PLOS Genetics

2005 - 2025

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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

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

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

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

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

Takintayo Akinbiyi, Mary Sara McPeek and Mark Abney

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

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

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

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

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

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

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

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

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

Hanmin Guo, Alexander Eckehart Urban and Wing Hung Wong

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

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

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

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

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

Volume 19, issue 12, 2023

Uncovering associations between pre-existing conditions and COVID-19 Severity: A polygenic risk score approach across three large biobanks pp. 1-28

Lars G Fritsche, Kisung Nam, Jiacong Du, Ritoban Kundu, Maxwell Salvatore, Xu Shi, Seunggeun Lee, Stephen Burgess and Bhramar Mukherjee

FiMAP: A fast identity-by-descent mapping test for biobank-scale cohorts pp. 1-20

Han Chen, Ardalan Naseri and Degui Zhi

cLD: Rare-variant linkage disequilibrium between genomic regions identifies novel genomic interactions pp. 1-21

Dinghao Wang, Deshan Perera, Jingni He, Chen Cao, Pathum Kossinna, Qing Li, William Zhang, Xingyi Guo, Alexander Platt, Jingjing Wu and Qingrun Zhang

Volume 19, issue 11, 2023

Transfer learning with false negative control improves polygenic risk prediction pp. 1-17

Xinge Jessie Jeng, Yifei Hu, Vaishnavi Venkat, Tzu-Pin Lu and Jung-Ying Tzeng

Phosphorylation of AHR by PLK1 promotes metastasis of LUAD via DIO2-TH signaling pp. 1-27

Chaohao Li, Derek B Allison, Daheng He, Fengyi Mao, Xinyi Wang, Piotr Rychahou, Ibrahim A Imam, Yifan Kong, Qiongsi Zhang, Yanquan Zhang, Jinghui Liu, Ruixin Wang, Xiongjian Rao, Sai Wu, B Mark Evers, Qing Shao, Chi Wang, Zhiguo Li and Xiaoqi Liu

Inferring multi-locus selection in admixed populations pp. 1-27

Nicolas M Ayala, Maximilian Genetti and Russell Corbett-Detig

BRASS: Permutation methods for binary traits in genetic association studies with structured samples pp. 1-21

Joelle Mbatchou, Mark Abney and Mary Sara McPeek

Methods for mediation analysis with high-dimensional DNA methylation data: Possible choices and comparisons pp. 1-26

Dylan Clark-Boucher, Xiang Zhou, Jiacong Du, Yongmei Liu, Belinda L Needham, Jennifer A Smith and Bhramar Mukherjee

Volume 19, issue 10, 2023

Meta-analysis of genome-wide association studies of gestational duration and spontaneous preterm birth identifies new maternal risk loci pp. 1-19

Anu Pasanen, Minna K Karjalainen, FinnGen, Ge Zhang, Heli Tiensuu, Antti M Haapalainen, Marja Ojaniemi, Bjarke Feenstra, Bo Jacobsson, Aarno Palotie, Hannele Laivuori, Louis J Muglia, Mika Rämet and Mikko Hallman

SMASH: Scalable Method for Analyzing Spatial Heterogeneity of genes in spatial transcriptomics data pp. 1-25

Souvik Seal, Benjamin G Bitler and Debashis Ghosh

Volume 19, issue 9, 2023

Saturation genome editing of 11 codons and exon 13 of BRCA2 coupled with chemotherapeutic drug response accurately determines pathogenicity of variants pp. 1-28

Sounak Sahu, Teresa L Sullivan, Alexander Y Mitrophanov, Mélissa Galloux, Darryl Nousome, Eileen Southon, Dylan Caylor, Arun Prakash Mishra, Christine N Evans, Michelle E Clapp, Sandra Burkett, Tyler Malys, Raj Chari, Kajal Biswas and Shyam K Sharan

Inferring gene regulatory network from single-cell transcriptomes with graph autoencoder model pp. 1-28

Jiacheng Wang, Yaojia Chen and Quan Zou

Review and further developments in statistical corrections for Winner’s Curse in genetic association studies pp. 1-29

Amanda Forde, Gibran Hemani and John Ferguson

Large-scale whole exome sequencing studies identify two genes,CTSL and APOE, associated with lung cancer pp. 1-13

Jingxiong Xu, Wei Xu, Jiyeon Choi, Yonathan Brhane, David C Christiani, Jui Kothari, James McKay, John K Field, Michael P A Davies, Geoffrey Liu, Christopher I Amos, Rayjean J Hung and Laurent Briollais

Evolutionary conserved circular MEF2A RNAs regulate myogenic differentiation and skeletal muscle development pp. 1-32

Xiaoxu Shen, Xiyu Zhao, Haorong He, Jing Zhao, Yuanhang Wei, Yuqi Chen, Shunshun Han, Yifeng Zhu, Yao Zhang, Qing Zhu and Huadong Yin

On the interpretation of transcriptome-wide association studies pp. 1-23

Christiaan de Leeuw, Josefin Werme, Jeanne E Savage, Wouter J Peyrot and Danielle Posthuma

Volume 19, issue 8, 2023

Accurate detection of shared genetic architecture from GWAS summary statistics in the small-sample context pp. 1-19

Thomas W Willis and Chris Wallace

Volume 19, issue 7, 2023

Organization and replicon interactions within the highly segmented genome of Borrelia burgdorferi pp. 1-27

Zhongqing Ren, Constantin N Takacs, Hugo B Brandão, Christine Jacobs-Wagner and Xindan Wang

A flexible empirical Bayes approach to multivariate multiple regression, and its improved accuracy in predicting multi-tissue gene expression from genotypes pp. 1-21

Fabio Morgante, Peter Carbonetto, Gao Wang, Yuxin Zou, Abhishek Sarkar and Matthew Stephens

Regularized sequence-context mutational trees capture variation in mutation rates across the human genome pp. 1-22

Christopher J Adams, Mitchell Conery, Benjamin J Auerbach, Shane T Jensen, Iain Mathieson and Benjamin F Voight

A genetic tradeoff for tolerance to moderate and severe heat stress in US hybrid maize pp. 1-29

Aaron Kusmec, Lakshmi Attigala, Xiongtao Dai, Srikant Srinivasan, Cheng-Ting “Eddy” Yeh and Patrick S Schnable

A Van Gogh/Vangl tyrosine phosphorylation switch regulates its interaction with core Planar Cell Polarity factors Prickle and Dishevelled pp. 1-26

Ashley C Humphries, Claudia Molina-Pelayo, Parijat Sil, C Clayton Hazelett, Danelle Devenport and Marek Mlodzik

Volume 19, issue 6, 2023

Combinations of genes at the 16p11.2 and 22q11.2 CNVs contribute to neurobehavioral traits pp. 1-20

Mikhail Vysotskiy, Autism Working Group of the Psychiatric Genomics Consortium, Bipolar Disorder Working Group of the Psychiatric Genomics Consortium, Schizophrenia Working Group of the Psychiatric Genomics Consortium and Lauren A Weiss

Relaxing parametric assumptions for non-linear Mendelian randomization using a doubly-ranked stratification method pp. 1-22

Haodong Tian, Amy M Mason, Cunhao Liu and Stephen Burgess

Volume 19, issue 5, 2023

The molecular mechanism for carbon catabolite repression of the chitin response in Vibrio cholerae pp. 1-26

Virginia E Green, Catherine A Klancher, Shouji Yamamoto and Ankur B Dalia

Transcriptome-wide gene-gene interaction associations elucidate pathways and functional enrichment of complex traits pp. 1-32

Luke M Evans, Christopher H Arehart, Andrew D Grotzinger, Travis J Mize, Maizy S Brasher, Jerry A Stitzel, Marissa A Ehringer and Charles A Hoeffer

Volume 19, issue 4, 2023

Imputed genomes and haplotype-based analyses of the Picts of early medieval Scotland reveal fine-scale relatedness between Iron Age, early medieval and the modern people of the UK pp. 1-25

Adeline Morez, Kate Britton, Gordon Noble, Torsten Günther, Anders Götherström, Ricardo Rodríguez-Varela, Natalija Kashuba, Rui Martiniano, Sahra Talamo, Nicholas J Evans, Joel D Irish, Christina Donald and Linus Girdland-Flink

Volume 19, issue 3, 2023

Tuberculosis severity associates with variants and eQTLs related to vascular biology and infection-induced inflammation pp. 1-25

Michael L McHenry, Jason Simmons, Hyejeong Hong, LaShaunda L Malone, Harriet Mayanja-Kizza, William S Bush, W Henry Boom, Thomas R Hawn, Scott M Williams and Catherine M Stein

Volume 19, issue 2, 2023

The identification of mediating effects using genome-based restricted maximum likelihood estimation pp. 1-17

Cornelius A Rietveld, Ronald de Vlaming and Eric A W Slob

Bayesian inference of admixture graphs on Native American and Arctic populations pp. 1-22

Svend V Nielsen, Andrew H Vaughn, Kalle Leppälä, Michael J Landis, Thomas Mailund and Rasmus Nielsen

Volume 19, issue 1, 2023

Historic samples reveal loss of wild genotype through domestic chicken introgression during the Anthropocene pp. 1-19

Meng Yue Wu, Giovanni Forcina, Gabriel Weijie Low, Keren R Sadanandan, Chyi Yin Gwee, Hein van Grouw, Shaoyuan Wu, Scott V Edwards, Maude W Baldwin and Frank E Rheindt

Decomposing heritability and genetic covariance by direct and indirect effect paths pp. 1-17

Jie Song, Yiqing Zou, Yuchang Wu, Jiacheng Miao, Ze Yu, Jason M Fletcher and Qiongshi Lu