| 2025 | AISTATS | Towards Regulatory-Confirmed Adaptive Clinical Trials: Machine Learning Opportunities and Solutions. | Omer Noy Klein, Alihan Hyk, Ron Shamir, Uri Shalit, Mihaela van der Schaar |
| 2016 | CPM | A Linear-Time Algorithm for the Copy Number Transformation Problem. | Ron Shamir, Meirav Zehavi, Ron Zeira |
| 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 |
| 2016 | WABI | Compact Universal k-mer Hitting Sets. | Yaron Orenstein, David Pellow, Guillaume Marais, Ron Shamir, Carl Kingsford |
| 2015 | CPM | Sorting by Cuts, Joins and Whole Chromosome Duplications. | Ron Zeira, Ron Shamir |
| 2012 | CPM | Gene Regulation, Protein Networks and Disease: A Computational Perspective. | Ron Shamir |
| 2011 | RECOMB | Understanding Gene Sequence Variation in the Context of Transcription Regulation in Yeast. | Irit Gat-Viks, Renana Meller, Martin Kupiec, Ron Shamir |
| 2010 | RECOMB | Detecting Highways of Horizontal Gene Transfer. | Mukul S. Bansal, J. Peter Gogarten, Ron Shamir |
| 2010 | RECOMB | Discovering Transcriptional Modules by Combined Analysis of Expression Profiles and Regulatory Sequences. | Yonit Halperin, Chaim Linhart, Igor Ulitsky, Ron Shamir |
| 2009 | RECOMB | Topology-Free Querying of Protein Interaction Networks. | Sharon Bruckner, Falk Hffner, Richard M. Karp, Ron Shamir, Roded Sharan |
| 2008 | RECOMB | Sorting Cancer Karyotypes by Elementary Operations. | Michal Ozery-Flato, Ron Shamir |
| 2008 | RECOMB | Detecting Disease-Specific Dysregulated Pathways Via Analysis of Clinical Expression Profiles. | Igor Ulitsky, Richard M. Karp, Ron Shamir |
| 2008 | WABI | A Faster Algorithm for RNA Co-folding. | Michal Ziv-Ukelson, Irit Gat-Viks, Ydo Wexler, Ron Shamir |
| 2007 | RECOMB | Rearrangements in Genomes with Centromeres Part I: Translocations. | Michal Ozery-Flato, Ron Shamir |
| 2006 | CPM | An O(n | Michal Ozery-Flato, Ron Shamir |
| 2006 | ESA | Some Computational Challenges in Today's Bio-medicine. | Ron Shamir |
| 2006 | RECOMB | Sorting by Translocations Via Reversals Theory. | Michal Ozery-Flato, Ron Shamir |
| 2005 | ISMB | Tag SNP selection in genotype data for maximizing SNP prediction accuracy. | Eran Halperin, Gad Kimmel, Ron Shamir |
| 2005 | RECOMB | The Factor Graph Network Model for Biological Systems. | Irit Gat-Viks, Amos Tanay, Daniela Raijman, Ron Shamir |
| 2004 | CPM | Computational Problems in Perfect Phylogeny Haplotyping: Xor-Genotypes and Tag SNPs. | Tamar Barzuza, Jacques S. Beckmann, Ron Shamir, Itsik Pe'er |
| 2004 | PSB | Reconstructing Chain Functions in Genetic Networks. | Irit Gat-Viks, Ron Shamir, Richard M. Karp, Roded Sharan |
| 2004 | RECOMB | Modeling and Analysis of Heterogeneous Regulation in Biological Networks. | Irit Gat-Viks, Amos Tanay, Ron Shamir |
| 2004 | RECOMB | Maximum likelihood resolution of multi-block genotypes. | Gad Kimmel, Ron Shamir |
| 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 |
| 2003 | ISMB | Chain functions and scoring functions in genetic networks. | Irit Gat-Viks, Ron Shamir |
| 2003 | RECOMB | Modeling transcription programs: inferring binding site activity and dose-response model optimization. | Amos Tanay, Ron Shamir |
| 2003 | WABI | Identifying Blocks and Sub-populations in Noisy SNP Data. | Gad Kimmel, Roded Sharan, Ron Shamir |
| 2002 | ISMB | The degenerate primer design problem. | Chaim Linhart, Ron Shamir |
| 2002 | ISMB | Discovering statistically significant biclusters in gene expression data. | Amos Tanay, Roded Sharan, Ron Shamir |
| 2002 | RECOMB | The restriction scaffold problem. | Amir Ben-Dor, Richard M. Karp, Benno Schwikowski, Ron Shamir |
| 2002 | RECOMB | Handling long targets and errors in sequencing by hybridization. | Eran Halperin, Shay Halperin, Tzvika Hartman, Ron Shamir |
| 2002 | WG | Cluster Graph Modification Problems. | Ron Shamir, Roded Sharan, Dekel Tsur |
| 2001 | ISMB | Computational expansion of genetic networks. | Amos Tanay, Ron Shamir |
| 2001 | RECOMB | Large scale sequencing by hybridization. | Ron Shamir, 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 | Spectrum Alignment: Efficient Resequencing by Hybridization. | Itsik Pe'er, Ron Shamir |
| 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 | ISMB | An Algorithm Combining Discrete and Continuous Methods for Optical Mapping. | Richard M. Karp, Itsik Pe'er, Ron Shamir |
| 1999 | RECOMB | An algorithm for clustering cDNAs for gene expression analysis. | Erez Hartuv, Armin O. Schmitt, Jrg Lange, Sebastian Meier-Ewert, Hans Lehrach, Ron Shamir |
| 1999 | RECOMB | Construction of physical maps from oligonucleotide fingerprints data. | Guy Mayraz, Ron Shamir |
| 1999 | WG | Complexity Classification of Some Edge Modification Problems. | Assaf Natanzon, Ron Shamir, Roded Sharan |
| 1998 | RECOMB | Algorithms for optical mapping. | Richard M. Karp, Ron Shamir |
| 1998 | SODA | The Maximum Subforest Problem: Approximation and Exact Algorithms (Extended Abstract). | Ron Shamir, Dekel Tsur |
| 1998 | STOC | A Polynomial Approximation Algorithm for the Minimum Fill-In Problem. | Assaf Natanzon, Ron Shamir, Roded Sharan |
| 1997 | RECOMB | Faster and simpler algorithm for sorting signed permutations by reversals. | Haim Kaplan, Ron Shamir, Robert Endre Tarjan |
| 1997 | SODA | Faster and Simpler Algorithm for Sorting Signed Permutations by Reversals. | Haim Kaplan, Ron Shamir, Robert Endre Tarjan |
| 1995 | ESA | Interval Graphs with Side (and Size) Constraints. | Itsik Pe'er, Ron Shamir |
| 1994 | FOCS | Tractability of parameterized completion problems on chordal and interval graphs: Minimum Fill-in and Physical Mapping | Haim Kaplan, Ron Shamir, Robert Endre Tarjan |
| 1993 | WG | Algorithms and Complexity of Sandwich Problems in Graphs (Extended Abstract). | Martin Charles Golumbic, Haim Kaplan, Ron Shamir |
| 1992 | AAAI | Algorithms and Complexity for Reasoning about Time. | Martin Charles Golumbic, Ron Shamir |
| 1990 | SODA | Characterization and Algorithms for Greedily Solvable Transportation Problems. | Ron Shamir, Brenda L. Dietrich |