"><em>Journal of Computational Biology Volume 12, Number 10, pp. 1243-1260, 2005<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Integrative analysis of genome-wide experiments in the context of a large high-throughput data compendium<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/qubic.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>A. Tanay, I. Steinfeld, M. Kupiec and R. Shamir<\/h4>\n     <a href=\"http:\/\/www.nature.com\/msb\/journal\/v1\/n1\/full\/msb4100005.html\"><em>Molecular Systems Biology doi: 10.1038\/msb4100005 (2005)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>A global view of pleiotropy and phenotypically derived gene function in yeast<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/aimee.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>A. M. Dudley, D. M. Janse, A. Tanay, R. Shamir, G. M. Church<\/h4>\n     <a href=\"http:\/\/www.nature.com\/msb\/journal\/v1\/n1\/full\/msb4100004.html\"><em>Molecular Systems Biology doi: 10.1038\/msb4100004 (2005)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Accurate identification of alternatively spliced exons using support vector machine<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/splicing-svm.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Gideon Dror, Rotem Sorek and Ron Shamir<\/h4>\n     <a href=\"http:\/\/bioinformatics.oupjournals.org\/cgi\/reprint\/21\/7\/897\"><em>Bioinformatics (21) 897-901 (2005)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>The degenerate primer design problem: Theory and applications<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/dpd-theory-final.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>C. Linhart and R. Shamir<\/h4>\n     <a href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&#038;db=PubMed&#038;list_uids=15882141&#038;dopt=Abstract\"><em>Journal of Computational Biology 12 (4) 431-456 (2005)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>The Incomplete Perfect Phylogeny Haplotype Problem<\/h3>\n  <h4>Gad Kimmel and Ron Shamir<\/h4>\n     <a href=\"http:\/\/www.worldscinet.com\/jbcb\/03\/0302\/S0219720005001090.html\"><em>Journal of Bioinformatics and Computational Biology Vol. 3 No. 2 1-25 (2005)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>>Modeling and analysis of heterogeneous regulation in biological networks<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/metareg-recomb-satellite.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>I. Gat-Viks, A. Tanay, R. Shamir<\/h4>\n    <em>Proc. of the first RECOMB Bioinformatics<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>GERBIL: GEnotype Resolution and Block Identification using Likelihood<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/gerbil-pnas.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>G.Kimmel and R. Shamir<\/h4>\n     <a href=\"http:\/\/www.pnas.org\/cgi\/content\/abstract\/102\/1\/158\"><em>Proc. National Academy of Science USA 102: 158-162 (2005) (website and supplementary material)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>A fully dynamic algorithms for modular decomposition and representation of cographs<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/dcog-DAM04.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>R. Shamir and R. Sharan<\/h4>\n    <em>Discrete Applied Mathematics<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>A note on tolerance graph recognition<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/tol.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Ryan B. Hayward and Ron Shamir<\/h4>\n    <em>Discrete Applied Mathematics<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Maximum likelihood resolution of multi-block genotypes<\/h3>\n  <h4>G. Kimmel and R. Shamir<\/h4>\n    <em>Proc. of RECOMB<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Multi-level Modeling and Inference of Transcription Regulation<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/TanayShamir.ps\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>A. Tanay and R. Shamir<\/h4>\n     <a href=\"http:\/\/www.liebertonline.com\/doi\/abs\/10.1089\/1066527041410364\"><em>Journal of Computational Biology Vol. 11 No. 2-3, pp. 357-376 (2004)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Cluster Graph Modification Problems<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/cmod.ps\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Ron Shamir, Roded Sharan and Dekel Tsur<\/h4>\n    <em>Discrete Applied Mathematics<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>How prevalent is functional alternative splicing in the human genome?<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/casp_TG.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>R. Sorek, R. Shamir, G. Ast<\/h4>\n     <a href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/query.fcgi?cmd=Retrieve&#038;db=PubMed&#038;list_uids=14746986&#038;dopt=Abstract\"><em>Trends in Genetics 20 (2), 68-71 (2004)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>The Canine Olfactory Subgenome<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/dog-or.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Tsviya Olender, Tania Fuchs, Chaim Linhart, Ron Shamir, Mark Adams,Francis Kalush, Miriam Khen and Doron Lancet<\/h4>\n     <a href=\"http:\/\/www.sciencedirect.com\/science?_ob=ArticleURL&#038;_udi=B6WG1-4B5JMTD-1&#038;_user=48161&#038;_coverDate=03%2F31%2F2004&#038;_rdoc=4&#038;_fmt=full&#038;_orig=browse&#038;_srch=doc-info(%23toc%236809%232004%23999169996%23479352%23FLA%23display%23Volume)&#038;_cdi=6809&#038;_sort=d&#038;_docanchor=&#038;view=c&#038;_ct=21&#038;_acct=C000005078&#038;_version=1&#038;_urlVersion=0&#038;_userid=48161&#038;md5=982db76953c4ec72e17ab045e69b25ed\"><em>Genomics 83, 361-372 (2004)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>PIVOT: Protein Interactions VisualizatiOn Tool<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/pivot.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Nir Orlev, Ron Shamir and Yosef Shiloh<\/h4>\n     <a href=\"http:\/\/bioinformatics.oxfordjournals.org\/cgi\/content\/abstract\/btg426v1\"><em>Bioinformatics 30 (3), 424-425 (2004)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/\/biobic-pnas.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>A. Tanay, R. Sharan, M. Kupiec, R. Shamir<\/h4>\n     <a href=\"http:\/\/www.pnas.org\/cgi\/reprint\/0308661100v1\"><em>Proc. National Academy of Science USA 101 (9) 2981-2986 (March 2004) (website and supplementary material)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Computational Problems in Perfect Phylogeny Haplotyping: Xor-Genotypes and Tag SNPs<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/xpph-cpm.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Tamar Barzuza, Jacques S. Beckmann, Ron Shamir and Itsik Peer<\/h4>\n    <em>Proc. of CPM<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>A Global View of the Selection Forces in the Evolution of Yeast Cis-Regulation<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/prevo.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>A. Tanay, I. Gat-Viks, and R. Shamir<\/h4>\n     <a href=\"http:\/\/www.genome.org\/cgi\/content\/full\/14\/5\/829\"><em>Genome Research 14: 829-834 (2004) (website and supplementary material)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>A non-EST based method for exon-skipping prediction<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/altsp-classifier.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>R. Sorek, R. Shemesh, Y. Cohen, O. Basechess, G. Ast, R. Shamir<\/h4>\n     <a href=\"http:\/\/www.genome.org\/cgi\/content\/abstract\/14\/8\/1617\"><em>Genome Research 14 pp. 1617-1623 (2004)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Reconstructing Chain Functions in Genetic Networks<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/rchain_PSB.zip\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>I. Gat-Viks, R. Shamir, R.M. Karp and R. Sharan<\/h4>\n    <em>Pacific Symposium on Biocomputing<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Modeling and Analysis of Heterogeneous Regulation in Biological Networks<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/metareg_JCB.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>I. Gat-Viks, A. Tanay and R. Shamir<\/h4>\n     <a href=\"http:\/\/www.liebertonline.com\/doi\/abs\/10.1089%2Fcmb.2004.11.1034\"><em>Journal of Computational Biology Vol. 11 No. 6 pp. 1034-1049 (2004)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Towards Optimally Multiplexed Applications of Universal Arrays<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/snp_jcb.ps\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>A. Ben-Dor, T. Hartman, R. M. Karp, B. Schwikowski, R. Sharan and Z. Yakhini<\/h4>\n     <a href=\"http:\/\/www.liebertonline.com\/doi\/abs\/10.1089%2F1066527041410373\"><em>Journal of Computational Biology 11(2-3), pp. 477-494 (2004)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Designing Multi-Route Synthesis in Combinatorial Chemistry<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/combichem.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>A. Akavia, H. Senderowitz, A. Lerner and R. Shamir<\/h4>\n    <em>Journal of Combinatorial Chemistry<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Computational Problems in Noisy SNP and Haplotype Analysis: Block Scores, Block Identification and Population Stratification<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/blocks-informs.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Gad Kimmel, Roded Sharan and Ron Shamir<\/h4>\n    <em>INFORMS Journal on Computing<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>In silico identification of transcriptional regulators associated with c-Myc<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/Myc-NAR.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>R. Elkon, K. Zeller, C. Linhart, C. Dang, R. Shamir and Y. Shiloh<\/h4>\n     <a href=\"http:\/\/nar.oxfordjournals.org\/cgi\/content\/abstract\/32\/17\/4955\"><em>Nucleic Acid Research Vol. 32 No. 17, pp. 4955-4961 (2004)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Two notes on genome rearrangements<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/2notesonGR.ps\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Michal Ozery-Flato and Ron Shamir<\/h4>\n    <em>Journal of Bioinformatics and Computational Biology<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Genome-Wide In Silico Identification of Transcriptional Regulators Controlling the Cell Cycle in Human Cells<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/prima.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Ran Elkon, Chaim Linhart, Roded Sharan, Ron Shamir, and Yosef Shiloh<\/h4>\n     <a href=\"http:\/\/www.genome.org\/cgi\/content\/abstract\/13\/5\/773\"><em>Genome Research Vol. 13(5), pp. 773-780, (2003) (website and supplementary material)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Identifying Blocks and Sub-Populations in Noisy SNP Data<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/blocks-wabi03.ps\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Gad Kimmel, Roded Sharan and Ron Shamir<\/h4>\n    <em>Proc. of WABI<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Chain functions and scoring functions in genetic networks<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/chain-ismb03.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Irit Gat-Viks and Ron Shamir<\/h4>\n    <em>Bioinformatics<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Simpler 1.5-Approximation Algorithm for Sorting by Transpositions<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/CPM2003.ps\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Tzvika Hartman<\/h4>\n    <em>Proc. of CPM<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Towards Optimally Multiplexed Applications of Universal DNA Tag Systems<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/snp.ps\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Amir Ben-Dor, Tzvika Hartman, Benno Schwikowski , Roded Sharan , and Zohar Yakhini<\/h4>\n    <em>Proc. of RECOMB<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Detecting Excess Radical Replacements in Phylogenetic Trees<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/pos_sel.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>T. Pupko, R. Sharan, M. Hasegawa, R. Shamir and D. Graur<\/h4>\n     <a href=\"http:\/\/www.sciencedirect.com\/science?_ob=ArticleURL&#038;_udi=B6T39-49R5KF3-1&#038;_user=48161&#038;_coverDate=11%2F13%2F2003&#038;_rdoc=1&#038;_fmt=&#038;_orig=search&#038;_sort=d&#038;view=c&#038;_acct=C000005078&#038;_version=1&#038;_urlVersion=0&#038;_userid=48161&#038;md5=80db8819a334f1ea441a3a4cffccb17c\"><em>Gene 319, pp. 127-135, 2003<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Advanced Computational Techniques for Resequencing DNA with Polymerase Signaling Assay Arrays<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/specalign-orchid-PV.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Itsik Pe'er, Naama Arbili, Yi Liu, Colby Enck, Craig Gelfand, Ron Shamir<\/h4>\n     <a href=\"http:\/\/nar.oxfordjournals.org\/cgi\/content\/full\/31\/19\/5667\"><em>Nucleic Acids Research 31(19):5667-75 (2003)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>CLICK and EXPANDER: A System for Clustering and Visualizing Gene Expression Data<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/1787.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Roded Sharan, Adi Maron-Katz and Ron Shamir<\/h4>\n    <em>Bioinformatics<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Improved Algorithms for the Random Cluster Graph Model<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/cluster.ps.gz\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>R. Shamir and D. Tsur<\/h4>\n     <a href=\"http:\/\/www.springerlink.com\/content\/7hxc9mg2cvr3cnn7\/\"><em>Lecture Notes In Computer Science Vol. 2368<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>The Restriction Scaffold Problem<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/rsp.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>A. Ben-Dor, R. M. Karp, B. Schwikowski, R. Shamir<\/h4>\n    <em>Proc. of RECOMB 2002<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Handling Long Targets and Errors in Sequencing by Hybridization<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/esbh-recomb02.ps\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>E. Halperin, S. Halperin, T. Hartman and R. Shamir<\/h4>\n    <em>Proc. of RECOMB<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Scoring clustering solutions by their biological relevance<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/cl-eval-bioinfo.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>I. Gat-Viks, R. Sharan, R. Shamir<\/h4>\n     <a href=\"http:\/\/bioinformatics.oxfordjournals.org\/cgi\/content\/abstract\/19\/18\/2381\"><em>Bioinformatics 19: 2381-2389 (2003)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Modeling transcription programs: inferring binding site activity and dose-response model optimization<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/p085-tanay.ps.gz\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>A. Tanay and R. Shamir<\/h4>\n    <em>Proc. of RECOMB<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Algorithmic Approaches to Clustering Gene Expression Data<\/h3>\n  <h4>Ron Shamir and Roded Sharan<\/h4>\n    <em>Current Topics in Computational Molecular Biology<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Cluster Analysis and its Applications to Gene Expression Data<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/schering.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Roded Sharan, Rani Elkon and Ron Shamir<\/h4>\n    <em>Ernst Schering workshop on Bioinformatics and Genome Analysis<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Discovering Statistically Significant Biclusters in Gene Expression Data<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/bic-ismb02.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>A. Tanay, R. Sharan, R. Shamir<\/h4>\n     <a href=\"http:\/\/bioinformatics.oxfordjournals.org\/cgi\/content\/abstract\/18\/suppl_1\/S136\"><em>Proc. of ISMB 2002; Bioinformatics Vol. 18 Suppl. 1 S136-S144<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>The Degenerate Primer Design Problem<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/dpd-ismb02.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>C. Linhart, R. Shamir<\/h4>\n    <em>Proc. of ISMB<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>On the Properties of Sequences of Reversals that Sort a Signed Permutation<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/jobim.ps\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Anne Bergeron, Cedric Chauve, Tzvika Hartman and Karine St-Onge<\/h4>\n    <em>Proc. of JOBIM<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>DEFOG: A Practical Scheme for Deciphering Families of Genes<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/defog-genomics.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Tania Fuchs, Barbora Malecova, Chaim Linhart, Roded Sharan, Miriam Khen, Ralf Herwig, Dmitry Shmulevich, Rani Elkon, Matthias Steinfath, John K. O'Brien, Uwe Radelof, Hans Lehrach, Doron Lancet, and Ron Shamir<\/h4>\n     <a href=\"http:\/\/www.sciencedirect.com\/science?_ob=ArticleURL&#038;_udi=B6WG1-46MK1FM-8&#038;_user=48161&#038;_coverDate=09%2F30%2F2002&#038;_rdoc=1&#038;_fmt=&#038;_orig=search&#038;_sort=d&#038;view=c&#038;_acct=C000005078&#038;_version=1&#038;_urlVersion=0&#038;_userid=48161&#038;md5=8c807da6c18b3f8d64b411d108574f67\"><em>Genomics Vol. 80, No. 3, 295-302 (2002)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>A computational method for resequencing long DNA targets by universal oligonucleotide arrays<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/PNAS02.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>I. Pe'er, N. Arbili and R. Shamir<\/h4>\n     <a href=\"http:\/\/www.pnas.org\/content\/vol99\/issue24\/index.shtml\"><em>Proc. National Academy of Science USA Vol. 99 pp. 15497-15500 (2002)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Complexity Classification of Some Edge Modification Problems<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/mod.ps\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>A. Natanzon, R. Shamir and R.Sharan<\/h4>\n    <em>Discrete Applied Mathematics<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Large Scale Sequencing By Hybridization<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/msbh.ps\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Ron Shamir and Dekel Tsur<\/h4>\n    <em>Proc. of RECOMB<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Computational Expansion of Genetic Networks<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/TanayShamirISMB01.ps\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>A. Tanay and Ron Shamir<\/h4>\n     <a href=\"http:\/\/bioinformatics.oxfordjournals.org\/cgi\/content\/abstract\/17\/suppl_1\/S270\"><em>Proc. of ISMB 2001; Bioinformatics Vol. 17, Supplement 1, pp. S270-S278 (2001)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>A Chemical Distance Based Test for Positive Darwinian Selection<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/ps.ps.gz\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>T. Pupko, R. Sharan, M. Hasegawa, R. Shamir and D. Graur<\/h4>\n    <em>Proc. of WABI<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Incomplete Directed Perfect Phylogeny<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/sines.ps\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Itsik Pe'er, Ron Shamir and Roded Sharan<\/h4>\n    <em>Proc. of CPM<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>On the Complexity of Positional Sequencing by Hybridization<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/psbh.ps\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Ben-Dor, I. Pe'er, R. Shamir and R. Sharan<\/h4>\n    <em>Proc. of CPM<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>A Fully Dynamic Algorithm for Recognizing and Representing Proper Interval Graphs<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/dpig.ps\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Pavol Hell, Ron Shamir and Roded Sharan<\/h4>\n    <em>Proc. of ESA<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>An Algorithm for Clustering cDNAs for Gene Expression Analysis Using Short Oligonucleotide Fingerprints<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/recomb99a.ps.gz\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>E. Hartuv, A. Schmitt, J. Lange, S. Meier-Ewert, H. Lehrach and R. Shamir<\/h4>\n    <em>Proc. of RECOMB<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>A Clustering Algorithm based on Graph Connectivity<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/hcs.ps\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>E. Hartuv, R. Shamir<\/h4>\n    <em>Information Processing Letters<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Fast Algorithm for Reconstruction of Ancestral Amino-Acid Sequences<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/ancestral.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Tal Pupko, Itsik Pe'er, Ron Shamir and Dan Graur<\/h4>\n    <em>Molecular Biology and Evolution<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>An Algorithm Combining Discrete and Continuous Methods for Optical Mapping<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/om2.ps\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Richard M. Karp, Itsik Pe'er, Ron Shamir<\/h4>\n    <em>Proc. of ISMB<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Approximation Algorithms for the Median Problem in the Breakpoint Model<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/breakpt-median-approx.ps\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Itsik Pe'er and Ron Shamir<\/h4>\n    <em>Comparative Genomics<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>CLICK: A Clustering Algorithm with Applications to Gene Expression Analysis<\/h3>\n  <h4>Roded Sharan and Ron Shamir<\/h4>\n    <em>Currents in Compuational Molecular Biology<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Spectrum Alignment: Efficient Resequencing by Hybridization<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/specalign.ps\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Itsik Pe'er and Ron Shamir<\/h4>\n    <em>Proc. of ISMB<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Bounded Degree Interval Sandwich Problems<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/degree.ps\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Haim Kaplan and Ron Shamir<\/h4>\n     <a href=\"http:\/\/link.springer.de\/link\/service\/journals\/00453\/bibs\/24n2p96.html\"><em>Algorithmica, Vol. 24, No. 2, pp. 96-104 (1999)<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Tractability of parameterized completion problems on chordal, strongly chordal and proper interval graphs<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/paracomp.ps\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Haim Kaplan, Ron Shamir and Robert E. Tarjan<\/h4>\n    <em>SIAM Journal of Computing<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Faster Subtree Isomorphism<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/subtree.ps\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Ron Shamir, Dekel Tzur<\/h4>\n    <em>Journal of Algorithms<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Construction of Physical Maps From Oligonucleotide Fingerprints Data<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/guymap.ps.gz\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>G. Mayraz, R. Shamir<\/h4>\n    <em>Journal of Computational Biology<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Clustering Gene Expression Patterns<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/bioclust.zip\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>A. Ben-Dor, R. Shamir, Z. Yakhini<\/h4>\n    <em>Journal of Computational Biology<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Perfect Completion and Deletion in Random Graphs<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/gap.ps\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Assaf Natanzon, Ron Shamir<\/h4>\n    <em>Technical Report<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Optimizing the BAC-End Strategy for Sequencing the Human Genome<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/stc.ps\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Kichard M. Karp, Ron Shamir<\/h4>\n    <em>Technical Report<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Algorithms for Optical Mapping<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/recomb98.ps\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>R. M. Karp, R. Shamir<\/h4>\n    <em>Proc. of RECOMB<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>A Polynomial Approximation Algorithm for the Minimum Fill-In Problem<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/fillin-approx.ps\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>A. Natanzon, R. Shamir and R.Sharan<\/h4>\n    <em>Proc. of STOC<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Faster and Simpler Algorithm for Sorting Signed Permutations by Reversals<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/soda97.ps\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Haim Kaplan, Ron Shamir and Robert E. Tarjan<\/h4>\n    <em>Proc. of SODA<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>The maximum subforest problem: Approximation and exact algorithms<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/soda98.ps\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Ron Shamir, Dekel Tzur<\/h4>\n    <em>Proc. of SODA<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Realizing interval graphs with size and distance constraints<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/mig.ps\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Itsik Pe'er and Ron Shamir<\/h4>\n    <em>SIAM Journal of Discrete Mathematics<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Satisfiability Problems on Intervals and Unit Intervals<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/tcs.ps\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Itsik Pe'er and Ron Shamir<\/h4>\n    <em>Theoretical Computer Science<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Pathwidth, Bandwidth and Completion Problems to Proper Interval Graphs with Small Cliques<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/pw.ps\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Haim Kaplan, Ron Shamir<\/h4>\n    <em>SIAM J. Computing<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Physical Maps and Interval Sandwich Problems: Bounded Degrees Help<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/istcs96.ps\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Haim Kaplan and Ron Shamir<\/h4>\n    <em>Proc. of ISTCS<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Interval Graphs with Side (and Size) Constraints<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/esa.ps\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Itsik Pe'er and Ron Shamir<\/h4>\n    <em>Proc. of the Third European Symposium on Algorithms (ESA 95)<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Four Strikes Against Physical Mapping of DNA<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/4strikes.ps\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Paul W. Goldberg, Martin C. Golumbic, Haim Kaplan and Ron Shamir<\/h4>\n    <em>Journal of Computational Biology<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Algorithms and Complexity of Sandwich Problems in Graphs<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/sand_wg93.ps\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Martin Golumbic Haim Kaplan, Ron Shamir<\/h4>\n    <em>Proc. of WG<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Tractability of parameterized completion problems on chordal and interval graphs: Minimum Fill-in and Physical Mapping<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/pwfocs.ps\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Haim Kaplan, Ron Shamir, Robert E. Tarjan<\/h4>\n    <em>Proc. of FOCS<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><\/div>\n  <div class=\"col-md-10\"><h3>Complexity and algorithms for reasoning about time: a graph-theoretic approach<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/02\/rat.ps\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Martin Golumbic, Ron Shamir<\/h4>\n    <em>JACM<\/em> <\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/06\/BMC_genomics.png\" title=\"BMC_genomics.png\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Reduced changes in protein compared to mRNA levels across non-proliferating tissues<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2019\/06\/Kobi_BMC_Genomics_art3A10.11862Fs12864-017-3683-9.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>K. Perl, K. Ushakov, Y. Pozniak, O. Yizhar-Barnea, Y. Bhonker, S. Shivatzki, T. Geiger, K.B. Avraham and R. Shamir<\/h4>\n     <a href=\"https:\/\/bmcgenomics.biomedcentral.com\/articles\/10.1186\/s12864-017-3683-9\"><em>BMC Genomics, 18:305, DOI 10.1186\/s12864-017-3683-9 (2017).  <\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/06\/HBM-wpcf_80x100.jpg\" title=\"HBM.jpg\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Tired and misconnected: A breakdown of brain modularity following sleep deprivation.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/06\/Adi_MK_Simon_et_al-2017-Human_Brain_Mapping.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>E. Ben Simon, A. Maron-Katz, N. Lahav, R. Shamir and T. Hendler.<\/h4>\n     <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/28370703\"><em>Human Brain Mapping, 38(6):3300-3314. doi: 10.1002\/hbm.23596 (2017).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/06\/BIORXIV2017-3-wpcf_80x100.png\" title=\"BIORXIV2017-3.png\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Reconstructing cancer karyotypes from short read data: the half full and half empty glass<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/06\/Rami_152447.full_.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>R. Eitan, R. Shamir.<\/h4>\n     <a href=\"http:\/\/biorxiv.org\/content\/early\/2017\/06\/20\/152447\"><em>bioRxiv 152447; doi: https:\/\/doi.org\/10.1101\/152447 (2017).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/07\/bioinformatics-j-wpcf_80x100.jpg\" title=\"bioinformatics-j.jpg\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Improving the performance of minimizers and winnowing schemes<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/07\/David_Pellow_104075.full_.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>G. Marcais, D. Pellow, D. Bork, Y. Orenstein, R. Shamir, C. Kingsford.<\/h4>\n     <a href=\"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/14\/i110\/3953951\/Improving-the-performance-of-minimizers-and?guestAccessKey=594c6ca5-e053-4713-b23f-28a1481be865\"><em>Bioinformatics, special issue of ISMB\/ECCB 2017, Vol. 33, i110\u2013i117 doi: 10.1093\/bioinformatics\/btx235 (2017).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/07\/Algorithms_for_Molecular_Biology-wpcf_80x100.jpg\" title=\"Algorithms_for_Molecular_Biology.jpg\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Complexity and algorithms for copy-number evolution problems<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/07\/Ron_Zeira_s13015-017-0103-2.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>M. El-Kebir, B. J. Raphael, R. Shamir, R. Sharan, S. Zaccaria, M. Zehavi and R. Zeira<\/h4>\n     <a href=\"https:\/\/almob.biomedcentral.com\/articles\/10.1186\/s13015-017-0103-2\"><em>Algorithms for Molecular Biology, 12(1), 13 (2017).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/07\/bioinformatics-j-2-wpcf_80x100.jpg\" title=\"bioinformatics-j-2.jpg\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Faucet: streaming de novo assembly graph construction<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/12\/Roye_Rozov_btx471.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>R. Rozov,  G. Goldshlager,  E. Halperin,  R. Shamir.<\/h4>\n     <a href=\"https:\/\/doi.org\/10.1093\/bioinformatics\/btx471\"><em>Bioinformatics,  34 (1) 147\u2013154 (2018).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/08\/Plos_comp_bio_download-wpcf_80x100.jpg\" title=\"Plos_comp_bio_download.jpg\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Extracting replicable associations across multiple studies: Empirical Bayes algorithms for controlling the false discovery rate<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/08\/Didi_journal.pcbi_.1005700.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>D. Amar, R. Shamir, D. Yekutieli.<\/h4>\n     <a href=\"http:\/\/journals.plos.org\/ploscompbiol\/article?id=10.1371\/journal.pcbi.1005700\"><em>PLoS Computational Biology 13(8): e1005700 (2017).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/09\/BIORXIV2017-wpcf_80x100.png\" title=\"BIORXIV2017.png\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>An extensive enhancer-promoter map generated by genome-scale analysis of enhancer and gene activity patterns<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/09\/Tom_190231.1.full_Sept2017.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>T. A. Hait, D. Amar, R. Shamir and R. Elkon.<\/h4>\n     <a href=\"http:\/\/www.biorxiv.org\/content\/early\/2017\/09\/18\/190231.1\"><em>BioRxiv, doi: https:\/\/doi.org\/10.1101\/190231 (2017).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/10\/Com_Bio-wpcf_80x100.jpg\" title=\"Com_Bio.jpg\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>A Linear-Time Algorithm for the Copy Number Transformation Problem<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/10\/Ron_Zeira_cmb.2017.0060.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>R. Zeira, M. Zehavi and R. Shamir<\/h4>\n     <a href=\"http:\/\/online.liebertpub.com\/doi\/abs\/10.1089\/cmb.2017.0060\"><em>Journal of Computational Biology, DOI: 10.1089\/cmb.2017.0060 (2017).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/11\/Plos_comp_bio_download-wpcf_80x100.jpg\" title=\"Plos_comp_bio_download.jpg\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Designing small universal k-mer hitting sets for improved analysis of high throughput sequencing<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/11\/Pellow_journal.pcbi_.1005777.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Y. Orenstein, D. Pellow, G. Marcais, R. Shamir, C. Kingsford.<\/h4>\n     <a href=\"http:\/\/journals.plos.org\/ploscompbiol\/article?id=10.1371\/journal.pcbi.1005777\"><em>PLoS Computational Biology, 13(10): e1005777  (2017).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/11\/Neurology_Oct17-wpcf_80x100.jpg\" title=\"Neurology_Oct17.jpg\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Analysis of blood-based gene expression in idiopathic Parkinson disease<\/h3>\n  <h4>R. Shamir, C. Klein, D. Amar, E. J. Vollstedt, M. Bonin, M. Usenovic, Y. C. Wong, A. Maver, A. Troiano, S. Poths, H. Safer, J.-C. Corvol, S. Lesage, O. Lavi, G. Deuschl, G. Kuhlenbaeumer, H. Pawlack, I. Ulitsky, M. Kasten, O. Riess, A. Brice, B. Peterlin, D. Krainc.\r\n<\/h4>\n     <a href=\"http:\/\/www.neurology.org\/content\/early\/2017\/09\/15\/WNL.0000000000004516.abstract \"><em>Neurology, 89(16):1676-1683 (2017).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/11\/BMC_bioinformatics-wpcf_80x100.gif\" title=\"BMC_bioinformatics.gif\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Reconstructing cancer karyotypes from short read data: the half full and half empty glass<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/11\/Rami_Eitan_s12859-017-1929-9.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>R. Eitan, R. Shamir.<\/h4>\n     <a href=\"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-017-1929-9\"><em>BMC Bioinformatics, 18:488, 2017.  Preliminary version:  bioRxiv 152447; doi: https:\/\/doi.org\/10.1101\/152447 (2017).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/12\/frontiers_behavioral_neuroscience-wpcf_80x100.jpg\" title=\"frontiers_behavioral_neuroscience.jpg\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Tracing the neural carryover effects of interpersonal anger on resting-state fMRI\u00a0and their relation to traumatic stress symptoms in a subsample of soldiers<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2017\/12\/Adi_fnbeh-11-00252.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>G. Gilam, A. Maron-Katz, E. Kliper, T. Lin, E. Fruchter, R. Shamir, T. Hendler.<\/h4>\n     <a href=\"https:\/\/www.frontiersin.org\/articles\/10.3389\/fnbeh.2017.00252\/full\"><em>Frontiers in Behavioral Neuroscience, doi: 10.3389\/fnbeh.2017.00252 (2017).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2018\/01\/bioinformatics-j-wpcf_80x100.jpg\" title=\"bioinformatics-j.jpg\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>ADEPTUS: A discovery tool for disease prediction, enrichment and network analysis based on profiles from many diseases<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2018\/01\/Didi_Amir_ADEPTUS2_Jan2018.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>D. Amar,  A. Vizel, C. Levy  & R. Shamir.<\/h4>\n     <a href=\"https:\/\/academic.oup.com\/bioinformatics\/advance-article\/doi\/10.1093\/bioinformatics\/bty027\/4817619\"><em>Bioinformatics, bty027, https:\/\/doi.org\/10.1093\/bioinformatics\/bty027 (2018).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2018\/03\/Frontiers_Plant_Science-wpcf_80x100.jpg\" title=\"Frontiers_Plant_Science.jpg\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>MorphDB: Prioritizing Genes for Specialized Metabolism Pathways and Gene Ontology Categories in Plants<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2018\/03\/Tzfadia_Amar_Shamir_pls-09-00352.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>A. Zwaenepoel, T. Diels, D. Amar, T. Van Parys, R. Shamir, Y. Van de Peer and O. Tzfadia.<\/h4>\n     <a href=\"https:\/\/www.frontiersin.org\/articles\/10.3389\/fpls.2018.00352\/full\"><em>Front. Plant Sci., https:\/\/doi.org\/10.3389\/fpls.2018.0035 (2018).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2018\/05\/Genome_Biology-wpcf_80x100.jpg\" title=\"Genome_Biology.jpg\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>FOCS: a novel method for analyzing enhancer and gene activity patterns infers an extensive enhancer\u2013promoter map<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2018\/05\/Tom_Hait_s13059-018-1432-2.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>T. A. Hait, D. Amar, R. Shamir, R. Elkon.<\/h4>\n     <a href=\"https:\/\/genomebiology.biomedcentral.com\/articles\/10.1186\/s13059-018-1432-2\"><em>Genome Biology, 19:56, https:\/\/doi.org\/10.1186\/s13059-018-1432-2 (2018).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2018\/05\/bioinformatics-j-wpcf_80x100.jpg\" title=\"bioinformatics-j.jpg\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Sorting cancer karyotypes using double-cut-and-joins, duplications and deletions<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2018\/05\/Ron_Zeira_bty381.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>R. Zeira and R. Shamir.<\/h4>\n     <a href=\"https:\/\/academic.oup.com\/bioinformatics\/advance-article\/doi\/10.1093\/bioinformatics\/bty381\/4992148\"><em>Bioinformatics, bty381, https:\/\/doi.org\/10.1093\/bioinformatics\/bty381 (2018).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2018\/06\/Human_Genomics-wpcf_80x100.jpg\" title=\"Human_Genomics.jpg\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Computational analysis of mRNA expression profiling in the inner ear reveals candidate transcription factors associated with proliferation, differentiation, and deafness<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2018\/06\/Kobi_s40246-018-0161-7.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>K. Perl, R. Shamir and K. B. Avraham<\/h4>\n     <a href=\"https:\/\/humgenomics.biomedcentral.com\/articles\/10.1186\/s40246-018-0161-7\"><em>Human Genomics,  12:30, https:\/\/doi.org\/10.1186\/s40246-018-0161-7 (2018).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2019\/05\/bioinformatics_and_phylogenetics-wpcf_80x100.png\" title=\"bioinformatics_and_phylogenetics.png\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Genome Rearrangement Problems with Single and Multiple Gene Copies: A Review<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2018\/08\/Ron_Zeira_genome-rearrangement-problems-second-revision_updated_12Aug2018.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>R. Zeira and R. Shamir.<\/h4>\n     <a href=\"https:\/\/www.springer.com\/gp\/book\/9783030108366\"><em>Bioinformatics and Phylogenetics: Seminal contributions of Bernard Moret, T. Warnow, Editor, pp. 205--242, Springer Nature Switzerland AG (2019).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2018\/10\/NAR2018-wpcf_80x100.jpg\" title=\"NAR2018.jpg\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Multi-omic and multi-view clustering algorithms: review and cancer benchmark<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2018\/10\/Nimrod_NAR_gky889.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>N. Rappoport & R. Shamir<\/h4>\n     <a href=\"https:\/\/academic.oup.com\/nar\/article\/46\/20\/10546\/5123392?guestAccessKey=a38211b7-14be-452b-9fd5-a8ae64e116a8\"><em>Nucleic Acids Research, 46 (20) pp. 10546\u2013-10562 (2018).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2018\/09\/epigenetics_and_chromatin-wpcf_80x100.jpg\" title=\"epigenetics_and_chromatin.jpg\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Genomic meta-analysis of the interplay between 3D chromatin organization and gene expression programs under basal and stress conditions<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2018\/09\/Idan_s13072-018-0220-2.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>I. Nurick, R. Shamir and R. Elkon.<\/h4>\n     <a href=\"https:\/\/epigeneticsandchromatin.biomedcentral.com\/articles\/10.1186\/s13072-018-0220-2\"><em>Epigenetics & Chromatin (2018) 11:49 https:\/\/doi.org\/10.1186\/s13072-018-0220-2 (2018).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2018\/09\/npj-Biofilms-and-Microbiomes-228x300-wpcf_80x100.jpg\" title=\"npj-Biofilms-and-Microbiomes-228x300.jpg\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>GePMI: A statistical model for personal intestinal microbiome identification <\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2018\/09\/Ting_Chen_Ron_Shamir_s41522-018-0065-2.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Z. Wang, H. Lou, R. Shamir, R. Jiang, T. Chen.<\/h4>\n     <a href=\"https:\/\/www.nature.com\/articles\/s41522-018-0065-2\"><em>npj Biofilm and Microbiome} 4: 20, https:\/\/doi.org\/10.1038\/s41522-018-0065-2 (2018).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2019\/05\/bioinformatics.png\" title=\"bioinformatics.png\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>NEMO: cancer subtyping by integration of partial multi-omic data<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2019\/05\/Nimrod_Rappoport_btz058.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>N. Rappoport and R. Shamir.<\/h4>\n     <a href=\"https:\/\/academic.oup.com\/bioinformatics\/advance-article\/doi\/10.1093\/bioinformatics\/btz058\/5304361\"><em>Bioinformatics, https:\/\/doi.org\/10.1093\/bioinformatics\/btz058 (2018).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2019\/06\/JMB-wpcf_80x100.gif\" title=\"JMB.gif\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>The EXPANDER integrated platform for transcriptome analysis<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2019\/06\/expander_tom_june2019_1-s2.0-S0022283619302803-main.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>T. A. Hait, A.Maron-Katz., D. Sagir, D. Amar, I. Ulitsky, C. Linhart, A. Tanay, R. Sharan, Y. Shiloh, R. Elkon, R.Shamir.<\/h4>\n     <a href=\"https:\/\/doi.org\/10.1016\/j.jmb.2019.05.013\"><em>Journal of Molecular Biology, https:\/\/doi.org\/10.1016\/j.jmb.2019.05.013 (2019).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2019\/07\/BIORXIV2017-wpcf_80x100.png\" title=\"BIORXIV2017.png\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>CT-FOCS: a novel method for inferring cell type-specific enhancer-promoter maps<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2021\/09\/ct_focs_updated_sept2021_707158v3.full_.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>T. Hait, R. Elkon, R. Shamir.<\/h4>\n     <a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/707158v3\"><em>BioRxiv, https:\/\/www.biorxiv.org\/content\/10.1101\/707158v3 (2019).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2019\/08\/PLOS_ONE-wpcf_80x87.jpg\" title=\"PLOS_ONE.jpg\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Personalized prediction of adverse heart and kidney events using baseline and longitudinal data from SPRINT and ACCORD<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2019\/08\/Gal_Dinstag_journal.pone_.0219728_Aug2019.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>G. Dinstag, D. Amar, E. Ingelsson, E. Ashley and R. Shamir.<\/h4>\n     <a href=\"https:\/\/doi.org\/10.1371\/journal.pone.0219728\"><em>PLOS ONE, https:\/\/doi.org\/10.1371\/journal.pone.0219728 (2019).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2019\/08\/molecular_systems_biology-wpcf_80x100.png\" title=\"molecular_systems_biology.png\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Inaccuracy of the log\u2010rank approximation in cancer data analysis<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2019\/08\/nimrod_rappoport_msb.20188754_aug2019.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>N. Rappoport and R. Shamir.<\/h4>\n     <a href=\"https:\/\/www.embopress.org\/doi\/10.15252\/msb.20188754\"><em>Molecular Systems Biology (2019) 15:e8754https:\/\/doi.org\/10.15252\/msb.20188754 (2019).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2019\/11\/bioinformatics-j-wpcf_80x100.jpg\" title=\"bioinformatics-j.jpg\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Prodigy: personalized prioritization of driver genes<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2019\/11\/Gal_Dinstag_Prodigy_btz815.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>G. Dinstag, R. Shamir.<\/h4>\n     <a href=\"https:\/\/academic.oup.com\/bioinformatics\/advance-article\/doi\/10.1093\/bioinformatics\/btz815\/5612092?guestAccessKey=99652dc9-9980-47c8-a568-2fe53c366aee\"><em>Bioinformatics btz815, https:\/\/doi.org\/10.1093\/bioinformatics\/btz815 (2019).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2019\/12\/environmental_microbiology-wpcf_80x100.jpg\" title=\"environmental_microbiology.jpg\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Unravelling plasmidome distribution and interaction with its hosting microbiome<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2019\/12\/aimee_environmental_microbiology_dec2019.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>A. Kav Brown, R. Rozov, D. Bogmil, S. J. Sorensen, I. Benhar, E. Halperin, R. Shamir, I. Mizrahi.<\/h4>\n     <a href=\"https:\/\/sfamjournals.onlinelibrary.wiley.com\/doi\/full\/10.1111\/1462-2920.14813\"><em>Environmental Microbiology, https:\/\/doi.org\/10.1111\/1462-2920.14813 (2019).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2019\/12\/bioinformatics-j-wpcf_80x100.jpg\" title=\"bioinformatics-j.jpg\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>PROMO: an interactive tool for analyzing clinically-labeled multi-omic cancer datasets<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2019\/12\/dvir_netanely_promo_dec2019_s12859-019-3142-5.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>D. Netanely, N. Stern, I. Laufer,  R. Shamir.<\/h4>\n     <a href=\"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-019-3142-5#citeas\"><em>BMC Bioinformatics 20:732, https:\/\/doi.org\/10.1186\/s12859-019-3142-5 (2019).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2020\/01\/infection-wpcf_80x100.jpg\" title=\"infection.jpg\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Using the kinetics of C-reactive protein response to improve the differential diagnosis between acute bacterial and viral infections<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2020\/01\/Coster2019_Article_UsingTheKineticsOfC-reactivePr.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>D. Coster, A. Wasserman, E. Fisher, O. Rogowski, D. Zeltser, I. Shapira, D. Bernstein, Ahuva Meilik, E. Raykhshtat, P. Halpern, S. Berliner, S. Shenhar-Tsarfaty, R. Shamir.<\/h4>\n     <a href=\"https:\/\/link.springer.com\/article\/10.1007\/s15010-019-01383-6\"><em>Infection,  https:\/\/doi.org\/10.1007\/s15010-019-01383-6 (2020).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2021\/01\/molecular_SYSTEM_BIOLOGY-wpcf_80x100.jpg\" title=\"molecular_SYSTEM_BIOLOGY.jpg\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>DOMINO: a novel network-based module detection algorithm with reduced rate of false calls<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2021\/01\/Hagai_DOMINO_msb.20209593.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>H. Levi, R. Elkon, R. Shamir.<\/h4>\n     <a href=\"https:\/\/www.embopress.org\/doi\/full\/10.15252\/msb.20209593\"><em>Molecular Systems Biology 17:e9593 (2021).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2020\/04\/cancer_research-1-wpcf_80x100.jpg\" title=\"cancer_research-1.jpg\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Melanoma-secreted lysosomes trigger monocyte-derived dendritic cell apoptosis and limit cancer immunotherapy<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2020\/04\/Netanely_Shamir_cancer_research_journal_0008-5472.CAN-19-2944.full_.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>N. S. Magal , L. Farhat-Younis , D. Rasoulouniriana , A. Glieberman , A. Gutwillig , L. Tal , D. Netanely, R. Shamir , R. Blau , H. Gutman ,P. Rider, Y. Carmi.<\/h4>\n     <a href=\"https:\/\/cancerres.aacrjournals.org\/content\/early\/2020\/03\/03\/0008-5472.CAN-19-2944\"><em>Cancer Research, doi: 10.1158\/0008-5472.CAN-19-2944 (2020).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2020\/05\/plos_comp_bio-wpcf_80x100.png\" title=\"plos_comp_bio.png\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>PlasClass improves plasmid sequence classification<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2020\/05\/David_Pellow_may2020_journal.pcbi_.1007781.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>D. Pellow, I. Mizrahi, R. Shamir.<\/h4>\n     <a href=\"https:\/\/journals.plos.org\/ploscompbiol\/article?id=10.1371\/journal.pcbi.1007781\"><em>PLoS Comput Biol, 16(4): e1007781. https:\/\/doi.org\/10.1371\/journal.pcbi.1007781 (2020).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2020\/09\/PLOS_COMP_BIO_2020-wpcf_80x100.png\" title=\"PLOS_COMP_BIO_2020.png\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>MONET: Multi-omic patient module detection by omic selection<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2020\/09\/Nimrod_monet_journal.pcbi_.1008182.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>N. Rappoport, R. Safra, R. Shamir.<\/h4>\n     <a href=\"https:\/\/journals.plos.org\/ploscompbiol\/article?id=10.1371\/journal.pcbi.1008182\"><em>PLoS Computational Biology 16 (9) e1008182 (2020).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2021\/08\/ACM-BCB-wpcf_80x100.jpg\" title=\"ACM-BCB.jpg\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Improving the efficiency of de Bruijn graph construction using compact universal hitting sets<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2021\/08\/yael_ben-ari_ACMBCB-proceedings.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Y. Ben-Ari, D. Flomin, L. Pu, Y. Orenstein, R. Shamir.\r\n\r\n<\/h4>\n     <a href=\"https:\/\/dl.acm.org\/doi\/10.1145\/3459930.3469520\"><em>Proc. ACM Conference on Bioinformatics, Computational Biology and Health Informatics (ACM-BCB), August 2021, Article No.: 4, pp 1\u20139, https:\/\/dl.acm.org\/doi\/10.1145\/3459930.3469520 (2021).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2021\/01\/fss23-wpcf_80x100.jpg\" title=\"fss23\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Risk Modeling of Time-Varying Covariates Using an Ensemble of Survival Trees: Predicting Future Cancer Events<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2021\/01\/27711-Article-Text-31762-1-2-20240122.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>D. Coster, E. Fischer, S. Shenhar-Tsarfaty, T. Menes, S. Berliner, O. Rogowski, D. Zeltser, I. Shapira, E. Halperin, S. Rosset, M. Gorfine, R. Shamir.<\/h4>\n     <a href=\"https:\/\/ojs.aaai.org\/index.php\/AAAI-SS\/article\/view\/27711\"><em>Proceedings of the AAAI Symposium Series, 2(1), 429-442. https:\/\/doi.org\/10.1609\/aaaiss.v2i1.27711 (2023).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2021\/02\/oncogene_2021-wpcf_80x100.jpg\" title=\"oncogene_2021.jpg\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Classification of node-positive melanomas into prognostic subgroups using keratin, immune and melanogenesis expression patterns<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2021\/02\/dvir_oncogene_s41388-021-01665-0.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>D. Netanely, S. Leibou, R. Parikh, N. Stern, H. Vaknine, R. Brenner, S. Amar, R. Haiat Factor, T. Perluk, J. Frand, E Nizri, D. Hershkovitz, V. Zemser-Werner, C. Levy, R. Shamir.<\/h4>\n     <a href=\"https:\/\/www.nature.com\/articles\/s41388-021-01665-0\"><em>Oncogene https:\/\/doi.org\/10.1038\/s41388-021-01665-0 (2021).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2021\/06\/Microbiome-wpcf_80x100.jpg\" title=\"Microbiome.jpg\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>SCAPP: An algorithm for improved plasmid assembly in metagenomes<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2021\/06\/David_Pellow_SCAPP_micobiome_journal_June2021.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>D. Pellow, M. Probst, O. Furman, A. Zorea, A. Segal, I. Mizrahi, R. Shamir.<\/h4>\n     <a href=\"https:\/\/microbiomejournal.biomedcentral.com\/articles\/10.1186\/s40168-021-01068-z\"><em>Microbiome 9, 144 (2021), https:\/\/doi.org\/10.1186\/s40168-021-01068-z (2021).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2021\/10\/bmc_womens_health-wpcf_80x100.jpg\" title=\"bmc_womens_health.jpg\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Contribution of clinical breast exam to cancer detection in women participating in a modern screening program.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2021\/10\/dan_coster_BMC_women_health_12905-021-01507-x.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>T.S. Menes,  D. Coster  and S. Shenhar-Tsarfaty.<\/h4>\n     <a href=\"https:\/\/bmcwomenshealth.biomedcentral.com\/articles\/10.1186\/s12905-021-01507-x\"><em>BMC Women's Health, 21(1) 368, pp.1-8., https:\/\/doi.org\/10.1186\/s12905-021-01507-x (2021).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2021\/12\/BMC_ifectious_diseases-wpcf_80x100.jpg\" title=\"BMC_ifectious_diseases.jpg\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>C-reactive protein velocity discriminates between acute viral and bacterial infections in patients who present with relatively low CRP concentrations<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2021\/12\/dan_coster_BMC_s12879-021-06878-y.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>D. Bernstein, D. Coster, S. Berliner, I. Shapira, D. Zeltser, O. Rogowski, A. Adler, O. Halutz, T. Levinson, O. Ritter, S. Shenhar-Tsarfaty & A. Wasserman.<\/h4>\n     <a href=\"https:\/\/bmcinfectdis.biomedcentral.com\/articles\/10.1186\/s12879-021-06878-y\"><em>BMC Infect Dis 21, 1210 (2021). https:\/\/doi.org\/10.1186\/s12879-021-06878-y (2021).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2022\/02\/nar_2021-wpcf_80x100.jpg\" title=\"nar_2021.jpg\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>CT-FOCS: a novel method for inferring cell type-specific enhancer-promoter maps.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2022\/02\/Tom_Hait_gkac048_1_Feb2022.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>T.A. Hait, R. Elkon, R. Shamir.\r\n<\/h4>\n     <a href=\"https:\/\/academic.oup.com\/nar\/advance-article\/doi\/10.1093\/nar\/gkac048\/6517947\"><em>Nucleic Acids Research gkac048, https:\/\/doi.org\/10.1093\/nar\/gkac048 (2022).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2022\/02\/bioinformatics-j-wpcf_80x100.jpg\" title=\"bioinformatics-j.jpg\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>The DOMINO web-server for active module identification analysis.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2022\/02\/Hagai_domino_in_bioinformatics_journal_btac067_feb2022.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>H. Levi, N. Rahmanian, R. Elkon, R. Shamir.<\/h4>\n     <a href=\"https:\/\/academic.oup.com\/bioinformatics\/advance-article\/doi\/10.1093\/bioinformatics\/btac067\/6525218?login=true\"><em>Bioinformatics, btac067, https:\/\/doi.org\/10.1093\/bioinformatics\/btac067 (2022).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2022\/02\/Nature_Scientific_Reports-wpcf_80x100.jpg\" title=\"Nature_Scientific_Reports.jpg\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>A machine learning model for predicting deterioration of COVID-19 inpatients<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2022\/02\/Omer_Noy_Dan_Coster_Nature_Sciientific_Reports_s41598-022-05822-7-1.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>O. Noy*, D. Coster*, M. Metzger, I. Attar, S. Shenhar-Tsafraty, S. Berliner, G. Rahav, O.Rogowski, R. Shamir.<\/h4>\n     <a href=\"https:\/\/www.nature.com\/articles\/s41598-022-05822-7\"><em>Nature Scientific Reports Article 2630 DOI 10.1038\/s41598-022-05822-7 (2022).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2022\/03\/CancerResearch.png\" title=\"CancerResearch.png\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Whole-genome duplication shapes the aneuploidy landscape of human cancers.<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2022\/03\/hagai_uri_BD_can-21-2065.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Prasad, M. Bloomfield, H. Levi, K. Keuper, S. V. Bernhard, N. C. Baudoin, G. Leor, Y. Eliezer, M. Giam, C. Kit Wong, G. Rancati, Z. Storchov\u00e1, D. Cimini, U. Ben-David.<\/h4>\n     <a href=\"https:\/\/aacrjournals.org\/cancerres\/article\/doi\/10.1158\/0008-5472.CAN-21-2065\/681796\/Whole-genome-duplication-shapes-the-aneuploidy\"><em>Cancer Res, https:\/\/doi.org\/10.1158\/0008-5472.CAN-21-2065 (2022).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2022\/05\/actaDV-wpcf_80x100.png\" title=\"actaDV.png\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Relationship Between Pemphigus Vulgaris Severity and PCR-positive Herpes Simplex Virus<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2022\/05\/DanCo_ActaDV_may2022.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Baum, I.  Atar,  D. Coster,  S. Dovrat,  M. Solomon,  E. Sprecher,  T. Zeeli  and  A. Barzilai.<\/h4>\n     <a href=\"https:\/\/medicaljournalssweden.se\/actadv\/article\/view\/917\"><em>ActaDV, Vol. 102 (2022), DOI: https:\/\/doi.org\/10.2340\/actadv.v102.917 (2022).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2022\/06\/Com_Bio-wpcf_80x100.jpg\" title=\"Com_Bio.jpg\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Data Set-Adaptive Minimizer Order Reduces Memory Usage in k-Mer Counting<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2022\/06\/Flomin_cmb.2021.0599.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>D. Flomin, D. Pellow and R. Shamir.<\/h4>\n     <a href=\"https:\/\/www.liebertpub.com\/doi\/10.1089\/cmb.2021.0599\"><em>Journal of Computational Biology, Vol. 29, Pp. 1\u201314 DOI: 10.1089\/cmb.2021.0599 (2022).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2022\/09\/bioinformatics-j-wpcf_80x100.jpg\" title=\"bioinformatics-j.jpg\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>3CAC: improving the classification of phages and plasmids in metagenomic assemblies using assembly graphs<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2022\/09\/Lianrong_btac468.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>L. Pu and R. Shamir.<\/h4>\n     <a href=\"https:\/\/academic.oup.com\/bioinformatics\/article\/38\/Supplement_2\/ii56\/6702013\"><em>Bioinformatics, Volume 38, Issue Supplement 2, September 2022, Pages ii56\u2013ii61, https:\/\/doi.org\/10.1093\/bioinformatics\/btac468 (2022).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2022\/02\/NAR.png\" title=\"NAR.png\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Integration of gene expression and DNA methylation data across different experiments<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2022\/09\/gkad566.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Y. Itai, N. Rappoport, R. Shamir.<\/h4>\n     <a href=\"https:\/\/academic.oup.com\/nar\/advance-article\/doi\/10.1093\/nar\/gkad566\/7217038\"><em>Nucleic Acids Research,  gkad566, https:\/\/doi.org\/10.1093\/nar\/gkad566 (2023).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2022\/10\/Brain_Str_Fun_logo-wpcf_80x100.jpg\" title=\"Brain_Str_Fun_logo\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Clustering the cortical laminae: in vivo parcellation<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2022\/10\/s00429-023-02748-2.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>I. Shamir, Y. Assaf, R. Shamir.<\/h4>\n     <a href=\"https:\/\/link.springer.com\/article\/10.1007\/s00429-023-02748-2?utm_source=rct_congratemailt&#038;utm_medium=email&#038;utm_campaign=oa_20240109&#038;utm_content=10.1007\/s00429-023-02748-2\"><em>Brain Structure and Function, https:\/\/doi.org\/10.1007\/s00429-023-02748-2 (2024).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2020\/09\/PLOS_COMP_BIO_2020-wpcf_80x100.png\" title=\"PLOS_COMP_BIO_2020.png\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Parameterized syncmer schemes improve long-read mapping<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2022\/12\/abhinav_pellow_journal.pcbi_.1010638.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>A. Dutta, D. Pellow, R. Shamir.<\/h4>\n     <a href=\"https:\/\/journals.plos.org\/ploscompbiol\/article?id=10.1371\/journal.pcbi.1010638\"><em>PLOS Comp Bio, https:\/\/doi.org\/10.1371\/journal.pcbi.1010638 (2022).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2023\/04\/arxiv_logo-wpcf_80x100.jpg\" title=\"arxiv_logo\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Time-dependent Iterative Imputation for Multivariate Longitudinal Clinical Data<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2023\/04\/2304.07821.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Omer Noy, Ron Shamir<\/h4>\n     <a href=\"https:\/\/arxiv.org\/abs\/2304.07821\"><em>arXiv  https:\/\/doi.org\/10.48550\/arXiv.2304.07821 (2023).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2019\/08\/PLOS_ONE-wpcf_80x87.jpg\" title=\"PLOS_ONE.jpg\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>The Effect of Body Mass Index Reduction on Intraocular Pressure in a Large, Prospective Population-based Cohort Study in Israel<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2023\/05\/journal.pone_.0285759.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>D. Coster, A. Rafie, N. Savion, R. Rachmiel, S. Kurtz, S. Berliner, I. Shapira, D. Zeltser, O. Rogowski, S. Shenhar-Tsarfaty, M. Waisbourd<\/h4>\n     <a href=\"https:\/\/doi.org\/10.1371\/journal.pone.0285759\"><em>PLoS One, https:\/\/doi.org\/10.1371\/journal.pone.0285759 (2023).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2022\/02\/Nature_Scientific_Reports-wpcf_80x100.jpg\" title=\"Nature_Scientific_Reports.jpg\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Clustering of clinical-echocardiographic phenotypes of covid-19 disease using machine-learning techniques<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2023\/06\/s41598-023-35449-1.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>E. Shpigelman*, A. Hochstadt*, D. Coster, I. Merdler, E. Ghantous, Y. Szekely, Y, Lichter, P. Taieb, A. Banai, O. Sapir, Y. Granot, L. Lupu, A. Borohovitz, S. Sadon, S. Banai, R. Rubinshtein, Y. Topilsky, R. Shamir.<\/h4>\n     <a href=\"https:\/\/www.nature.com\/articles\/s41598-023-35449-1\"><em>Scientific Reports 13:8832 doi: 10.1038\/s41598-023-35449-1 (2023).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2023\/07\/nature-comm-cover-wpcf_80x100.jpg\" title=\"nature-comm-cover\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Single cell Hi-C identifies plastic chromosome conformations underlying the gastrulation enhancer landscape<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2023\/07\/41467_2023_Article_39549.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>N. Rappaport, E. Chomsky, T. Nagano, C. Seibert, Y. Lubling, Y. Baran, A. Lifshitz, W. Leung, Z. Mukamel, R. Shamir, P. Fraser, A. Tanay.<\/h4>\n     <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC10310791\/\"><em>Nature Communications 14(1):3844. doi: 10.1038\/s41467-023-39549-4 (2023).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2023\/07\/download-e1689576023577-wpcf_80x100.png\" title=\"download\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Evaluation of European-based polygenic risk score for breast cancer on Ashkenazi Jewish women<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2023\/07\/jmg-2023-109185.full_.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>H. Levi, S. Carmi, S. Rosset, R. Yerushalmi, A. Zick, T. Yablonski-Peretz, .... (127 members of the BCAC Consortium)..., S. Ben-Shachar, N. Elefant*, R. Shamir* and R. Elkon*.<\/h4>\n     <a href=\"https:\/\/jmg.bmj.com\/content\/early\/2023\/07\/13\/jmg-2023-109185\"><em>Journal of Medical Genetics doi:10.1136\/jmg-2023-109185 (2023).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2023\/08\/GR_Logo-wpcf_80x100.png\" title=\"GR_Logo\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Efficient minimizer orders for large values of $k$ using minimum decycling sets<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2023\/08\/Genome-Res.-2023-Pellow-gr.277644.123.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>D. Pellow, L. Pu, B. Ekim, L. Kotlar, B. Berger, R. Shamir, Y. Orenstein<\/h4>\n     <a href=\"https:\/\/genome.cshlp.org\/content\/early\/2023\/08\/09\/gr.277644.123.long\"><em>Genome Research DOI: 10.1101\/gr.277644.123 (2023).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2023\/08\/logoResearchSquare-wpcf_80x100.jpg\" title=\"logoResearchSquare\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Inferring transcriptional activation and repression activity maps in single-nucleotide resolution using deep-learning<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2023\/08\/a10f3978-451a-4ed6-b30c-67229c5f2a4c.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>T. Hait, R. Elkon, R. Shamir.<\/h4>\n     <a href=\"https:\/\/www.researchsquare.com\/article\/rs-3270775\/v1\"><em>Research Square https:\/\/doi.org\/10.21203\/rs.3.rs-3270775\/v1 (2023).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2023\/10\/medrxiv_logo-wpcf_80x100.jpg\" title=\"medrxiv_logo\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>A feature ranking algorithm for clustering medical data<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2023\/10\/2023.09.30.23296349v1.full_.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>E. Shpigelman, R. Shamir.<\/h4>\n     <a href=\"https:\/\/medrxiv.org\/cgi\/content\/short\/2023.09.30.23296349v1\"><em>MedRxiv doi: 10.1101\/2023.09.30.23296349 (2023).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2019\/12\/bioinformatics-j-wpcf_80x100.jpg\" title=\"bioinformatics-j.jpg\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>The predictive capacity of polygenic risk scores for disease risk is only moderately influenced by imputation panels tailored to the target population<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2024\/01\/btae036.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>H. Levi, R. Elkon*, R. Shamir*.<\/h4>\n     <a href=\"https:\/\/academic.oup.com\/bioinformatics\/advance-article\/doi\/10.1093\/bioinformatics\/btae036\/7587512?login=true\"><em>Bioinformatics, btae036, https:\/\/doi.org\/10.1093\/bioinformatics\/btae036 (2024).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2023\/07\/nature-comm-cover-wpcf_80x100.jpg\" title=\"nature-comm-cover\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Plasmids in the human gut reveal neutral dispersal and recombination that is overpowered by inflammatory diseases<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2024\/05\/s41467-024-47272-x.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>A. Zorea, D. Pellow, L. Levin, S. Pilosof, J. Friedman, R. Shamir, I. Mizrahi.<\/h4>\n     <a href=\"https:\/\/www.nature.com\/articles\/s41467-024-47272-x\"><em>Nature Communications 15, Article number: 3147, https:\/\/doi.org\/10.1038\/s41467-024-47272-x (2024).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2022\/02\/NAR.png\" title=\"NAR.png\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Drugst.One -- A plug-and-play solution for online systems medicine and network-based drug repurposing<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2024\/05\/gkae388.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>A. Maier, M. Hartung, M. Abovsky, K. Adamowicz, G. D. Bader, S. Baier, D. B. Blumenthal, J. Chen, M. L. Elkjaer, C. Garcia-Hernandez, M. Hoffmann, I. Jurisica, M. Kotlyar, O. Lazareva, H. Levi, M. List, S. Lobentanzer, J. Loscalzo, N. Malod-Dognin, Q. Manz, J. Matschinske, M. Oubounyt, A. R. Pico, R. T. Pillich, J. M. Poschenrieder, D. Pratt, N. Pr\u017eulj, S. Sadegh, J. Saez-Rodriguez, S. Sakar, G. Shaked, R. Shamir, N. Trummer, U. Turhan, R. Wang, O. Zolotareva, J. Baumbach.<\/h4>\n     <a href=\"https:\/\/doi.org\/10.1093\/nar\/gkae388\"><em>Nucleic Acids Research gkae388 (2024).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2024\/06\/microbiology_spect_logo.jpg\" title=\"microbiology_spect_logo\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Race-dependent variability in the human tumor mycobiome<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2026\/04\/coster-et-al-2026.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>D. Coster, T. Margalit, R. Ben-Ami, B. Boursi*, R. Shamir*.<\/h4>\n     <a href=\"https:\/\/doi.org\/10.1128\/spectrum.02310-25\"><em>Microbiology Spectrum, https:\/\/doi.org\/10.1128\/spectrum.02310-25 (2026).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2024\/09\/NAR_logo-wpcf_80x100.jpeg\" title=\"NAR_logo\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>4CAC: 4-class classifier of metagenomic assemblies using machine learning and assembly graphs<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2024\/09\/gkae799.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>L. Pu, R. Shamir.<\/h4>\n     <a href=\"https:\/\/academic.oup.com\/nar\/advance-article\/doi\/10.1093\/nar\/gkae799\/7759139\"><em>Nucleic Acids Research gkae799, https:\/\/doi.org\/10.1093\/nar\/gkae799 (2024).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2024\/10\/ng_logo-wpcf_80x100.png\" title=\"ng_logo\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Aneuploidy as a driver of human cancer<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2024\/10\/s41588-024-01916-2.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>E. Sdeor, H. Okada, R. Saad, T. Ben-Yishay, U. Ben-David.<\/h4>\n     <a href=\"https:\/\/www.nature.com\/articles\/s41588-024-01916-2\"><em>Nature Genetics s41588-024-01916-2, https:\/\/doi.org\/10.1038\/s41588-024-01916-2 (2024).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2024\/10\/CD_logo-wpcf_80x100.jpg\" title=\"CD_logo\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Increased RNA and Protein Degradation Is Required for Counteracting Transcriptional Burden and Proteotoxic Stress in Human Aneuploid Cells<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2024\/10\/cd-23-0309.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>M. R. Ippolito, J. Zerbib, Y. Eliezer, E. Reuveni, S. Vigan\u00f2, G. De Feudis, E. D. Shulman, A. S. Kadmon, R. Slutsky, T. Chang, E. M. Campagnolo, S. Taglietti, S. Scorzoni, S. Gianotti, S. Martin, J. Muenzner, M. M\u00fclleder, N. Rozenblum, C. Rubolino, T. Ben-Yishay, K. Laue, Y. Cohen-Sharir, I. Vigorito, F. Nicassio, E. Ruppin, M. Ralser, F. Vazquez, S. Santaguida, U. Ben-David<\/h4>\n     <a href=\"https:\/\/aacrjournals.org\/cancerdiscovery\/article-abstract\/doi\/10.1158\/2159-8290.CD-23-0309\/748735\/Increased-RNA-and-Protein-Degradation-Is-Required?redirectedFrom=fulltext\"><em>Cancer Discovery CD-23-0309 https:\/\/doi.org\/10.1158\/2159-8290.CD-23-0309 (2024).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2024\/10\/science_logo-wpcf_80x100.jpeg\" title=\"science_logo\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>A p62-dependent rheostat dictates micronuclei catastrophe and chromosome rearrangements<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2024\/10\/science.adj7446.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>S. Martin, S. Scorzoni, S. Cordone, A. Mazzagatti, G. V. Beznoussenko, A. L. Gunn, M. Di Bona, Y. Eliezer, G. Leor, T. Ben-Yishay, A. Loffreda, V. Cancila, M. C. Rainone, M. R. Ippolito, V. Martis, F. Bedin, M. Garr\u00e9, L. P. Vaites, P. Vasapolli, S. Polo, D. Parazzoli, C. Tripodi, A. A. Mironov, A. Cuomo, U. Ben-David, S. F. Bakhoum, E. M. Hatch, P. Ly, S. Santaguida.<\/h4>\n     <a href=\"https:\/\/www.science.org\/doi\/10.1126\/science.adj7446\"><em>Science adj7446, https:\/\/doi.org\/10.1126\/science.adj7446 (2024).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2025\/01\/PNAS_logo-e1736338544545-wpcf_80x79.png\" title=\"PNAS_logo\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>The cGAS\u2013STING, p38 MAPK, and p53 pathways link genome instability to accelerated cellular senescence in ATM-deficient murine lung fibroblasts<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2025\/01\/haj-et-al-2025-the-cgas-sting-p38-mapk-and-p53-pathways-link-genome-instability-to-accelerated-cellular-senescence-in.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>M. Haj, Y. Frey, A. Levon, A. Maliah, T. Ben-Yishay, R. Slutsky, R. Smoom, Y. Tzfati, U. Ben-David, C. Levy, R. Elkon, Y. Ziv, Y. Shiloh<\/h4>\n     <a href=\"https:\/\/www.pnas.org\/doi\/10.1073\/pnas.2419196122\"><em>PNAS 122 (2) e2419196122, https:\/\/doi.org\/10.1073\/pnas.2419196122 (2025).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2025\/02\/npg_dig_med_logo-1-wpcf_80x100.jpg\" title=\"npg_dig_med_logo\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Predicting appropriateness of antibiotic treatment among ICU patients with hospital acquired infection<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2025\/02\/s41746-024-01426-9.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>E. Rannon, E. Goldschmidt, D. Bernstein, A. Wasserman, M. Roimi, A. Shrot, D. Coster, R. Shamir.<\/h4>\n     <a href=\"https:\/\/www.nature.com\/articles\/s41746-024-01426-9\"><em>npj Digit. Med. 8, 87 https:\/\/doi.org\/10.1038\/s41746-024-01426-9 (2025).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2025\/03\/PMLR_logo-2-wpcf_80x41.png\" title=\"PMLR_logo\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Towards Regulatory-Confirmed Adaptive Clinical Trials: Machine Learning Opportunities and Solutions<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2025\/03\/klein25a.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>O. Noy Klein, A. H\u00fcy\u00fck, R. Shamir, U. Shalit, M. van der Schaar<\/h4>\n     <a href=\"https:\/\/proceedings.mlr.press\/v258\/klein25a.html\"><em>Proc. 28th International Conference on Artificial Intelligence and Statistics (AISTATS), PMLR 258:4969-4977 (2025).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2025\/06\/nature_med_logo-1-wpcf_80x55.png\" title=\"nature_med_logo\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>A reference model for circulating hematopoietic stem cells with applications to diagnostics<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2025\/06\/s41591-025-03716-5.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Furer N.*, Rappoport N.*, O. Milman, Tavor S., Lifshitz A., Bercovich A., Ben-Kiki O., Danin A., Kedmi M., Shipony Z., Lipson D., Meiri E., Yanai G., Shapira S., Arber N., Berdichevsky S., Tyner J., Joshi S., Landau D., Ganesan S., Dusaj N., Chamely P., Kaushansky N., Chapal-Ilani N., Shamir R., Tanay A., Shlush LI.<\/h4>\n     <a href=\"https:\/\/www.nature.com\/articles\/s41591-025-03716-5\"><em>Nature Medicine https:\/\/doi.org\/10.1038\/s41591-025-03716-5 (2025).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2024\/09\/NAR_logo-wpcf_80x100.jpeg\" title=\"NAR_logo\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Transcriptional programs of cell identity and p53-induced stress responses are associated with distinctive features of spatial genome organization<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2025\/07\/gkaf607.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>G. Shanel, T-H. S. Hsieh, C. Cattoglio, H. Amira Haham, H-J. Chou, J. Li, R. Shamir, X. Darzacq, R. Elkon.<\/h4>\n     <a href=\"https:\/\/academic.oup.com\/nar\/article\/53\/13\/gkaf607\/8192815\"><em>Nucleic Acids Research 53 (13), gkaf607 (2025).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2023\/04\/arxiv_logo-wpcf_80x100.jpg\" title=\"arxiv_logo\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>From Observational Data to Clinical Recommendations: A Causal Framework for Estimating Patient-level Treatment Effects and Learning Policies<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2025\/07\/2507.11381v2.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>R. Gutman, S. Sheiba, O. Noy Klein, N. Dekel Bird, A. Gruber, D. Aronson, O. Caspi, U. Shalit<\/h4>\n     <a href=\"https:\/\/arxiv.org\/abs\/2507.11381\"><em>arXiv https:\/\/doi.org\/10.48550\/arXiv.2507.11381 (2025).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2025\/08\/npj_park_logo-2.png\" title=\"npj_park_logo\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Optimizing Parkinson\u2019s Disease progression scales using computational methods<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2025\/08\/s41531-026-01259-1.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>A. Benesh, R. N. Alcalay, A. Mirelman, R. Shamir.<\/h4>\n     <a href=\"https:\/\/www.nature.com\/articles\/s41531-026-01259-1\"><em>npj Parkinson's Disease 12, 46 https:\/\/doi.org\/10.1038\/s41531-026-01259-1 (2026).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2025\/10\/RqjUmuNy_400x400-wpcf_80x100.jpg\" title=\"RqjUmuNy_400x400\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Integrating gene expression, mutation and copy number data to identify driver genes of recurrent chromosome-arm losses<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2025\/10\/1-s2.0-S2211124725012264-main.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>R. Saad, R. Shamir*, U. Ben-David*.<\/h4>\n     <a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S2211124725012264\"><em>Cell Reports 44 (11), 25 November 2025, 116455 (2025).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2025\/12\/msb-3-wpcf_80x53.png\" title=\"msb\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3><\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2025\/12\/s44320-025-00170-w.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>P. Bheda, J. Hou, R. Aebersold, U. Alon, J. S. Bader, L. Bardwell, E. T. Liu, J. C. W. Locke, M. Mann, A. J. Millar, F. Naef, Y. Pilpel, R. Shamir, D. Vitkup.<\/h4>\n     <a href=\"https:\/\/link.springer.com\/article\/10.1038\/s44320-025-00170-w\"><em>Molecular Systems Biology 12: 1667-1673. doi: 10.1038\/s44320-025-00170-w (2025).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2022\/10\/BIORXIV2017-1-wpcf_80x100.png\" title=\"BIORXIV2017-1.png\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Pan-cancer analysis reveals genomic fidelity and evolution of patient-derived organoids<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2025\/12\/2025.12.10.693393v1.full_.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Linoy Raz, Tal Ben-Yishay, Haia Khoury, Ron Saad, Amjad Zoabi, Giulia Orlandi, Sara Donzelli, Giovanni Blandino, Uri Ben-David<\/h4>\n     <a href=\"https:\/\/www.biorxiv.org\/content\/10.64898\/2025.12.10.693393v1\"><em>bioRxiv https:\/\/doi.org\/10.64898\/2025.12.10.693393 (2025).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2025\/12\/cell_logo-wpcf_80x100.jpeg\" title=\"cell_logo\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>HLA Export by Melanoma Cells Decoys Cytotoxic T Cells to Promote Immune Evasion<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2025\/12\/1-s2.0-S0092867425013169-main.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>Y. Chemla, O. Itzhaki, S. Melamed, C. Weller, Y. Sade, P. Manich, K. Reshef, N. Xenidis, A. Maliah, G. Levy, R. Parikh, O. Bartok, O. Levy, I. Tal, G. Aziel, A. Nissani, S. Yunger, D. Likonen, V. Kliminsky, T. Golan, C. Capron, V. Ace, R. Levy, D. Rasoulouniriana, Z. Eyal, Y. Barzilay, R. Balaban, A. Khateeb, R. Khosravi, A. Grau, T. Ziv, P. Greenberg, D. Netanely, H. Vaknin, X. Wu, Y. Amitay, R. Brenner, J. Mar\u00eda Mart\u00ednez G\u00f3mez, D. Hershkovitz, T. Yardeni, V. Zemser-Werner, O. Kobiler, Y. Friedmann, D. Bassan, R. Shamir, L. Eisenbach, N. Santana-Magal, M. Milyavsky, G. Eisenberg, L. Keren, M. Cohen, D. Gur, B. Barak, M. Lotem, D. Sprinzak, S. Greenberger, D. Fisher, M. J. Besser, M. Khaled, P. Close, R. Shapira, S. Apcher, A. Madi, M. P. Levesque, F. Rapino, Y. Carmi, S. Parikh, Y. Samuels, C. Levy.<\/h4>\n     <a href=\"https:\/\/www.cell.com\/cell\/fulltext\/S0092-8674(25)01316-9?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867425013169%3Fshowall%3Dtrue\"><em>Cell https:\/\/doi.org\/10.1016\/j.cell.2025.11.020 (2025).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2026\/01\/microbiome_logo-wpcf_80x100.jpg\" title=\"microbiome_logo\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>ProFiT-SPEci-FISH: A Novel Approach for Linking Plasmids to Hosts in Complex Microbial Communities at the Single-Cell Level'<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2026\/01\/s40168-025-02238-z.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>A. Zorea, S. Mora\u00efs, D. Pellow, O. Gershoni-Yahalom, M. Probst, S. Nadler, R. Shamir, B. Rosental, N. Elia, I. Mizrahi.<\/h4>\n     <a href=\"https:\/\/link.springer.com\/article\/10.1186\/s40168-025-02238-z\"><em>Microbiome 10.1186\/s40168-025-02238-z (2025).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2026\/04\/CJASN_logo-wpcf_80x33.png\" title=\"CJASN_logo\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>The Impact of Nephrology Referral on Chronic Kidney Disease Outcomes in Israel<\/h3>\n  <h4>T. Wertheimer, O. Noy-Klein, N. Erlich,  S. Kushnir, B. Rozen Zvi*, R. Shamir*, D. Bielopolski.<\/h4>\n     <a href=\"https:\/\/journals.lww.com\/cjasn\/abstract\/9900\/the_impact_of_nephrology_referral_on_chronic.888.aspx\"><em>Clinical Journal of the American Society of Nephrology   DOI: 10.2215\/CJN.0000001026 (2026).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\t\n\t\t<div class=\"row \">\n\t\t\t<div class=\"col-sm-12\"><div class=\"well\">\n  <div class=\"row\">\n  <div class=\"col-md-2\"><img decoding=\"async\" src=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2023\/04\/arxiv_logo-wpcf_80x100.jpg\" title=\"arxiv_logo\" class=\"aligncenter img-thumbnail\" \/><\/div>\n  <div class=\"col-md-10\"><h3>Perspective on Bias in Biomedical AI: Preventing Downstream Healthcare Disparities<\/h3><span style=\"float: right;\"><a href=\"https:\/\/acgt.cs.tau.ac.il\/wp-content\/uploads\/2026\/04\/2604.14514v1.pdf\"><button class=\"btn btn-default\" type=\"button\">PDF<\/button><\/a><\/span>\n  <h4>M. Rosen-Zvi, Y. Kan-Tor, M. Danziger, A. Ferretti, J. Aula-Blasco, J. Falcao, R. Shamir, M. Muszkat.<\/h4>\n     <a href=\"https:\/\/arxiv.org\/abs\/2604.14514\"><em>arXiv:2604.14514 (2026).<\/em><\/a><\/div>\n<\/div>    \n  <\/div>\n<\/div>\n\t\t<\/div>\n\t\t\n\t\n\t\n\t\n<\/div>\n<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Publications Go to latest publications<\/p>\n","protected":false},"author":9,"featured_media":0,"parent":0,"menu_order":17,"comment_status":"closed","ping_status":"closed","template":"","meta":[],"_links":{"self":[{"href":"https:\/\/acgt.cs.tau.ac.il\/index.php?rest_route=\/wp\/v2\/pages\/3925"}],"collection":[{"href":"https:\/\/acgt.cs.tau.ac.il\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/acgt.cs.tau.ac.il\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/acgt.cs.tau.ac.il\/index.php?rest_route=\/wp\/v2\/users\/9"}],"replies":[{"embeddable":true,"href":"https:\/\/acgt.cs.tau.ac.il\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=3925"}],"version-history":[{"count":11,"href":"https:\/\/acgt.cs.tau.ac.il\/index.php?rest_route=\/wp\/v2\/pages\/3925\/revisions"}],"predecessor-version":[{"id":5167,"href":"https:\/\/acgt.cs.tau.ac.il\/index.php?rest_route=\/wp\/v2\/pages\/3925\/revisions\/5167"}],"wp:attachment":[{"href":"https:\/\/acgt.cs.tau.ac.il\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=3925"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}