| 2025 | AAAI | Memorize and Rank: Elevating Large Language Models for Clinical Diagnosis Prediction. | Mingyu Derek Ma, Xiaoxuan Wang, Yijia Xiao, Anthony Cuturrufo, Vijay S. Nori, Eran Halperin, Wei Wang |
| 2019 | RECOMB | Distinguishing Biological from Technical Sources of Variation Using a Combination of Methylation Datasets. | Mike Thompson, Zeyuan Johnson Chen, Elior Rahmani, Eran Halperin |
| 2018 | RECOMB | Tensor Composition Analysis Detects Cell-Type Specific Associations in Epigenetic Studies. | Elior Rahmani, Regev Schweiger, Saharon Rosset, Sriram Sankararaman, Eran Halperin |
| 2017 | RECOMB | A Bayesian Framework for Estimating Cell Type Composition from DNA Methylation Without the Need for Methylation Reference. | Elior Rahmani, Regev Schweiger, Liat Shenhav, Eleazar Eskin, Eran Halperin |
| 2017 | RECOMB | Using Stochastic Approximation Techniques to Efficiently Construct Confidence Intervals for Heritability. | Regev Schweiger, Eyal Fisher, Elior Rahmani, Liat Shenhav, Saharon Rosset, Eran Halperin |
| 2015 | WABI | Multiple-Ancestor Localization for Recently Admixed Individuals. | Yaron Margalit, Yael Baran, Eran Halperin |
| 2013 | RECOMB | eALPS: Estimating Abundance Levels in Pooled Sequencing Using Available Genotyping Data. | Itamar Eskin, Farhad Hormozdiari, Luca Conde, Jacques Riby, Chris Skibola, Eleazar Eskin, Eran Halperin |
| 2013 | RECOMB | Learning Natural Selection from the Site Frequency Spectrum. | Roy Ronen, Nitin Udpa, Eran Halperin, Vineet Bafna |
| 2012 | RECOMB | CNVeM: Copy Number Variation Detection Using Uncertainty of Read Mapping. | Zhanyong Wang, Farhad Hormozdiari, Wen-Yun Yang, Eran Halperin, Eleazar Eskin |
| 2012 | RECOMB | Probabilistic Inference of Viral Quasispecies Subject to Recombination. | Osvaldo Zagordi, Armin Tpfer, Sandhya Prabhakaran, Volker Roth, Eran Halperin, Niko Beerenwinkel |
| 2011 | RECOMB | Pedigree Reconstruction Using Identity by Descent. | Bonnie Kirkpatrick, Shuai Cheng Li, Richard M. Karp, Eran Halperin |
| 2010 | RECOMB | Accurate Estimation of Expression Levels of Homologous Genes in RNA-seq Experiments. | Bogdan Pasaniuc, Noah Zaitlen, Eran Halperin |
| 2009 | RECOMB | Haplotype Inference in Complex Pedigrees. | Bonnie Kirkpatrick, Javier Rosa, Eran Halperin, Richard M. Karp |
| 2008 | RECOMB | On the Inference of Ancestries in Admixed Populations. | Sriram Sankararaman, Gad Kimmel, Eran Halperin, Michael I. Jordan |
| 2007 | RECOMB | An Efficient and Accurate Graph-Based Approach to Detect Population Substructure. | Srinath Sridhar, Satish Rao, Eran Halperin |
| 2007 | SODA | A rigorous analysis of population stratification with limited data. | Kamalika Chaudhuri, Eran Halperin, Satish Rao, Shuheng Zhou |
| 2006 | CPM | SNP and Haplotype Analysis - Algorithms and Applications. | Eran Halperin |
| 2006 | ICALP | Fixed Parameter Tractability of Binary Near-Perfect Phylogenetic Tree Reconstruction. | Guy E. Blelloch, Kedar Dhamdhere, Eran Halperin, R. Ravi, Russell Schwartz, Srinath Sridhar |
| 2006 | ICCS | Simple Reconstruction of Binary Near-Perfect Phylogenetic Trees. | Srinath Sridhar, Kedar Dhamdhere, Guy E. Blelloch, Eran Halperin, R. Ravi, Russell Schwartz |
| 2005 | ISMB | Tag SNP selection in genotype data for maximizing SNP prediction accuracy. | Eran Halperin, Gad Kimmel, Ron Shamir |
| 2005 | RECOMB | HAPLOFREQ - Estimating Haplotype Frequencies E.ciently. | Eran Halperin, Elad Hazan |
| 2004 | ICALP | The Minimum-Entropy Set Cover Problem. | Eran Halperin, Richard M. Karp |
| 2004 | RECOMB | Perfect phylogeny and haplotype assignment. | Eran Halperin, Richard M. Karp |
| 2004 | STOC | Asymmetric k-center is log | Julia Chuzhoy, Sudipto Guha, Eran Halperin, Sanjeev Khanna, Guy Kortsarz, Joseph Naor |
| 2003 | ICALP | An Improved Approximation Algorithm for Vertex Cover with Hard Capacities. | Rajiv Gandhi, Eran Halperin, Samir Khuller, Guy Kortsarz, Aravind Srinivasan |
| 2003 | ISMB | Detecting protein sequence conservation via metric embeddings. | Eran Halperin, Jeremy Buhler, Richard M. Karp, Robert Krauthgamer, Ben Westover |
| 2003 | RECOMB | Large scale reconstruction of haplotypes from genotype data. | Eleazar Eskin, Eran Halperin, Richard M. Karp |
| 2003 | SODA | Integrality ratio for group Steiner trees and directed steiner trees. | Eran Halperin, Guy Kortsarz, Robert Krauthgamer, Aravind Srinivasan, Nan Wang |
| 2003 | STOC | A stochastic process on the hypercube with applications to peer-to-peer networks. | Micah Adler, Eran Halperin, Richard M. Karp, Vijay V. Vazirani |
| 2003 | STOC | Polylogarithmic inapproximability. | Eran Halperin, Robert Krauthgamer |
| 2002 | RECOMB | Handling long targets and errors in sequencing by hybridization. | Eran Halperin, Shay Halperin, Tzvika Hartman, Ron Shamir |
| 2002 | SODA | Reachability and distance queries via 2-hop labels. | Edith Cohen, Eran Halperin, Haim Kaplan, Uri Zwick |
| 2002 | SODA | MAX CUT in cubic graphs. | Eran Halperin, Dror Livnat, Uri Zwick |
| 2001 | ICALP | Performance Aspects of Distributed Caches Using TTL-Based Consistency. | Edith Cohen, Eran Halperin, Haim Kaplan |
| 2001 | IPCO | A Unified Framework for Obtaining Improved Approximation Algorithms for Maximum Graph Bisection Problems. | Eran Halperin, Uri Zwick |
| 2001 | SODA | Coloring k-colorable graphs using smaller palettes. | Eran Halperin, Ram Nathaniel, Uri Zwick |
| 2001 | SODA | Combinatorial approximation algorithms for the maximum directed cut problem. | Eran Halperin, Uri Zwick |
| 2000 | SODA | Improved approximation algorithms for the vertex cover problem in graphs and hypergraphs. | Eran Halperin |
| 1999 | IPCO | Approximation Algorithms for MAX 4-SAT and Rounding Procedures for Semidefinite Programs. | Eran Halperin, Uri Zwick |