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Assistant Professor
Biography
Dr. Evan Koch is a population geneticist and computational biologist with a research focus on the genetic and evolutionary basis of human traits and diseases. He earned his PhD in Ecology and Evolution at the University of Chicago in the lab of John Novembre, developing theoretical and empirical approaches to describe how mutation, selection, and drift affect genetic variation and how mutation and population history shape the distribution of complex trait variation. As a postdoctoral research fellow with Shamil Sunyaev at Harvard Medical School, he worked on a fine-scale mutation rate map for the human genome and created population genetics models and statistical methods using GWAS data to study selection. At Yale School of Medicine, his group develops quantitative methods that bridge classical population genetics with contemporary genomic and phenotypic data.
Last Updated on November 05, 2025.
Appointments
Genetics
Assistant ProfessorPrimary
Other Departments & Organizations
- Genetics
- Human Genome Sciences
- Yale Combined Program in the Biological and Biomedical Sciences (BBS)
Education & Training
- Research Associate
- Harvard Medical School (2025)
- Postdoctoral Associate
- Harvard Medical School (2023)
- PhD
- University of Chicago, Ecology and Evolution (2018)
- BS
- University of Texas at Austin, Biology (2012)
Research
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Overview
Medical Research Interests
Biological Evolution; Genetics, Population; Models, Statistical
ORCID
0000-0002-1124-4559
Research at a Glance
Publications Timeline
A big-picture view of Evan Koch's research output by year.
Research Interests
Research topics Evan Koch is interested in exploring.
16Publications
376Citations
Genetics, Population
Publications
2025
Hotspots of human mutation point to clonal expansions in spermatogonia
Seplyarskiy V, Moldovan M, Koch E, Kar P, Neville M, Rahbari R, Sunyaev S. Hotspots of human mutation point to clonal expansions in spermatogonia. Nature 2025, 647: 429-435. PMID: 41062699, PMCID: PMC12714578, DOI: 10.1038/s41586-025-09579-7.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsHuman de novo mutationsRate of de novo mutationsEffects of negative selectionExcess of mutationsLoss-of-functionClonal expansionPolymorphism levelMale germlinePositive selectionControl triosMissense mutationsSomatic tissuesPrevalence of genetic disordersMutation rateDriver candidatesPopulation variationDisease associationsGenesMutationsNegative selectionRenewing tissuesSpermatogoniaGenetic disordersHuman populationTrios
2023
A mutation rate model at the basepair resolution identifies the mutagenic effect of polymerase III transcription
Seplyarskiy V, Koch E, Lee D, Lichtman J, Luan H, Sunyaev S. A mutation rate model at the basepair resolution identifies the mutagenic effect of polymerase III transcription. Nature Genetics 2023, 55: 2235-2242. PMID: 38036792, PMCID: PMC11348951, DOI: 10.1038/s41588-023-01562-0.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsLocal mutation rateMutation rate modelMutation rateBasepair resolutionRare disease genesPolymerase III transcriptionElevated mutation ratesDe novo mutationsHuman mutation rateRestricted to sitesDemographic historyGenomic locationsIII transcriptionDisease genesPol IIISequence contextEstimates of population growthDNA strandsMutagenic mechanismsMutagenic effectsSelection intensityMutationsBasepairsTranscriptionGenesMutation rates and adaptive variation among the clinically dominant clusters of Mycobacterium abscessus
Commins N, Sullivan M, McGowen K, Koch E, Rubin E, Farhat M. Mutation rates and adaptive variation among the clinically dominant clusters of Mycobacterium abscessus. Proceedings Of The National Academy Of Sciences Of The United States Of America 2023, 120: e2302033120. PMID: 37216535, PMCID: PMC10235944, DOI: 10.1073/pnas.2302033120.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsMolecular clock rateWhole-genome sequencingPhylogenetic clusteringGenetic clustersAnalysis of whole genome sequencesCluster of clinical isolatesMutation rateLong internal branchesDNA repair machineryMultidrug-resistant pathogensPhylogenetic inferenceCoalescent analysesTransmission inferenceDNA repair genesAdaptive variationClinical isolatesFacultative pathogensRepair machineryPatient-to-patient transmissionHost environmentRate in vitroMycobacterium abscessusInternal branchesPatient isolatesRepair genesRecurrent mutation in the ancestry of a rare variant
Wakeley J, Fan W, Koch E, Sunyaev S. Recurrent mutation in the ancestry of a rare variant. Genetics 2023, 224: iyad049. PMID: 36967220, PMCID: PMC10324944, DOI: 10.1093/genetics/iyad049.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsSite-frequency spectrumRecurrent mutationsRare variantsPopulation of constant sizeModels of population geneticsNeutral coalescentPopulations of varying sizeAllele-frequencyHuman SNPsExponentially growing populationsAllele TracingHuman genomePopulation geneticsCoalescent treeMutation rateMultiple copiesEwens sampling formulaMutationsAllelesStatistical independenceAncestrySampling formulaVariantsCopySampling theory
2021
Maintenance of Complex Trait Variation: Classic Theory and Modern Data
Koch E, Sunyaev S. Maintenance of Complex Trait Variation: Classic Theory and Modern Data. Frontiers In Genetics 2021, 12: 763363. PMID: 34868244, PMCID: PMC8636146, DOI: 10.3389/fgene.2021.763363.Peer-Reviewed Original ResearchCitationsAltmetricPopulation sequencing data reveal a compendium of mutational processes in the human germ line
Seplyarskiy V, Soldatov R, Koch E, McGinty R, Goldmann J, Hernandez R, Barnes K, Correa A, Burchard E, Ellinor P, McGarvey S, Mitchell B, Vasan R, Redline S, Silverman E, Weiss S, Arnett D, Blangero J, Boerwinkle E, He J, Montgomery C, Rao D, Rotter J, Taylor K, Brody J, Chen Y, de las Fuentes L, Hwu C, Rich S, Manichaikul A, Mychaleckyj J, Palmer N, Smith J, Kardia S, Peyser P, Bielak L, O’Connor T, Emery L, Consortium‡ N, Group T, Gilissen C, Wong W, Kharchenko P, Sunyaev S. Population sequencing data reveal a compendium of mutational processes in the human germ line. Science 2021, 373: 1030-1035. PMID: 34385354, PMCID: PMC9217108, DOI: 10.1126/science.aba7408.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsPopulation sequencing dataSequence dataLong interspersed nuclear elementsHuman germline mutationsSpectrum of mutationsSequencing datasetsReplication timingActive demethylationHuman germ lineRegulatory regionsMutagenic effectsGerm lineReplication forksNuclear elementsBulky DNA lesionsMutational propertiesMutational processesBiological interpretationGermline mutationsDNA lesionsMutationsBiological mechanismsReplicationTOPMedGenomePopulation-specific causal disease effect sizes in functionally important regions impacted by selection
Shi H, Gazal S, Kanai M, Koch E, Schoech A, Siewert K, Kim S, Luo Y, Amariuta T, Huang H, Okada Y, Raychaudhuri S, Sunyaev S, Price A. Population-specific causal disease effect sizes in functionally important regions impacted by selection. Nature Communications 2021, 12: 1098. PMID: 33597505, PMCID: PMC7889654, DOI: 10.1038/s41467-021-21286-1.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsPopulation-specificGenome-wide summary statisticsPolygenic risk predictionEffect sizeGenetic correlationsGenome annotationComplex traitsRegulatory regionsGene-environment interactionsPositive selectionBrain genesImmune genesSummary statisticsGenesEast AsiansRisk predictionLociTraitsRegionAnnotationSelectionPolygenic adaptation of rosette growth in Arabidopsis thaliana
Wieters B, Steige K, He F, Koch E, Ramos-Onsins S, Gu H, Guo Y, Sunyaev S, de Meaux J. Polygenic adaptation of rosette growth in Arabidopsis thaliana. PLOS Genetics 2021, 17: e1008748. PMID: 33493157, PMCID: PMC7861555, DOI: 10.1371/journal.pgen.1008748.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsPolygenic adaptationArabidopsis thalianaRosette growthPolygenic basisGenetic variationLevels of genetic variationBurden of deleterious mutationsGenome-wide association studiesEvolution of growth rateGrowth rateMaladaptive evolutionAdaptive divergencePhenotypic divergenceSets of genotypesFunctional traitsDeleterious mutationsAssociation studiesNatural populationsGrowth plasticityPlant ecologyRosette diameterStabilizing selectionPlant sizeEcological relevancePlant growthMaintenance of Adaptive Dynamics and No Detectable Load in a Range-Edge Outcrossing Plant Population
Takou M, Hämälä T, Koch E, Steige K, Dittberner H, Yant L, Genete M, Sunyaev S, Castric V, Vekemans X, Savolainen O, de Meaux J. Maintenance of Adaptive Dynamics and No Detectable Load in a Range-Edge Outcrossing Plant Population. Molecular Biology And Evolution 2021, 38: 1820-1836. PMID: 33480994, PMCID: PMC8097302, DOI: 10.1093/molbev/msaa322.Peer-Reviewed Original ResearchCitationsAltmetricMeSH Keywords and ConceptsConceptsRange-edge populationsDemographic historyNonsynonymous variantsDeleterious mutationsGenomic burdenModel of allele frequenciesRemoval of deleterious mutationsEffects of range expansionFitness effects of mutationsNegative frequency-dependent selectionBurden of deleterious mutationsFitness effectsA. lyrata sspEffective population sizeArabidopsis lyrata sspSelf-incompatibility locusFrequency-dependent selectionEffects of mutationsAdaptive dynamicsEdge populationsGenetic driftAllelic diversityGenomic footprintingDeleterious variantsGarden experiment
2019
De Novo Mutation Rate Estimation in Wolves of Known Pedigree
Koch E, Schweizer R, Schweizer T, Stahler D, Smith D, Wayne R, Novembre J. De Novo Mutation Rate Estimation in Wolves of Known Pedigree. Molecular Biology And Evolution 2019, 36: 2536-2547. PMID: 31297530, PMCID: PMC6805234, DOI: 10.1093/molbev/msz159.Peer-Reviewed Original ResearchCitationsAltmetricConceptsMutation rate estimatesDemographic historyDe novo mutationsMutation rateAncestral populationsKnowledge of mutation ratesSanger sequencingNuclear mutation rateWhole-genome sequencingPopulation genetic modelsMutation rate evolutionSequencing of parentsSanger sequencing of parentsDivergence timesAncient DNAEurasian wolvesStringent filtersCoalescence modelGenetic modelsMutationsPedigreeWolvesGenomeRate estimatesSanger
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