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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.


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

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. GrŸtz, L. Lee, R. Rosales, N. BrŸggemann, 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.

HTS-IBIS: fast and accurate inference of binding site motifs from HT-SELEX data

Y. Orenstein and R. Shamir

BioRxiv ,, 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. ThŽvenin, 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.

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

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, 2011

Selected 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, 2011

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

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

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. Fršhlich, 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., HŸffner, 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) .

Torque: topology-free querying of protein interaction networks

S. Bruckner, F. HŸffner, 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. HŸffner, 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).

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.)

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)

Sorting Genomes with Centromeres by Translocations

M. Ozery-Flato and R. Shamir

Journal of Computational Biology (2008) Vol. 15 No. 7

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

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.2007-1081

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).

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. 1 101-9

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

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

On 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)

Rearrangements in genomes with centromeres part I: translocations

M. Ozery-Flato and R. Shamir.


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)

Sorting by translocations via reversals theory

M. Ozery-Flato and R. Shamir

Proc. 4th RECOMB Satellite on Comparative Genomics, Lecture Notes in Computer Science

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)

An O(n3/2Ãlog(n)) algorithm for sorting by reciprocal translocations

M. Ozery-Flato and R. Shamir

Proc. of CPM

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)

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

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 2005

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)

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)

Factor graph network models for biological systems

I. Gat-Viks, A. Tanay, D. Raijman, R. Shamir

Proc. of RECOMB

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 2005

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

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

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)

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)

>Modeling and analysis of heterogeneous regulation in biological networks

I. Gat-Viks, A. Tanay, R. Shamir

Proc. of the first RECOMB Bioinformatics

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)

A fully dynamic algorithms for modular decomposition and representation of cographs

R. Shamir and R. Sharan

Discrete Applied Mathematics

A note on tolerance graph recognition

Ryan B. Hayward and Ron Shamir

Discrete Applied Mathematics

Maximum likelihood resolution of multi-block genotypes

G. Kimmel and R. Shamir

Proc. of RECOMB

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)

Cluster Graph Modification Problems

Ron Shamir, Roded Sharan and Dekel Tsur

Discrete Applied Mathematics

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)

Computational Problems in Perfect Phylogeny Haplotyping: Xor-Genotypes and Tag SNPs

Tamar Barzuza, Jacques S. Beckmann, Ron Shamir and Itsik Peer

Proc. of CPM

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)

Reconstructing Chain Functions in Genetic Networks

I. Gat-Viks, R. Shamir, R.M. Karp and R. Sharan

Pacific Symposium on Biocomputing

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)

Designing Multi-Route Synthesis in Combinatorial Chemistry

A. Akavia, H. Senderowitz, A. Lerner and R. Shamir

Journal of Combinatorial Chemistry

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

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)

Two notes on genome rearrangements

Michal Ozery-Flato and Ron Shamir

Journal of Bioinformatics and Computational Biology

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)

Identifying Blocks and Sub-Populations in Noisy SNP Data

Gad Kimmel, Roded Sharan and Ron Shamir

Proc. of WABI

Chain functions and scoring functions in genetic networks

Irit Gat-Viks and Ron Shamir


Simpler 1.5-Approximation Algorithm for Sorting by Transpositions

Tzvika Hartman

Proc. of CPM

Towards Optimally Multiplexed Applications of Universal DNA Tag Systems

Amir Ben-Dor, Tzvika Hartman, Benno Schwikowski , Roded Sharan , and Zohar Yakhini

Proc. of RECOMB

Detecting Excess Radical Replacements in Phylogenetic Trees

T. Pupko, R. Sharan, M. Hasegawa, R. Shamir and D. Graur

Gene 319, pp. 127-135, 2003

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)

CLICK and EXPANDER: A System for Clustering and Visualizing Gene Expression Data

Roded Sharan, Adi Maron-Katz and Ron Shamir


Improved Algorithms for the Random Cluster Graph Model

R. Shamir and D. Tsur

Lecture Notes In Computer Science Vol. 2368

The Restriction Scaffold Problem

A. Ben-Dor, R. M. Karp, B. Schwikowski, R. Shamir

Proc. of RECOMB 2002

Handling Long Targets and Errors in Sequencing by Hybridization

E. Halperin, S. Halperin, T. Hartman and R. Shamir

Proc. of RECOMB

Scoring clustering solutions by their biological relevance

I. Gat-Viks, R. Sharan, R. Shamir

Bioinformatics 19: 2381-2389 (2003)

Modeling transcription programs: inferring binding site activity and dose-response model optimization

A. Tanay and R. Shamir

Proc. of RECOMB

Algorithmic Approaches to Clustering Gene Expression Data

Ron Shamir and Roded Sharan

Current Topics in Computational Molecular Biology

Cluster Analysis and its Applications to Gene Expression Data

Roded Sharan, Rani Elkon and Ron Shamir

Ernst Schering workshop on Bioinformatics and Genome Analysis

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

The Degenerate Primer Design Problem

C. Linhart, R. Shamir

Proc. of ISMB

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

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)

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)

Complexity Classification of Some Edge Modification Problems

A. Natanzon, R. Shamir and R.Sharan

Discrete Applied Mathematics

Large Scale Sequencing By Hybridization

Ron Shamir and Dekel Tsur

Proc. of RECOMB

Computational Expansion of Genetic Networks

A. Tanay and Ron Shamir

Proc. of ISMB 2001; Bioinformatics Vol. 17, Supplement 1, pp. S270-S278 (2001)

A Chemical Distance Based Test for Positive Darwinian Selection

T. Pupko, R. Sharan, M. Hasegawa, R. Shamir and D. Graur

Proc. of WABI

Incomplete Directed Perfect Phylogeny

Itsik Pe'er, Ron Shamir and Roded Sharan

Proc. of CPM

On the Complexity of Positional Sequencing by Hybridization

Ben-Dor, I. Pe'er, R. Shamir and R. Sharan

Proc. of CPM

A Fully Dynamic Algorithm for Recognizing and Representing Proper Interval Graphs

Pavol Hell, Ron Shamir and Roded Sharan

Proc. of ESA

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

A Clustering Algorithm based on Graph Connectivity

E. Hartuv, R. Shamir

Information Processing Letters

Fast Algorithm for Reconstruction of Ancestral Amino-Acid Sequences

Tal Pupko, Itsik Pe'er, Ron Shamir and Dan Graur

Molecular Biology and Evolution

An Algorithm Combining Discrete and Continuous Methods for Optical Mapping

Richard M. Karp, Itsik Pe'er, Ron Shamir

Proc. of ISMB

Approximation Algorithms for the Median Problem in the Breakpoint Model

Itsik Pe'er and Ron Shamir

Comparative Genomics

CLICK: A Clustering Algorithm with Applications to Gene Expression Analysis

Roded Sharan and Ron Shamir

Currents in Compuational Molecular Biology

Spectrum Alignment: Efficient Resequencing by Hybridization

Itsik Pe'er and Ron Shamir

Proc. of ISMB

Bounded Degree Interval Sandwich Problems

Haim Kaplan and Ron Shamir

Algorithmica, Vol. 24, No. 2, pp. 96-104 (1999)

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

Faster Subtree Isomorphism

Ron Shamir, Dekel Tzur

Journal of Algorithms

Construction of Physical Maps From Oligonucleotide Fingerprints Data

G. Mayraz, R. Shamir

Journal of Computational Biology

Clustering Gene Expression Patterns

A. Ben-Dor, R. Shamir, Z. Yakhini

Journal of Computational Biology

Perfect Completion and Deletion in Random Graphs

Assaf Natanzon, Ron Shamir

Technical Report

Optimizing the BAC-End Strategy for Sequencing the Human Genome

Kichard M. Karp, Ron Shamir

Technical Report

Faucet: streaming de novo assembly graph construction

R. Rozov, G. Goldshlager, E. Halperin, R. Shamir

BioRxiv, doi:, 2017

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.

Reconstructing cancer karyotypes from short read data: the half full and half empty glass

R. Eitan, R. Shamir.

bioRxiv 152447; doi:

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.


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: