Bipartite subgraphs of integer weighted graphs. - Noga Alon; Eran Halperin (Discret. Math., 1998)

FramePlus: aligning DNA to protein sequences. - Eran Halperin; Simchon Faigler; Raveh Gill-More (Bioinform., 1999)

Coloring k-colorable graphs using smaller palettes. - Eran Halperin; Ram Nathaniel; Uri Zwick (SODA, 2001)

Combinatorial approximation algorithms for the maximum directed cut problem. - Eran Halperin; Uri Zwick (SODA, 2001)

Approximation Algorithms for MAX 4-SAT and Rounding Procedures for Semidefinite Programs. - Eran Halperin; Uri Zwick (J. Algorithms, 2001)

Improved Approximation Algorithms for the Partial Vertex Cover Problem. - Eran Halperin; Aravind Srinivasan (APPROX, 2002)

Coloring k-colorable graphs using relatively small palettes. - Eran Halperin; Ram Nathaniel; Uri Zwick (J. Algorithms, 2002)

A unified framework for obtaining improved approximation algorithms for maximum graph bisection problems. - Eran Halperin; Uri Zwick (Random Struct. Algorithms, 2002)

Improved Approximation Algorithms for the Vertex Cover Problem in Graphs and Hypergraphs. - Eran Halperin (SIAM J. Comput., 2002)

Detecting protein sequence conservation via metric embeddings. - Eran Halperin; Jeremy Buhler; Richard M. Karp; Robert Krauthgamer; Ben Westover (ISMB (Supplement of Bioinformatics), 2003)

Large scale reconstruction of haplotypes from genotype data. - Eleazar Eskin; Eran Halperin; Richard M. Karp (RECOMB, 2003)

A stochastic process on the hypercube with applications to peer-to-peer networks. - Micah Adler; Eran Halperin; Richard M. Karp; Vijay V. Vazirani (STOC, 2003)

Polylogarithmic inapproximability. - Eran Halperin; Robert Krauthgamer (STOC, 2003)

Tight lower bounds for the asymmetric k-center problem - Eran Halperin; Guy Kortsarz; Robert Krauthgamer (Electron. Colloquium Comput. Complex., 2003)

Handling Long Targets and Errors in Sequencing by Hybridization. - Eran Halperin; Shay Halperin; Tzvika Hartman; Ron Shamir (J. Comput. Biol., 2003)

Reachability and Distance Queries via 2-Hop Labels. - Edith Cohen; Eran Halperin; Haim Kaplan; Uri Zwick (SIAM J. Comput., 2003)

Perfect phylogeny and haplotype assignment. - Eran Halperin; Richard M. Karp (RECOMB, 2004)

Asymmetric k-center is log* n-hard to approximate. - Julia Chuzhoy; Sudipto Guha; Eran Halperin; Sanjeev Khanna; Guy Kortsarz; Joseph Naor (STOC, 2004)

Haplotype reconstruction from genotype data using Imperfect Phylogeny. - Eran Halperin; Eleazar Eskin (Bioinform., 2004)

MAX CUT in cubic graphs. - Eran Halperin; Dror Livnat; Uri Zwick (J. Algorithms, 2004)

Tag SNP selection in genotype data for maximizing SNP prediction accuracy. - Eran Halperin; Gad Kimmel; Ron Shamir (ISMB (Supplement of Bioinformatics), 2005)

HAPLOFREQ - Estimating Haplotype Frequencies E.ciently. - Eran Halperin; Elad Hazan (RECOMB, 2005)

Asymmetric k-center is log* n-hard to approximate. - Julia Chuzhoy; Sudipto Guha; Eran Halperin; Sanjeev Khanna; Guy Kortsarz; Robert Krauthgamer; Joseph Naor (J. ACM, 2005)

Performance aspects of distributed caches using TTL-based consistency. - Edith Cohen; Eran Halperin; Haim Kaplan (Theor. Comput. Sci., 2005)

The minimum-entropy set cover problem. - Eran Halperin; Richard M. Karp (Theor. Comput. Sci., 2005)

SNP and Haplotype Analysis - Algorithms and Applications. - Eran Halperin (CPM, 2006)

Fixed Parameter Tractability of Binary Near-Perfect Phylogenetic Tree Reconstruction. - Guy E. Blelloch; Kedar Dhamdhere; Eran Halperin; R. Ravi 001; Russell Schwartz; Srinath Sridhar 001 (ICALP (1), 2006)

Simple Reconstruction of Binary Near-Perfect Phylogenetic Trees. - Srinath Sridhar 001; Kedar Dhamdhere; Guy E. Blelloch; Eran Halperin; R. Ravi 001; Russell Schwartz (International Conference on Computational Science (2), 2006)

A Note on Phasing Long Genomic Regions Using Local Haplotype Predictions. - Eleazar Eskin; Roded Sharan; Eran Halperin (J. Bioinform. Comput. Biol., 2006)

HAPLOFREQ-Estimating Haplotype Frequencies Efficiently. - Eran Halperin; Elad Hazan (J. Comput. Biol., 2006)

An improved approximation algorithm for vertex cover with hard capacities. - Rajiv Gandhi; Eran Halperin; Samir Khuller; Guy Kortsarz; Aravind Srinivasan (J. Comput. Syst. Sci., 2006)

An Efficient and Accurate Graph-Based Approach to Detect Population Substructure. - Srinath Sridhar 001; Satish Rao; Eran Halperin (RECOMB, 2007)

A rigorous analysis of population stratification with limited data. - Kamalika Chaudhuri; Eran Halperin; Satish Rao; Shuheng Zhou 002 (SODA, 2007)

HAPLOPOOL: improving haplotype frequency estimation through DNA pools and phylogenetic modeling. - Bonnie Kirkpatrick; Carlos Santos Armendariz; Richard M. Karp; Eran Halperin (Bioinform., 2007)

Integrality Ratio for Group Steiner Trees and Directed Steiner Trees. - Eran Halperin; Guy Kortsarz; Robert Krauthgamer; Aravind Srinivasan; Nan Wang 001 (SIAM J. Comput., 2007)

Algorithms for Efficient Near-Perfect Phylogenetic Tree Reconstruction in Theory and Practice. - Srinath Sridhar 001; Kedar Dhamdhere; Guy E. Blelloch; Eran Halperin; R. Ravi 001; Russell Schwartz (IEEE ACM Trans. Comput. Biol. Bioinform., 2007)

On the Inference of Ancestries in Admixed Populations. - Sriram Sankararaman; Gad Kimmel; Eran Halperin; Michael I. Jordan (RECOMB, 2008)

Haplotype Inference in Complex Pedigrees. - Bonnie Kirkpatrick; Javier Rosa; Eran Halperin; Richard M. Karp (RECOMB, 2009)

Inference of locus-specific ancestry in closely related populations. - Bogdan Pasaniuc; Sriram Sankararaman; Gad Kimmel; Eran Halperin (Bioinform., 2009)

Increasing the Power of Association Studies by Imputation-based Sparse Tag SNP Selection. - Ofir Davidovich; Eran Halperin; Gad Kimmel; Ron Shamir (Commun. Inf. Syst., 2009)

miRNAkey: a software for microRNA deep sequencing analysis. - Roy Ronen; Ido Gan; Shira Modai; Alona Sukacheov; Gideon Dror; Eran Halperin; Noam Shomron (Bioinform., 2010)

Haplotype Inference in Complex Pedigrees. - Bonnie Kirkpatrick; Eran Halperin; Richard M. Karp (J. Comput. Biol., 2010)

Genotyping common and rare variation using overlapping pool sequencing. - Dan He 001; Noah Zaitlen; Bogdan Pasaniuc; Eleazar Eskin; Eran Halperin (BMC Bioinform., 2011)

Pedigree Reconstruction Using Identity by Descent. - Bonnie Kirkpatrick; Shuai Cheng Li 001; Richard M. Karp; Eran Halperin (J. Comput. Biol., 2011)

Accurate Estimation of Expression Levels of Homologous Genes in RNA-seq Experiments. - Bogdan Pasaniuc; Noah Zaitlen; Eran Halperin (J. Comput. Biol., 2011)

Fast and accurate inference of local ancestry in Latino populations. - Yael Baran; Bogdan Pasaniuc; Sriram Sankararaman; Dara G. Torgerson; Christopher Gignoux; Celeste Eng; William Rodriguez-Cintron; Rocio Chapela; Jean G. Ford; Pedro C. Avila; Jose Rodriguez-Santana; Esteban Gonzàlez Burchard; et al. (Bioinform., 2012)

Haplotype reconstruction using perfect phylogeny and sequence data. - Anatoly Efros; Eran Halperin (BMC Bioinform., 2012)

MGMR: leveraging RNA-Seq population data to optimize expression estimation. - Roye Rozov; Eran Halperin; Ron Shamir (BMC Bioinform., 2012)

Joint Analysis of Multiple Metagenomic Samples. - Yael Baran; Eran Halperin (PLoS Comput. Biol., 2012)

Learning Natural Selection from the Site Frequency Spectrum. - Roy Ronen; Nitin Udpa; Eran Halperin; Vineet Bafna (RECOMB, 2013)

Analysis of Latino populations from GALA and MEC studies reveals genomic loci with biased local ancestry estimation. - Bogdan Pasaniuc; Sriram Sankararaman; Dara G. Torgerson; Christopher Gignoux; Noah Zaitlen; Celeste Eng; William Rodriguez-Cintron; Rocio Chapela; Jean G. Ford; Pedro C. Avila; Jose Rodriguez-Santana; Gary K. Chen; et al. (Bioinform., 2013)

eALPS: Estimating Abundance Levels in Pooled Sequencing Using Available Genotyping Data. - Itamar Eskin; Farhad Hormozdiari; Lucía Conde; Jacques Riby; Christine F. Skibola; Eleazar Eskin; Eran Halperin (J. Comput. Biol., 2013)

Probabilistic Inference of Viral Quasispecies Subject to Recombination. - Armin Töpfer; Osvaldo Zagordi; Sandhya Prabhakaran; Volker Roth 001; Eran Halperin; Niko Beerenwinkel (J. Comput. Biol., 2013)

CNVeM: Copy Number Variation Detection Using Uncertainty of Read Mapping. - Zhanyong Wang; Farhad Hormozdiari; Wen-Yun Yang; Eran Halperin; Eleazar Eskin (J. Comput. Biol., 2013)

EPIQ - efficient detection of SNP-SNP epistatic interactions for quantitative traits. - Ya'ara Arkin; Elior Rahmani; Marcus E. Kleber; Reijo Laaksonen; Winfried März; Eran Halperin (Bioinform., 2014)

Fast lossless compression via cascading Bloom filters. - Roye Rozov; Ron Shamir; Eran Halperin (BMC Bioinform., 2014)

Historical Pedigree Reconstruction from Extant Populations Using PArtitioning of RElatives (PREPARE). - Doron Shem-Tov; Eran Halperin (PLoS Comput. Biol., 2014)

Multiple-Ancestor Localization for Recently Admixed Individuals. - Yaron Margalit; Yael Baran; Eran Halperin (WABI, 2015)

Inferring parental genomic ancestries using pooled semi-Markov processes. - James Y. Zou; Eran Halperin; Esteban Gonzàlez Burchard; Sriram Sankararaman (Bioinform., 2015)

A Note on the Relations Between Spatio-Genetic Models. - Yael Baran; Eran Halperin (J. Comput. Biol., 2015)

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 (RECOMB, 2017)

GLINT: a user-friendly toolset for the analysis of high-throughput DNA-methylation array data. - Elior Rahmani; Reut Yedidim; Liat Shenhav; Regev Schweiger; Omer Weissbrod; Noah Zaitlen; Eran Halperin (Bioinform., 2017)

Recycler: an algorithm for detecting plasmids from de novo assembly graphs. - Roye Rozov; Aya Brown Kav; David Bogumil; Naama Shterzer; Eran Halperin; Itzhak Mizrahi; Ron Shamir (Bioinform., 2017)

Association testing of bisulfite-sequencing methylation data via a Laplace approximation. - Omer Weissbrod; Elior Rahmani; Regev Schweiger; Saharon Rosset; Eran Halperin (Bioinform., 2017)

Tensor Composition Analysis Detects Cell-Type Specific Associations in Epigenetic Studies. - Elior Rahmani; Regev Schweiger; Saharon Rosset; Sriram Sankararaman; Eran Halperin (RECOMB, 2018)

Faucet: streaming de novo assembly graph construction. - Roye Rozov; Gil Goldshlager; Eran Halperin; Ron Shamir (Bioinform., 2018)

Using Stochastic Approximation Techniques to Efficiently Construct Confidence Intervals for Heritability. - Regev Schweiger; Eyal Fisher; Elior Rahmani; Liat Shenhav; Saharon Rosset; Eran Halperin (J. Comput. Biol., 2018)

Distinguishing Biological from Technical Sources of Variation Using a Combination of Methylation Datasets. - Mike Thompson; Zeyuan Johnson Chen; Elior Rahmani; Eran Halperin (RECOMB, 2019)

Modeling the temporal dynamics of the gut microbial community in adults and infants. - Liat Shenhav; Ori Furman; Leah Briscoe; Mike Thompson; Justin D. Silverman; Itzhak Mizrahi; Eran Halperin (PLoS Comput. Biol., 2019)

Compositional Lotka-Volterra describes microbial dynamics in the simplex. - Tyler A. Joseph; Liat Shenhav; João B. Xavier; Eran Halperin; Itsik Pe'er (PLoS Comput. Biol., 2020)

The Effect of Model Directionality on Cell-Type-Specific Differential DNA Methylation Analysis. - Elior Rahmani; Brandon Jew; Eran Halperin (Frontiers Bioinform., 2021)

Virtual reality-based conflict resolution: The impact of immersive 360° video on changing view points and moral judgment in the context of violent intergroup conflict. - Béatrice S. Hasler; Daniel H. Landau; Yossi Hasson; Noa Schori-Eyal; Jonathan Giron; Jonathan Levy; Eran Halperin; Doron Friedman (New Media Soc., 2021)

Automated identification of clinical features from sparsely annotated 3-dimensional medical imaging. - Nadav Rakocz; Jeffrey N. Chiang; Muneeswar G. Nittala; Giulia Corradetti; Liran Tiosano; Swetha Velaga; Michael Thompson; Brian L. Hill; Sriram Sankararaman; Jonathan L. Haines; Margaret A. Pericak-Vance; Dwight Stambolian; et al. (npj Digit. Medicine, 2021)

Extend and Explain: Interpreting Very Long Language Models. - Joel Stremmel; Brian L. Hill; Jeffrey Hertzberg; Jaime Murillo; Llewelyn Allotey; Eran Halperin (ML4H@NeurIPS, 2022)

Evaluating supervised and unsupervised background noise correction in human gut microbiome data. - Leah Briscoe; Brunilda Balliu; Sriram Sankararaman; Eran Halperin; Nandita R. Garud (PLoS Comput. Biol., 2022)

Understanding and Predicting the Effect of Environmental Factors on People with Type 2 Diabetes. - Kailas Vodrahalli; Gregory D. Lyng; Brian L. Hill; Kimmo Kärkkäinen; Jeffrey Hertzberg; James Zou 001; Eran Halperin (CHIL, 2023)

Collecting data when missingness is unknown: a method for improving model performance given under-reporting in patient populations. - Kevin Wu; Dominik Dahlem; Christopher Hane; Eran Halperin; James Zou 001 (CHIL, 2023)

Surpassing GPT-4 Medical Coding with a Two-Stage Approach. - Zhichao Yang 001; Sanjit Singh Batra; Joel Stremmel; Eran Halperin (CoRR, 2023)

XAIQA: Explainer-Based Data Augmentation for Extractive Question Answering. - Joel Stremmel; Ardavan Saeedi; Hamid Hassanzadeh; Sanjit S. Batra; Jeffrey Hertzberg; Jaime Murillo; Eran Halperin (CoRR, 2023)

Personalized mood prediction from patterns of behavior collected with smartphones. - Brunilda Balliu; Chris Douglas; Darsol Seok; Liat Shenhav; Yue Wu; Doxa Chatzopoulou; William Kaiser; Victor Chen; Jennifer Kim; Sandeep Deverasetty; Inna Arnaudova; Robert Gibbons; et al. (npj Digit. Medicine, 2024)

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 010 (AAAI, 2025)

Guided Discrete Diffusion for Electronic Health Record Generation. - Jun Han; Zixiang Chen; Yongqian Li; Yiwen Kou; Eran Halperin; Robert E. Tillman; Quanquan Gu (Trans. Mach. Learn. Res., 2025)