PLOS Genetics

2005 - 2025

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Volume 21, issue 11, 2025

Modeling the length distribution of gene conversion tracts in humans from the UK Biobank sequence data pp. 1-21

Nobuaki Masaki and Sharon R Browning

Volume 21, issue 10, 2025

Genome-wide analysis identifies susceptibility loci for heart failure and nonischemic cardiomyopathy subtype in the East Asian populations pp. 1-26

Yi Han, Yun Hong, Yan Gao, Jiapeng Lu, Bowang Chen, Lihua Zhang, Xiaofang Yan, Ying Sun, Liping Zhang, Jiangling Liu, Hao Dai, Libo Hou, Xi Li and Jing Li

Modelling transcription with explainable AI uncovers context-specific epigenetic gene regulation at promoters and gene bodies pp. 1-22

Kashyap Chhatbar, Adrian Bird and Guido Sanguinetti

Volume 21, issue 9, 2025

Conservation of heat stress acclimation by the IPK2-type kinases that control the synthesis of the inositol pyrophosphate 4/6-InsP7 in land plants pp. 1-35

Ranjana Yadav, Guizhen Liu, Priyanshi Rana, Naga Jyothi Pullagurla, Danye Qiu, Henning J Jessen and Debabrata Laha

Genome-wide association study provides novel insight into the genetic architecture of severe obesity pp. 1-27

Mohanraj Krishnan, Mohammad Yaser Anwar, Anne E Justice, Geetha Chittoor, Hung-Hsin Chen, Rashedeh Roshani, Alyssa Scartozzi, Rachel R Dickerson, Roelof A J Smit, Michael H Preuss, Nathalie Chami, Benjamin S Hadad, Esteban J Parra, Miguel Cruz, Qin Hui, Peter W F Wilson, Yan V Sun, Xiaoyu Zhang, Gregorio V Linchangco, Sharon L R Kardia, Jessica D Faul, David R Weir, Lawrence F Bielak, Heather M Highland, Kristin L Young, Baiyu Qi, Yujie Wang, Myriam Fornage, Christopher Haiman, Iona Cheng, Ulrike Peters, Charles Kooperberg, Steven Buyske, Joseph B McCormick, Susan P Fisher-Hoch, Frida Lona-Durazo, Jesus Peralta, Jamie Gomez-Zamudio, Stephen S Rich, Kendra R Ferrier, Ethan M Lange, Christopher R Gignoux, Eimear E Kenny, Genevieve L Wojcik, Kelly Cho, Michael J Gaziano, Luc Djousse, Shuwei Liu, Dhananjay Vaidya, Renée de Mutsert, Navya S Josyula, Christopher R Bauer, Wei Zhao, Ryan W Walker, Jennifer A Smith, Leslie A Lange, Mariah C Meyer, Ching-Ti Liu, Lisa R Yanek, Miryoung Lee, Laura M Raffield, Ruth J F Loos, Penny Gordon-Larsen, Jennifer E Below, Kari E North and Mariaelisa Graff

Variants in CALD1, ESRP1, and RBFOX1 are associated with orofacial cleft risk pp. 1-21

Jenna C Carlson, Xinyi Zhang, Zeynep Erdogan-Yildirim, Terri H Beaty, Azeez Butali, Carmen J Buxó, Lord JJ Gowans, Jacqueline T Hecht, Ross E Long, Lina Moreno, Jeffrey C Murray, Ieda M Orioli, Carmencita Padilla, George L Wehby, Eleanor Feingold, Elizabeth J Leslie-Clarkson, Seth M Weinberg, Mary L Marazita and John R Shaffer

Ripply3 overdosage induces mid-face shortening through Tbx1 downregulation in Down syndrome models pp. 1-23

José Tomás Ahumada Saavedra, Claire Chevalier, Agnes Bloch Zupan and Yann Herault

Volume 21, issue 8, 2025

Detecting latent interaction effects when analyzing binary traits pp. 1-17

Ziang Zhang, Jerald F Lawless, Andrew D Paterson and Lei Sun

Gene dosage and protein valency impact phase separation and fungal cell fate pp. 1-33

Collin Ganser, Peiling He, Corey Frazer, Damian J Krysan and Richard J Bennett

Understanding the alcohol harm paradox: A multivariable mendelian randomization approach pp. 1-15

Gemma Sawyer, Hannah Sallis, Marcus Munafò, Liam Mahedy and Jasmine Khouja

Volume 21, issue 7, 2025

Genomic organization, domain assortments, and nucleotide-binding domain diversity of NLR proteins in Sordariales fungi pp. 1-28

Lucas Bonometti, Florian Charriat, Noah Hensen, Silvia Miñana-Posada, Hanna Johannesson and Pierre Gladieux

Systematically identification of survival-associated eQTLs in a Japanese kidney cancer cohort pp. 1-28

Xiya Song, Han Jin, Xiangyu Li, Meng Yuan, Hong Yang, Yusuke Sato, Haruki Kume, Seishi Ogawa, Cheng Zhang and Adil Mardinoglu

Expectations for papers performing Mendelian randomization analyses pp. 1-4

Scott M Williams, Hua Tang, Gregory M Cooper, Anne O’Donnell-Luria, Santhosh Girirajan, Aimée M Dudley, Anne Goriely, Zoltán Kutalik, Xiaofeng Zhu, Giorgio Sirugo and Michael P Epstein

A novel expectation-maximization approach to infer general diploid selection from time-series genetic data pp. 1-38

Adam G Fine and Matthias Steinrücken

Genetic and environmental influences on the distributions of three chromosomal drive haplotypes in maize pp. 1-19

Meghan J Brady and R Kelly Dawe

Volume 21, issue 6, 2025

Environmental data provide marginal benefit for predicting climate adaptation pp. 1-31

Forrest Li, Daniel J Gates, Edward S Buckler, Matthew B Hufford, Garrett M Janzen, Rubén Rellán-Álvarez, Fausto Rodríguez-Zapata, J Alberto Romero Navarro, Ruairidh J H Sawers, Samantha J Snodgrass, Kai Sonder, Martha C Willcox, Sarah J Hearne, Jeffrey Ross-Ibarra and Daniel E Runcie

Defining the high-translational readthrough stop codon context pp. 1-17

Daniela Smoljanow, Dennis Lebeda, Julia Hofhuis and Sven Thoms

Volume 21, issue 5, 2025

New composite phenotypes enhance chronic kidney disease classification and genetic associations pp. 1-15

Kim Ngan Tran, Heidi G Sutherland, Andrew J Mallett, Lyn R Griffiths and Rodney A Lea

Volume 21, issue 4, 2025

Probabilistic classification of gene-by-treatment interactions on molecular count phenotypes pp. 1-33

Yuriko Harigaya, Nana Matoba, Brandon D Le, Jordan M Valone, Jason L Stein, Michael I Love and William Valdar

Probing the limits of cis-acting gene regulation using a model of allelic imbalance quantitative trait loci pp. 1-19

Cathal Seoighe, Seán Connaire and Mehak Chopra

Volume 21, issue 3, 2025

Haplotype-based analysis distinguishes maternal-fetal genetic contribution to pregnancy-related outcomes pp. 1-33

Amit K Srivastava, Julius Juodakis, Pol Sole-Navais, Jing Chen, Jonas Bacelis, Kari Teramo, Mikko Hallman, Pal R Njølstad, David M Evans, Bo Jacobsson, Louis J Muglia and Ge Zhang

RatXcan: A framework for cross-species integration of genome-wide association and gene expression data pp. 1-18

Natasha Santhanam, Sandra Sanchez-Roige, Sabrina Mi, Yanyu Liang, Apurva S Chitre, Daniel Munro, Denghui Chen, Jianjun Gao, Angel Garcia-Martinez, Anthony M George, Alexander F Gileta, Wenyan Han, Katie Holl, Alesa Hughson, Christopher P King, Alexander C Lamparelli, Connor D Martin, Festus Nyasimi, Celine L St. Pierre, Sarah Sumner, Jordan Tripi, Tengfei Wang, Hao Chen, Shelly Flagel, Keita Ishiwari, Paul Meyer, Oksana Polesskaya, Laura Saba, Leah C Solberg Woods, Abraham A Palmer and Hae Kyung Im

Local genetic covariance analysis with lipid traits identifies novel loci for early-onset Alzheimer’s Disease pp. 1-16

Nicholas R Ray, Joseph Bradley, Elanur Yilmaz, Caghan Kizil, Jiji T Kurup, Eden R Martin, Hans-Ulrich Klein, Brian W Kunkle, David A Bennett, Philip L De Jager, Alzheimer’s Disease Genetics Consortium, Gary W Beecham, Carlos Cruchaga and Christiane Reitz

Volume 21, issue 2, 2025

Two transmembrane transcriptional regulators coordinate to activate chitin-induced natural transformation in Vibrio cholerae pp. 1-20

Allison C Hullinger, Virginia E Green, Catherine A Klancher, Triana N Dalia and Ankur B Dalia

Volume 21, issue 1, 2025

Estimating evolutionary and demographic parameters via ARG-derived IBD pp. 1-16

Zhendong Huang, Jerome Kelleher, Yao-ban Chan and David Balding

metaGE: Investigating genotype x environment interactions through GWAS meta-analysis pp. 1-26

Annaïg De Walsche, Alexis Vergne, Renaud Rincent, Fabrice Roux, Stéphane Nicolas, Claude Welcker, Sofiane Mezmouk, Alain Charcosset and Tristan Mary-Huard

ADELLE: A global testing method for trans-eQTL mapping pp. 1-22

Takintayo Akinbiyi, Mary Sara McPeek and Mark Abney

Refining fine-mapping: Effect sizes and regional heritability pp. 1-21

Christian Benner, Anubha Mahajan and Matti Pirinen

Volume 20, issue 12, 2024

Disentangling the consequences of type 2 diabetes on targeted metabolite profiles using causal inference and interaction QTL analyses pp. 1-20

Ozvan Bocher, Archit Singh, Yue Huang, Urmo Võsa, Ene Reimann, Ana Arruda, Andrei Barysenska, Anastassia Kolde, Nigel W Rayner, Estonian Biobank research Team, Tõnu Esko, Reedik Mägi and Eleftheria Zeggini

Adjusting for principal components can induce collider bias in genome-wide association studies pp. 1-29

Kelsey E Grinde, Brian L Browning, Alexander P Reiner, Timothy A Thornton and Sharon R Browning

FABIO: TWAS fine-mapping to prioritize causal genes for binary traits pp. 1-26

Haihan Zhang, Kevin He, Zheng Li, Lam C Tsoi and Xiang Zhou

Integrin adhesome axis inhibits the RPM-1 ubiquitin ligase signaling hub to regulate growth cone and axon development pp. 1-30

Jonathan Amezquita, Muriel Desbois, Karla J Opperman, Joseph S Pak, Elyse L Christensen, Nikki T Nguyen, Karen Diaz-Garcia, Melissa A Borgen and Brock Grill

Volume 20, issue 11, 2024

Prediction of causal genes at GWAS loci with pleiotropic gene regulatory effects using sets of correlated instrumental variables pp. 1-29

Mariyam Khan, Adriaan-Alexander Ludl, Sean Bankier, Johan L M Björkegren and Tom Michoel

A novel statistical framework for meta-analysis of total mediation effect with high-dimensional omics mediators in large-scale genomic consortia pp. 1-23

Zhichao Xu and Peng Wei

Volume 20, issue 10, 2024

STAREG: Statistical replicability analysis of high throughput experiments with applications to spatial transcriptomic studies pp. 1-19

Yan Li, Xiang Zhou, Rui Chen, Xianyang Zhang and Hongyuan Cao

Dual role for Headcase in hemocyte progenitor fate determination in Drosophila melanogaster pp. 1-25

Bayan Kharrat, Erika Gábor, Nikolett Virág, Rita Sinka, Ferenc Jankovics, Ildikó Kristó, Péter Vilmos, Gábor Csordás and Viktor Honti

Volume 20, issue 9, 2024

Constraining models of dominance for nonsynonymous mutations in the human genome pp. 1-25

Christopher C Kyriazis and Kirk E Lohmueller

MR-SPLIT: A novel method to address selection and weak instrument bias in one-sample Mendelian randomization studies pp. 1-23

Ruxin Shi, Ling Wang, Stephen Burgess and Yuehua Cui

Upstream open reading frames repress the translation from the iab-8 RNA pp. 1-18

Yohan Frei, Clément Immarigeon, Maxime Revel, François Karch and Robert K Maeda

Prioritizing disease-related rare variants by integrating gene expression data pp. 1-16

Hanmin Guo, Alexander Eckehart Urban and Wing Hung Wong

Volume 20, issue 8, 2024

Enhancing portability of trans-ancestral polygenic risk scores through tissue-specific functional genomic data integration pp. 1-18

Bradley Crone and Alan P Boyle

Finemap-MiXeR: A variational Bayesian approach for genetic finemapping pp. 1-21

Bayram Cevdet Akdeniz, Oleksandr Frei, Alexey Shadrin, Dmitry Vetrov, Dmitry Kropotov, Eivind Hovig, Ole A Andreassen and Anders M Dale

Volume 20, issue 7, 2024

Improving population scale statistical phasing with whole-genome sequencing data pp. 1-22

Rick Wertenbroek, Robin J Hofmeister, Ioannis Xenarios, Yann Thoma and Olivier Delaneau

Volume 20, issue 6, 2024

TGF-β ligand cross-subfamily interactions in the response of Caenorhabditis elegans to a bacterial pathogen pp. 1-20

Emma Jo Ciccarelli, Zachary Wing, Moshe Bendelstein, Ramandeep Kaur Johal, Gurjot Singh, Ayelet Monas and Cathy Savage-Dunn

Volume 20, issue 5, 2024

Transcription decouples estrogen-dependent changes in enhancer-promoter contact frequencies and spatial proximity pp. 1-27

Luciana I Gómez Acuña, Ilya Flyamer, Shelagh Boyle, Elias T Friman and Wendy A Bickmore

Simultaneous estimation of genotype error and uncalled deletion rates in whole genome sequence data pp. 1-18

Nobuaki Masaki, Sharon R Browning and Brian L Browning

Volume 20, issue 4, 2024

Correlation-based tests for the formal comparison of polygenic scores in multiple populations pp. 1-17

Sophia Gunn and Kathryn L Lunetta

Collider bias correction for multiple covariates in GWAS using robust multivariable Mendelian randomization pp. 1-27

Peiyao Wang, Zhaotong Lin, Haoran Xue and Wei Pan

Better together against genetic heterogeneity: A sex-combined joint main and interaction analysis of 290 quantitative traits in the UK Biobank pp. 1-23

Boxi Lin, Andrew D Paterson and Lei Sun

Volume 20, issue 3, 2024

Canadian COVID-19 host genetics cohort replicates known severity associations pp. 1-25

Elika Garg, Paola Arguello-Pascualli, Olga Vishnyakova, Anat R Halevy, Samantha Yoo, Jennifer D Brooks, Shelley B Bull, France Gagnon, Celia M T Greenwood, Rayjean J Hung, Jerald F Lawless, Jordan Lerner-Ellis, Jessica K Dennis, Rohan J S Abraham, Jean-Michel Garant, Bhooma Thiruvahindrapuram, Steven J M Jones, CGEn HostSeq Initiative, Lisa J Strug, Andrew D Paterson, Lei Sun and Lloyd T Elliott

Volume 20, issue 2, 2024

Maintenance of proteostasis by Drosophila Rer1 is essential for competitive cell survival and Myc-driven overgrowth pp. 1-28

Pranab Kumar Paul, Shruti Umarvaish, Shivani Bajaj, Rishana Farin S., Hrudya Mohan, Wim Annaert and Varun Chaudhary

TRAILS: Tree reconstruction of ancestry using incomplete lineage sorting pp. 1-21

Iker Rivas-González, Mikkel H Schierup, John Wakeley and Asger Hobolth