Gur Yaari
Associate Professor of PathologyCards
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Associate Professor of Pathology
Biography
Gur Yaari is an Associate Professor in the Department of Pathology, Yale School of Medicine. He received his B.Sc. degree in physics and math, M.Sc. in high energy physics, and Ph.D. in interdisciplinary physics, all from HUJI. He was a postdoctoral fellow at Yale University, and served as an assistant, associate and full professor at Bar Ilan Univerrsity from 2013 till 2025. His current research interest focuses on the development of computational and statistical tools to process and analyze high-throughput biological data, with a special spotlight on the adaptive immune system.
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Pathology
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Overview
Our lab develops computational and statistical tools to process and analyze high-throughput biological data. The research is multidisciplinary and involves elements from mathematics, statistics, physics, computer science, biology and medicine. Our main focus is studying the adaptive immune system from a system/repertoire perspective. In particular, we are interested in understanding lymphocyte (T and B cells) repertoire dynamics in healthy individuals as well as in illness states such as infections, autoimmune diseases, aging and cancer. We apply advanced molecular biology methods to produce large sequencing data sets of human lymphocyte receptors, and analyze them using dedicated computational pipelines, in order to obtain meaningful biological insights into the adaptive immune system.
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Research at a Glance
Yale Co-Authors
Publications Timeline
Ayelet Peres
Steven Kleinstein, PhD
David A. Hafler, MD, FANA
Kevin C O'Connor, PhD
Publications
2025
Enhancing sequence alignment of adaptive immune receptors through multi-task deep learning.
Konstantinovsky T, Peres A, Eisenberg R, Polak P, Lindenbaum O, Yaari G. Enhancing sequence alignment of adaptive immune receptors through multi-task deep learning. Nucleic Acids Res 2025, 53 PMID: 40650972, DOI: 10.1093/nar/gkaf651.Peer-Reviewed Original Research
2023
IGHV allele similarity clustering improves genotype inference from adaptive immune receptor repertoire sequencing data
Peres A, Lees W, Rodriguez O, Lee N, Polak P, Hope R, Kedmi M, Collins A, Ohlin M, Kleinstein S, Watson C, Yaari G. IGHV allele similarity clustering improves genotype inference from adaptive immune receptor repertoire sequencing data. Nucleic Acids Research 2023, 51: e86-e86. PMID: 37548401, PMCID: PMC10484671, DOI: 10.1093/nar/gkad603.Peer-Reviewed Original ResearchCitationsAltmetricA novel approach to T-cell receptor beta chain (TCRB) repertoire encoding using lossless string compression.
Konstantinovsky T, Yaari G. A novel approach to T-cell receptor beta chain (TCRB) repertoire encoding using lossless string compression. Bioinformatics 2023, 39 PMID: 37417959, DOI: 10.1093/bioinformatics/btad426.Peer-Reviewed Original ResearchA somatic hypermutation-based machine learning model stratifies individuals with Crohn's disease and controls.
Safra M, Werner L, Peres A, Polak P, Salamon N, Schvimer M, Weiss B, Barshack I, Shouval DS, Yaari G. A somatic hypermutation-based machine learning model stratifies individuals with Crohn's disease and controls. Genome Res 2023, 33: 71-79. PMID: 36526432, DOI: 10.1101/gr.276683.122.Peer-Reviewed Original Research
2021
Immune2vec: Embedding B/T Cell Receptor Sequences in ℝ (N) Using Natural Language Processing.
Ostrovsky-Berman M, Frankel B, Polak P, Yaari G. Immune2vec: Embedding B/T Cell Receptor Sequences in ℝ (N) Using Natural Language Processing. Front Immunol 2021, 12: 680687. PMID: 34367141, DOI: 10.3389/fimmu.2021.680687.Peer-Reviewed Original Research
2020
VDJbase: an adaptive immune receptor genotype and haplotype database.
Omer A, Shemesh O, Peres A, Polak P, Shepherd AJ, Watson CT, Boyd SD, Collins AM, Lees W, Yaari G. VDJbase: an adaptive immune receptor genotype and haplotype database. Nucleic Acids Res 2020, 48: D1051-D1056. PMID: 31602484, DOI: 10.1093/nar/gkz872.Peer-Reviewed Original Research
2019
Mosaic deletion patterns of the human antibody heavy chain gene locus shown by Bayesian haplotyping.
Gidoni M, Snir O, Peres A, Polak P, Lindeman I, Mikocziova I, Sarna VK, Lundin KEA, Clouser C, Vigneault F, Collins AM, Sollid LM, Yaari G. Mosaic deletion patterns of the human antibody heavy chain gene locus shown by Bayesian haplotyping. Nat Commun 2019, 10: 628. PMID: 30733445, DOI: 10.1038/s41467-019-08489-3.Peer-Reviewed Original Research
2015
Practical guidelines for B-cell receptor repertoire sequencing analysis
Yaari G, Kleinstein SH. Practical guidelines for B-cell receptor repertoire sequencing analysis. Genome Medicine 2015, 7: 121. PMID: 26589402, PMCID: PMC4654805, DOI: 10.1186/s13073-015-0243-2.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and Concepts
2013
Quantitative set analysis for gene expression: a method to quantify gene set differential expression including gene-gene correlations
Yaari G, Bolen CR, Thakar J, Kleinstein SH. Quantitative set analysis for gene expression: a method to quantify gene set differential expression including gene-gene correlations. Nucleic Acids Research 2013, 41: e170-e170. PMID: 23921631, PMCID: PMC3794608, DOI: 10.1093/nar/gkt660.Peer-Reviewed Original ResearchCitationsAltmetricModels of Somatic Hypermutation Targeting and Substitution Based on Synonymous Mutations from High-Throughput Immunoglobulin Sequencing Data
Yaari G, Vander Heiden J, Uduman M, Gadala-Maria D, Gupta N, Stern JN, O’Connor K, Hafler DA, Laserson U, Vigneault F, Kleinstein SH. Models of Somatic Hypermutation Targeting and Substitution Based on Synonymous Mutations from High-Throughput Immunoglobulin Sequencing Data. Frontiers In Immunology 2013, 4: 358. PMID: 24298272, PMCID: PMC3828525, DOI: 10.3389/fimmu.2013.00358.Peer-Reviewed Original ResearchCitationsAltmetricConceptsAccurate background modelSynonymous mutationsNon-coding regionsParticular codon usageNon-functional sequencesComputational analysis methodsObserved mutation patternExisting modelsBackground modelInfluence of selectionCodon usageSHM targetingBase compositionImproved modelSequencing dataNucleotide substitutionsAnalysis methodStatistical analysisFunctional sequencesMutation targetingB-cell cancersModelSomatic hypermutation patternsMutationsHypermutation patterns
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activity Immunoinformatics
2022 - PresentJournal ServiceEditor-in-Chief
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New Haven, CT 06511