PLOS Genetics

2005 - 2022

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Volume 18, issue 4, 2022

A spatially aware likelihood test to detect sweeps from haplotype distributions pp. 1-37

Michael DeGiorgio and Zachary A Szpiech

Analyzing human knockouts to validate GPR151 as a therapeutic target for reduction of body mass index pp. 1-13

Allan Gurtan, John Dominy, Shareef Khalid, Linh Vong, Shari Caplan, Treeve Currie, Sean Richards, Lindsey Lamarche, Daniel Denning, Diana Shpektor, Anastasia Gurinovich, Asif Rasheed, Shahid Hameed, Subhan Saeed, Imran Saleem, Anjum Jalal, Shahid Abbas, Raffat Sultana, Syed Zahed Rasheed, Fazal-ur-Rehman Memon, Nabi Shah, Mohammad Ishaq, Amit V Khera, John Danesh, Philippe Frossard and Danish Saleheen

Volume 18, issue 3, 2022

THUNDER: A reference-free deconvolution method to infer cell type proportions from bulk Hi-C data pp. 1-18

Bryce Rowland, Ruth Huh, Zoey Hou, Cheynna Crowley, Jia Wen, Yin Shen, Ming Hu, Paola Giusti-Rodríguez, Patrick F Sullivan and Yun Li

BmPMFBP1 regulates the development of eupyrene sperm in the silkworm, Bombyx mori pp. 1-20

Dehong Yang, Jun Xu, Kai Chen, Yujia Liu, Xu Yang, Linmeng Tang, Xingyu Luo, Zulian Liu, Muwang Li, James R Walters and Yongping Huang

Significant sparse polygenic risk scores across 813 traits in UK Biobank pp. 1-21

Yosuke Tanigawa, Junyang Qian, Guhan Venkataraman, Johanne Marie Justesen, Ruilin Li, Robert Tibshirani, Trevor Hastie and Manuel A Rivas

Impact of nonrandom selection mechanisms on the causal effect estimation for two-sample Mendelian randomization methods pp. 1-21

Yuanyuan Yu, Lei Hou, Xu Shi, Xiaoru Sun, Xinhui Liu, Yifan Yu, Zhongshang Yuan, Hongkai Li and Fuzhong Xue

Volume 18, issue 2, 2022

Genomic legacy of migration in endangered caribou pp. 1-25

Maria Cavedon, Bridgett vonHoldt, Mark Hebblewhite, Troy Hegel, Elizabeth Heppenheimer, Dave Hervieux, Stefano Mariani, Helen Schwantje, Robin Steenweg, Jessica Theoret, Megan Watters and Marco Musiani

From musk to body odor: Decoding olfaction through genetic variation pp. 1-27

Bingjie Li, Marissa L Kamarck, Qianqian Peng, Fei-Ling Lim, Andreas Keller, Monique A M Smeets, Joel D Mainland and Sijia Wang

Soft selective sweeps: Addressing new definitions, evaluating competing models, and interpreting empirical outliers pp. 1-12

Parul Johri, Wolfgang Stephan and Jeffrey D Jensen

Volume 18, issue 1, 2022

Noise-augmented directional clustering of genetic association data identifies distinct mechanisms underlying obesity pp. 1-24

Andrew J Grant, Dipender Gill, Paul D W Kirk and Stephen Burgess

Redundant neural circuits regulate olfactory integration pp. 1-26

Wenxing Yang, Taihong Wu, Shasha Tu, Yuang Qin, Chengchen Shen, Jiangyun Li, Myung-Kyu Choi, Fengyun Duan and Yun Zhang

Bacterial recognition by PGRP-SA and downstream signalling by Toll/DIF sustain commensal gut bacteria in Drosophila pp. 1-27

Shivohum Bahuguna, Magda Atilano, Marcus Glittenberg, Dohun Lee, Srishti Arora, Lihui Wang, Jun Zhou, Siamak Redhai, Michael Boutros and Petros Ligoxygakis

Comprehensive patient-level classification and quantification of driver events in TCGA PanCanAtlas cohorts pp. 1-23

Alexey D Vyatkin, Danila V Otnyukov, Sergey V Leonov and Aleksey V Belikov

Volume 17, issue 11, 2021

The effects of introgression across thousands of quantitative traits revealed by gene expression in wild tomatoes pp. 1-20

Mark S Hibbins and Matthew W Hahn

Prediction of heterosis in the recent rapeseed (Brassica napus) polyploid by pairing parental nucleotide sequences pp. 1-22

Qian Wang, Tao Yan, Zhengbiao Long, Luna Yue Huang, Yang Zhu, Ying Xu, Xiaoyang Chen, Haksong Pak, Jiqiang Li, Dezhi Wu, Yang Xu, Shuijin Hua and Lixi Jiang

Evolution of ColE1-like plasmids across γ-Proteobacteria: From bacteriocin production to antimicrobial resistance pp. 1-24

Manuel Ares-Arroyo, Eduardo P C Rocha and Bruno Gonzalez-Zorn

Combining the strengths of inverse-variance weighting and Egger regression in Mendelian randomization using a mixture of regressions model pp. 1-25

Zhaotong Lin, Yangqing Deng and Wei Pan

Network-based protein-protein interaction prediction method maps perturbations of cancer interactome pp. 1-19

Jiajun Qiu, Kui Chen, Chunlong Zhong, Sihao Zhu and Xiao Ma

Volume 17, issue 10, 2021

Haplotype associated RNA expression (HARE) improves prediction of complex traits in maize pp. 1-24

Anju Giri, Merritt Khaipho-Burch, Edward S Buckler and Guillaume P Ramstein

Leveraging auxiliary data from arbitrary distributions to boost GWAS discovery with Flexible cFDR pp. 1-37

Anna Hutchinson, Guillermo Reales, Thomas Willis and Chris Wallace

Metabolic flux from the Krebs cycle to glutamate transmission tunes a neural brake on seizure onset pp. 1-27

Jiwon Jeong, Jongbin Lee, Ji-hyung Kim and Chunghun Lim

Machine learning to predict the source of campylobacteriosis using whole genome data pp. 1-17

Nicolas Arning, Samuel K Sheppard, Sion Bayliss, David A Clifton and Daniel J Wilson

Volume 17, issue 9, 2021

A more accurate method for colocalisation analysis allowing for multiple causal variants pp. 1-11

Chris Wallace

Rare variants in the endocytic pathway are associated with Alzheimer’s disease, its related phenotypes, and functional consequences pp. 1-38

Lingyu Zhan, Jiajin Li, Brandon Jew and Jae Hoon Sul

Identifying causal variants by fine mapping across multiple studies pp. 1-19

Nathan LaPierre, Kodi Taraszka, Helen Huang, Rosemary He, Farhad Hormozdiari and Eleazar Eskin

Genome-wide methylation data improves dissection of the effect of smoking on body mass index pp. 1-19

Carmen Amador, Yanni Zeng, Michael Barber, Rosie M Walker, Archie Campbell, Andrew M McIntosh, Kathryn L Evans, David J Porteous, Caroline Hayward, James F Wilson, Pau Navarro and Chris S Haley

Dynamic neurogenomic responses to social interactions and dominance outcomes in female paper wasps pp. 1-25

Floria M K Uy, Christopher M Jernigan, Natalie C Zaba, Eshan Mehrotra, Sara E Miller and Michael J Sheehan

A scalable Drosophila assay for clinical interpretation of human PTEN variants in suppression of PI3K/AKT induced cellular proliferation pp. 1-28

Payel Ganguly, Landiso Madonsela, Jesse T Chao, Christopher J R Loewen, Timothy P O’Connor, Esther M Verheyen and Douglas W Allan

A Bayesian network approach incorporating imputation of missing data enables exploratory analysis of complex causal biological relationships pp. 1-28

Richard Howey, Alexander D Clark, Najib Naamane, Louise N Reynard, Arthur G Pratt and Heather J Cordell

Volume 17, issue 8, 2021

Multitrait GWAS to connect disease variants and biological mechanisms pp. 1-36

Hanna Julienne, Vincent Laville, Zachary R McCaw, Zihuai He, Vincent Guillemot, Carla Lasry, Andrey Ziyatdinov, Cyril Nerin, Amaury Vaysse, Pierre Lechat, Hervé Ménager, Wilfried Le Goff, Marie-Pierre Dube, Peter Kraft, Iuliana Ionita-Laza, Bjarni J Vilhjálmsson and Hugues Aschard

Forecasting of phenotypic and genetic outcomes of experimental evolution in Pseudomonas protegens pp. 1-24

Jennifer T Pentz and Peter A Lind

Average semivariance yields accurate estimates of the fraction of marker-associated genetic variance and heritability in complex trait analyses pp. 1-27

Mitchell J Feldmann, Hans-Peter Piepho, William C Bridges and Steven J Knapp

Exploiting collider bias to apply two-sample summary data Mendelian randomization methods to one-sample individual level data pp. 1-26

Ciarrah Barry, Junxi Liu, Rebecca Richmond, Martin K Rutter, Deborah A Lawlor, Frank Dudbridge and Jack Bowden

Volume 17, issue 7, 2021

A fast and robust Bayesian nonparametric method for prediction of complex traits using summary statistics pp. 1-17

Geyu Zhou and Hongyu Zhao

A spectral theory for Wright’s inbreeding coefficients and related quantities pp. 1-24

Olivier François and Clément Gain

Pleiotropy method reveals genetic overlap between orofacial clefts at multiple novel loci from GWAS of multi-ethnic trios pp. 1-28

Debashree Ray, Sowmya Venkataraghavan, Wanying Zhang, Elizabeth J Leslie, Jacqueline B Hetmanski, Seth M Weinberg, Jeffrey C Murray, Mary L Marazita, Ingo Ruczinski, Margaret A Taub and Terri H Beaty

Meiosis in Quarantine discussions lead to an action plan to increase diversity and inclusion within the genetics community pp. 1-11

Katherine K Billmyre, María Angélica Bravo Núñez, Douglas K Bishop and Francesca Cole

Volume 17, issue 6, 2021

A genome-wide association study identifies 5 loci associated with frozen shoulder and implicates diabetes as a causal risk factor pp. 1-13

Harry D Green, Alistair Jones, Jonathan P Evans, Andrew R Wood, Robin N Beaumont, Jessica Tyrrell, Timothy M Frayling, Christopher Smith and Michael N Weedon

An autoregulatory negative feedback loop controls thermomorphogenesis in Arabidopsis pp. 1-21

Sanghwa Lee, Ling Zhu and Enamul Huq

Predicting population genetic change in an autocorrelated random environment: Insights from a large automated experiment pp. 1-23

Marie Rescan, Daphné Grulois, Enrique Ortega Aboud, Pierre de Villemereuil and Luis-Miguel Chevin

Volume 17, issue 5, 2021

Evaluation of polygenic prediction methodology within a reference-standardized framework pp. 1-22

Oliver Pain, Kylie P Glanville, Saskia P Hagenaars, Saskia Selzam, Anna E Fürtjes, Héléna A Gaspar, Jonathan R I Coleman, Kaili Rimfeld, Gerome Breen, Robert Plomin, Lasse Folkersen and Cathryn M Lewis

Gene action, genetic variation, and GWAS: A user-friendly web tool pp. 1-9

Valentin Hivert, Naomi R Wray and Peter M Visscher

Genetic variation affects morphological retinal phenotypes extracted from UK Biobank optical coherence tomography images pp. 1-27

Hannah Currant, Pirro Hysi, Tomas W Fitzgerald, Puya Gharahkhani, Pieter W M Bonnemaijer, Anne Senabouth, Alex W Hewitt, UK Biobank Eye and Vision Consortium, International Glaucoma Genetics Consortium, Denize Atan, Tin Aung, Jason Charng, Hélène Choquet, Jamie Craig, Peng T Khaw, Caroline C W Klaver, Michiaki Kubo, Jue-Sheng Ong, Louis R Pasquale, Charles A Reisman, Maciej Daniszewski, Joseph E Powell, Alice Pébay, Mark J Simcoe, Alberta A H J Thiadens, Cornelia M van Duijn, Seyhan Yazar, Eric Jorgenson, Stuart MacGregor, Chris J Hammond, David A Mackey, Janey L Wiggs, Paul J Foster, Praveen J Patel, Ewan Birney and Anthony P Khawaja

Evolution of plasticity in production and transgenerational inheritance of small RNAs under dynamic environmental conditions pp. 1-25

Willian T A F Silva, Sarah P Otto and Simone Immler

Volume 17, issue 4, 2021

Leveraging expression from multiple tissues using sparse canonical correlation analysis and aggregate tests improves the power of transcriptome-wide association studies pp. 1-21

Helian Feng, Nicholas Mancuso, Alexander Gusev, Arunabha Majumdar, Megan Major, Bogdan Pasaniuc and Peter Kraft

MRLocus: Identifying causal genes mediating a trait through Bayesian estimation of allelic heterogeneity pp. 1-24

Anqi Zhu, Nana Matoba, Emma P Wilson, Amanda L Tapia, Yun Li, Joseph G Ibrahim, Jason L Stein and Michael I Love

Sex-stratified genome-wide association study of multisite chronic pain in UK Biobank pp. 1-27

Keira J A Johnston, Joey Ward, Pradipta R Ray, Mark J Adams, Andrew M McIntosh, Blair H Smith, Rona J Strawbridge, Theodore J Price, Daniel J Smith, Barbara I Nicholl and Mark E S Bailey

Volume 17, issue 3, 2021

Genome-wide association meta-analysis identifies pleiotropic risk loci for aerodigestive squamous cell cancers pp. 1-19

Corina Lesseur, Aida Ferreiro-Iglesias, James D McKay, Yohan Bossé, Mattias Johansson, Valerie Gaborieau, Maria Teresa Landi, David C Christiani, Neil C Caporaso, Stig E Bojesen, Christopher I Amos, Sanjay Shete, Geoffrey Liu, Gadi Rennert, Demetrios Albanes, Melinda C Aldrich, Adonina Tardon, Chu Chen, Liloglou Triantafillos, John K Field, Marion Dawn Teare, Lambertus A Kiemeney, Brenda Diergaarde, Robert L Ferris, Shanbeh Zienolddiny, Stephen Lam, Andrew F Olshan, Mark C Weissler, Martin Lacko, Angela Risch, Heike Bickeböller, Andy R Ness, Steve Thomas, Loic Le Marchand, Matthew B Schabath, Victor Wünsch-Filho, Eloiza H Tajara, Angeline S Andrew, Gary M Clifford, Philip Lazarus, Kjell Grankvist, Mikael Johansson, Susanne Arnold, Olle Melander, Hans Brunnström, Stefania Boccia, Gabriella Cadoni, Wim Timens, Ma’en Obeidat, Xiangjun Xiao, Richard S Houlston, Rayjean J Hung and Paul Brennan

Genome-wide association study of fish oil supplementation on lipid traits in 81,246 individuals reveals new gene-diet interaction loci pp. 1-20

Michael Francis, Changwei Li, Yitang Sun, Jingqi Zhou, Xiang Li, J Thomas Brenna and Kaixiong Ye

Changes in the fine-scale genetic structure of Finland through the 20th century pp. 1-26

Sini Kerminen, Nicola Cerioli, Darius Pacauskas, Aki S Havulinna, Markus Perola, Pekka Jousilahti, Veikko Salomaa, Mark J Daly, Rupesh Vyas, Samuli Ripatti and Matti Pirinen

MOSTWAS: Multi-Omic Strategies for Transcriptome-Wide Association Studies pp. 1-30

Arjun Bhattacharya, Yun Li and Michael I Love

Volume 17, issue 2, 2021

Transcriptome-wide transmission disequilibrium analysis identifies novel risk genes for autism spectrum disorder pp. 1-25

Kunling Huang, Yuchang Wu, Junha Shin, Ye Zheng, Alireza Fotuhi Siahpirani, Yupei Lin, Zheng Ni, Jiawen Chen, Jing You, Sunduz Keles, Daifeng Wang, Sushmita Roy and Qiongshi Lu

Glucocerebrosidase reduces the spread of protein aggregation in a Drosophila melanogaster model of neurodegeneration by regulating proteins trafficked by extracellular vesicles pp. 1-28

Kathryn A Jewett, Ruth E Thomas, Chi Q Phan, Bernice Lin, Gillian Milstein, Selina Yu, Lisa F Bettcher, Fausto Carnevale Neto, Danijel Djukovic, Daniel Raftery, Leo J Pallanck and Marie Y Davis

Power analysis of transcriptome-wide association study: Implications for practical protocol choice pp. 1-20

Chen Cao, Bowei Ding, Qing Li, Devin Kwok, Jingjing Wu and Quan Long

Hippocampal transcriptome-wide association study and neurobiological pathway analysis for Alzheimer’s disease pp. 1-22

Nana Liu, Jiayuan Xu, Huaigui Liu, Shijie Zhang, Miaoxin Li, Yao Zhou, Wen Qin, Mulin Jun Li, Chunshui Yu and for the Alzheimer’s disease Neuroimaging Initiative

Volume 17, issue 1, 2021

Population structure of indigenous inhabitants of Arabia pp. 1-18

Katsuhiko Mineta, Kosuke Goto, Takashi Gojobori and Fowzan S Alkuraya

Identifying drug targets for neurological and psychiatric disease via genetics and the brain transcriptome pp. 1-26

Denis A Baird, Jimmy Z Liu, Jie Zheng, Solveig K Sieberts, Thanneer Perumal, Benjamin Elsworth, Tom G Richardson, Chia-Yen Chen, Minerva M Carrasquillo, Mariet Allen, Joseph S Reddy, Philip L De Jager, Nilufer Ertekin-Taner, Lara M Mangravite, Ben Logsdon, Karol Estrada, Philip C Haycock, Gibran Hemani, Heiko Runz, George Davey Smith, Tom R Gaunt and eQTL working group Amp-Ad

Adaptation is influenced by the complexity of environmental change during evolution in a dynamic environment pp. 1-27

Sébastien Boyer, Lucas Hérissant and Gavin Sherlock

Ciona Brachyury proximal and distal enhancers have different FGF dose-response relationships pp. 1-23

Matthew J Harder, Julie Hix, Wendy M Reeves and Michael T Veeman

Estimating FST and kinship for arbitrary population structures pp. 1-36

Alejandro Ochoa and John D Storey

RAFFI: Accurate and fast familial relationship inference in large scale biobank studies using RaPID pp. 1-19

Ardalan Naseri, Junjie Shi, Xihong Lin, Shaojie Zhang and Degui Zhi

Accurate genetic and environmental covariance estimation with composite likelihood in genome-wide association studies pp. 1-25

Boran Gao, Can Yang, Jin Liu and Xiang Zhou