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 Biology19(1): 30-41, 2012.
|
|
|
2011
|
|
| 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(n3/2√log(n)) algorithm for sorting by reciprocal translocations.
|
| M. Ozery-Flato, R. Shamir. | |
Journal of Discrete Algorithms, Volume 9, Issue 4, Pages 344-357(2011),
|
|
|
| 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
|
|
 |
| 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. |
|
To appear in Journal of Computational Biology, 18 (7), 2011.
|
|
 |
| 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.
|
|
|
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).
|
|
 |
| 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).
|
|
|
| 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. 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).
|
|
|
|
|
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).
|
|
|
|
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).
|
|
|
2009
|
|
|
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).
|
|
|
|
|
|
|
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. 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.
|
|
|
|
|
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.
|
|
|
| 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. Hüffner, 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).
|
|
|
2008
|
|
| 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.), 8th International Workshop, WABI 2008, LNBI 5251, 174-185, Karlsruh, Germany, September 15-17, (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. 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
|
|
|
2007
|
|
| On the frequency of genome rearrangement events in cancer karyotypes |
| M. Ozery-Flato and R. Shamir. |
|
Proc. RECOMB satellite on Computational Cancer Biology, 2007
|
|
 |
| Improved algorithms for the random cluster graph model |
| R. Shamir and D. Tsur |
|
Random Structures and Algorithms
31(4):418-449, 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) |
|
 |
|
 |
| 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. |
| Proc. RECOMB 2007, , pp. 339--353, LNBI 4453, Springer, Berlin (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)
|
|
|
2006
|
|
| 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, Vol. 4205, pp. 87-98, Springer, Berlin (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)
|
|
|
| An O(n3/2√log(n)) algorithm for sorting by reciprocal translocations |
| M. Ozery-Flato and R. Shamir |
| Proc. of CPM 2006, LNCS, Vol. 4009, pp. 258-269 (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) |
|
 |
| 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)
|
|
 |
|
 |
| 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)
|
|
|
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 Vol. 12 No. 6 pp. 835-846 (2005)
|
|
| 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 2005 pp. 31-47, Lecture Notes in Bioinformatics 3500, Springer, Berlin, 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 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 satellite workshop on Regulatory Genomics, E. Eskin and C. Workman (editors), Lecture Notes in Bioinformatics, Vol. 3318 pp. 98-113, Springer, Berlin (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) |
|
|
2004
|
| 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)
|
|
| A note on tolerance graph recognition |
| Ryan B. Hayward and Ron Shamir |
| Discrete Applied Mathematics, Vol. 143, No. 307-311 (2004) |
|
| Maximum likelihood resolution of multi-block genotypes |
| G. Kimmel and R. Shamir |
| Proc. of RECOMB 2004, pp. 2-9 (2004)
|
|
| 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)
|
|
| 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
|
|
| 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)
|
|
| 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)
|
|
| Cluster Graph Modification Problems |
| Ron Shamir, Roded Sharan and Dekel Tsur |
| Discrete Applied Mathematics, Vol. 144, pp. 173-182 (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) |
|
| 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)
|
|
| 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 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)
|
|
| 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)
|
|
| 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)
|
|
| 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)
|
|
|
2003
|
| 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)
|
|
| 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)
|
|
| 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)
|
|
| 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 2003, pp. 303-319 (2003)
|
|
| Chain functions and scoring functions in genetic networks |
| Irit Gat-Viks and Ron Shamir |
| Bioinformatics, Vol. 19, Supplement 1, pp. i108-i117 (2003)
|
|
| Simpler 1.5-Approximation Algorithm for Sorting by Transpositions |
| Tzvika Hartman |
| Proc. of CPM 2003, pp. 156-169
|
|
| 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
|
|
| 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 |
| Bioinformatics, Vol. 19, No. 14, pp. 1787-1799 (2003)
(website) |
|
| Improved Algorithms for the Random Cluster Graph Model |
| R. Shamir and D. Tsur |
| Lecture Notes In Computer Science Vol. 2368
|
|
| 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 2003, pp. 301-310
|
|
|
2002
|
| 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)
|
|
| 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
|
|
| 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
|
|
| The Restriction Scaffold Problem |
| A. Ben-Dor, R. M. Karp, B. Schwikowski, R. Shamir |
| Proc. of RECOMB 2002, (extended abstract)
|
|
| 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
|
|
| 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)
|
|
| The Degenerate Primer Design Problem |
| C. Linhart, R. Shamir |
| Proc. of ISMB 2002; Bioinformatics, Vol. 18, Suppl. 1 S172-S180
(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
|
|
| 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)
|
|
|
2001
|
| 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)
|
|
| 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)
|
|
| Large Scale Sequencing By Hybridization |
| Ron Shamir and Dekel Tsur |
| Proc. of RECOMB 2001, pp. 267-279, ACM Press, New York, NY (2001)
|
|
| 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 2001 (extended abstract)
|
|
|
2000
|
| Algorithms for Optical Mapping |
| R. M. Karp, R. Shamir |
| Journal of Computational Biology Vol. 7, No. 1/2, pp. 303-316 (2000)
|
|
| 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)
|
|
| 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)
|
|
| A Clustering Algorithm based on Graph Connectivity |
| E. Hartuv, R. Shamir |
| Information Processing Letters, Vol. 76, pp. 175-181 (2000)
|
|
| 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)
|
|
| 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)
|
|
| 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
|
|
| 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)
; Proc. of ISMB 2000, pp. 307-316, AAAI Press, Menlo Park, CA (2000) (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)
|
|
| Incomplete Directed Perfect Phylogeny |
| Itsik Pe'er, Ron Shamir and Roded Sharan |
| Proc. of CPM 2000, pp. 143-153
|
|
|
1999
|
| 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, Vol. 28, No. 5, pp. 1906-1922 (1999)
|
|
| 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)
|
|
| Faster Subtree Isomorphism |
| Ron Shamir, Dekel Tzur |
| Journal of Algorithms, Vol. 33, pp. 267-280 (1999)
|
|
| Construction of Physical Maps From Oligonucleotide Fingerprints Data |
| G. Mayraz, R. Shamir |
| Journal of Computational Biology, Vol. 6, No. 2, pp. 237-252 (1999)
|
|
| 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)
|
|
| Clustering Gene Expression Patterns |
| A. Ben-Dor, R. Shamir, Z. Yakhini |
| Journal of Computational Biology, Vol. 6, No. 3/4, pp. 281-297 (1999)
|
|
| 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)
|
|
| 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)
|
|
| Perfect Completion and Deletion in Random Graphs |
| Assaf Natanzon, Ron Shamir |
| Technical Report, 1999
|
|
| Optimizing the BAC-End Strategy for Sequencing the Human Genome |
| Kichard M. Karp, Ron Shamir |
| Technical Report, April 1999
|
|
| 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
|
|
|
1998 and before
|
| Algorithms for Optical Mapping |
| R. M. Karp, R. Shamir |
|
Proc. of RECOMB 1998, pp. 117-124 (extended abstract)
|
|
| A Polynomial Approximation Algorithm for the Minimum Fill-In Problem |
| A. Natanzon, R. Shamir and R.Sharan |
| Proc. of STOC 1998, pp. 41-47
|
|
| The maximum subforest problem: Approximation and exact algorithms |
| Ron Shamir, Dekel Tzur |
| Proc. of SODA 1998, pp. 394-399
|
|
| 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
; 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)
|
|
| Satisfiability Problems on Intervals and Unit Intervals |
| Itsik Pe'er and Ron Shamir |
| Theoretical Computer Science, Vol. 175, No. 2, pp. 349-372 (1997)
|
|
| 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)
|
|
| 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
|
|
| 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
|
|
| 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)
|
|
| 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
|
|
| 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
|
|
| Complexity and algorithms for reasoning about time: a graph-theoretic approach |
| Martin Golumbic, Ron Shamir |
| JACM, Vol. 40, pp. 1108-1133 (1993)
|
|
|
Copyright notice
|
|
The documents distributed here have been provided as a means to ensure timely dissemination of scholarly and technical work
on a noncommercial basis. Copyright and all rights therein are maintained by the authors or by other copyright holders,
notwithstanding that they have offered their works here electronically. It is understood that all persons copying this information
will adhere to the terms and constraints invoked by each author's copyright. These works may not be reposted without the explicit
permission of the copyright holder.
|
|
