Publications

Ma Z, Starr AL, Gokhman D, and Fraser HB (2026)
The causes and consequences of human-specific DNA methylation
doi: 10.64898/2026.01.20.700710 . bioRxiv : The Preprint Server for Biology
Starr AL, Palmer ME, Gao J, Nichols CG, and Fraser HB (2025)
A framework to detect positive selection using variant effect predictions reveals widespread adaptive evolution of human neurons
doi: 10.1101/2025.09.11.675696 . bioRxiv : The Preprint Server for Biology
Starr AL, Palmer ME, and Fraser HB (2025)
In silico genome transplants and the cis-regulatory basis of biodiversity.
doi: 10.1016/j.tig.2025.10.012 . Trends in Genetics
Starr AL, and Fraser HB (2025)
A General Principle of Neuronal Evolution Reveals a Human-Accelerated Neuron Type Potentially Underlying the High Prevalence of Autism in Humans.
doi: 10.1093/molbev/msaf189 . Molecular Biology and Evolution , 42 (9)
Starr AL, Nishimura T, Igarashi KJ, Funamoto C, Nakauchi H, and Fraser HB (2025)
Disentangling cell-intrinsic and cell-extrinsic factors underlying evolution.
doi: 10.1016/j.xgen.2025.100891 . Cell Genomics , 5 (8) : 100891
Aguilar-Rodriguez J, Vila JCC, Chen SA, Razo-Mejia M, Ghosh OM, Jarosz DF, Fraser HB, and Petrov DA (2025)
Massively parallel interrogation of the fitness of natural variants in ancient signaling pathways reveals pervasive local adaptation.
doi: 10.1101/2024.10.30.621178 . bioRxiv : The Preprint Server for Biology
Wang B, Starr AL, and Fraser HB (2024)
Cell-type-specific cis-regulatory divergence in gene expression and chromatin accessibility revealed by human-chimpanzee hybrid cells.
doi: 10.7554/eLife.89594 . eLife , 12
Pettie KP, Mumbach M, Lea AJ, Ayroles J, Chang HY, Kasowski M, and Fraser HB (2024)
Chromatin activity identifies differential gene regulation across human ancestries.
doi: 10.1186/s13059-024-03165-2 . Genome Biology , 25 (1) : 21
Mack KL, Talbott HE, Griffin MF, Parker JBL, Guardino NJ, Spielman AF, Davitt MF, Mascharak S, Downer M, Morgan A, Valencia C, Akras D, Berger MJ, Wan DC, Fraser HB, and Longaker MT (2023)
Allele-specific expression reveals genetic drivers of tissue regeneration in mice.
doi: 10.1016/j.stem.2023.08.010 . Cell Stem Cell , 30 (10) : 1368-1381.e6
Chen SA, Kern AF, Ang RML, Xie Y, and Fraser HB (2023)
Gene-by-environment interactions are pervasive among natural genetic variants.
doi: 10.1016/j.xgen.2023.100273 . Cell Genomics , 3 (4) : 100273
Ang RML, Chen SA, Kern AF, Xie Y, and Fraser HB (2023)
Widespread epistasis among beneficial genetic variants revealed by high-throughput genome editing.
doi: 10.1016/j.xgen.2023.100260 . Cell Genomics , 3 (4) : 100260
Mack KL, Square TA, Zhao B, Miller CT, and Fraser HB (2023)
Evolution of Spatial and Temporal cis-Regulatory Divergence in Sticklebacks.
doi: 10.1093/molbev/msad034 . Molecular Biology and Evolution , 40 (3)
Starr AL, Gokhman D, and Fraser HB (2023)
Accounting for cis-regulatory constraint prioritizes genes likely to affect species-specific traits.
doi: 10.1186/s13059-023-02846-8 . Genome Biology , 24 (1) : 11
Fraser HB (2022)
Existing methods are effective at measuring natural selection on gene expression.
doi: 10.1038/s41559-022-01889-7 . Nature Ecology & Evolution , 6 (12) : 1836-1837
García-Nieto PE, Wang B, and Fraser HB (2022)
Transcriptome diversity is a systematic source of variation in RNA-sequencing data.
doi: 10.1371/journal.pcbi.1009939 . PLoS Computational Biology , 18 (3) : e1009939
Hu CK, York RA, Metz HC, Bedford NL, Fraser HB, and Hoekstra HE (2022)
cis-Regulatory changes in locomotor genes are associated with the evolution of burrowing behavior.
doi: 10.1016/j.celrep.2022.110360 . Cell Reports , 38 (7) : 110360
Zhao B, Chen SA, Lee J, and Fraser HB (2022)
Bacterial Retrons Enable Precise Gene Editing in Human Cells.
doi: 10.1089/crispr.2021.0065 . The CRISPR Journal , 5 (1) : 31-39
Kern AF, Yang GX, Khosla NM, Ang RML, Snyder MP, and Fraser HB (2021)
Divergent patterns of selection on metabolite levels and gene expression.
doi: 10.1186/s12862-021-01915-5 . BMC Ecology and Evolution , 21 (1) : 185
Nivina A, Herrera Paredes S, Fraser HB, and Khosla C (2021)
GRINS: Genetic elements that recode assembly-line polyketide synthases and accelerate their diversification.
doi: 10.1073/pnas.2100751118 . PNAS , 118 (26)
Weiss CV, Harshman L, Inoue F, Fraser HB, Petrov DA, Ahituv N, and Gokhman D (2021)
The cis-regulatory effects of modern human-specific variants.
doi: 10.7554/eLife.63713 . eLife , 10
Gokhman D, Agoglia RM, Kinnebrew M, Gordon W, Sun D, Bajpai VK, Naqvi S, Chen C, Chan A, Chen C, Petrov DA, Ahituv N, Zhang H, Mishina Y, Wysocka J, Rohatgi R, and Fraser HB (2021)
Human-chimpanzee fused cells reveal cis-regulatory divergence underlying skeletal evolution.
doi: 10.1038/s41588-021-00804-3 . Nature Genetics , 53 (4) : 467-476
Agoglia RM, Sun D, Birey F, Yoon SJ, Miura Y, Sabatini K, Pașca SP, and Fraser HB (2021)
Primate cell fusion disentangles gene regulatory divergence in neurodevelopment.
doi: 10.1038/s41586-021-03343-3 . Nature , 592 (7854) : 421-427
Singh-Babak SD, Babak T, Fraser HB, and Johnson AD (2021)
Lineage-specific selection and the evolution of virulence in the Candida clade.
doi: 10.1073/pnas.2016818118 . PNAS , 118 (12)
Fraser HB (2021)
Reply to Zhang and Xu: Environment is indeed important in any phenotypic study.
doi: 10.1073/pnas.2022917118 . PNAS , 118 (9)
Fraser HB (2020)
Detecting selection with a genetic cross.
doi: 10.1073/pnas.2014277117 . PNAS , 117 (36) : 22323-22330
Zhao Q, Dacre M, Nguyen T, Pjanic M, Liu B, Iyer D, Cheng P, Wirka R, Kim JB, Fraser HB, and Quertermous T (2020)
Molecular mechanisms of coronary disease revealed using quantitative trait loci for TCF21 binding, chromatin accessibility, and chromosomal looping.
doi: 10.1186/s13059-020-02049-5 . Genome Biology , 21 (1) : 135
García-Nieto PE, Morrison AJ, and Fraser HB (2019)
The somatic mutation landscape of the human body.
doi: 10.1186/s13059-019-1919-5 . Genome Biology , 20 (1) : 298
Tehranchi A, Hie B, Dacre M, Kaplow I, Pettie K, Combs P, and Fraser HB (2019)
Fine-mapping cis-regulatory variants in diverse human populations.
doi: 10.7554/eLife.39595 . eLife , 8
Combs PA, Krupp JJ, Khosla NM, Bua D, Petrov DA, Levine JD, and Fraser HB (2018)
Tissue-Specific cis-Regulatory Divergence Implicates eloF in Inhibiting Interspecies Mating in Drosophila.
doi: 10.1016/j.cub.2018.10.036 . Current Biology : CB , 28 (24) : 3969-3975.e3
Martin T, and Fraser HB (2018)
Comparative expression profiling reveals widespread coordinated evolution of gene expression across eukaryotes.
doi: 10.1038/s41467-018-07436-y . Nature Communications , 9 (1) : 4963
York RA, Patil C, Abdilleh K, Johnson ZV, Conte MA, Genner MJ, McGrath PT, Fraser HB, Fernald RD, and Streelman JT (2018)
Behavior-dependent cis regulation reveals genes and pathways associated with bower building in cichlid fishes.
doi: 10.1073/pnas.1810140115 . PNAS , 115 (47) : E11081-E11090
Combs PA, and Fraser HB (2018)
Spatially varying cis-regulatory divergence in Drosophila embryos elucidates cis-regulatory logic.
doi: 10.1371/journal.pgen.1007631 . PLoS Genetics , 14 (11) : e1007631
Fraser HB (2018)
Improving Estimates of Compensatory cis-trans Regulatory Divergence.
doi: 10.1016/j.tig.2018.09.003 . Trends in Genetics , 35 (1) : 3-5
Sharon E, Chen SA, Khosla NM, Smith JD, Pritchard JK, and Fraser HB (2018)
Functional Genetic Variants Revealed by Massively Parallel Precise Genome Editing.
doi: 10.1016/j.cell.2018.08.057 . Cell , 175 (2) : 544-557.e16
Carja O, MacIsaac JL, Mah SM, Henn BM, Kobor MS, Feldman MW, and Fraser HB (2017)
Worldwide patterns of human epigenetic variation.
doi: 10.1038/s41559-017-0299-z . Nature Ecology & Evolution , 1 (10) : 1577-1583
Kita R, Venkataram S, Zhou Y, and Fraser HB (2017)
High-resolution mapping of cis-regulatory variation in budding yeast.
doi: 10.1073/pnas.1717421114 . PNAS , 114 (50) : E10736-E10744
Artieri CG, Naor A, Turgeman-Grott I, Zhou Y, York R, Gophna U, and Fraser HB (2017)
Cis-regulatory evolution in prokaryotes revealed by interspecific archaeal hybrids.
doi: 10.1038/s41598-017-04278-4 . Scientific Reports , 7 (1) : 3986
Kita R, and Fraser HB (2016)
Local Adaptation of Sun-Exposure-Dependent Gene Expression Regulation in Human Skin.
doi: 10.1371/journal.pgen.1006382 . PLoS Genetics , 12 (10) : e1006382
Sharon E, Sibener LV, Battle A, Fraser HB, Garcia KC, and Pritchard JK (2016)
Genetic variation in MHC proteins is associated with T cell receptor expression biases.
doi: 10.1038/ng.3625 . Nature Genetics , 48 (9) : 995-1002
Tehranchi AK, Myrthil M, Martin T, Hie BL, Golan D, and Fraser HB (2016)
Pooled ChIP-Seq Links Variation in Transcription Factor Binding to Complex Disease Risk.
doi: 10.1016/j.cell.2016.03.041 . Cell , 165 (3) : 730-41
Naranjo S, Smith JD, Artieri CG, Zhang M, Zhou Y, Palmer ME, and Fraser HB (2015)
Dissecting the Genetic Basis of a Complex cis-Regulatory Adaptation.
doi: 10.1371/journal.pgen.1005751 . PLoS Genetics , 11 (12) : e1005751
Agoglia RM, and Fraser HB (2015)
Disentangling Sources of Selection on Exonic Transcriptional Enhancers.
doi: 10.1093/molbev/msv234 . Molecular Biology and Evolution , 33 (2) : 585-90
Kaplow IM, MacIsaac JL, Mah SM, McEwen LM, Kobor MS, and Fraser HB (2015)
A pooling-based approach to mapping genetic variants associated with DNA methylation.
doi: 10.1101/gr.183749.114 . Genome Research , 25 (6) : 907-17
McCoy RC, Demko Z, Ryan A, Banjevic M, Hill M, Sigurjonsson S, Rabinowitz M, Fraser HB, and Petrov DA (2015)
Common variants spanning PLK4 are associated with mitotic-origin aneuploidy in human embryos.
doi: 10.1126/science.aaa3337 . Science , 348 (6231) : 235-8
Babak T, DeVeale B, Tsang EK, Zhou Y, Li X, Smith KS, Kukurba KR, Zhang R, Li JB, van der Kooy D, Montgomery SB, and Fraser HB (2015)
Genetic conflict reflected in tissue-specific maps of genomic imprinting in human and mouse.
doi: 10.1038/ng.3274 . Nature Genetics , 47 (5) : 544-9
Jiang R, Jones MJ, Chen E, Neumann SM, Fraser HB, Miller GE, and Kobor MS (2015)
Discordance of DNA methylation variance between two accessible human tissues.
doi: 10.1038/srep08257 . Scientific Reports , 5 : 8257
Artieri CG, and Fraser HB (2014)
Accounting for biases in riboprofiling data indicates a major role for proline in stalling translation.
doi: 10.1101/gr.175893.114 . Genome Research , 24 (12) : 2011-21
Artieri CG, and Fraser HB (2014)
Transcript length mediates developmental timing of gene expression across Drosophila.
doi: 10.1093/molbev/msu226 . Molecular Biology and Evolution , 31 (11) : 2879-89
Artieri CG, and Fraser HB (2013)
Evolution at two levels of gene expression in yeast.
doi: 10.1101/gr.165522.113 . Genome Research , 24 (3) : 411-21
Fraser HB (2013)
Cell-cycle regulated transcription associates with DNA replication timing in yeast and human.
doi: 10.1186/gb-2013-14-10-r111 . Genome Biology , 14 (10) : R111
Chang J, Zhou Y, Hu X, Lam L, Henry C, Green EM, Kita R, Kobor MS, and Fraser HB (2013)
The molecular mechanism of a cis-regulatory adaptation in yeast.
doi: 10.1371/journal.pgen.1003813 . PLoS Genetics , 9 (9) : e1003813
Smith JD, McManus KF, and Fraser HB (2013)
A novel test for selection on cis-regulatory elements reveals positive and negative selection acting on mammalian transcriptional enhancers.
doi: 10.1093/molbev/mst134 . Molecular Biology and Evolution , 30 (11) : 2509-18
Irimia M, Maeso I, Roy SW, and Fraser HB (2013)
Ancient cis-regulatory constraints and the evolution of genome architecture.
doi: 10.1016/j.tig.2013.05.008 . Trends in Genetics , 29 (9) : 521-8
Lam LL, Emberly E, Fraser HB, Neumann SM, Chen E, Miller GE, and Kobor MS (2013)
Reply to Suderman et al.: Importance of accounting for blood cell composition in epigenetic studies.
doi: 10.1073/pnas.1222104110 . PNAS , 110 (14) : E1247
Fraser HB (2013)
Gene expression drives local adaptation in humans.
doi: 10.1101/gr.152710.112 . Genome Research , 23 (7) : 1089-96
Ariza-Cosano A, Visel A, Pennacchio LA, Fraser HB, Gómez-Skarmeta JL, Irimia M, and Bessa J (2012)
Differences in enhancer activity in mouse and zebrafish reporter assays are often associated with changes in gene expression.
doi: 10.1186/1471-2164-13-713 . BMC Genomics , 13 : 713
Lam LL, Emberly E, Fraser HB, Neumann SM, Chen E, Miller GE, and Kobor MS (2012)
Factors underlying variable DNA methylation in a human community cohort.
doi: 10.1073/pnas.1121249109 . PNAS , 109 Suppl 2 (Suppl 2) : 17253-60
Irimia M, Tena JJ, Alexis MS, Fernandez-Miñan A, Maeso I, Bogdanovic O, de la Calle-Mustienes E, Roy SW, Gómez-Skarmeta JL, and Fraser HB (2012)
Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints.
doi: 10.1101/gr.139725.112 . Genome Research , 22 (12) : 2356-67
Fraser HB, Levy S, Chavan A, Shah HB, Perez JC, Zhou Y, Siegal ML, and Sinha H (2012)
Polygenic cis-regulatory adaptation in the evolution of yeast pathogenicity.
doi: 10.1101/gr.134080.111 . Genome Research , 22 (10) : 1930-9
Fraser HB, Lam LL, Neumann SM, and Kobor MS (2012)
Population-specificity of human DNA methylation.
doi: 10.1186/gb-2012-13-2-r8 . Genome Biology , 13 (2) : R8
Lamb JR, Zhang C, Xie T, Wang K, Zhang B, Hao K, Chudin E, Fraser HB, Millstein J, Ferguson M, Suver C, Ivanovska I, Scott M, Philippar U, Bansal D, Zhang Z, Burchard J, Smith R, Greenawalt D, Cleary M, Derry J, Loboda A, Watters J, Poon RT, Fan ST, Yeung C, Lee NP, Guinney J, Molony C, Emilsson V, Buser-Doepner C, Zhu J, Friend S, Mao M, Shaw PM, Dai H, Luk JM, and Schadt EE (2011)
Predictive genes in adjacent normal tissue are preferentially altered by sCNV during tumorigenesis in liver cancer and may rate limiting.
doi: 10.1371/journal.pone.0020090 . PloS One , 6 (7) : e20090
Fraser HB (2011)
Genome-wide approaches to the study of adaptive gene expression evolution: systematic studies of evolutionary adaptations involving gene expression will allow many fundamental questions in evolutionary biology to be addressed.
doi: 10.1002/bies.201000094 . BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology , 33 (6) : 469-77
Fraser HB, Babak T, Tsang J, Zhou Y, Zhang B, Mehrabian M, and Schadt EE (2011)
Systematic detection of polygenic cis-regulatory evolution.
doi: 10.1371/journal.pgen.1002023 . PLoS Genetics , 7 (3) : e1002023
Babak T, Garrett-Engele P, Armour CD, Raymond CK, Keller MP, Chen R, Rohl CA, Johnson JM, Attie AD, Fraser HB, and Schadt EE (2010)
Genetic validation of whole-transcriptome sequencing for mapping expression affected by cis-regulatory variation.
doi: 10.1186/1471-2164-11-473 . BMC Genomics , 11 : 473
Fraser HB, Moses AM, and Schadt EE (2010)
Evidence for widespread adaptive evolution of gene expression in budding yeast.
doi: 10.1073/pnas.0912245107 . PNAS , 107 (7) : 2977-82
Fraser HB, and Schadt EE (2010)
The quantitative genetics of phenotypic robustness.
doi: 10.1371/journal.pone.0008635 . PloS One , 5 (1) : e8635
Yassour M, Kaplan T, Fraser HB, Levin JZ, Pfiffner J, Adiconis X, Schroth G, Luo S, Khrebtukova I, Gnirke A, Nusbaum C, Thompson DA, Friedman N, and Regev A (2009)
Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing.
doi: 10.1073/pnas.0812841106 . PNAS , 106 (9) : 3264-9
Fraser HB, and Xie X (2009)
Common polymorphic transcript variation in human disease.
doi: 10.1101/gr.083477.108 . Genome Research , 19 (4) : 567-75
Fraser HB, and Plotkin JB (2007)
Using protein complexes to predict phenotypic effects of gene mutation.
doi: 10.1186/gb-2007-8-11-r252 . Genome Biology , 8 (11) : R252
Bertin N, Simonis N, Dupuy D, Cusick ME, Han JD, Fraser HB, Roth FP, and Vidal M (2007)
Confirmation of organized modularity in the yeast interactome.
doi: 10.1371/journal.pbio.0050153 . PLoS Biology , 5 (6) : e153
Plotkin JB, and Fraser HB (2007)
Assessing the determinants of evolutionary rates in the presence of noise.
doi: 10.1093/molbev/msm044 . Molecular Biology and Evolution , 24 (5) : 1113-21
Plotkin JB, Dushoff J, Desai MM, and Fraser HB (2006)
Codon usage and selection on proteins.
doi: 10.1007/s00239-005-0233-x . Journal of Molecular Evolution , 63 (5) : 635-53
Fraser HB (2006)
Coevolution, modularity and human disease.
doi: 10.1016/j.gde.2006.09.001 . Current Opinion in Genetics & Development , 16 (6) : 637-44
Plotkin JB, Dushoff J, Desai MM, and Fraser HB (2006)
Estimating selection pressures from limited comparative data.
doi: 10.1093/molbev/msl021 . Molecular Biology and Evolution , 23 (8) : 1457-9
Fraser HB, Khaitovich P, Plotkin JB, Pääbo S, and Eisen MB (2005)
Aging and gene expression in the primate brain.
doi: 10.1371/journal.pbio.0030274 . PLoS Biology , 3 (9) : e274
Lynch PJ, Fraser HB, Sevastopoulos E, Rine J, and Rusche LN (2005)
Sum1p, the origin recognition complex, and the spreading of a promoter-specific repressor in Saccharomyces cerevisiae.
doi: 10.1128/MCB.25.14.5920-5932.2005 . Molecular and Cellular Biology , 25 (14) : 5920-32
Wall DP, Hirsh AE, Fraser HB, Kumm J, Giaever G, Eisen MB, and Feldman MW (2005)
Functional genomic analysis of the rates of protein evolution.
doi: 10.1073/pnas.0501761102 . PNAS , 102 (15) : 5483-8
Fraser HB (2005)
Modularity and evolutionary constraint on proteins.
doi: 10.1038/ng1530 . Nature Genetics , 37 (4) : 351-2
Wall DP, Fraser HB, and Hirsh AE (2003)
Detecting putative orthologs.
doi: 10.1093/bioinformatics/btg213 . Bioinformatics , 19 (13) : 1710-1
Gasch AP, Moses AM, Chiang DY, Fraser HB, Berardini M, and Eisen MB (2004)
Conservation and evolution of cis-regulatory systems in ascomycete fungi.
doi: 10.1371/journal.pbio.0020398 . PLoS Biology , 2 (12) : e398
Hirsh AE, Fraser HB, and Wall DP (2004)
Adjusting for selection on synonymous sites in estimates of evolutionary distance.
doi: 10.1093/molbev/msh265 . Molecular Biology and Evolution , 22 (1) : 174-7
Fraser HB, Hirsh AE, Wall DP, and Eisen MB (2004)
Coevolution of gene expression among interacting proteins.
doi: 10.1073/pnas.0402591101 . PNAS , 101 (24) : 9033-8
Fraser HB, and Hirsh AE (2004)
Evolutionary rate depends on number of protein-protein interactions independently of gene expression level.
doi: 10.1186/1471-2148-4-13 . BMC Evolutionary Biology , 4 : 13
Fraser HB, Hirsh AE, Giaever G, Kumm J, and Eisen MB (2004)
Noise minimization in eukaryotic gene expression.
doi: 10.1371/journal.pbio.0020137 . PLoS Biology , 2 (6) : e137
Plotkin JB, Dushoff J, and Fraser HB (2004)
Detecting selection using a single genome sequence of M. tuberculosis and P. falciparum.
doi: 10.1038/nature02458 . Nature , 428 (6986) : 942-5
Fraser HB, Wall DP, and Hirsh AE (2003)
A simple dependence between protein evolution rate and the number of protein-protein interactions.
doi: 10.1186/1471-2148-3-11 . BMC Evolutionary Biology , 3 : 11
Fraser HB, Hirsh AE, Steinmetz LM, Scharfe C, and Feldman MW (2002)
Evolutionary rate in the protein interaction network.
doi: 10.1126/science.1068696 . Science , 296 (5568) : 750-2
Weitz JS, and Fraser HB (2001)
Explaining mortality rate plateaus.
doi: 10.1073/pnas.261228098 . PNAS , 98 (26) : 15383-6
Snapper SB, Takeshima F, Antón I, Liu CH, Thomas SM, Nguyen D, Dudley D, Fraser H, Purich D, Lopez-Ilasaca M, Klein C, Davidson L, Bronson R, Mulligan RC, Southwick F, Geha R, Goldberg MB, Rosen FS, Hartwig JH, and Alt FW (2001)
N-WASP deficiency reveals distinct pathways for cell surface projections and microbial actin-based motility.
doi: 10.1038/ncb1001-897 . Nature Cell Biology , 3 (10) : 897-904
Hirsh AE, and Fraser HB (2001)
Protein dispensability and rate of evolution.
doi: 10.1038/35082561 . Nature , 411 (6841) : 1046-9

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To view our full list of publications on PubMed, please visit: Fraser Lab Publications.