Publications

2017 2016 2015 2014 2013 2012 2011 2010 2009 2008 2007 2006 2005 2004 2003 2002 2001 2000 1999 1998 and before Copyright notice
2017  Top
Molecular Systems Biology
Transcription factor family-specific DNA shape readout revealed by quantitative specificity models
L. Yang, Y. Orenstein, A. Jolma, Y. Yin, J. Taipale, R. Shamir and R. Rohs.
Molecular Systems Biology, 13, 910, DOI 10.15252/msb.20167238, 2017. pdf
BioRxiv
Improving the performance of minimizers and winnowing schemes
G. Marcais, D. Pellow, D. Bork, Y. Orenstein, R. Shamir, C. Kingsford.
BioarXiv, https://doi.org/10.1101/104075(2017). pdf
Oncogene
Utilizing somatic mutation data from numerous studies for cancer research: proof of concept and applications
D. Amar, S. Izraeli and R. Shamir.
Oncogene, doi:10.1038/onc.2016.489 (2017). pdf
2016  Top
Bioinformatics
Recycler: an algorithm for detecting plasmids from de novo assembly graphs
R. Rozov, A. Brown Kav, D. Bogumil, N. Shterzer, E. Halperin, I. Mizrahi, and R. Shamir.
Bioinformatics 10.1093/bioinformatics/btw651,(2016). pdf
Journal of Computational Biology
Sorting by cuts, joins and duplications
R. Zeira, R. Shamir.
Journal of Computational Biology Vol 23 No 0. pp 1-11 (2016). pdf
Frontiers in Genetics
Dissecting the effect of genetic variation on the hepatic expression of drug disposition genes across the collaborative cross mouse strains
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.
Frontiers in Genetics Vol 7, Article 172, doi: 10.3389/fgene.2016.00172 (2016). pdf
Scientific Reports
SELMAP - SELEX affinity landscape MAPping of transcription factor binding sites using integrated microfluidics
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.
Scientific Reports 6, 33351; doi: 10.1038/srep33351, 2016. pdf
Proceedings of WABI, LNCS 2016, Algorithms in Bioinformatics
Copy-Number Evolution Problems: Complexity and Algorithms
M. El-Kebir, B. Raphael, R. Shamir, R. Sharan, S. Zaccaria, M. Zehavi, R. Zeira.
Proceedings of WABI 2016, Aarhus, Denmark, August, 2016, LNCS, 9838 pp. 137-149 (2016). pdf
Proceedings of WABI, LNCS 2016, Algorithms in Bioinformatics
Compact universal k-mer hitting sets
Y. Orenstein, D. Pellow, G. Marcais, R. Shamir, C. Kingsford.
Proceedings of WABI 2016, Aarhus, Denmark, August, 2016, LNCS, 9838 pp. 257--268 (2016). pdf
Briefings in Functional Genomics
Modeling protein-DNA binding via high throughput in vitro technologies
Y. Orenstein, R. Shamir.
Briefings in Functional Genomics, doi: 10.1093/bfgp/elw030 (2016). pdf
PLoS One
RichMind: a tool for improved inference from large-scale neuroimaging results
A. Maron-Katz, D. Amar, E. Ben-Simon, T. Hendler, R. Shamir.
PLoS One, DOI:10.1371/journal.pone.0159643 (2016). pdf
Breast Cancer Research
Expression and methylation signatures partition Luminal-A breast tumors into distinct prognostic subgroups
D. Netanely, A. Avraham, A. Ben-Baruch, E. Evron, R. Shamir
Breast Cancer Research, 18:74,DOI 10.1186/s13058-016-0724-2 (2016). pdf Erratum
LIPICs
A linear-time algorithm for the Copy Number Transformation Problem
R. Shamir, M. Zehavi, R. Zeira
Proc. 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016), R. Grossi and M. Lewenstein (Editors), Dagstuhl, Germany, LIPIcs, vol. 54, pp. 16:1–16:13. pdf
Genome Research
Enhancer methylation dynamics contribute to cancer plasticity and patient mortality
R. E. Bell, T. Golan, D. Sheinboim, H. Malcov, D. Amar, A. Salamon, T. Liron, S. Gelfman, Y. Gabet, R. Shamir and C. Levy.
Genome Research, 26 ( 5 ) pp. 601 - 611. pdf
Scientific Reports
A large-scale perspective on stress-induced alterations in resting-state networks
A. Maron-Katz, S. Vaisvaser, T. Lin, T. Hendler, R. Shamir.
Scientific Reports, 6, Article number: 21503, doi:10.1038/srep21503 (2016). pdf
 Cellular & Molecular Life Sciences
Evidence of TAF1 dysfunction in peripheral models of X-linked dystonia-parkinsonism.
A. Domingo, D. Amar, K. Grütz, L. Lee, R. Rosales, N. Brüggemann, R. D. Jamora, E. Cutiongco dela-Paz, K. Lohmann, R. Shamir, C. Klein, A. Westenberger.
Cellular and Molecular Life Sciences , DOI 10.1007/s00018-016-2159-4 (2016).
2015  Top
NAR
Integrated microfluidic approach for quantitative high-throughput measurements of transcription factor binding affinities.
Y. Glick, Y. Orenstein, D. Chen, D. Avrahami, T. Zor, R. Shamir R, D. Gerber
Nucl. Acids Res, doi: 10.1093/nar/gkv1327. pdf
BioRxiv
Recycler: an algorithm for detecting plasmids from de novo assembly graphs
R. Rozov, A. Kav Brown, D. Bogumil, E. Halperin, I. Mizrahi, R. Shamir.
BioRxiv, http://dx.doi.org/10.1101/029926, (26 Oct 2015, revised 7 February 2016). pdf
NAR
Integrated analysis of numerous heterogeneous gene expression profiles for detecting robust disease-specific biomarkers and proposing drug targets
D. Amar, T. Hait, S. Izraeli and R. Shamir.
Nucleic Acids Research , 43 (16): 7779-7789, 2015. pdf
Transcription
ElemeNT: a computational tool for detecting core promoter elements
A. Sloutskin, Y. M. Danino, Y. Zehavi, Y. Orenstein, T. Doniger, R. Shamir, T. Juven-Gershon
Transcription , 6:3, 41-50, 2015. pdf
LNCS
Sorting by cuts, joins and and whole chromosome duplications
R. Zeira and R. Shamir
Proceedings of CPM 2015, Ischia Island, Italy, June 2015. (F. Cicalese, E. Porat, U. Vaccaro, editors) LNCS , Vol 9133, pp 396-409, 2015. pdf
BioRxiv
HTS-IBIS: fast and accurate inference of binding site motifs from HT-SELEX data
Y. Orenstein and R. Shamir
BioRxiv , doi.org/10.1101/022277, 2015. pdf
Development
MicroRNAs of the RPE are essential for RPE differentiation and photoreceptor maturation
R. Ohana, B. Weiman-Kelman, S. Raviv, E. Tamm, M. Pasmanik-Chor, A. Rinon, D. Netanely, R. Shamir, AS.Salomon, R. Ashery-Padan.
Development , Jun 10. doi: 10.1242/dev.121533, 2015.
Bioinformatics
A hierarchical Bayesian model for flexible module discovery in three-way time-series data
D. Amar, D. Yekutieli, A. Maron-Katz, T. Hendler and R. Shamir.
Bioinformatics , 31 (12): i17-i26, ISMB/ECCB 2015, proceedings paper, doi: 10.1093/bioinformatics/btv228, 2015. pdf
Physiologia_Plantarum
The MORPH-R web server and software tool for predicting missing genes in biological pathways
D. Amar, I. Frades, T. Diels, D. Zaltzman, N. Ghatan, P. E. Hedley, E. Alexandersson, O. Tzfadia and R. Shamir
Physiologia_Plantarum , doi:10.1111/ppl.12326, 2015. pdf
2014  Top
 BMC Plant Biology
Evaluation and integration of functional annotation pipelines for newly sequenced organisms: the potato genome as a test case.
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.
BMC Plant Biology , 5;14(1):329, 2014. pdf
Genes and Development
Drosophila TRF2 is a preferential core promoter regulator.
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
Genes and Development, 28 (19) pp. 2163 - 2174, 2014. pdf
 BMC
Fast lossless compression via cascading Bloom filters.
R. Rozov, R. Shamir, E. Halperin
BMC Bioinformatics, 15(Suppl 9):S7, 2014. pdf
 Frontiers in Genetics
Examination of Exhaustive Cloning Attempts Reveals that C. elegans piRNAs, Transposons, and Repeat Sequences are Efficiently Cloned in Yeast, but not in Bacteria.
O. Sagy, R. Shamir and O. Rechavi
Frontiers in Genetics, 5:275, doi: 10.3389/fgene.2014.00275. pdf
 Nucleic Acids Research
Functional gene groups are concentrated within chromosomes, among chromosomes and in the nuclear space of the human genome.
A. Thévenin, L. Ein-Dor, M. Ozery-Flato and R. Shamir
Nucleic Acids Research, doi: 10.1093/nar/gku667. pdf
 Science Signaling
Parallel Profiling of the Transcriptome, Cistrome, and Epigenome in the Cellular Response to Ionizing Radiation.
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.
Science Signaling Vol. 7, 325, RS3, 2014. pdf
 Nucleic Acids Research
A comparative analysis of transcription factor binding models learned from PBM, HT-SELEX and ChIP data.
Y. Orenstein and R. Shamir
Nucleic Acids Research doi: 10.1093/nar/gku117, 2014. pdf
 Nucleic Acids Research
Constructing module maps for integrated analysis of heterogeneous biological networks.
D. Amar and R. Shamir
Nucleic Acids Research doi:10.1093/nar/gku102, 2014. pdf
2013  Top
 Plos Genetics
Environmental stresses disrupt telomere length homeostasis.
G.H. Romano, Y. Harar, T. Yehuda, A. Podhorzer, L. Rubinstein, R. Shamir, A. Gottlieb, Y. Silberberg, D. Pe’er, E. Ruppin, R. Sharan, M. Kupiec
PLoS Genetics,9(9):e1003721. doi: 10.1371/journal.pgen.1003721. Epub 2013. pdf
J. Investigative Dermatology
Transcription Factor/microRNA Axis Blocks Melanoma Invasion Program by miR-211 Targeting NUAK1.
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
Journal of Investigative Dermatology, doi: 10.1038/jid.2013.340, 2013. pdf
Computational Biologygy
Design of shortest double-stranded DNA sequences covering all k-mers with applications to protein-binding microarrays and synthetic enhancers.
Y. Orenstein, and R. Shamir
Bioinformatics, Vol. 29 ISMB/ECCB, i71-i79, 2013. pdf
Computational Biologygy
RAP: Accurate and fast motif finding based on protein binding microarray data.
Y. Orenstein, E. Mick and R. Shamir
Journal of Computational Biology, Vol. 20, No. 5: 375-382 , 2013. pdf
Nature Biotechnology
Dissection of Regulatory Networks that Are Altered in Disease via Differential Co-expression.
D. Amar, H. Safer, R. Shamir
PLOS Computational Biology, Vol. 9, No. 3. e1002955, 2013. pdf
PLOS Computational Biology
Evaluation of methods for modeling transcription factor sequence specificity.
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.
Nature Biotechnology,31(2):126-34, 2013. pdf
The Plant Cell
Systematic Inference of Highways of Horizontal Gene Transfer in Prokaryotes.
M.S. Bansal, G. Banay, T.J. Harlow, J.P. Gogarten, R. Shamir.
Bioinformatics, 29 ( 5 ) pp. 571 - 579, 2013. pdf
2012  Top
The Plant Cell
The MORPH Algorithm: Ranking Candidate Genes for Membership in Arabidopsis and Tomato Pathways.
O. Tzfadia, D. Amar, L.M.T. Bradbury, E.T. Wurtzel, and R. Shamir.
The Plant Cell, 24(11):4389-406, 2012. pdf
Plos One
Assessment of algorithms for inferring positional weight matrix motifs of transcription factor binding sites using protein binding microarray data.
Y. Orenstein, C. Linhart , R. Shamir.
PLoS ONE, 7 (9) e46145, 2012. pdf
MolOncology
Wisdom of crowds for robust gene network inference.
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.
Nature Methods, 9(8):796-804, 2012. pdf
MolOncology
Network-Induced Classification Kernels for Gene Expression Profile Analysis.
O. Lavi, G. Dror, and R. Shamir.
Journal of Computational Biology, 19(6), 694-709, 2012. pdf
MolOncology
MGMR: leveraging RNA-Seq population data to optimize expression estimation.
R. Rozov, E. Halperin and R. Shamir.
BMC Bioinformatics, Proceedings of the Second Annual RECOMB Satellite Workshop on Massively Parallel Sequencing (RECOMB-seq 2012), 13(Suppl 6):S2, 2012. pdf
MolOncology
Transcriptional and Proteomic Analysis of the Aspergillus fumigatus DprtT Protease-Deficient Mutant.
S.Hagag, P. Kubitschek-Barreira, G. W. P. Neves, D. Amar, W. Nierman, I. Shalit, R. Shamir, L. Lopes-Bezerra, N. Osherov.
PLoS ONE, Volume 7, Issue 4, e33604, 2012. pdf
MolOncology
A novel candidate cis-regulatory motif pair in the promoters of germline and oogenesis genes in C. elegans.
C. Linhart, Y. Halperin, A. Darom, S. Kidron, L. Broday and R. Shamir.
Genome Research, 22(1):76-83, 2012. pdf
MolOncology
Constructing logical models of gene regulatory networks by integrating transcription factor-DNA interactions with expression data: an entropy based approach.
G. Karlebach and R. Shamir.
Journal of Computational Biology, 19(1):30-41, 2012. pdf
2011  Top
MolOncology
A Point Mutation in Translation Initiation Factor eIF2B Leads to Function- and Time-Specific Changes in Brain Gene Expression.
L. Marom, I. Ulitsky, Y. Cabilly, R. Shamir, O. Elroy-Stein.
PLoS ONE, 6, 269920, 2011. pdf
MolOncology
Bioinformatics for Biologists.
P. Pevzner and R. Shamir, editors .
Textbook. Cambridge University Press, UK, 2011.
Journal of Discrete Algorithms
An O(n3/2log(n)) algorithm for sorting by reciprocal translocations.
M. Ozery-Flato, R. Shamir.
Journal of Discrete Algorithms, Volume 9, Issue 4, Pages 344-357(2011),  pdf
MolOncology
Detecting Highways of Horizontal Gene Transfer.
M. S. Bansal, G. Banay, J. P. Gogarten and R. Shamir.
J. of Computational Biology, September 2011, 18(9): 1087-1114. doi:10.1089/cmb.2011.0066 pdf
MolOncology
Transcriptional Modulation Induced By Ionizing Radiation: P53 Remains A Central Player.
S.Rashi-Elkeles, R. Elkona, S. Shavit, Y. Lerenthal, C. Linhart, A. Kupershtein, N. Amariglio, G. Rechavi, R. Shamir and Y. Shiloh.
Molecular Oncology, 5, 336-348, 2011 pdf
Genome Biology 2011
Large-scale analysis of chromosomal aberrations in cancer karyotypes reveals two distinct paths to aneuploidy.
Ozery-Flato M, Linhart C, Trakhtenbrot L, Izraeli S, Shamir R.
Genome Biology, 29;12(6):R61, 2011 pdf
Com_Bio
Selected papers from the 2nd RECOMB satellite meeting on Bioinformatics Education (RECOMB-BE).
P. A. Pevzner, R. Shamir, editors.
To appear in Journal of Computational Biology, 18 (7), 2011.
164
A note on the fixed parameter tractability of the gene-duplication problem.
Bansal, M.S. and Shamir, R.
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8 (3), art. no. 5557848, pp. 848-850, 2011 pdf
PLOS_ONE
Integration of Transcriptomics, Proteomics, and MicroRNA Analyses Reveals Novel MicroRNA Regulation of Targets in the Mammalian Inner Ear.
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.
PLoS One, Volume 6,Issue 4, e18195, 2011 pdf
PLOS ONE
PrtT-Regulated Proteins Secreted by Aspergillus fumigatus Activate MAPK Signaling in Exposed A549 Lung Cells Leading to Necrotic Cell Death.
H. Sharon, D. Amar, E. Levdansky, G. Mircus, Y. Shadkchan, R. Shamir, N. Osherov.
PLoS One, Volume 6, Issue 3, e17509, 2011  pdf
Cell Stemcell
Dynamic Changes in the Copy Number of Pluripotency and Cell Proliferation Genes in Human ESCs and iPSCs during Reprogramming and Time in Culture.
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.
Cell Stem Cell, doi: 10.1016/j.stem.2010.12.003,2011.  pdf
NAR
SPIKE: a database of highly curated human signaling pathways.
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.
Nucleic Acids Research, Vol. 39, Database issue D793-D799, 2011.  pdf
2010  Top
PLOS ONE
DEGAS: De Novo Discovery of Dysregulated Pathways in Human Diseases.
Igor Ulitsky, Akshay Krishnamurthy, Richard M. Karp, Ron Shamir.
PLoS One , 5 (10) e13367 (2010).  pdf
lncs
Detecting Highways of Horizontal Gene Transfer.
Mukul S. Bansal, J. Peter Gogarten, and Ron Shamir.
8th Annual RECOMB Comparative Genomics Workshop (RECOMB-CG 2010), LNCS, 6398: 109-120 (2010).  pdf
lncs
PAKDD Data Mining Competition 2009: New Ways of Using Known Methods.
Chaim Linhart, Guy Harari, Sharon Abramovich and Altina Buchris.
Lecture Notes in Computer Science, Volume 5669/2010, 99-105, DOI: 10.1007/978-3-642-14640-4_7 (2010).
Journal of Computational Biology
A Faster Algorithm for Simultaneous Alignment and Folding of RNA.
Ziv-Ukelson M, Gat-Viks I, Wexler Y, Shamir R.
Journal of Computational Biology,17(8):1051-65,2010.  pdf
NAR
Towards computational prediction of microRNA function and activity.
I. Ulitsky, L. C. Laurent and R. Shamir.
Nucleic Acids Research, 38 (15): e160. pp 1-13 (2010).  pdf
NSMB
A plasma-membrane E-MAP reveals links of the eisosome with sphingolipid metabolism and endosomal trafficking.
P.S. Aguilar, F. Fröhlich, 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.
Nature Structural and Molecular Biology , Vol. 17 no. 7, pp 901-909(2010).  pdf
Journal of Computation  Biology
Topology-free querying of protein interaction networks.
Bruckner, S., Hüffner, F., Karp, R.M., Shamir, R., Sharan, R.
Journal of Computational Biology , 17 (3), pp. 237-252 (2010).  pdf
BMC Systems Biology
Minimally perturbing a gene regulatory network to avoid a disease phenotype: the glioma network as a test case.
G. Karlebach, R. Shamir .
BMC Systems Biology , 4:15 doi:10.1186/1752-0509-4-15(2010).  pdf
International Journal of Cancer
Ras inhibits ER Stress in Human Cancer Cells with Amplified Myc.
S. Yaari-Stark, M. Shaked, Y. Nevo-Caspi, J. Jacob-Hircsh, R. Shamir, G. Rechavi, Y. Kloog.
International Journal of Cancer , Vol 126, 2268--2281 (2010).  pdf
Communication in Information and Systems
Special issues dedicated to Michael Waterman on the occasion of his 67th birthday.
S. Istrail, P. Pevzner, R. Shamir. F. Sun, guest editors.
Communication in Information and Systems , Vol 9 3-4 (2009), Vol 10 1-2 (2010).
Molecular Systems Biology
Different sets of QTLs influence fitness variation in yeast.
G. H. Romano, Y. Gurvich, O. Lavi, I. Ulitsky, R. Shamir, M. Kupiec.
Molecular Systems Biology 6:346, doi:10.1038/msb.2010.1, 2010 .  pdf
Nature protocols
Expander: from expression microarrays to networks and functions.
I. Ulitsky, A. Maron-Katz, S. Shavit, D. Sagir, C. Linhart, R. Elkon, A. Tanay, R. Sharan, Y. Shiloh, R. Shamir.
Nature Protocols Vol 5, pp 303 - 322, 2010 .  pdf
PLoS
Understanding gene sequence variation in the context of transcription regulation in yeast.
I. Gat-Viks, R. Meller, M. Kupiec, R. Shamir.
PLoS Genetics , Vol. 6 No. 1 e1000800 (2010).  pdf
2009  Top
Genome biology
Towards accurate imputation of quantitative genetic interactions.
I. Ulitsky, N.J. Krogan and R. Shamir.
Genome Biology , Volume 10:R140 2009 .  pdf
Advances in Bioinformatics
Assessing the Quality of Whole Genome Alignments in Bacteria.
F. Swidan, R. Shamir.
Advances in Bioinformatics , Volume 2009, Article ID 749027, 8 pages doi:10.1155/2009/749027 (2009).  pdf
Journal of Computation  Biology
Sorting Cancer Karyotypes by Elementary Operations.
M. Ozery-Flato, R. Shamir.
Journal of Computational Biology Vol. 16. no. 10, pp. 1445 - 1460, October 2009.  pdf
AAAS
Computing Has Changed Biology - Biology Education Must Catch Up.
P. Pevzner, R. Shamir.
Education Forum in Science Vol. 325. no. 5940, pp. 541 - 542 (31 July 2009).  pdf
PLOS ONE
SlimPLS: a method for feature selection in gene expression-based disease classification.
M. Gutkin, G. Dror, R. Shamir.
PLoS One Vol. 4 No. 7 e6416 (2009) .  pdf
IWPEC
A faster fixed-parameter approach to drawing binary tanglegrams.
S. Bocker, F. Hüffner, A. Truss, and M. Wahlstrom.
In Proceedings of the 4th International Workshop on Parameterized and Exact Computation,(IWPEC '09) Copenhagen,Denmark,September 2009 Lecture Notes in Computer Science, Springer.   pdf
NAR
Torque: topology-free querying of protein interaction networks
S. Bruckner, F. Hüffner, R. M. Karp, R. Shamir, R. Sharan.
Nucleic Acids Research doi: 10.1093/nar/gkp474.   pdf
Communication in Information and Systems
Increasing the Power of Association Studies by Imputation-based Sparse Tag SNP Selection
O. Davidovich, G. Kimmel, E. Halperin, R. Shamir.
Communications in Information and Systems 9 (3) 269-282 (2009)  pdf
Bioinformatics
Identifying functional modules using expression profiles and confidence-scored protein interactions
I. Ulitsky and R. Shamir.
Bioinformatics Vol. 25 no. 9 pages 1158-1164 (2009) .  pdf
lncs
Topology-free querying of protein interaction networks
S. Bruckner, F. Hüffner, R. M. Karp, R. Shamir, R. Sharan.
Proceedings of RECOMB 2009 LNCS 5541 74-89,  pdf
JCSS
Faster Pattern Matching with Character Classes using Prime Number Encoding
C. Linhart and R. Shamir.
Journal of Computers and System Sciences , 75, 155--162 (2009).   pdf
NAR
Allegro: Analyzing expression and sequence in concert to discover regulatory programs
Y. Halperin, C. Linhart, I. Ulitsky and R. Shamir.
Nucleic Acids Research 37:5, 1566-1579.   pdf
IPL
Matching with don't-cares and a small number of mismatches
C. Linhart and R. Shamir.
Information Processing Letters Volume 109, Number 5, p. 273-277 (2009).   pdf
2008  Top
lncs
Sorting cancer karyotypes by elementary operations
M. Ozery-Flato and R. Shamir.
Proceedings of the 6th RECOMB Satellite Workshop on Comparative Genomics 2008, LNCS Vol. 5267 pp. 211-225 (2008).  pdf
lncs
A faster algorithm for RNA co-folding
M. Ziv-Ukelson, I. Gat-Viks, Y. Wexler and R. Shamir.
Proc. Algorithms in Bioinformatics, Keith A. Crandall and Jens Lagergren (Eds.), 8th International Workshop, WABI 2008, LNBI 5251, 174-185, Karlsruh, Germany, September 15-17, (2008).   pdf
nrm
Modeling and Analysis of Regulatory Networks
G. Karlebach and R. Shamir.
Nature Reviews Molecular Cell Biology, Vol. 9 771--780 doi:10.1038/nrm2503 (2008)  pdf
SCM Nature
Regulatory networks define phenotypic classes of human stem cell lines.
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.
Nature. Vol. 455 No. 7211 p. 401-405 (2008) 
CSB08
Detecting pathways transcriptionally correlated with clinical parameters
I. Ulitsky and R. Shamir
Proc. 7th Annual International Conference on Computational Systems Bioinformatics (CSB 08) pp. 249--258, Imperial College Press, London, UK (2008)  pdf
JCB
Sorting Genomes with Centromeres by Translocations
M. Ozery-Flato and R. Shamir
Journal of Computational Biology (2008) Vol. 15 No. 7  pdf
Molecular Systems Biology
From E-MAPs to module maps: dissecting quantitative genetic interactions using physical interactions
I. Ulitsky, T. Shlomi, M. Kupiec and R. Shamir
Molecular Systems Biology (2008) Vol. 4 doi:10.1038/msb.2008.42  pdf
Genome research
Transcription factor and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets
C. Linhart, Y. Halperin and R. Shamir
Genome Research (2008) Vol. 18 No. 7 1180-1189  pdf
StemCells
Comprehensive MicroRNA Profiling Reveals a Unique Human Embryonic Stem Cell Signature Dominated by a Single Seed Sequence
L.C. Laurent, J. Chen, I. Ulitsky, F.J. Mueller, C. Lu, R. Shamir, J.B. Fan and J.F. Loring
Stem Cells doi: 10.1634/stemcells.2007-1081 pdf
lncs
Detecting Disease-Specific Dysregulated Pathways Via Analysis of Clinical Expression Profiles
I. Ulitsky, R.M. Karp and R. Shamir
Proc. RECOMB 2008, pp. 347--359, LNBI 4955, Springer, Berlin, (2008).  pdf
BMC
SPIKE - a database, visualization and analysis tool of cellular signaling pathways
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
BMC Bioinformatics (2008) Vol. 9 No. 11   pdf
TCBB
Computational Problems in Perfect Phylogeny Haplotyping: Typing without Calling the Allele
T. Barzuza, J.S. Beckmann, R. Shamir and I. Pe'er
IEEE Transactions on Computational Biology and Bioinformatics (2008) Vol. 5 No. 1 101-9
PLoS
Evolution and Selection in Yeast Promoters: Analyzing the Combined Effect of Diverse Transcription Factor Binding Sites
D. Raijman, R. Shamir and A. Tanay
PLoS Computational Biology (2008) Vol. 4 No. 1  pdf
Genome biology
MetaReg: A platform for modeling, analysis and visualization of biological systems using large-scale experimental data
I. Ulitsky, I. Gat-Viks and R. Shamir
Genome Biology (2008) Vol. 9 No. R1   pdf
2007  Top
lncs
On the frequency of genome rearrangement events in cancer karyotypes
M. Ozery-Flato and R. Shamir.
Proc. RECOMB satellite on Computational Cancer Biology, 2007  pdf
rsa
Improved algorithms for the random cluster graph model
R. Shamir and D. Tsur
Random Structures and Algorithms 31(4):418-449, 2007  pdf
IBD
Pediatric Onset Crohn's Disease is Characterized by Age and Genotype- Related Colonic Susceptibility
A. Levine, S. Kugathasan, A. Vito, V. Biank, E. Leshinsky-Silver, O. Davidovich, G. Kimmel, R. Shamir, P. Orazio, U. Broeckel, S. Cucchiara.
Inflammatory Bowel Disease (2007) Vol. 13 No. 12 1509-15
BMC Genomics
Functional genomic delineation of TLR-induced transcriptional networks
R. Elkon, C. Linhart, Y. Halperin, Y. Shiloh and R. Shamir
BMC Genomics (2007) Vol. 8 No. 394  pdf
AJHG
A randomization test for controlling population stratification in whole-genome association studies
G. Kimmel, M.I. Jordan, E. Halperin, R. Shamir and R.M. Karp RM
American Journal of Human Genetics (2007) , Vol. 81 No. 5, 895-905 (2007) pdf
PCR Primer Design
Degenerate Primer Design: Theoretical Analysis and the HYDEN program
C. Linhart and R. Shamir.
PCR primer design, A. Yuryev, editor. The Methods in Molecular Biology series, Humana Press (2007)  pdf
AMJG
Risk factors for perianal Crohn's disease: the role of genotype, phenotype, and ethnicity.
A. Karban, M. Itay, O. Davidovich, E. Leshinsky-Silver G. Kimmel, H. Fidder, R. Shamir, M. Waterman, R. Eliakim and A. Levine
The American Journal of Gastroenterology, Vol 102, No. 8 1702-8 (2007)  pdf
JCSS
Third special issue on Computational Biology
R. M. Karp, M. Li, P. Pevzner, R. Shamir, Guest editors.
Journal of Computers and System Sciences Vol. 73, No. 7 (2007)
Molecular Systems Biology
Pathway redundancy and protein essentiality revealed in the Saccharomyces cerevisiae interaction networks
I. Ulitsky and R. Shamir
Molecular Systems Biology, Vol. 3, No. 88 (2007)  pdf
lncs
Rearrangements in genomes with centromeres part I: translocations
M. Ozery-Flato and R. Shamir.
Proc. RECOMB 2007, , pp. 339--353, LNBI 4453, Springer, Berlin (2007) pdf
Molecular Systems Biology
Network-based prediction of protein function
R. Sharan, I. Ulitsky and R. Shamir
Molecular Systems Biology, Vol. 3, No. 88 (2007)  pdf
Jounral of Colorectal Disease
Lack of association of the 3'-UTR polymorphism in the NFKBIA gene with Crohn's disease in an Israeli cohort
E. Leshinsky-Silver, A. Karban, S. Cohen, M. Fridlander, O. Davidowich, G. Kimmel, R. Shamir and A. Levine
International Journal of Colorectal Disease (2007)  pdf
JCB
Sorting by reciprocal translocations via reversals theory
M. Ozery-Flato and R. Shamir
Journal of Computational Biology , Vol. 14 No. 4 (2007)  pdf
Nature Genetics
A genome-wide analysis in Saccharomyces cerevisiae demonstrates the influence of chromatin modifiers on transcription
I. Steinfeld, R. Shamir and M. Kupiec
Nature Genetics, Vol. 39, No. 3 (2007) .  pdf
Discrete Applied Mathematics
Fifth Special Issue in the Computational Molecular Biology Series
S. Istrail, P. Pevzner, R. Shamir, Editors
Discrete Applied Mathematics, Vol. 155, No. 6-7 (2007)
Genome Research
Refinement and expansion of signaling pathways: The osmotic response network in yeast
I. Gat-Viks and R. Shamir
Genome Research, Vol. 17, No. 3 (2007)  pdf
BMC
GEVALT: An integrated software tool for genotype analysis
O. Davidovich, G. Kimmel and R. Shamir
BMC Bioinformatics, Vol. 8, No. 36 (2007)  pdf
BMC
Identification of functional modules using network topology and high-throughput data
I. Ulitsky and R. Shamir
BMC Systems Biology, Vol. 1, No. 8 (2007)  pdf
2006  Top
BMC
Assessing the number of ancestral alternatively spliced exons in the human genome
R. Sorek, G. Dror and R. Shamir
BMC Genomics, Vol. 7, pp. 273 (2006)  pdf
lncs
Sorting by translocations via reversals theory
M. Ozery-Flato and R. Shamir
Proc. 4th RECOMB Satellite on Comparative Genomics, Lecture Notes in Computer Science, Vol. 4205, pp. 87-98, Springer, Berlin (2006)  pdf
PNAS
Quantification of protein half-lives in the budding yeast proteome
A. Belle, A. Tanay, L. Bitincka, R. Shamir and E.K. O'Shea
Proc. National Academy of Science USA, Vol. 103, No. 35, pp. 13004-13009 (2006)  pdf
Journal of Cancer
E2F1 identified by promoter and biochemical analysis as a central target of glioblastoma cell-cycle arrest in response to RAS inhbibition
R. Blum, I. Nakdimon, R. Elkon, R. Shamir, G. Rechavi and Y. Kloog
International Journal of Cancer, Vol. 119, No. 3, pp. 527-538 (2006)  pdf
AJHG
A Fast Method for Computing High-Significance Disease Association in Large Population-Based Studies
G. Kimmel and R. Shamir
American Journal of Human Genetics, Vol. 79, pp. 481-492 (2006)  pdf
lncs
An O(n3/2log(n)) algorithm for sorting by reciprocal translocations
M. Ozery-Flato and R. Shamir
Proc. of CPM 2006, LNCS, Vol. 4009, pp. 258-269 (2006)  pdf
JCB
A probabilistic methodology for integrating knowledge and experiments on biological networks
I. Gat-Viks, A. Tanay, D. Raijman and R. Shamir
Journal of Computational Biology 2006 Mar;13(2):165-81 pdf
Journal of Cancer
RAD51 haplotypes and breast cancer risk in Jewish non-Ashkenazi high risk women
I. Gal, G. Kimmel, R. Gershoni-Baruch, M. Z. Papa, E. Dagan, R. Shamir, E. Friedman
European Journal of Cancer 42(8) pp. 1129-34 (2006) pdf
BJC
ATM haplotypes and breast cancer risk in Jewish high risk women
M. Koren, G. Kimmel, E. Ben-Asher, I. Gal, M. Z. Papa, J. S. Beckman, D. Lancet, R. Shamir, E. Friedman
British Journal of Cancer 94 (10) pp. 1537-1543 (2006)  pdf
Handbook of Computational Molecular Biology
Biclustering Algorithms: A Survey
Amos Tanay, Roded Sharan and Ron Shamir
Handbook of Computational Molecular Biology , S. Aluru, editor, pp. 26-1 - 26-17, Chapman and Hall / CRC Press (2006)  pdf
Information And Computation
A simpler and faster 1.5-approximation algorithm for sorting by transpositions
T. Hartman and R. Shamir
Information and Computation 204 (2) 275-290 (2006)  pdf
Oncogene
Parallel induction of ATM-dependent pro- and anti-apoptotic signals in response to ionizing radiation in murine lymphoid tissue
S. Rashi-Elkeles, R. Elkon, N. Weizman, C. Linhart, N. Amariglio, G. Sternberg, G. Rechavi, A. Barzilai, R. Shamir, Y. Shiloh
Oncogene 25, 1584-1592 (2006)  pdf
2005  Top
Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data
R. Sharan, T. Ideker, B. Kelley, R. Shamir, R. M. Karp
Journal of Computational Biology Vol. 12 No. 6 pp. 835-846 (2005)  pdf
Deciphering Transcriptional Regulatory Elements That Encode Specific Cell-Cycle Phasing by Comparative Genomics Analysis
C. Linhart, R. Elkon, Y. Shiloh, and R. Shamir
Cell Cycle Vol. 4(12), pp. 1788-1797 Dec 2005  pdf
EXPANDER: an integrative suite for microarray data analysis
R. Shamir, A. Maron-Katz, A. Tanay, C. Linhart, I. Steinfeld, R.Sharan, Y. Shiloh, R. Elkon
BMC Bioinformatics 6:232 (2005)  pdf
A catalog of stability-associated sequence elements in 3~R UTRs of yeast mRNAs
R. Shalgi, M. Lapidot, R. Shamir, Y. Pilpel
Genome Biology 6:R86 (2005)  pdf (website)
Tag SNP Selection in Genotype Data for Maximizing SNP Prediction Accuracy
E. Halperin, G. Kimmel, R. Shamir.
Proc. of ISMB 2005; Bioinformatics Vol. 21 Suppl. 1 pp. i195-i203 (2005)  pdf
Typing without calling the allele: a strategy for inferring SNP haplotypes
T. Barzuza, J. S. Beckmann, R. Shamir and I. Pe'er
European Journal of Human Genetics Vol. 13, pp. 898-901 (2005)  pdf
Conservation and evolvability in regulatory networks: The evolution of ribosomal regulation in yeast
A. Tanay, A. Regev, R. Shamir
Proc. National Academy of Science USA Vol. 102 No. 20, pp. 7203-7208 (2005)  pdf
Factor graph network models for biological systems
I. Gat-Viks, A. Tanay, D. Raijman, R. Shamir
Proc. of RECOMB 2005 pp. 31-47, Lecture Notes in Bioinformatics 3500, Springer, Berlin, 2005  pdf
Dissection of a DNA damage-induced transcriptional network using a combination of microarrays, RNAi and computational promoter analysis
R. Elkon, S. Rashi-Elkeles, Y. Lerenthal, C. Linhart, T. Tenne, N. Amariglio, G. Rechavi, R. Shamir, Y. Shiloh
Genome Biology 6: R43 (2005)  pdf
2nd special issue of JCSS on Computational Biology
R. M. Karp, M. Li, P. Pevzner, R. Shamir, guest editors
Journal of Computers and System Sciences Volume 70, No. 3, May 2005  pdf
A Block-Free Hidden Markov Model for Genotypes and Its Application to Disease Association
G. Kimmel and R. Shamir
Journal of Computational Biology Volume 12, Number 10, pp. 1243-1260, 2005  pdf
Integrative analysis of genome-wide experiments in the context of a large high-throughput data compendium
A. Tanay, I. Steinfeld, M. Kupiec and R. Shamir
Molecular Systems Biology doi: 10.1038/msb4100005 (2005)  pdf
A global view of pleiotropy and phenotypically derived gene function in yeast
A. M. Dudley, D. M. Janse, A. Tanay, R. Shamir, G. M. Church
Molecular Systems Biology doi: 10.1038/msb4100004 (2005)  pdf
Accurate identification of alternatively spliced exons using support vector machine
Gideon Dror, Rotem Sorek and Ron Shamir
Bioinformatics (21) 897-901 (2005)  pdf
The degenerate primer design problem: Theory and applications
C. Linhart and R. Shamir
Journal of Computational Biology 12 (4) 431-456 (2005)  pdf
The Incomplete Perfect Phylogeny Haplotype Problem
Gad Kimmel and Ron Shamir
Journal of Bioinformatics and Computational Biology Vol. 3 No. 2 1-25 (2005)  pdf  ps
>Modeling and analysis of heterogeneous regulation in biological networks
I. Gat-Viks, A. Tanay, R. Shamir
Proc. of the first RECOMB satellite workshop on Regulatory Genomics, E. Eskin and C. Workman (editors), Lecture Notes in Bioinformatics, Vol. 3318 pp. 98-113, Springer, Berlin (2005)  pdf
GERBIL: GEnotype Resolution and Block Identification using Likelihood
G.Kimmel and R. Shamir
Proc. National Academy of Science USA 102: 158-162 (2005)  pdf (website and supplementary material)
2004  Top
A fully dynamic algorithms for modular decomposition and representation of cographs
R. Shamir and R. Sharan
Discrete Applied Mathematics, Vol. 136, No. 2-3, Pages 329-340 (2004)  pdf
A note on tolerance graph recognition
Ryan B. Hayward and Ron Shamir
Discrete Applied Mathematics, Vol. 143, No. 307-311 (2004) pdf
Maximum likelihood resolution of multi-block genotypes
G. Kimmel and R. Shamir
Proc. of RECOMB 2004, pp. 2-9 (2004)  pdf ps 
Identification of Protein Complexes by Comparative Analysis of Yeast and Bacterial Protein Interaction Data
R. Sharan, T. Ideker, B. Kelley, R. Shamir, R. M. Karp
Proc. of RECOMB 2004, pp. 282-289 (2004)  ps
Identification of Protein Complexes by Comparative Analysis of Yeast and Bacterial Protein Interaction Data
R. Sharan, T. Ideker, B. Kelley, R. Shamir, R. M. Karp
Journal of Computational Biology Volume 12, pp. 835-846, 2005  pdf
Multi-level Modeling and Inference of Transcription Regulation
A. Tanay and R. Shamir
Journal of Computational Biology Vol. 11 No. 2-3, pp. 357-376 (2004)  ps
Incomplete Directed Perfect Phylogeny
Itsik Pe'er, Tal Pupko, Ron Shamir and Roded Sharan
SIAM Journal on Computing Vol. 33 No. 3, 590-607 (2004)  ps 
Cluster Graph Modification Problems
Ron Shamir, Roded Sharan and Dekel Tsur
Discrete Applied Mathematics, Vol. 144, pp. 173-182 (2004)   ps
How prevalent is functional alternative splicing in the human genome?
R. Sorek, R. Shamir, G. Ast
Trends in Genetics 20 (2), 68-71 (2004)  pdf
The Canine Olfactory Subgenome
Tsviya Olender, Tania Fuchs, Chaim Linhart, Ron Shamir, Mark Adams,Francis Kalush, Miriam Khen and Doron Lancet
Genomics 83, 361-372 (2004)  pdf
PIVOT: Protein Interactions VisualizatiOn Tool
Nir Orlev, Ron Shamir and Yosef Shiloh
Bioinformatics 30 (3), 424-425 (2004)  pdf
Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data
A. Tanay, R. Sharan, M. Kupiec, R. Shamir
Proc. National Academy of Science USA 101 (9) 2981-2986 (March 2004)  pdf (website and supplementary material)
Computational Problems in Perfect Phylogeny Haplotyping: Xor-Genotypes and Tag SNPs
Tamar Barzuza, Jacques S. Beckmann, Ron Shamir and Itsik Peer
Proc. of CPM 2004, LNCS 3109, pp. 14-31 (2004)  pdf
A Global View of the Selection Forces in the Evolution of Yeast Cis-Regulation
A. Tanay, I. Gat-Viks, and R. Shamir
Genome Research 14: 829-834 (2004)  pdf (website and supplementary material)
A non-EST based method for exon-skipping prediction
R. Sorek, R. Shemesh, Y. Cohen, O. Basechess, G. Ast, R. Shamir
Genome Research 14 pp. 1617-1623 (2004) pdf
Reconstructing Chain Functions in Genetic Networks
I. Gat-Viks, R. Shamir, R.M. Karp and R. Sharan
Pacific Symposium on Biocomputing 2004  ps
Modeling and Analysis of Heterogeneous Regulation in Biological Networks
I. Gat-Viks, A. Tanay and R. Shamir
Journal of Computational Biology Vol. 11 No. 6 pp. 1034-1049 (2004)  pdf
Towards Optimally Multiplexed Applications of Universal Arrays
A. Ben-Dor, T. Hartman, R. M. Karp, B. Schwikowski, R. Sharan and Z. Yakhini
Journal of Computational Biology 11(2-3), pp. 477-494 (2004)  ps 
Designing Multi-Route Synthesis in Combinatorial Chemistry
A. Akavia, H. Senderowitz, A. Lerner and R. Shamir
Journal of Combinatorial Chemistry, Vol. 6, No. 4, pp. 540-548 (2004)  pdf
Computational Problems in Noisy SNP and Haplotype Analysis: Block Scores, Block Identification and Population Stratification
Gad Kimmel, Roded Sharan and Ron Shamir
INFORMS Journal on Computing, Vol. 16, No. 4, pp. 360-370 (2004)  pdf
In silico identification of transcriptional regulators associated with c-Myc
R. Elkon, K. Zeller, C. Linhart, C. Dang, R. Shamir and Y. Shiloh
Nucleic Acid Research Vol. 32 No. 17, pp. 4955-4961 (2004)  pdf
2003  Top
The Restriction Scaffold Problem
A. Ben-Dor, R. M. Karp, B. Schwikowski, R. Shamir
Computational Biology Vol. 10 No. 3-4, pp. 385-398 (2003)  pdf
Handling Long Targets and Errors in Sequencing by Hybridization
E. Halperin, S. Halperin, T. Hartman and R. Shamir
Journal of Computational Biology Vol. 10 No. 3-4, pp. 483-498 (2003)  ps 
Two notes on genome rearrangements
Michal Ozery-Flato and Ron Shamir
Journal of Bioinformatics and Computational Biology, Vol. 1, No. 1, pp. 71-94 (2003)  ps 
Genome-Wide In Silico Identification of Transcriptional Regulators Controlling the Cell Cycle in Human Cells
Ran Elkon, Chaim Linhart, Roded Sharan, Ron Shamir, and Yosef Shiloh
Genome Research Vol. 13(5), pp. 773-780, (2003)  pdf  (website and supplementary material)
Identifying Blocks and Sub-Populations in Noisy SNP Data
Gad Kimmel, Roded Sharan and Ron Shamir
Proc. of WABI 2003, pp. 303-319 (2003)  ps 
Chain functions and scoring functions in genetic networks
Irit Gat-Viks and Ron Shamir
Bioinformatics, Vol. 19, Supplement 1, pp. i108-i117 (2003)  pdf
Simpler 1.5-Approximation Algorithm for Sorting by Transpositions
Tzvika Hartman
Proc. of CPM 2003, pp. 156-169  ps
Towards Optimally Multiplexed Applications of Universal DNA Tag Systems
Amir Ben-Dor, Tzvika Hartman, Benno Schwikowski , Roded Sharan , and Zohar Yakhini
Proc. of RECOMB 2003, pp. 48-56  ps
Detecting Excess Radical Replacements in Phylogenetic Trees
T. Pupko, R. Sharan, M. Hasegawa, R. Shamir and D. Graur
Gene 319, pp. 127-135, 2003  pdf
Advanced Computational Techniques for Resequencing DNA with Polymerase Signaling Assay Arrays
Itsik Pe'er, Naama Arbili, Yi Liu, Colby Enck, Craig Gelfand, Ron Shamir
Nucleic Acids Research 31(19):5667-75 (2003)  pdf
CLICK and EXPANDER: A System for Clustering and Visualizing Gene Expression Data
Roded Sharan, Adi Maron-Katz and Ron Shamir
Bioinformatics, Vol. 19, No. 14, pp. 1787-1799 (2003)  pdf  (website)
Improved Algorithms for the Random Cluster Graph Model
R. Shamir and D. Tsur
Lecture Notes In Computer Science Vol. 2368  ps 
Scoring clustering solutions by their biological relevance
I. Gat-Viks, R. Sharan, R. Shamir
Bioinformatics 19: 2381-2389 (2003)  pdf
Modeling transcription programs: inferring binding site activity and dose-response model optimization
A. Tanay and R. Shamir
Proc. of RECOMB 2003, pp. 301-310  ps
2002  Top
On the Complexity of Positional Sequencing by Hybridization
Ben-Dor, I. Pe'er, R. Shamir and R. Sharan
Journal of Computational Biology Vol. 8 No. 4, pp. 361-371 (2002)  pdf
Algorithmic Approaches to Clustering Gene Expression Data
Ron Shamir and Roded Sharan
Current Topics in Computational Molecular Biology, T.Jiang, T. Smith, Y. Xu, M. Q. Zhang (editors), pp. 269-300, MIT Press, 2002  pdf ps 
Cluster Analysis and its Applications to Gene Expression Data
Roded Sharan, Rani Elkon and Ron Shamir
Ernst Schering workshop on Bioinformatics and Genome Analysis, pp. 83-108, Springer Verlag, Berlin 2002  pdf
The Restriction Scaffold Problem
A. Ben-Dor, R. M. Karp, B. Schwikowski, R. Shamir
Proc. of RECOMB 2002, (extended abstract)  pdf
Discovering Statistically Significant Biclusters in Gene Expression Data
A. Tanay, R. Sharan, R. Shamir
Proc. of ISMB 2002; Bioinformatics Vol. 18 Suppl. 1 S136-S144  pdf
Handling Long Targets and Errors in Sequencing by Hybridization
E. Halperin, S. Halperin, T. Hartman and R. Shamir
Proc. of RECOMB 2002, pp. 176-185 (extended abstract)  ps
The Degenerate Primer Design Problem
C. Linhart, R. Shamir
Proc. of ISMB 2002; Bioinformatics, Vol. 18, Suppl. 1 S172-S180  pdf  (website)
On the Properties of Sequences of Reversals that Sort a Signed Permutation
Anne Bergeron, Cedric Chauve, Tzvika Hartman and Karine St-Onge
Proc. of JOBIM 2002, pp. 99-108  ps
DEFOG: A Practical Scheme for Deciphering Families of Genes
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
Genomics Vol. 80, No. 3, 295-302 (2002)  pdf
A computational method for resequencing long DNA targets by universal oligonucleotide arrays
I. Pe'er, N. Arbili and R. Shamir
Proc. National Academy of Science USA Vol. 99 pp. 15497-15500 (2002)  pdf
2001  Top
Complexity Classification of Some Edge Modification Problems
A. Natanzon, R. Shamir and R.Sharan
Discrete Applied Mathematics, Vol. 113, No. 1, pp. 109-128 (2001)  ps
A Fully Dynamic Algorithm for Recognizing and Representing Proper Interval Graphs
Pavol Hell, Ron Shamir and Roded Sharan
SIAM Journal on Computing Vol. 31, No. 1, pp. 289-305 (2001)  ps
Large Scale Sequencing By Hybridization
Ron Shamir and Dekel Tsur
Proc. of RECOMB 2001, pp. 267-279, ACM Press, New York, NY (2001)  ps
Computational Expansion of Genetic Networks
A. Tanay and Ron Shamir
Proc. of ISMB 2001; Bioinformatics Vol. 17, Supplement 1, pp. S270-S278 (2001)  ps
A Chemical Distance Based Test for Positive Darwinian Selection
T. Pupko, R. Sharan, M. Hasegawa, R. Shamir and D. Graur
Proc. of WABI 2001 (extended abstract)  ps
2000  Top
Algorithms for Optical Mapping
R. M. Karp, R. Shamir
Journal of Computational Biology Vol. 7, No. 1/2, pp. 303-316 (2000)  ps
A Polynomial Approximation Algorithm for the Minimum Fill-In Problem
A. Natanzon, R. Shamir and R.Sharan
SIAM Journal on Computing, Vol. 30, No. 4, pp. 1067-1079 (2000)  ps
An Algorithm for Clustering cDNAs for Gene Expression Analysis Using Short Oligonucleotide Fingerprints
E. Hartuv, A. Schmitt, J. Lange, S. Meier-Ewert, H. Lehrach and R. Shamir
Genomics , Vol. 66, No. 3, pp. 249-256 (2000)  pdf
A Clustering Algorithm based on Graph Connectivity
E. Hartuv, R. Shamir
Information Processing Letters, Vol. 76, pp. 175-181 (2000)  ps
Fast Algorithm for Reconstruction of Ancestral Amino-Acid Sequences
Tal Pupko, Itsik Pe'er, Ron Shamir and Dan Graur
Molecular Biology and Evolution, Vol. 17, No. 6, pp. 890-896 (2000)  pdf
An Algorithm Combining Discrete and Continuous Methods for Optical Mapping
Richard M. Karp, Itsik Pe'er, Ron Shamir
J. Computational Biology, Vol. 7, No. 1/2, pp. 303-316 (2000)  ps
Approximation Algorithms for the Median Problem in the Breakpoint Model
Itsik Pe'er and Ron Shamir
Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment and the Evolution of Gene Families (D. Sankoff and J. H. Nadeau, editors), Kluwer Academic Press (Dordrecht), 2000  ps
CLICK: A Clustering Algorithm with Applications to Gene Expression Analysis
Roded Sharan and Ron Shamir
Currents in Compuational Molecular Biology, pp. 6-7, S. Miyano, R. Shamir and T. Takagi (editors) Universal Academy Press, 2000 (short summary)  ps ; Proc. of ISMB 2000, pp. 307-316, AAAI Press, Menlo Park, CA (2000) ps (Expander Home page)
Spectrum Alignment: Efficient Resequencing by Hybridization
Itsik Pe'er and Ron Shamir
Proc. of ISMB 2000, pp. 260-268, AAAI Press, Menlo Park, CA (2000)  ps
Incomplete Directed Perfect Phylogeny
Itsik Pe'er, Ron Shamir and Roded Sharan
Proc. of CPM 2000, pp. 143-153  ps
1999  Top
Bounded Degree Interval Sandwich Problems
Haim Kaplan and Ron Shamir
Algorithmica, Vol. 24, No. 2, pp. 96-104 (1999)  ps
Tractability of parameterized completion problems on chordal, strongly chordal and proper interval graphs
Haim Kaplan, Ron Shamir and Robert E. Tarjan
SIAM Journal of Computing, Vol. 28, No. 5, pp. 1906-1922 (1999)  ps
Faster and Simpler Algorithm for Sorting Signed Permutations by Reversals
Haim Kaplan, Ron Shamir and Robert E. Tarjan
SIAM Journal on Computing, Vol. 29, No. 3, pp. 880-892 (1999)  ps
Faster Subtree Isomorphism
Ron Shamir, Dekel Tzur
Journal of Algorithms, Vol. 33, pp. 267-280 (1999)  ps
Construction of Physical Maps From Oligonucleotide Fingerprints Data
G. Mayraz, R. Shamir
Journal of Computational Biology, Vol. 6, No. 2, pp. 237-252 (1999)  ps
An Algorithm for Clustering cDNAs for Gene Expression Analysis Using Short Oligonucleotide Fingerprints
E. Hartuv, A. Schmitt, J. Lange, S. Meier-Ewert, H. Lehrach and R. Shamir
Proc. of RECOMB 1999, pp. 188-197 (extended abstract)  ps
Clustering Gene Expression Patterns
A. Ben-Dor, R. Shamir, Z. Yakhini
Journal of Computational Biology, Vol. 6, No. 3/4, pp. 281-297 (1999)  ps
On the Complexity of Positional Sequencing by Hybridization
Ben-Dor, I. Pe'er, R. Shamir and R. Sharan
Proc. of CPM 1999, (LNCS 1645) pp. 88-100 (extended abstract)  ps
An Algorithm Combining Discrete and Continuous Methods for Optical Mapping
Richard M. Karp, Itsik Pe'er, Ron Shamir
Proc. of ISMB 1999, pp. 159-168 (extended abstract)  ps
Perfect Completion and Deletion in Random Graphs
Assaf Natanzon, Ron Shamir
Technical Report, 1999  ps
Optimizing the BAC-End Strategy for Sequencing the Human Genome
Kichard M. Karp, Ron Shamir
Technical Report, April 1999  ps
A Fully Dynamic Algorithm for Recognizing and Representing Proper Interval Graphs
Pavol Hell, Ron Shamir and Roded Sharan
Proc. of ESA 1999, pp. 527-539, LNCS 1643  ps
1998 and before  Top
Algorithms for Optical Mapping
R. M. Karp, R. Shamir
Proc. of RECOMB 1998, pp. 117-124 (extended abstract)  ps
A Polynomial Approximation Algorithm for the Minimum Fill-In Problem
A. Natanzon, R. Shamir and R.Sharan
Proc. of STOC 1998, pp. 41-47  ps
The maximum subforest problem: Approximation and exact algorithms
Ron Shamir, Dekel Tzur
Proc. of SODA 1998, pp. 394-399  ps
Faster and Simpler Algorithm for Sorting Signed Permutations by Reversals
Haim Kaplan, Ron Shamir and Robert E. Tarjan
Proc. of SODA 1997, pp. 344-351  ps ; Also Proc. of RECOMB 1997, pp. 163
Realizing interval graphs with size and distance constraints
Itsik Pe'er and Ron Shamir
SIAM Journal of Discrete Mathematics, Vol. 10, No. 4, pp. 662-687 (1997)  ps 
Satisfiability Problems on Intervals and Unit Intervals
Itsik Pe'er and Ron Shamir
Theoretical Computer Science, Vol. 175, No. 2, pp. 349-372 (1997)  ps 
Pathwidth, Bandwidth and Completion Problems to Proper Interval Graphs with Small Cliques
Haim Kaplan, Ron Shamir
SIAM J. Computing, Vol. 25, No. 3, pp. 540-561 (1996)  ps
Physical Maps and Interval Sandwich Problems: Bounded Degrees Help
Haim Kaplan and Ron Shamir
Proc. of ISTCS 1996, IEEE Computer Science Press, pp. 195-201  ps
Interval Graphs with Side (and Size) Constraints
Itsik Pe'er and Ron Shamir
Proc. of the Third European Symposium on Algorithms (ESA 95), Springer, Berlin, pp. 142-154  ps
Four Strikes Against Physical Mapping of DNA
Paul W. Goldberg, Martin C. Golumbic, Haim Kaplan and Ron Shamir
Journal of Computational Biology, Vol. 2, No. 1, pp. 139-152 (1995)  ps
Algorithms and Complexity of Sandwich Problems in Graphs
Martin Golumbic Haim Kaplan, Ron Shamir
Proc. of WG 1993, pp. 57-69, LNCS 790, Springer, Berlin, 1994  ps
Tractability of parameterized completion problems on chordal and interval graphs: Minimum Fill-in and Physical Mapping
Haim Kaplan, Ron Shamir, Robert E. Tarjan
Proc. of FOCS 1994, pp. 780-791  ps
Complexity and algorithms for reasoning about time: a graph-theoretic approach
Martin Golumbic, Ron Shamir
JACM, Vol. 40, pp. 1108-1133 (1993)  ps
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