Towards Multidocument Summarization by Reformulation: Progress and Prospects. - Kathleen R. McKeown; Judith Klavans; Vasileios Hatzivassiloglou; Regina Barzilay; Eleazar Eskin (AAAI/IAAI, 1999)

Detecting Text Similarity over Short Passages: Exploring Linguistic Feature Combinations via Machine Learning. - Vasileios Hatzivassiloglou; Judith L. Klavans; Eleazar Eskin (EMNLP, 1999)

Genetic programming applied to Othello: introducing students to machine learning research. - Eleazar Eskin; Eric V. Siegel (SIGCSE, 1999)

Detecting Errors within a Corpus using Anomaly Detection. - Eleazar Eskin (ANLP, 2000)

Combining Strategies for Extracting Relations from Text Collections. - Eugene Agichtein; Eleazar Eskin; Luis Gravano (ACM SIGMOD Workshop on Research Issues in Data Mining and Knowledge Discovery, 2000)

Anomaly Detection over Noisy Data using Learned Probability Distributions. - Eleazar Eskin (ICML, 2000)

Using mixtures of common ancestors for estimating the probabilities of discrete events in biological sequences. - Eleazar Eskin; William Noble Grundy; Yoram Singer (ISMB (Supplement of Bioinformatics), 2001)

Data Mining Methods for Detection of New Malicious Executables. - Matthew G. Schultz; Eleazar Eskin; Erez Zadok; Salvatore J. Stolfo (S&P, 2001)

MEF: Malicious Email Filter - A UNIX Mail Filter That Detects Malicious Windows Executables. - Matthew G. Schultz; Eleazar Eskin; Erez Zadok; Manasi Bhattacharyya; Salvatore J. Stolfo (USENIX ATC, FREENIX Track, 2001)

Data Mining-based Intrusion Detectors: An Overview of the Columbia IDS Project. - Salvatore J. Stolfo; Wenke Lee; Philip K. Chan; Wei Fan 001; Eleazar Eskin (SIGMOD Rec., 2001)

A Geometric Framework for Unsupervised Anomaly Detection. - Eleazar Eskin; Andrew Arnold; Michael J. Prerau; Leonid Portnoy; Salvatore J. Stolfo (Applications of Data Mining in Computer Security, 2002)

Adaptive Model Generation. - Andrew Honig; Andrew Howard; Eleazar Eskin; Salvatore J. Stolfo (Applications of Data Mining in Computer Security, 2002)

Finding composite regulatory patterns in DNA sequences. - Eleazar Eskin; Pavel A. Pevzner (ISMB, 2002)

Mismatch String Kernels for SVM Protein Classification. - Christina S. Leslie; Eleazar Eskin; Jason Weston; William Stafford Noble (NIPS, 2002)

MET: an experimental system for Malicious Email Tracking. - Manasi Bhattacharyya; Shlomo Hershkop; Eleazar Eskin (NSPW, 2002)

A Kernel Approach for Learning from Almost Orthogonal Patterns. - Bernhard Schölkopf; Jason Weston; Eleazar Eskin; Christina S. Leslie; William Stafford Noble (PKDD, 2002)

The Spectrum Kernel: A String Kernel for SVM Protein Classification. - Christina S. Leslie; Eleazar Eskin; William Stafford Noble (Pacific Symposium on Biocomputing, 2002)

Detecting Malicious Software by Monitoring Anomalous Windows Registry Accesses. - Frank Apap; Andrew Honig; Shlomo Hershkop; Eleazar Eskin; Salvatore J. Stolfo (RAID, 2002)

Using Substitution Matrices to Estimate Probability Distributions for Biological Sequences. - Eleazar Eskin; William Stafford Noble; Yoram Singer (J. Comput. Biol., 2002)

Laplace Propagation. - Alexander J. Smola; Vishy Vishwanathan; Eleazar Eskin (NIPS, 2003)

Genome-Wide Analysis of Bacterial Promoter Regions. - Eleazar Eskin; Uri Keich; Mikhail S. Gelfand; Pavel A. Pevzner (Pacific Symposium on Biocomputing, 2003)

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

Protein Family Classification Using Sparse Markov Transducers. - Eleazar Eskin; William Stafford Noble; Yoram Singer (J. Comput. Biol., 2003)

Discrete profile alignment via constrained information bottleneck. - Sean O'Rourke; Gal Chechik; Robin Friedman; Eleazar Eskin (NIPS, 2004)

Combining Text Mining and Sequence Analysis to Discover Protein Functional Regions. - Eleazar Eskin; Eugene Agichtein (Pacific Symposium on Biocomputing, 2004)

From profiles to patterns and back again: a branch and bound algorithm for finding near optimal motif profiles. - Eleazar Eskin (RECOMB, 2004)

Using Expression Data to Discover RNA and DNA Regulatory Sequence Motifs. - Chaya Ben-Zaken Zilberstein; Eleazar Eskin; Zohar Yakhini (Regulatory Genomics, 2004)

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

Mismatch string kernels for discriminative protein classification. - Christina S. Leslie; Eleazar Eskin; Adiel Cohen; Jason Weston; William Stafford Noble (Bioinform., 2004)

The Homology Kernel: A Biologically Motivated Sequence Embedding into Euclidean Space. - Eleazar Eskin; Sagi Snir (CIBCB, 2005)

A comparative evaluation of two algorithms for Windows Registry Anomaly Detection. - Salvatore J. Stolfo; Frank Apap; Eleazar Eskin; Katherine A. Heller; Shlomo Hershkop; Andrew Honig; Krysta M. Svore (J. Comput. Secur., 2005)

Searching Genomes for Noncoding RNA Using FastR. - Shaojie Zhang 001; Brian Haas; Eleazar Eskin; Vineet Bafna (IEEE ACM Trans. Comput. Biol. Bioinform., 2005)

10 Years of the International Conference on Research in Computational Molecular Biology (RECOMB). - Sarah J. Aerni; Eleazar Eskin (RECOMB, 2006)

Discrete profile comparison using information bottleneck. - Sean O'Rourke; Gal Chechik; Robin Friedman; Eleazar Eskin (BMC Bioinform., 2006)

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

Identification of Deletion Polymorphisms from Haplotypes. - Erik Corona; Benjamin J. Raphael; Eleazar Eskin (RECOMB, 2007)

Reconstructing the Phylogeny of Mobile Elements. - Sean O'Rourke; Noah Zaitlen; Nebojsa Jojic; Eleazar Eskin (RECOMB, 2007)

Discovering tightly regulated and differentially expressed gene sets in whole genome expression data. - Chun Ye; Eleazar Eskin (Bioinform., 2007)

Incorporating homologues into Sequence Embeddings for protein Analysis. - Eleazar Eskin; Sagi Snir (J. Bioinform. Comput. Biol., 2007)

Increasing Power in Association Studies by Using Linkage Disequilibrium Structure and Molecular Function as Prior Information. - Eleazar Eskin (RECOMB, 2008)

Efficient Genome Wide Tagging by Reduction to SAT. - Arthur Choi; Noah Zaitlen; Buhm Han; Knot Pipatsrisawat; Adnan Darwiche; Eleazar Eskin (WABI, 2008)

An Adaptive and Memory Efficient Algorithm for Genotype Imputation. - Hyun Min Kang; Noah Zaitlen; Buhm Han; Eleazar Eskin (RECOMB, 2009)

Using Network Component Analysis to Dissect Regulatory Networks Mediated by Transcription Factors in Yeast. - Chun Ye; Simon J. Galbraith; James C. Liao; Eleazar Eskin (PLoS Comput. Biol., 2009)

Respecting Markov Equivalence in Computing Posterior Probabilities of Causal Graphical Features. - Eun Yong Kang; Ilya Shpitser; Eleazar Eskin (AAAI, 2010)

Effective Algorithms for Fusion Gene Detection. - Dan He 001; Eleazar Eskin (WABI, 2010)

Multi-marker tagging single nucleotide polymorphism selection using estimation of distribution algorithms. - Roberto Santana 001; Alexander Mendiburu; Noah Zaitlen; Eleazar Eskin; José Antonio Lozano 001 (Artif. Intell. Medicine, 2010)

Optimal algorithms for haplotype assembly from whole-genome sequence data. - Dan He 001; Arthur Choi; Knot Pipatsrisawat; Adnan Darwiche; Eleazar Eskin (Bioinform., 2010)

Detection and reconstruction of tandemly organized de novo copy number variations. - Dan He 001; Nicholas A. Furlotte; Eleazar Eskin (BMC Bioinform., 2010)

Detecting the Presence and Absence of Causal Relationships between Expression of Yeast Genes with Very Few Samples. - Eun Yong Kang; Chun Ye; Ilya Shpitser; Eleazar Eskin (J. Comput. Biol., 2010)

EMINIM: An Adaptive and Memory-Efficient Algorithm for Genotype Imputation. - Hyun Min Kang; Noah Zaitlen; Eleazar Eskin (J. Comput. Biol., 2010)

Genome-wide analysis reveals novel genes influencing temporal lobe structure with relevance to neurodegeneration in Alzheimer's disease. - Jason L. Stein; Xue Hua; Jonathan H. Morra; Suh Lee; Derrek P. Hibar; April J. Ho; Alex D. Leow; Arthur W. Toga; Jae Hoon Sul; Hyun Min Kang; Eleazar Eskin; Andrew J. Saykin; et al. (NeuroImage, 2010)

Using HLA binding prediction algorithms for epitope mapping in HIV vaccine clinical trials. - Dan He 001; Pratima Kunwar; Eleazar Eskin; Helen Horton; Peter B. Gilbert; Tomer Hertz (BCB, 2011)

Session Introduction. - Can Alkan; Emidio Capriotti; Eleazar Eskin; Fereydoun Hormozdiari; Maricel G. Kann (Pacific Symposium on Biocomputing, 2011)

Mixed-model coexpression: calculating gene coexpression while accounting for expression heterogeneity. - Nicholas A. Furlotte; Hyun Min Kang; Chun Ye; Eleazar Eskin (Bioinform., 2011)

Efficient algorithms for tandem copy number variation reconstruction in repeat-rich regions. - Dan He 001; Farhad Hormozdiari; Nicholas A. Furlotte; Eleazar Eskin (Bioinform., 2011)

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

Assembly of non-unique insertion content using next-generation sequencing. - Nathaniel Parrish; Farhad Hormozdiari; Eleazar Eskin (BMC Bioinform., 2011)

Gene networks associated with conditional fear in mice identified using a systems genetics approach. - Christopher C. Park; Greg D. Gale; Simone de Jong; Anatole Ghazalpour; Brian J. Bennett; Charles R. Farber; Peter Langfelder; Andy Lin; Arshad H. Khan; Eleazar Eskin; Steve Horvath; Aldons J. Lusis; et al. (BMC Syst. Biol., 2011)

Increasing Power of Groupwise Association Test with Likelihood Ratio Test. - Jae Hoon Sul; Buhm Han; Eleazar Eskin (J. Comput. Biol., 2011)

Efficient genotyping of individuals using overlapping pool sequencing and imputation. - Farhad Hormozdiari; Zhanyong Wang; Wen-Yun Yang; Eleazar Eskin (ACSCC, 2012)

Incorporating prior information into association studies. - Gregory Darnell; Dat Duong; Buhm Han; Eleazar Eskin (Bioinform., 2012)

IPEDX: An exact algorithm for pedigree reconstruction using genotype data. - Dan He 001; Eleazar Eskin (BIBM, 2013)

Leveraging reads that span multiple single nucleotide polymorphisms for haplotype inference from sequencing data. - Wen-Yun Yang; Farhad Hormozdiari; Zhanyong Wang; Dan He 001; Bogdan Pasaniuc; Eleazar Eskin (Bioinform., 2013)

Genome reassembly with high-throughput sequencing data. - Nathaniel Parrish; Benjamin Sudakov; Eleazar Eskin (BMC Genom., 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)

Hap-seq: An Optimal Algorithm for Haplotype Phasing with Imputation Using Sequencing Data. - Dan He 001; Buhm Han; Eleazar Eskin (J. Comput. Biol., 2013)

IPED: Inheritance Path-based Pedigree Reconstruction Algorithm Using Genotype Data. - Dan He 001; Zhanyong Wang; Buhm Han; Laxmi Parida; Eleazar Eskin (J. Comput. Biol., 2013)

Efficiently Identifying Significant Associations in Genome-wide Association Studies. - Emrah Kostem; Eleazar Eskin (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)

Identifying causal variants at loci with multiple signals of association. - Farhad Hormozdiari; Emrah Kostem; Eun Yong Kang; Bogdan Pasaniuc; Eleazar Eskin (BCB, 2014)

Reconstruction of influenza a virus variants from PacBio reads. - Alexander Artyomenko; Serghei Mangul; Nicholas C. Wu; Eleazar Eskin; Ren Sun; Alex Zelikovsky (ICCABS, 2014)

VGA: A method for viral quasispecies assembly from ultra-deep sequencing data. - Serghei Mangul; Nicholas C. Wu; Nicholas Mancuso; Alex Zelikovsky; Ren Sun; Eleazar Eskin (ICCABS, 2014)

A Spatial-Aware Haplotype Copying Model with Applications to Genotype Imputation. - Wen-Yun Yang; Farhad Hormozdiari; Eleazar Eskin; Bogdan Pasaniuc (RECOMB, 2014)

Fast pairwise IBD association testing in genome-wide association studies. - Buhm Han; Eun Yong Kang; Soumya Raychaudhuri; Paul I. W. de Bakker; Eleazar Eskin (Bioinform., 2014)

Privacy preserving protocol for detecting genetic relatives using rare variants. - Farhad Hormozdiari; Jong Wha J. Joo; Akshay Wadia; Feng Guan; Rafail Ostrovsky; Amit Sahai; Eleazar Eskin (Bioinform., 2014)

Accurate viral population assembly from ultra-deep sequencing data. - Serghei Mangul; Nicholas C. Wu; Nicholas Mancuso; Alex Zelikovsky; Ren Sun; Eleazar Eskin (Bioinform., 2014)

IPED2X: A robust pedigree reconstruction algorithm for complicated pedigrees. - Dan He 001; Eleazar Eskin (J. Bioinform. Comput. Biol., 2014)

2SNV: Quasispecies reconstruction from PacBio reads. - Alexander Artyomenko; Nicholas C. Wu; Serghei Mangul; Eleazar Eskin; Ren Sun; Alex Zelikovsky (ICCABS, 2015)

Efficient and Accurate Multiple-Phenotypes Regression Method for High Dimensional Data Considering Population Structure. - Jong Wha J. Joo; Eun Yong Kang; Elin Org; Nicholas A. Furlotte; Brian Parks; Aldons J. Lusis; Eleazar Eskin (RECOMB, 2015)

Identification of causal genes for complex traits. - Farhad Hormozdiari; Gleb Kichaev; Wen-Yun Yang; Bogdan Pasaniuc; Eleazar Eskin (Bioinform., 2015)

Discovering genes involved in disease and the mystery of missing heritability. - Eleazar Eskin (Commun. ACM, 2015)

Memory efficient assembly of human genome. - Farhad Hormozdiari; Eleazar Eskin (J. Bioinform. Comput. Biol., 2015)

Gene-Gene Interactions Detection Using a Two-stage Model. - Zhanyong Wang; Jae Hoon Sul; Sagi Snir; José Antonio Lozano 001; Eleazar Eskin (J. Comput. Biol., 2015)

A Spatial Haplotype Copying Model with Applications to Genotype Imputation. - Wen-Yun Yang; Farhad Hormozdiari; Eleazar Eskin; Bogdan Pasaniuc (J. Comput. Biol., 2015)

HapIso: An Accurate Method for the Haplotype-Specific Isoforms Reconstruction from Long Single-Molecule Reads. - Serghei Mangul; Harry (Taegyun) Yang; Farhad Hormozdiari; Elizabeth Tseng; Alex Zelikovsky; Eleazar Eskin (ISBRA, 2016)

Using genomic annotations increases statistical power to detect eGenes. - Dat Duong; Jennifer Zou; Farhad Hormozdiari; Jae Hoon Sul; Jason Ernst; Buhm Han; Eleazar Eskin (Bioinform., 2016)

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)

Applying meta-analysis to genotype-tissue expression data from multiple tissues to identify eQTLs and increase the number of eGenes. - Dat Duong; Lisa Gai; Sagi Snir; Eun Yong Kang; Buhm Han; Jae Hoon Sul; Eleazar Eskin (Bioinform., 2017)

Improved methods for multi-trait fine mapping of pleiotropic risk loci. - Gleb Kichaev; Megan Roytman; Ruth Johnson; Eleazar Eskin; Sara Lindström; Peter Kraft; Bogdan Pasaniuc (Bioinform., 2017)

Increasing the power of meta-analysis of genome-wide association studies to detect heterogeneous effects. - C. H. Lee; Eleazar Eskin; Buhm Han (Bioinform., 2017)

Long Single-Molecule Reads Can Resolve the Complexity of the Influenza Virus Composed of Rare, Closely Related Mutant Variants. - Alexander Artyomenko; Nicholas C. Wu; Serghei Mangul; Eleazar Eskin; Ren Sun; Alex Zelikovsky (J. Comput. Biol., 2017)

The impact of rare variation on gene expression across tissues. - Xin Li 130; Yungil Kim; Emily K. Tsang; Joe R. Davis; Farhan N. Damani; Colby Chiang; Gaelen T. Hess; Zachary Zappala; Benjamin J. Strober; Alexandra J. Scott; Amy Li; Andrea Ganna; et al. (Nat., 2017)

IPED2: Inheritance Path Based Pedigree Reconstruction Algorithm for Complicated Pedigrees. - Dan He 001; Zhanyong Wang; Laxmi Parida; Eleazar Eskin (IEEE ACM Trans. Comput. Biol. Bioinform., 2017)

A Unifying Framework for Summary Statistic Imputation. - Yue Wu; Eleazar Eskin; Sriram Sankararaman (RECOMB, 2018)

Finding associated variants in genome-wide association studies on multiple traits. - Lisa Gai; Eleazar Eskin (Bioinform., 2018)

Word and Sentence Embedding Tools to Measure Semantic Similarity of Gene Ontology Terms by Their Definitions. - Dat Duong; Wasi Uddin Ahmad; Eleazar Eskin; Kai-Wei Chang; Jingyi Jessica Li (J. Comput. Biol., 2019)

Improving Imputation Accuracy by Inferring Causal Variants in Genetic Studies. - Yue Wu; Farhad Hormozdiari; Jong Wha J. Joo; Eleazar Eskin (J. Comput. Biol., 2019)

Benchmarking of computational error-correction methods for next-generation sequencing data. - Keith Mitchell; Jaqueline J. Brito; Igor Mandric; Qiaozhen Wu; Sergey Knyazev; Sei Chang; Lana S. Martin; Aaron Karlsberg; Ekaterina Gerasimov; Russell Littman; Brian L. Hill; Nicholas C. Wu; et al. (BCB, 2020)

Identifying Causal Variants by Fine Mapping Across Multiple Studies. - Nathan LaPierre; Kodi Taraszka; Helen Huang; Rosemary He; Farhad Hormozdiari; Eleazar Eskin (RECOMB, 2020)

A Unifying Framework for Imputing Summary Statistics in Genome-Wide Association Studies. - Yue Wu; Eleazar Eskin; Sriram Sankararaman (J. Comput. Biol., 2020)

A comprehensive benchmarking of WGS-based deletion structural variant callers. - Varuni Sarwal; Sebastian Niehus; Ram Ayyala; Minyoung Kim; Aditya Sarkar; Sei Chang; Angela Lu; Neha Rajkumar; Nicholas Darci-Maher; Russell Littman; Karishma Chhugani; Arda Soylev; et al. (Briefings Bioinform., 2022)

Packaging, containerization, and virtualization of computational omics methods: Advances, challenges, and opportunities. - Mohammed Alser; Sharon Waymost; Ram Ayyala; Brendan Lawlor; Richard J. Abdill; Neha Rajkumar; Nathan LaPierre; Jaqueline J. Brito; Andre M. Ribeiro-dos-Santos; Can Firtina; Nour Almadhoun; Varuni Sarwal; et al. (CoRR, 2022)

VISTA: an integrated framework for structural variant discovery. - Varuni Sarwal; Seungmo Lee; Jianzhi Yang; Sriram Sankararaman; Mark Chaisson; Eleazar Eskin; Serghei Mangul (Briefings Bioinform., 2024)