| 2025 | RECOMB | An Adversarial Scheme for Integrating Multi-modal Data on Protein Function. | Rami Nasser, Leah V. Schaffer, Trey Ideker, Roded Sharan |
| 2025 | WABI | Mutational Signature Refitting on Sparse Pan-Cancer Data. | Gal Gilad, Teresa M. Przytycka, Roded Sharan |
| 2024 | RECOMB | An Integer Programming Framework for Identifying Stable Components in Asynchronous Boolean Networks. | Shani Jacobson, Roded Sharan |
| 2020 | PSB | Session Introduction. | Mark D. M. Leiserson, Teresa M. Przytycka, Roded Sharan |
| 2020 | PSB | DNA Repair Footprint Uncovers Contribution of DNA Repair Mechanism to MutationalSignatures. | Damian Wjtowicz, Mark D. M. Leiserson, Roded Sharan, Teresa M. Przytycka |
| 2020 | RECOMB | A Mixture Model for Signature Discovery from Sparse Mutation Data. | Itay Sason, Yuexi Chen, Mark D. M. Leiserson, Roded Sharan |
| 2019 | RECOMB | A Sticky Multinomial Mixture Model of Strand-Coordinated Mutational Processes in Cancer. | Itay Sason, Damian Wjtowicz, Welles Robinson, Mark D. M. Leiserson, Teresa M. Przytycka, Roded Sharan |
| 2018 | RECOMB | ModulOmics: Integrating Multi-Omics Data to Identify Cancer Driver Modules. | Dana Silverbush, Simona Cristea, Gali Yanovich, Tamar Geiger, Niko Beerenwinkel, Roded Sharan |
| 2018 | WABI | A Dynamic Algorithm for Network Propagation. | Barak Sternberg, Roded Sharan |
| 2017 | RECOMB | BeWith: A Between-Within Method for Module Discovery in Cancer using Integrated Analysis of Mutual Exclusivity, Co-occurrence and Functional Interactions (Extended Abstract). | Phuong Dao, Yoo-Ah Kim, Sanna Madan, Roded Sharan, Teresa M. Przytycka |
| 2016 | PSB | Inference of Personalized Drug Targets via Network Propagation. | Ortal Shnaps, Eyal Perry, Dana Silverbush, Roded Sharan |
| 2016 | WABI | Copy-Number Evolution Problems: Complexity and Algorithms. | Mohammed El-Kebir, Benjamin J. Raphael, Ron Shamir, Roded Sharan, Simone Zaccaria, Meirav Zehavi, Ron Zeira |
| 2015 | RECOMB | Functional Alignment of Metabolic Networks. | Arnon Mazza, Allon Wagner, Eytan Ruppin, Roded Sharan |
| 2013 | WABI | A Minimum-Labeling Approach for Reconstructing Protein Networks across Multiple Conditions. | Arnon Mazza, Irit Gat-Viks, Hesso Farhan, Roded Sharan |
| 2012 | CPM | Approximation Algorithms and Hardness Results for Shortest Path Based Graph Orientations. | Dima Blokh, Danny Segev, Roded Sharan |
| 2012 | RECOMB | Reconstructing Boolean Models of Signaling. | Roded Sharan, Richard M. Karp |
| 2012 | WABI | Estimating Population Size via Line Graph Reconstruction. | Bjarni V. Halldrsson, Dima Blokh, Roded Sharan |
| 2012 | WABI | Sign Assignment Problems on Protein Networks. | Shay Houri, Roded Sharan |
| 2011 | CPM | Approximation Algorithms for Orienting Mixed Graphs. | Michael Elberfeld, Danny Segev, Colin R. Davidson, Dana Silverbush, Roded Sharan |
| 2011 | RECOMB | Optimally Orienting Physical Networks. | Dana Silverbush, Michael Elberfeld, Roded Sharan |
| 2011 | SISAP | Similarity-based methods to predict drug targets, indications and side-effects. | Roded Sharan |
| 2010 | RECOMB | An Algorithmic Framework for Predicting Side-Effects of Drugs. | Nir Atias, Roded Sharan |
| 2010 | WABI | Improved Orientations of Physical Networks. | Iftah Gamzu, Danny Segev, Roded Sharan |
| 2009 | RECOMB | Topology-Free Querying of Protein Interaction Networks. | Sharon Bruckner, Falk Hffner, Richard M. Karp, Ron Shamir, Roded Sharan |
| 2008 | ECCB | Improved network-based identification of protein orthologs. | Nir Yosef, Roded Sharan, William Stafford Noble |
| 2008 | RECOMB | Fast and Accurate Alignment of Multiple Protein Networks. | Maxim Kalaev, Vineet Bafna, Roded Sharan |
| 2008 | WABI | An Algorithm for Orienting Graphs Based on Cause-Effect Pairs and Its Applications to Orienting Protein Networks. | Alexander Medvedovsky, Vineet Bafna, Uri Zwick, Roded Sharan |
| 2007 | ISMB | SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments. | Oved Ourfali, Tomer Shlomi, Trey Ideker, Eytan Ruppin, Roded Sharan |
| 2007 | RECOMB | QNet: A Tool for Querying Protein Interaction Networks. | Banu Dost, Tomer Shlomi, Nitin Gupta, Eytan Ruppin, Vineet Bafna, Roded Sharan |
| 2006 | ISMB | A sequence-based filtering method for ncRNA identification and its application to searching for riboswitch elements. | Shaojie Zhang, Ilya Borovok, Yair Aharonowitz, Roded Sharan, Vineet Bafna |
| 2006 | WABI | On the Complexity of SNP Block Partitioning Under the Perfect Phylogeny Model. | Jens Gramm, Tzvika Hartman, Till Nierhoff, Roded Sharan, Till Tantau |
| 2006 | WABI | Flux-Based | Oleg Rokhlenko, Tomer Shlomi, Roded Sharan, Eytan Ruppin, Ron Y. Pinter |
| 2005 | ISMB | A motif-based framework for recognizing sequence families. | Roded Sharan, Eugene W. Myers |
| 2005 | RECOMB | Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks. | Jacob Scott, Trey Ideker, Richard M. Karp, Roded Sharan |
| 2005 | RECOMB | Comparison of Protein-Protein Interaction Confidence Assignment Schemes. | Silpa Suthram, Tomer Shlomi, Eytan Ruppin, Roded Sharan, Trey Ideker |
| 2004 | ICML | Bayesian haplo-type inference via the dirichlet process. | Eric P. Xing, Roded Sharan, Michael I. Jordan |
| 2004 | PSB | Reconstructing Chain Functions in Genetic Networks. | Irit Gat-Viks, Ron Shamir, Richard M. Karp, Roded Sharan |
| 2004 | PSB | Multiplexing Schemes for Generic SNP Genotyping Assays. | Roded Sharan, Amir Ben-Dor, Zohar Yakhini |
| 2004 | RECOMB | A discriminative model for identifying spatial cis-regulatory modules. | Eran Segal, Roded Sharan |
| 2004 | RECOMB | Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data. | Roded Sharan, Trey Ideker, Brian P. Kelley, Ron Shamir, Richard M. Karp |
| 2004 | WABI | A 1.5-Approximation Algorithm for Sorting by Transpositions and Transreversals. | Tzvika Hartman, Roded Sharan |
| 2003 | ISMB | CREME: a framework for identifying cis-regulatory modules in human-mouse conserved segments. | Roded Sharan, Ivan Ovcharenko, Asa Ben-Hur, Richard M. Karp |
| 2003 | RECOMB | Towards optimally multiplexed applications of universal DNA tag systems. | Amir Ben-Dor, Tzvika Hartman, Benno Schwikowski, Roded Sharan, Zohar Yakhini |
| 2003 | WABI | Identifying Blocks and Sub-populations in Noisy SNP Data. | Gad Kimmel, Roded Sharan, Ron Shamir |
| 2002 | ISMB | Discovering statistically significant biclusters in gene expression data. | Amos Tanay, Roded Sharan, Ron Shamir |
| 2002 | WG | Cluster Graph Modification Problems. | Ron Shamir, Roded Sharan, Dekel Tsur |
| 2001 | WABI | A Chemical-Distance-Based Test for Positive Darwinian Selection. | Tal Pupko, Roded Sharan, Masami Hasegawa, Ron Shamir, Dan Graur |
| 2000 | CPM | Incomplete Directed Perfect Phylogeny. | Itsik Pe'er, Ron Shamir, Roded Sharan |
| 2000 | ISMB | Center CLICK: A Clustering Algorithm with Applications to Gene Expression Analysis. | Roded Sharan, Ron Shamir |
| 1999 | CPM | On the Complexity of Positional Sequencing by Hybridization. | Amir Ben-Dor, Itsik Pe'er, Ron Shamir, Roded Sharan |
| 1999 | ESA | A Fully Dynamic Algorithm for Recognizing and Representing Proper Interval Graphs. | Pavol Hell, Ron Shamir, Roded Sharan |
| 1999 | WG | Complexity Classification of Some Edge Modification Problems. | Assaf Natanzon, Ron Shamir, Roded Sharan |
| 1998 | STOC | A Polynomial Approximation Algorithm for the Minimum Fill-In Problem. | Assaf Natanzon, Ron Shamir, Roded Sharan |