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- affiliation: Tel Aviv University, Blavatnik School of Computer Science, Israel
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Books and Theses
- 2002
[b1]Roded Sharan:
Graph modification problems and their applications to genomic research. Tel Aviv University, Israel, 2002
Journal Articles
- 2024
- [j87]Neta Zadok, Gil Ast, Roded Sharan:
A network-based method for associating genes with autism spectrum disorder. Frontiers Bioinform. 4 (2024) - 2023
- [j86]Itay Kahane
, Mark D. M. Leiserson, Roded Sharan:
A mutation-level covariate model for mutational signatures. PLoS Comput. Biol. 19(6) (2023) - 2022
- [j85]Asia Gervits, Roded Sharan:
Predicting genetic interactions, cell line dependencies and drug sensitivities with variational graph auto-encoder. Frontiers Bioinform. 2 (2022) - [j84]Rami Nasser, Yonina C. Eldar, Roded Sharan:
Deep Unfolding for Non-Negative Matrix Factorization with Application to Mutational Signature Analysis. J. Comput. Biol. 29(1): 45-55 (2022) - [j83]Nicholas Franzese, Jason Fan, Roded Sharan, Mark D. M. Leiserson:
ScalpelSig Designs Targeted Genomic Panels from Data to Detect Activity of Mutational Signatures. J. Comput. Biol. 29(1): 56-73 (2022) - 2021
- [j82]Sapir Margalit, Yotam Abramson, Hila Sharim, Zohar Manber, Surajit Bhattacharya, Yi-Wen Chen, Eric Vilain, Hayk Barseghyan, Ran Elkon, Roded Sharan, Yuval Ebenstein:
Long reads capture simultaneous enhancer-promoter methylation status for cell-type deconvolution. Bioinform. 37(Supplement): 327-333 (2021) - [j81]L. F. Signorini, T. Almozlino, Roded Sharan:
ANAT 3.0: a framework for elucidating functional protein subnetworks using graph-theoretic and machine learning approaches. BMC Bioinform. 22(3): 526 (2021) - [j80]Gal Gilad, Itay Sason, Roded Sharan:
An automated approach for determining the number of components in non-negative matrix factorization with application to mutational signature learning. Mach. Learn. Sci. Technol. 2(1): 15013 (2021) - [j79]Gal Gilad, Mark D. M. Leiserson, Roded Sharan:
A data-driven approach for constructing mutation categories for mutational signature analysis. PLoS Comput. Biol. 17(10) (2021) - 2020
- [j78]Ariel Bruner, Roded Sharan:
A Robustness Analysis of Dynamic Boolean Models of Cellular Circuits. J. Comput. Biol. 27(2): 133-143 (2020) - 2019
- [j77]Welles Robinson, Roded Sharan, Mark D. M. Leiserson:
Modeling clinical and molecular covariates of mutational process activity in cancer. Bioinform. 35(14): i492-i500 (2019) - 2018
- [j76]Sushant Patkar, Roded Sharan:
An optimization framework for network annotation. Bioinform. 34(13): i502-i508 (2018) - [j75]Tom Hartmann, Nicolas Wieseke, Roded Sharan, Martin Middendorf, Matthias Bernt:
Genome Rearrangement with ILP. IEEE ACM Trans. Comput. Biol. Bioinform. 15(5): 1585-1593 (2018) - 2017
- [j74]Mohammed El-Kebir, Benjamin J. Raphael, Ron Shamir, Roded Sharan, Simone Zaccaria, Meirav Zehavi, Ron Zeira:
Complexity and algorithms for copy-number evolution problems. Algorithms Mol. Biol. 12(1): 13:1-13:11 (2017) - [j73]Yomtov Almozlino, Nir Atias, Dana Silverbush, Roded Sharan:
ANAT 2.0: reconstructing functional protein subnetworks. BMC Bioinform. 18(1): 495 (2017) - [j72]Phuong Dao, Yoo-Ah Kim, Damian Wójtowicz, Sanna Madan, Roded Sharan, Teresa M. Przytycka:
BeWith: A Between-Within method to discover relationships between cancer modules via integrated analysis of mutual exclusivity, co-occurrence and functional interactions. PLoS Comput. Biol. 13(10) (2017) - [j71]Sushant Patkar, Assaf Magen, Roded Sharan, Sridhar Hannenhalli:
A network diffusion approach to inferring sample-specific function reveals functional changes associated with breast cancer. PLoS Comput. Biol. 13(11) (2017) - 2016
- [j70]Arnon Mazza, Konrad Klockmeier, Erich E. Wanker, Roded Sharan:
An integer programming framework for inferring disease complexes from network data. Bioinform. 32(12): 271-277 (2016) - [j69]Arnon Mazza, Konrad Klockmeier, Erich E. Wanker, Roded Sharan:
An integer programming framework for inferring disease complexes from network data. Bioinform. 32(24): 3855 (2016) - [j68]Arnon Mazza, Allon Wagner, Eytan Ruppin, Roded Sharan:
Functional Alignment of Metabolic Networks. J. Comput. Biol. 23(5): 390-399 (2016) - 2015
- [j67]Roded Sharan:
Preface. J. Comput. Biol. 22(5): 335 (2015) - [j66]Matthew Ruffalo, Mehmet Koyutürk, Roded Sharan:
Network-Based Integration of Disparate Omic Data To Identify "Silent Players" in Cancer. PLoS Comput. Biol. 11(12) (2015) - 2014
- [j65]Arnon Mazza, Irit Gat-Viks, Hesso Farhan, Roded Sharan:
A minimum-labeling approach for reconstructing protein networks across multiple conditions. Algorithms Mol. Biol. 9: 1 (2014) - [j64]Dana Silverbush, Roded Sharan:
Network orientation via shortest paths. Bioinform. 30(10): 1449-1455 (2014) - [j63]Nir Atias, Michal Gershenzon, Katia Labazin, Roded Sharan:
Experimental design schemes for learning Boolean network models. Bioinform. 30(17): 445-452 (2014) - [j62]Arnon Mazza, Irit Gat-Viks, Roded Sharan:
Elucidating Influenza Inhibition Pathways via Network Reconstruction. J. Comput. Biol. 21(5): 394-404 (2014) - 2013
- [j61]Bjarni V. Halldórsson, Dima Blokh, Roded Sharan:
Estimating population size via line graph reconstruction. Algorithms Mol. Biol. 8: 17 (2013) - [j60]Roded Sharan, Richard M. Karp:
Reconstructing Boolean Models of Signaling. J. Comput. Biol. 20(3): 249-257 (2013) - [j59]Dima Blokh, Danny Segev, Roded Sharan:
The Approximability of Shortest Path-Based Graph Orientations of Protein-Protein Interaction Networks. J. Comput. Biol. 20(12): 945-957 (2013) - [j58]Mark D. M. Leiserson, Dima Blokh, Roded Sharan, Benjamin J. Raphael:
Simultaneous Identification of Multiple Driver Pathways in Cancer. PLoS Comput. Biol. 9(5) (2013) - [j57]Michael Elberfeld, Danny Segev, Colin R. Davidson, Dana Silverbush, Roded Sharan:
Approximation algorithms for orienting mixed graphs. Theor. Comput. Sci. 483: 96-103 (2013) - 2012
- [j56]Nir Atias, Roded Sharan:
Comparative analysis of protein networks: hard problems, practical solutions. Commun. ACM 55(5): 88-97 (2012) - [j55]Yael Silberberg, Assaf Gottlieb, Martin Kupiec, Eytan Ruppin, Roded Sharan:
Large-Scale Elucidation of Drug Response Pathways in Humans. J. Comput. Biol. 19(2): 163-174 (2012) - [j54]Liram Vardi, Eytan Ruppin, Roded Sharan:
A Linearized Constraint-Based Approach for Modeling Signaling Networks. J. Comput. Biol. 19(2): 232-240 (2012) - [j53]Oded Magger, Yedael Y. Waldman, Eytan Ruppin, Roded Sharan:
Enhancing the Prioritization of Disease-Causing Genes through Tissue Specific Protein Interaction Networks. PLoS Comput. Biol. 8(9) (2012) - 2011
- [j52]Guy Geva, Roded Sharan:
Identification of protein complexes from co-immunoprecipitation data. Bioinform. 27(1): 111-117 (2011) - [j51]Assaf Gottlieb, Oded Magger, Igor Berman, Eytan Ruppin, Roded Sharan:
PRINCIPLE: a tool for associating genes with diseases via network propagation. Bioinform. 27(23): 3325-3326 (2011) - [j50]Michael Elberfeld, Vineet Bafna, Iftah Gamzu, Alexander Medvedovsky, Danny Segev, Dana Silverbush, Uri Zwick, Roded Sharan:
On the Approximability of Reachability-Preserving Network Orientations. Internet Math. 7(4): 209-232 (2011) - [j49]Liat Perlman, Assaf Gottlieb, Nir Atias, Eytan Ruppin, Roded Sharan:
Combining Drug and Gene Similarity Measures for Drug-Target Elucidation. J. Comput. Biol. 18(2): 133-145 (2011) - [j48]Nir Atias, Roded Sharan:
An Algorithmic Framework for Predicting Side Effects of Drugs. J. Comput. Biol. 18(3): 207-218 (2011) - [j47]Dana Silverbush, Michael Elberfeld, Roded Sharan:
Optimally Orienting Physical Networks. J. Comput. Biol. 18(11): 1437-1448 (2011) - [j46]Tomer Shlomi, Tomer Benyamini, Eyal Gottlieb, Roded Sharan, Eytan Ruppin:
Genome-Scale Metabolic Modeling Elucidates the Role of Proliferative Adaptation in Causing the Warburg Effect. PLoS Comput. Biol. 7(3) (2011) - [j45]Lior Wolf, Chen Goldberg, Nathan Manor, Roded Sharan, Eytan Ruppin:
Gene Expression in the Rodent Brain is Associated with Its Regional Connectivity. PLoS Comput. Biol. 7(5) (2011) - 2010
- [j44]Jens Gramm, Richard M. Karp, William S. Noble, Roded Sharan, Qianfei Wang, Nir Yosef:
Prediction of Phenotype Information from Genotype Data. Commun. Inf. Syst. 10(2): 99-114 (2010) - [j43]Misael Mongiovì, Raffaele Di Natale, Rosalba Giugno, Alfredo Pulvirenti, Alfredo Ferro, Roded Sharan:
Sigma: a Set-Cover-Based Inexact Graph Matching Algorithm. J. Bioinform. Comput. Biol. 8(2): 199-218 (2010) - [j42]Sharon Bruckner, Falk Hüffner, Richard M. Karp, Ron Shamir, Roded Sharan:
Topology-Free Querying of Protein Interaction Networks. J. Comput. Biol. 17(3): 237-252 (2010) - [j41]Tal Peleg, Nir Yosef, Eytan Ruppin, Roded Sharan:
Network-Free Inference of Knockout Effects in Yeast. PLoS Comput. Biol. 6(1) (2010) - [j40]Oron Vanunu, Oded Magger, Eytan Ruppin, Tomer Shlomi, Roded Sharan:
Associating Genes and Protein Complexes with Disease via Network Propagation. PLoS Comput. Biol. 6(1) (2010) - [j39]Shiri Freilich, Anat Kreimer, Elhanan Borenstein, Uri Gophna, Roded Sharan, Eytan Ruppin:
Decoupling Environment-Dependent and Independent Genetic Robustness across Bacterial Species. PLoS Comput. Biol. 6(2) (2010) - 2009
- [j38]Jens Gramm, Tzvika Hartman, Till Nierhoff, Roded Sharan, Till Tantau:
On the complexity of SNP block partitioning under the perfect phylogeny model. Discret. Math. 309(18): 5610-5617 (2009) - [j37]Shaul Karni, Hermona Soreq, Roded Sharan:
A Network-Based Method for Predicting Disease-Causing Genes. J. Comput. Biol. 16(2): 181-189 (2009) - [j36]Maxim Kalaev, Vineet Bafna, Roded Sharan:
Fast and Accurate Alignment of Multiple Protein Networks. J. Comput. Biol. 16(8): 989-999 (2009) - [j35]Sharon Bruckner, Falk Hüffner, Richard M. Karp, Ron Shamir, Roded Sharan:
Torque: topology-free querying of protein interaction networks. Nucleic Acids Res. 37(Web-Server-Issue): 106-108 (2009) - 2008
- [j34]Maxim Kalaev, Michael E. Smoot, Trey Ideker, Roded Sharan:
NetworkBLAST: comparative analysis of protein networks. Bioinform. 24(4): 594-596 (2008) - [j33]Oranit Dror, Dina Schneidman-Duhovny, Alexandra Shulman-Peleg, Ruth Nussinov, Haim J. Wolfson, Roded Sharan:
Structural similarity of genetically interacting proteins. BMC Syst. Biol. 2: 69 (2008) - [j32]Banu Dost, Tomer Shlomi, Nitin Gupta, Eytan Ruppin, Vineet Bafna, Roded Sharan:
QNet: A Tool for Querying Protein Interaction Networks. J. Comput. Biol. 15(7): 913-925 (2008) - 2007
- [j31]Nir Yosef, Zohar Yakhini, Anya Tsalenko, Vessela N. Kristensen, Anne-Lise Børresen-Dale, Eytan Ruppin, Roded Sharan:
A supervised approach for identifying discriminating genotype patterns and its application to breast cancer data. Bioinform. 23(2): 91-98 (2007) - [j30]Eitan Hirsh, Roded Sharan:
Identification of conserved protein complexes based on a model of protein network evolution. Bioinform. 23(2): 170-176 (2007) - [j29]Oleg Rokhlenko, Tomer Shlomi, Roded Sharan, Eytan Ruppin, Ron Y. Pinter:
Constraint-based functional similarity of metabolic genes: going beyond network topology. Bioinform. 23(16): 2139-2146 (2007) - [j28]Itay Mayrose, Osnat Penn, Elana Erez, Nimrod D. Rubinstein, Tomer Shlomi, Natalia Tarnovitski Freund, Erez M. Bublil, Eytan Ruppin, Roded Sharan, Jonathan M. Gershoni, Eric Martz, Tal Pupko:
Pepitope: epitope mapping from affinity-selected peptides. Bioinform. 23(23): 3244-3246 (2007) - [j27]Jens Gramm, Till Nierhoff, Roded Sharan, Till Tantau:
Haplotyping with missing data via perfect path phylogenies. Discret. Appl. Math. 155(6-7): 788-805 (2007) - [j26]Eric P. Xing, Michael I. Jordan, Roded Sharan:
Bayesian Haplotype Inference via the Dirichlet Process. J. Comput. Biol. 14(3): 267-284 (2007) - 2006
- [j25]Tomer Shlomi, Daniel Segal, Eytan Ruppin, Roded Sharan:
QPath: a method for querying pathways in a protein-protein interaction network. BMC Bioinform. 7: 199 (2006) - [j24]Silpa Suthram, Tomer Shlomi, Eytan Ruppin, Roded Sharan, Trey Ideker:
A direct comparison of protein interaction confidence assignment schemes. BMC Bioinform. 7: 360 (2006) - [j23]Anya Tsalenko, Roded Sharan, Vessela N. Kristensen, Hege Edvardsen, Anne-Lise Børresen-Dale, Amir Ben-Dor, Zohar Yakhini:
Analysis of Snp-expression Association Matrices. J. Bioinform. Comput. Biol. 4(2): 259-274 (2006) - [j22]Eleazar Eskin, Roded Sharan, Eran Halperin:
A Note on Phasing Long Genomic Regions Using Local Haplotype Predictions. J. Bioinform. Comput. Biol. 4(3): 639-648 (2006) - [j21]Jacob Scott, Trey Ideker, Richard M. Karp, Roded Sharan:
Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks. J. Comput. Biol. 13(2): 133-144 (2006) - [j20]Irit Gat-Viks, Richard M. Karp, Ron Shamir, Roded Sharan:
Reconstructing Chain Functions in Genetic Networks. SIAM J. Discret. Math. 20(3): 727-740 (2006) - [j19]Roded Sharan, Bjarni V. Halldórsson, Sorin Istrail:
Islands of Tractability for Parsimony Haplotyping. IEEE ACM Trans. Comput. Biol. Bioinform. 3(3): 303-311 (2006) - 2005
- [j18]Ron Shamir, Adi Maron-Katz, Amos Tanay, Chaim Linhart, Israel Steinfeld, Roded Sharan, Yosef Shiloh, Ran Elkon:
EXPANDER - an integrative program suite for microarray data analysis. BMC Bioinform. 6: 232 (2005) - [j17]Roded Sharan, Jens Gramm, Zohar Yakhini, Amir Ben-Dor:
Multiplexing Schemes for Generic SNP Genotyping Assays. J. Comput. Biol. 12(5): 514-533 (2005) - [j16]Eran Segal, Roded Sharan:
A Discriminative Model for Identifying Spatial cis-Regulatory Modules. J. Comput. Biol. 12(6): 822-834 (2005) - [j15]Roded Sharan, Trey Ideker, Brian P. Kelley, Ron Shamir, Richard M. Karp:
Identification of Protein Complexes by Comparative Analysis of Yeast and Bacterial Protein Interaction Data. J. Comput. Biol. 12(6): 835-846 (2005) - [j14]Tzvika Hartman, Roded Sharan:
A 1.5-approximation algorithm for sorting by transpositions and transreversals. J. Comput. Syst. Sci. 70(3): 300-320 (2005) - 2004
- [j13]Ron Shamir, Roded Sharan:
A fully dynamic algorithm for modular decomposition and recognition of cographs. Discret. Appl. Math. 136(2-3): 329-340 (2004) - [j12]Ron Shamir, Roded Sharan, Dekel Tsur:
Cluster graph modification problems. Discret. Appl. Math. 144(1-2): 173-182 (2004) - [j11]Gad Kimmel, Roded Sharan, Ron Shamir:
Computational Problems in Noisy SNP and Haplotype Analysis: Block Scores, Block Identification, and Population Stratification. INFORMS J. Comput. 16(4): 360-370 (2004) - [j10]Amir Ben-Dor, Tzvika Hartman, Richard M. Karp, Benno Schwikowski, Roded Sharan, Zohar Yakhini:
Towards Optimally Multiplexed Applications of Universal Arrays. J. Comput. Biol. 11(2/3): 476-492 (2004) - [j9]Brian P. Kelley, Bingbing Yuan, Fran Lewitter, Roded Sharan, Brent R. Stockwell, Trey Ideker:
PathBLAST: a tool for alignment of protein interaction networks. Nucleic Acids Res. 32(Web-Server-Issue): 83-88 (2004) - [j8]Roded Sharan, Asa Ben-Hur, Gabriela G. Loots, Ivan Ovcharenko:
CREME: Cis-Regulatory Module Explorer for the human genome. Nucleic Acids Res. 32(Web-Server-Issue): 253-256 (2004) - [j7]Itsik Pe'er, Tal Pupko, Ron Shamir, Roded Sharan:
Incomplete Directed Perfect Phylogeny. SIAM J. Comput. 33(3): 590-607 (2004) - 2003
- [j6]Roded Sharan, Adi Maron-Katz, Ron Shamir:
CLICK and EXPANDER: a system for clustering and visualizing gene expression data. Bioinform. 19(14): 1787-1799 (2003) - [j5]Irit Gat-Viks, Roded Sharan, Ron Shamir:
Scoring clustering solutions by their biological relevance. Bioinform. 19(18): 2381-2389 (2003) - 2002
- [j4]Amir Ben-Dor, Itsik Pe'er, Ron Shamir, Roded Sharan:
On the Complexity of Positional Sequencing by Hybridization. J. Comput. Biol. 8(4): 361-371 (2002) - 2001
- [j3]Assaf Natanzon, Ron Shamir, Roded Sharan:
Complexity classification of some edge modification problems. Discret. Appl. Math. 113(1): 109-128 (2001) - [j2]Pavol Hell, Ron Shamir, Roded Sharan:
A Fully Dynamic Algorithm for Recognizing and Representing Proper Interval Graphs. SIAM J. Comput. 31(1): 289-305 (2001) - 2000
- [j1]Assaf Natanzon, Ron Shamir, Roded Sharan:
A Polynomial Approximation Algorithm for the Minimum Fill-In Problem. SIAM J. Comput. 30(4): 1067-1079 (2000)
Conference and Workshop Papers
- 2024
- [c59]Barel I. Mashiach, Roded Sharan:
Integer Programming Based Algorithms for Overlapping Correlation Clustering. From Computational Logic to Computational Biology 2024: 115-127 - [c58]Shani Jacobson, Roded Sharan:
An Integer Programming Framework for Identifying Stable Components in Asynchronous Boolean Networks. RECOMB 2024: 86-98 - 2020
- [c57]Mark D. M. Leiserson, Teresa M. Przytycka, Roded Sharan:
Session Introduction. PSB 2020: 219-225 - [c56]Damian Wójtowicz, Mark D. M. Leiserson, Roded Sharan, Teresa M. Przytycka:
DNA Repair Footprint Uncovers Contribution of DNA Repair Mechanism to MutationalSignatures. PSB 2020: 262-273 - [c55]Itay Sason, Yuexi Chen, Mark D. M. Leiserson, Roded Sharan:
A Mixture Model for Signature Discovery from Sparse Mutation Data. RECOMB 2020: 271-272 - 2019
- [c54]Ariel Bruner, Roded Sharan:
A Robustness Analysis of Dynamic Boolean Models of Cellular Circuits. ISBRA 2019: 183-195 - [c53]Itay Sason, Damian Wójtowicz, Welles Robinson, Mark D. M. Leiserson, Teresa M. Przytycka, Roded Sharan:
A Sticky Multinomial Mixture Model of Strand-Coordinated Mutational Processes in Cancer. RECOMB 2019: 243-255 - 2018
- [c52]Dana Silverbush, Simona Cristea, Gali Yanovich, Tamar Geiger, Niko Beerenwinkel, Roded Sharan:
ModulOmics: Integrating Multi-Omics Data to Identify Cancer Driver Modules. RECOMB 2018: 283-284 - [c51]Barak Sternberg, Roded Sharan:
A Dynamic Algorithm for Network Propagation. WABI 2018: 7:1-7:13 - 2017
- [c50]Phuong Dao, Yoo-Ah Kim, Sanna Madan, Roded Sharan, Teresa M. Przytycka:
BeWith: A Between-Within Method for Module Discovery in Cancer using Integrated Analysis of Mutual Exclusivity, Co-occurrence and Functional Interactions (Extended Abstract). RECOMB 2017: 370-371 - 2016
- [c49]Ortal Shnaps, Eyal Perry, Dana Silverbush, Roded Sharan:
Inference of Personalized Drug Targets via Network Propagation. PSB 2016: 156-167 - [c48]Mohammed El-Kebir, Benjamin J. Raphael, Ron Shamir, Roded Sharan, Simone Zaccaria, Meirav Zehavi, Ron Zeira:
Copy-Number Evolution Problems: Complexity and Algorithms. WABI 2016: 137-149 - 2015
- [c47]Arnon Mazza, Allon Wagner, Eytan Ruppin, Roded Sharan:
Functional Alignment of Metabolic Networks. RECOMB 2015: 243-255 - 2013
- [c46]Arnon Mazza, Irit Gat-Viks, Hesso Farhan, Roded Sharan:
A Minimum-Labeling Approach for Reconstructing Protein Networks across Multiple Conditions. WABI 2013: 33-44 - 2012
- [c45]Dima Blokh, Danny Segev, Roded Sharan:
Approximation Algorithms and Hardness Results for Shortest Path Based Graph Orientations. CPM 2012: 70-82 - [c44]Roded Sharan:
Invited: From protein networks to disease mechanisms. ICCABS 2012: 1 - [c43]Roded Sharan, Richard M. Karp:
Reconstructing Boolean Models of Signaling. RECOMB 2012: 261-271 - [c42]Bjarni V. Halldórsson, Dima Blokh, Roded Sharan:
Estimating Population Size via Line Graph Reconstruction. WABI 2012: 69-80 - [c41]Shay Houri, Roded Sharan:
Sign Assignment Problems on Protein Networks. WABI 2012: 338-345 - 2011
- [c40]Michael Elberfeld, Danny Segev, Colin R. Davidson, Dana Silverbush, Roded Sharan:
Approximation Algorithms for Orienting Mixed Graphs. CPM 2011: 416-428 - [c39]Dana Silverbush, Michael Elberfeld, Roded Sharan:
Optimally Orienting Physical Networks. RECOMB 2011: 424-436 - [c38]Roded Sharan:
Similarity-based methods to predict drug targets, indications and side-effects. SISAP 2011: 5-6 - 2010
- [c37]Nir Atias, Roded Sharan:
An Algorithmic Framework for Predicting Side-Effects of Drugs. RECOMB 2010: 1-14 - [c36]Iftah Gamzu, Danny Segev, Roded Sharan:
Improved Orientations of Physical Networks. WABI 2010: 215-225 - 2009
- [c35]Sharon Bruckner, Falk Hüffner, Richard M. Karp, Ron Shamir, Roded Sharan:
Topology-Free Querying of Protein Interaction Networks. RECOMB 2009: 74-89 - 2008
- [c34]Nir Yosef, Roded Sharan, William Stafford Noble:
Improved network-based identification of protein orthologs. ECCB 2008: 200-206 - [c33]Oron Vanunu, Roded Sharan:
A Propagation-based Algorithm for Inferring Gene-Disease Assocations. German Conference on Bioinformatics 2008: 54-63 - [c32]Maxim Kalaev, Vineet Bafna, Roded Sharan:
Fast and Accurate Alignment of Multiple Protein Networks. RECOMB 2008: 246-256 - [c31]Alexander Medvedovsky, Vineet Bafna, Uri Zwick, Roded Sharan:
An Algorithm for Orienting Graphs Based on Cause-Effect Pairs and Its Applications to Orienting Protein Networks. WABI 2008: 222-232 - 2007
- [c30]Oved Ourfali, Tomer Shlomi, Trey Ideker, Eytan Ruppin, Roded Sharan:
SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments. ISMB/ECCB (Supplement of Bioinformatics) 2007: 359-366 - [c29]Banu Dost, Tomer Shlomi, Nitin Gupta, Eytan Ruppin, Vineet Bafna, Roded Sharan:
QNet: A Tool for Querying Protein Interaction Networks. RECOMB 2007: 1-15 - 2006
- [c28]Shaojie Zhang, Ilya Borovok, Yair Aharonowitz, Roded Sharan, Vineet Bafna:
A sequence-based filtering method for ncRNA identification and its application to searching for riboswitch elements. ISMB (Supplement of Bioinformatics) 2006: 557-565 - [c27]Jens Gramm, Tzvika Hartman, Till Nierhoff, Roded Sharan, Till Tantau:
On the Complexity of SNP Block Partitioning Under the Perfect Phylogeny Model. WABI 2006: 92-102 - [c26]Oleg Rokhlenko, Tomer Shlomi, Roded Sharan, Eytan Ruppin, Ron Y. Pinter:
Flux-Based vs. Topology-Based Similarity of Metabolic Genes. WABI 2006: 274-285 - 2005
- [c25]Roded Sharan, Bjarni V. Halldórsson, Sorin Istrail:
Islands of Tractability for Parsimony Haplotyping. CSB 2005: 65-72 - [c24]Anya Tsalenko, Roded Sharan, Hege Edvardsen, Vessela N. Kristensen, Anne-Lise Børresen-Dale, Amir Ben-Dor, Zohar Yakhini:
Analysis of SNP-Expression Association Matrices. CSB 2005: 135-143 - [c23]Roded Sharan, Eugene W. Myers:
A motif-based framework for recognizing sequence families. ISMB (Supplement of Bioinformatics) 2005: 387-393 - [c22]Jacob Scott, Trey Ideker, Richard M. Karp, Roded Sharan:
Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks. RECOMB 2005: 1-13 - [c21]Silpa Suthram, Tomer Shlomi, Eytan Ruppin, Roded Sharan, Trey Ideker:
Comparison of Protein-Protein Interaction Confidence Assignment Schemes. Systems Biology and Regulatory Genomics 2005: 39-50 - 2004
- [c20]Eric P. Xing, Roded Sharan, Michael I. Jordan:
Bayesian haplo-type inference via the dirichlet process. ICML 2004 - [c19]Roded Sharan, Amir Ben-Dor, Zohar Yakhini:
Multiplexing Schemes for Generic SNP Genotyping Assays. Pacific Symposium on Biocomputing 2004: 140-151 - [c18]Irit Gat-Viks, Ron Shamir, Richard M. Karp, Roded Sharan:
Reconstructing Chain Functions in Genetic Networks. Pacific Symposium on Biocomputing 2004: 498-509 - [c17]Eran Segal, Roded Sharan:
A discriminative model for identifying spatial cis-regulatory modules. RECOMB 2004: 141-149 - [c16]Roded Sharan, Trey Ideker, Brian P. Kelley, Ron Shamir, Richard M. Karp:
Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data. RECOMB 2004: 282-289 - [c15]Tzvika Hartman, Roded Sharan:
A 1.5-Approximation Algorithm for Sorting by Transpositions and Transreversals. WABI 2004: 50-61 - 2003
- [c14]Roded Sharan, Ivan Ovcharenko, Asa Ben-Hur, Richard M. Karp:
CREME: a framework for identifying cis-regulatory modules in human-mouse conserved segments. ISMB (Supplement of Bioinformatics) 2003: 283-291 - [c13]Amir Ben-Dor, Tzvika Hartman, Benno Schwikowski, Roded Sharan, Zohar Yakhini:
Towards optimally multiplexed applications of universal DNA tag systems. RECOMB 2003: 48-56 - [c12]Gad Kimmel, Roded Sharan, Ron Shamir:
Identifying Blocks and Sub-populations in Noisy SNP Data. WABI 2003: 303-319 - 2002
- [c11]Amos Tanay, Roded Sharan, Ron Shamir:
Discovering statistically significant biclusters in gene expression data. ISMB 2002: 136-144 - [c10]Itsik Pe'er, Ron Shamir, Roded Sharan:
On the Generality of Phylogenies from Incomplete Directed Characters. SWAT 2002: 358-367 - [c9]Ron Shamir, Roded Sharan, Dekel Tsur:
Cluster Graph Modification Problems. WG 2002: 379-390 - 2001
- [c8]Tal Pupko, Roded Sharan, Masami Hasegawa, Ron Shamir, Dan Graur:
A Chemical-Distance-Based Test for Positive Darwinian Selection. WABI 2001: 142-155 - 2000
- [c7]Itsik Pe'er, Ron Shamir, Roded Sharan:
Incomplete Directed Perfect Phylogeny. CPM 2000: 143-153 - [c6]Roded Sharan, Ron Shamir:
Center CLICK: A Clustering Algorithm with Applications to Gene Expression Analysis. ISMB 2000: 307-316 - 1999
- [c5]Amir Ben-Dor, Itsik Pe'er, Ron Shamir, Roded Sharan:
On the Complexity of Positional Sequencing by Hybridization. CPM 1999: 88-100 - [c4]Pavol Hell, Ron Shamir, Roded Sharan:
A Fully Dynamic Algorithm for Recognizing and Representing Proper Interval Graphs. ESA 1999: 527-539 - [c3]Assaf Natanzon, Ron Shamir, Roded Sharan:
Complexity Classification of Some Edge Modification Problems. WG 1999: 65-77 - 1998
- [c2]Assaf Natanzon, Ron Shamir, Roded Sharan:
A Polynomial Approximation Algorithm for the Minimum Fill-In Problem. STOC 1998: 41-47 - 1996
- [c1]Roded Sharan, Avi Wigderson:
A New NCAlgorithm for Perfect Matching in Bipartite Cubic Graphs. ISTCS 1996: 202-207
Parts in Books or Collections
- 2008
- [p1]Nir Yosef, Eytan Ruppin, Roded Sharan:
Cross-Species Analysis of Protein-protein Interaction Networks. Protein-protein Interactions and Networks 2008: 163-185
Editorship
- 2014
- [e1]Roded Sharan:
Research in Computational Molecular Biology - 18th Annual International Conference, RECOMB 2014, Pittsburgh, PA, USA, April 2-5, 2014, Proceedings. Lecture Notes in Computer Science 8394, Springer 2014, ISBN 978-3-319-05268-7 [contents]
Informal and Other Publications
- 2021
- [i2]Rami Nasser, Yonina C. Eldar, Roded Sharan:
deep unfolding for non-negative matrix factorization with application to mutational signature analysis. CoRR abs/2108.09138 (2021) - 2001
- [i1]Piotr Berman, Amir Ben-Dor, Itsik Pe'er, Roded Sharan, Ron Shamir:
On the Complexity of Positional Sequencing by Hybridization. Electron. Colloquium Comput. Complex. TR01 (2001)
Coauthor Index
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