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).
Improving the performance of minimizers and winnowing schemes
G. Marcais, D. Pellow, D. Bork, Y. Orenstein, R. Shamir, C. Kingsford.
Bioinformatics, 15; 33(14): i110–i117 (2017).
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).
Recycler: an algorithm for detecting plasmids from de novo assembly graphs
R. Rozov, A. Kav Brown, D. Bogumil, E. Halperin, I. Mizrahi, R. Shamir.
Bioinformatics, 10.1093/bioinformatics/btw651, 2016.
Sorting by cuts, joins and duplications
R. Zeira, R. Shamir.
Journal of Computational Biology Vol 23 No 0. pp 1-11 (2016).
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).
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.
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).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).
Modeling protein-DNA binding via high throughput in vitro technologies
Y. Orenstein, R. Shamir.
Briefings in Functional Genomics, doi: 10.1093/bfgp/elw030 (2016).
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).
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). Erratum
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. 16:1Ð16:13.
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.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).
Evidence of TAF1 dysfunction in peripheral models of X-linked dystonia-parkinsonism.
A. Domingo, D. Amar, K. Grtz, L. Lee, R. Rosales, N. Brggemann, 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).
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Fast lossless compression via cascading Bloom filters.
R. Rozov, R. Shamir, E. Halperin
BMC Bioinformatics, 15(Suppl 9):S7, 2014.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.
Functional gene groups are concentrated within chromosomes, among chromosomes and in the nuclear space of the human genome.
A. Thvenin, L. Ein-Dor, M. Ozery-Flato and R. Shamir
Nucleic Acids Research, doi: 10.1093/nar/gku667.
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
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.Constructing module maps for integrated analysis of heterogeneous biological networks.
D. Amar and R. Shamir
Nucleic Acids Research doi:10.1093/nar/gku102, 2014.
Environmental stresses disrupt telomere length homeostasis.
G.H. Romano, Y. Harar, T. Yehuda, A. Podhorzer, L. Rubinstein, R. Shamir, A. Gottlieb, Y. Silberberg, D. PeÕer, E. Ruppin, R. Sharan, M. Kupiec
PLoS Genetics,9(9):e1003721. doi: 10.1371/journal.pgen.1003721. Epub 2013.
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.
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.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.
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.
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.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.
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.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.
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.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.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.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.
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.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.
Bioinformatics for Biologists.
P. Pevzner and R. Shamir, editors .
Textbook. Cambridge University Press, UK, 2011.
An O(n3/2Ãlog(n)) algorithm for sorting by reciprocal translocations.
M. Ozery-Flato, R. Shamir.
Journal of Discrete Algorithms, Volume 9, Issue 4, Pages 344-357(2011),
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
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, 2011Selected papers from the 2nd RECOMB satellite meeting on Bioinformatics Education (RECOMB-BE).
P. A. Pevzner, R. Shamir, editors.
Journal of Computational Biology
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, 2011Integration 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, 2011PrtT-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
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.
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.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).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).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).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.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).
A plasma-membrane E-MAP reveals links of the eisosome with sphingolipid metabolism and endosomal trafficking.
P.S. Aguilar, F. Frhlich, 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).Topology-free querying of protein interaction networks.
Bruckner, S., Hffner, F., Karp, R.M., Shamir, R., Sharan, R.
Journal of Computational Biology , 17 (3), pp. 237-252 (2010).
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).
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).
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).
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 .
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 .
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).
Towards accurate imputation of quantitative genetic interactions.
I. Ulitsky, N.J. Krogan and R. Shamir.
Genome Biology , Volume 10:R140 2009 .
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).Sorting Cancer Karyotypes by Elementary Operations.
M. Ozery-Flato, R. Shamir.
Journal of Computational Biology Vol. 16. no. 10, pp. 1445 - 1460, October 2009.
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).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) .
A faster fixed-parameter approach to drawing binary tanglegrams.
S. Bocker, F. Hffner, 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.Torque: topology-free querying of protein interaction networks
S. Bruckner, F. Hffner, R. M. Karp, R. Shamir, R. Sharan.
Nucleic Acids Research doi: 10.1093/nar/gkp474.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)
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) .Topology-free querying of protein interaction networks
S. Bruckner, F. Hffner, R. M. Karp, R. Shamir, R. Sharan.
Proceedings of RECOMB 2009 LNCS 5541 74-89,
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).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.
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).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).
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)
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)
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)
Sorting Genomes with Centromeres by Translocations
M. Ozery-Flato and R. Shamir
Journal of Computational Biology (2008) Vol. 15 No. 7From 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
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
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.2007-1081Detecting 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).
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
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. 1 101-9Evolution 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. 1MetaReg: 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. R1On the frequency of genome rearrangement events in cancer karyotypes
M. Ozery-Flato and R. Shamir.
Proc. RECOMB satellite on Computational Cancer Biology, 2007
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
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
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)
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)
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)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)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)Network-based prediction of protein function
R. Sharan, I. Ulitsky and R. Shamir
Molecular Systems Biology, Vol. 3, No. 88 (2007)
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)Sorting by reciprocal translocations via reversals theory
M. Ozery-Flato and R. Shamir
Journal of Computational Biology , Vol. 14 No. 4 (2007)
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) .
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)
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)GEVALT: An integrated software tool for genotype analysis
O. Davidovich, G. Kimmel and R. Shamir
BMC Bioinformatics, Vol. 8, No. 36 (2007)Identification of functional modules using network topology and high-throughput data
I. Ulitsky and R. Shamir
BMC Systems Biology, Vol. 1, No. 8 (2007)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)
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)
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)
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)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
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)
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)
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)
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)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 2005EXPANDER: 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)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) (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)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)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)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)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 2005Identification 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, 2005A 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, 2005Integrative 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)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)Accurate identification of alternatively spliced exons using support vector machine
Gideon Dror, Rotem Sorek and Ron Shamir
Bioinformatics (21) 897-901 (2005)The degenerate primer design problem: Theory and applications
C. Linhart and R. Shamir
Journal of Computational Biology 12 (4) 431-456 (2005)The Incomplete Perfect Phylogeny Haplotype Problem
Gad Kimmel and Ron Shamir
Journal of Bioinformatics and Computational Biology Vol. 3 No. 2 1-25 (2005)GERBIL: GEnotype Resolution and Block Identification using Likelihood
G.Kimmel and R. Shamir
Proc. National Academy of Science USA 102: 158-162 (2005) (website and supplementary material)Maximum likelihood resolution of multi-block genotypes
G. Kimmel and R. Shamir
Proc. of RECOMBMulti-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)How prevalent is functional alternative splicing in the human genome?
R. Sorek, R. Shamir, G. Ast
Trends in Genetics 20 (2), 68-71 (2004)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)PIVOT: Protein Interactions VisualizatiOn Tool
Nir Orlev, Ron Shamir and Yosef Shiloh
Bioinformatics 30 (3), 424-425 (2004)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) (website and supplementary material)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) (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)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)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)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)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) (website and supplementary material)Detecting Excess Radical Replacements in Phylogenetic Trees
T. Pupko, R. Sharan, M. Hasegawa, R. Shamir and D. Graur
Gene 319, pp. 127-135, 2003Advanced 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)Improved Algorithms for the Random Cluster Graph Model
R. Shamir and D. Tsur
Lecture Notes In Computer Science Vol. 2368Scoring clustering solutions by their biological relevance
I. Gat-Viks, R. Sharan, R. Shamir
Bioinformatics 19: 2381-2389 (2003)Algorithmic Approaches to Clustering Gene Expression Data
Ron Shamir and Roded Sharan
Current Topics in Computational Molecular BiologyDiscovering Statistically Significant Biclusters in Gene Expression Data
A. Tanay, R. Sharan, R. Shamir
Proc. of ISMB 2002; Bioinformatics Vol. 18 Suppl. 1 S136-S144DEFOG: 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)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)Computational Expansion of Genetic Networks
A. Tanay and Ron Shamir
Proc. of ISMB 2001; Bioinformatics Vol. 17, Supplement 1, pp. S270-S278 (2001)CLICK: A Clustering Algorithm with Applications to Gene Expression Analysis
Roded Sharan and Ron Shamir
Currents in Compuational Molecular BiologyBounded Degree Interval Sandwich Problems
Haim Kaplan and Ron Shamir
Algorithmica, Vol. 24, No. 2, pp. 96-104 (1999)
Reduced changes in protein compared to mRNA levels across non-proliferating tissues
K. Perl, K. Ushakov, Y. Pozniak, O. Yizhar-Barnea, Y. Bhonker, S. Shivatzki, T. Geiger, K.B. Avraham and R. Shamir
BMC Genomics, 18:305, DOI 10.1186/s12864-017-3683-9 (2017).
Tired and misconnected: A breakdown of brain modularity following sleep deprivation.
E. Ben Simon, A. Maron-Katz, N. Lahav, R. Shamir and T. Hendler.
Human Brain Mapping, 38(6):3300-3314. doi: 10.1002/hbm.23596 (2017).
Reconstructing cancer karyotypes from short read data: the half full and half empty glass
R. Eitan, R. Shamir.
bioRxiv 152447; doi: https://doi.org/10.1101/152447 (2017).
Improving the performance of minimizers and winnowing schemes
G. Marcais, D. Pellow, D. Bork, Y. Orenstein, R. Shamir, C. Kingsford.
Bioinformatics, special issue of ISMB/ECCB 2017, Vol. 33, i110–i117 doi: 10.1093/bioinformatics/btx235 (2017).
Complexity and algorithms for copy-number evolution problems
M. El-Kebir, B. J. Raphael, R. Shamir, R. Sharan, S. Zaccaria, M. Zehavi and R. Zeira
Algorithms for Molecular Biology, 12(1), 13 (2017).
Faucet: streaming de novo assembly graph construction
R. Rozov, G. Goldshlager, E. Halperin, R. Shamir.
Bioinformatics, 34 (1) 147–154 (2018).
Extracting replicable associations across multiple studies: Empirical Bayes algorithms for controlling the false discovery rate
D. Amar, R. Shamir, D. Yekutieli.
PLoS Computational Biology 13(8): e1005700 (2017).
An extensive enhancer-promoter map generated by genome-scale analysis of enhancer and gene activity patterns
T. A. Hait, D. Amar, R. Shamir and R. Elkon.
BioRxiv, doi: https://doi.org/10.1101/190231 (2017).
A Linear-Time Algorithm for the Copy Number Transformation Problem
R. Zeira, M. Zehavi and R. Shamir
Journal of Computational Biology, DOI: 10.1089/cmb.2017.0060 (2017).
Designing small universal k-mer hitting sets for improved analysis of high throughput sequencing
Y. Orenstein, D. Pellow, G. Marcais, R. Shamir, C. Kingsford.
PLoS Computational Biology, 13(10): e1005777 (2017).
Analysis of blood-based gene expression in idiopathic Parkinson disease
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.
Neurology, 89(16):1676-1683 (2017).
Reconstructing cancer karyotypes from short read data: the half full and half empty glass
R. Eitan, R. Shamir.
BMC Bioinformatics, 18:488, 2017. Preliminary version: bioRxiv 152447; doi: https://doi.org/10.1101/152447 (2017).
Tracing the neural carryover effects of interpersonal anger on resting-state fMRI and their relation to traumatic stress symptoms in a subsample of soldiers
G. Gilam, A. Maron-Katz, E. Kliper, T. Lin, E. Fruchter, R. Shamir, T. Hendler.
Frontiers in Behavioral Neuroscience, doi: 10.3389/fnbeh.2017.00252 (2017).
ADEPTUS: A discovery tool for disease prediction, enrichment and network analysis based on profiles from many diseases
D. Amar, A. Vizel, C. Levy & R. Shamir.
Bioinformatics, bty027, https://doi.org/10.1093/bioinformatics/bty027 (2018).
MorphDB: Prioritizing Genes for Specialized Metabolism Pathways and Gene Ontology Categories in Plants
A. Zwaenepoel, T. Diels, D. Amar, T. Van Parys, R. Shamir, Y. Van de Peer and O. Tzfadia.
Front. Plant Sci., https://doi.org/10.3389/fpls.2018.0035 (2018).
FOCS: a novel method for analyzing enhancer and gene activity patterns infers an extensive enhancer–promoter map
T. A. Hait, D. Amar, R. Shamir, R. Elkon.
Genome Biology, 19:56, https://doi.org/10.1186/s13059-018-1432-2 (2018).
Sorting cancer karyotypes using double-cut-and-joins, duplications and deletions
R. Zeira and R. Shamir.
Bioinformatics, bty381, https://doi.org/10.1093/bioinformatics/bty381 (2018).
Computational analysis of mRNA expression profiling in the inner ear reveals candidate transcription factors associated with proliferation, differentiation, and deafness
K. Perl, R. Shamir and K. B. Avraham
Human Genomics, 12:30, https://doi.org/10.1186/s40246-018-0161-7 (2018).
Genome Rearrangement Problems with Single and Multiple Gene Copies: A Review
R. Zeira and R. Shamir.
Bioinformatics and Phylogenetics: Seminal contributions of Bernard Moret, T. Warnow, Editor, pp. 205--242, Springer Nature Switzerland AG (2019).
Multi-omic and multi-view clustering algorithms: review and cancer benchmark
N. Rappoport & R. Shamir
Nucleic Acids Research, 46 (20) pp. 10546–-10562 (2018).
Genomic meta-analysis of the interplay between 3D chromatin organization and gene expression programs under basal and stress conditions
I. Nurick, R. Shamir and R. Elkon.
Epigenetics & Chromatin (2018) 11:49 https://doi.org/10.1186/s13072-018-0220-2 (2018).
GePMI: A statistical model for personal intestinal microbiome identification
Z. Wang, H. Lou, R. Shamir, R. Jiang, T. Chen.
npj Biofilm and Microbiome} 4: 20, https://doi.org/10.1038/s41522-018-0065-2 (2018).
NEMO: cancer subtyping by integration of partial multi-omic data
N. Rappoport and R. Shamir.
Bioinformatics, https://doi.org/10.1093/bioinformatics/btz058 (2018).
The EXPANDER integrated platform for transcriptome analysis
T. A. Hait, A.Maron-Katz., D. Sagir, D. Amar, I. Ulitsky, C. Linhart, A. Tanay, R. Sharan, Y. Shiloh, R. Elkon, R.Shamir.
Journal of Molecular Biology, https://doi.org/10.1016/j.jmb.2019.05.013 (2019).
CT-FOCS: a novel method for inferring cell type-specific enhancer-promoter maps
T. Hait, R. Elkon, R. Shamir.
BioRxiv, https://www.biorxiv.org/content/10.1101/707158v3 (2019).
Personalized prediction of adverse heart and kidney events using baseline and longitudinal data from SPRINT and ACCORD
G. Dinstag, D. Amar, E. Ingelsson, E. Ashley and R. Shamir.
PLOS ONE, https://doi.org/10.1371/journal.pone.0219728 (2019).
Inaccuracy of the log‐rank approximation in cancer data analysis
N. Rappoport and R. Shamir.
Molecular Systems Biology (2019) 15:e8754https://doi.org/10.15252/msb.20188754 (2019).
Prodigy: personalized prioritization of driver genes
G. Dinstag, R. Shamir.
Bioinformatics btz815, https://doi.org/10.1093/bioinformatics/btz815 (2019).
Unravelling plasmidome distribution and interaction with its hosting microbiome
A. Kav Brown, R. Rozov, D. Bogmil, S. J. Sorensen, I. Benhar, E. Halperin, R. Shamir, I. Mizrahi.
Environmental Microbiology, https://doi.org/10.1111/1462-2920.14813 (2019).
PROMO: an interactive tool for analyzing clinically-labeled multi-omic cancer datasets
D. Netanely, N. Stern, I. Laufer, R. Shamir.
BMC Bioinformatics 20:732, https://doi.org/10.1186/s12859-019-3142-5 (2019).
Using the kinetics of C-reactive protein response to improve the differential diagnosis between acute bacterial and viral infections
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.
Infection, https://doi.org/10.1007/s15010-019-01383-6 (2020).
DOMINO: a novel network-based module detection algorithm with reduced rate of false calls
H. Levi, R. Elkon, R. Shamir.
Molecular Systems Biology 17:e9593 (2021).
Melanoma-secreted lysosomes trigger monocyte-derived dendritic cell apoptosis and limit cancer immunotherapy
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.
Cancer Research, doi: 10.1158/0008-5472.CAN-19-2944 (2020).
PlasClass improves plasmid sequence classification
D. Pellow, I. Mizrahi, R. Shamir.
PLoS Comput Biol, 16(4): e1007781. https://doi.org/10.1371/journal.pcbi.1007781 (2020).
MONET: Multi-omic patient module detection by omic selection
N. Rappoport, R. Safra, R. Shamir.
PLoS Computational Biology 16 (9) e1008182 (2020).
Improving the efficiency of de Bruijn graph construction using compact universal hitting sets
Y. Ben-Ari, D. Flomin, L. Pu, Y. Orenstein, R. Shamir.
Proc. ACM Conference on Bioinformatics, Computational Biology and Health Informatics (ACM-BCB), August 2021, Article No.: 4, pp 1–9, https://dl.acm.org/doi/10.1145/3459930.3469520 (2021).
Early detection of prostate gland and breast cancer risk based on routine check-up data using survival analysis trees for left-truncated and right-censored data
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.
MedRxiv, doi: https://doi.org/10.1101/2021.01.11.21249491 (2021).
Classification of node-positive melanomas into prognostic subgroups using keratin, immune and melanogenesis expression patterns
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.
Oncogene https://doi.org/10.1038/s41388-021-01665-0 (2021).
SCAPP: An algorithm for improved plasmid assembly in metagenomes
D. Pellow, M. Probst, O. Furman, A. Zorea, A. Segal, I. Mizrahi, R. Shamir.
Microbiome 9, 144 (2021), https://doi.org/10.1186/s40168-021-01068-z (2021).
Contribution of clinical breast exam to cancer detection in women participating in a modern screening program.
T.S. Menes, D. Coster and S. Shenhar-Tsarfaty.
BMC Women's Health, 21(1) 368, pp.1-8., https://doi.org/10.1186/s12905-021-01507-x (2021).
C-reactive protein velocity discriminates between acute viral and bacterial infections in patients who present with relatively low CRP concentrations
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.
BMC Infect Dis 21, 1210 (2021). https://doi.org/10.1186/s12879-021-06878-y (2021).
Using syncmers improves long-read mapping
A. Dutta, D. Pellow, R. Shamir.
BioRxiv 2022.01.10.475696 (2022).
CT-FOCS: a novel method for inferring cell type-specific enhancer-promoter maps.
T.A. Hait, R. Elkon, R. Shamir.
Nucleic Acids Research gkac048, https://doi.org/10.1093/nar/gkac048 (2022).
The DOMINO web-server for active module identification analysis.
H. Levi, N. Rahmanian, R. Elkon, R. Shamir.
Bioinformatics, btac067, https://doi.org/10.1093/bioinformatics/btac067 (2022).
A machine learning model for predicting deterioration of COVID-19 inpatients
O. Noy*, D. Coster*, M. Metzger, I. Attar, S. Shenhar-Tsafraty, S. Berliner, G. Rahav, O.Rogowski, R. Shamir.
Nature Scientific Reports Article 2630 DOI 10.1038/s41598-022-05822-7 (2022).
Whole-genome duplication shapes the aneuploidy landscape of human cancers.
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. Storchová, D. Cimini, U. Ben-David.
Cancer Res, https://doi.org/10.1158/0008-5472.CAN-21-2065 (2022).
Relationship Between Pemphigus Vulgaris Severity and PCR-positive Herpes Simplex Virus
Baum, I. Atar, D. Coster, S. Dovrat, M. Solomon, E. Sprecher, T. Zeeli and A. Barzilai.
ActaDV, Vol. 102 (2022), DOI: https://doi.org/10.2340/actadv.v102.917 (2022).
Data Set-Adaptive Minimizer Order Reduces Memory Usage in k-Mer Counting
D. Flomin, D. Pellow and R. Shamir.
Journal of Computational Biology, Vol. 29, Pp. 1–14 DOI: 10.1089/cmb.2021.0599 (2022).
3CAC: improving the classification of phages and plasmids in metagenomic assemblies using assembly graphs
L. Pu and R. Shamir.
Bioinformatics, Volume 38, Issue Supplement 2, September 2022, Pages ii56–ii61, https://doi.org/10.1093/bioinformatics/btac468 (2022).
Integration of gene expression and DNA methylation data across different experiments
Y. Itai, N. Rappoport, R. Shamir.
Nucleic Acids Research, gkad566, https://doi.org/10.1093/nar/gkad566 (2023).
Clustering the cortical laminae: in vivo parcellation
I. Shamir, Y. Assaf, R. Shamir.
Brain Structure and Function, https://doi.org/10.1007/s00429-023-02748-2 (2024).Parameterized syncmer schemes improve long-read mapping
A. Dutta, D. Pellow, R. Shamir.
PLOS Comp Bio, https://doi.org/10.1371/journal.pcbi.1010638 (2022).
4CAC: 4-class classification of metagenomic assemblies using machine learning and assembly graphs
L. Pu, R. Shamir.
BioRxiv 2023.01.20.524935 doi: https://doi.org/10.1101/2023.01.20.524935 (2023).
Time-dependent Iterative Imputation for Multivariate Longitudinal Clinical Data
Omer Noy, Ron Shamir
arXiv https://doi.org/10.48550/arXiv.2304.07821 (2023).The Effect of Body Mass Index Reduction on Intraocular Pressure in a Large, Prospective Population-based Cohort Study in Israel
D. Coster, A. Rafie, N. Savion, R. Rachmiel, S. Kurtz, S. Berliner, I. Shapira, D. Zeltser, O. Rogowski, S. Shenhar-Tsarfaty, M. Waisbourd
PLoS One, https://doi.org/10.1371/journal.pone.0285759 (2023).Drugst.One -- A plug-and-play solution for online systems medicine and network-based drug repurposing
Andreas Maier, Michael Hartung, Mark Abovsky, Klaudia Adamowicz, Gary D. Bader, Sylvie Baier, David B. Blumenthal, Jing Chen, Maria L. Elkjaer, Carlos Garcia-Hernandez, Markus Hoffmann, Igor Jurisica, Max Kotlyar, Olga Lazareva, Hagai Levi, Markus List, Sebastian Lobentanzer, Joseph Loscalzo, Noel Malod-Dognin, Quirin Manz, Julian Matschinske, Mhaned Oubounyt, Alexander R. Pico, Rudolf T. Pillich, Julian M. Poschenrieder, Dexter Pratt, Nataša Pržulj, Sepideh Sadegh, Julio Saez-Rodriguez, Suryadipto Sakar, Gideon Shaked, Ron Shamir, Nico Trummer, Ugur Turhan, Ruisheng Wang, Olga Zolotareva, Jan Baumbach.
arXiv https://doi.org/10.48550/arXiv.2305.15453 (2023).Clustering of clinical-echocardiographic phenotypes of covid-19 disease using machine-learning techniques
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.
Scientific Reports 13:8832 doi: 10.1038/s41598-023-35449-1 (2023).
Single cell Hi-C identifies plastic chromosome conformations underlying the gastrulation enhancer landscape
N. Rappaport, E. Chomsky, T. Nagano, C. Seibert, Y. Lubling, Y. Baran, A. Lifshitz, W. Leung, Z. Mukamel, R. Shamir, P. Fraser, A. Tanay.
Nature Communications 14(1):3844. doi: 10.1038/s41467-023-39549-4 (2023).
Evaluation of European-based polygenic risk score for breast cancer on Ashkenazi Jewish women
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*.
Journal of Medical Genetics doi:10.1136/jmg-2023-109185 (2023).
Efficient minimizer orders for large values of $k$ using minimum decycling sets
D. Pellow, L. Pu, B. Ekim, L. Kotlar, B. Berger, R. Shamir, Y. Orenstein
Genome Research DOI: 10.1101/gr.277644.123 (2023).
Predicting appropriateness of antibiotic treatment among ICU patients with hospital acquired infection
E. Rannon, E. Goldschmidt, D. Bernstein, A. Wasserman, D. Coster, R. Shamir
medRxiv doi: https://doi.org/10.1101/2023.08.15.23294109 (2023).
Inferring transcriptional activation and repression activity maps in single-nucleotide resolution using deep-learning
T. Hait, R. Elkon, R. Shamir.
Research Square https://doi.org/10.21203/rs.3.rs-3270775/v1 (2023).
A feature ranking algorithm for clustering medical data
E. Shpigelman, R. Shamir.
MedRxiv doi: 10.1101/2023.09.30.23296349 (2023).