PLOS Genetics

2005 - 2022

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Volume 16, issue 12, 2020

Super-resolution visualization of distinct stalled and broken replication fork structures pp. 1-28

Donna R Whelan, Wei Ting C Lee, Frances Marks, Yu Tina Kong, Yandong Yin and Eli Rothenberg

Integrating comprehensive functional annotations to boost power and accuracy in gene-based association analysis pp. 1-23

Corbin Quick, Xiaoquan Wen, Gonçalo Abecasis, Michael Boehnke and Hyun Min Kang

A powerful method for pleiotropic analysis under composite null hypothesis identifies novel shared loci between Type 2 Diabetes and Prostate Cancer pp. 1-25

Debashree Ray and Nilanjan Chatterjee

Common maternal and fetal genetic variants show expected polygenic effects on risk of small- or large-for-gestational-age (SGA or LGA), except in the smallest 3% of babies pp. 1-15

Robin N Beaumont, Sarah J Kotecha, Andrew R Wood, Bridget A Knight, Sylvain Sebert, Mark I McCarthy, Andrew T Hattersley, Marjo-Riitta Järvelin, Nicholas J Timpson, Rachel M Freathy and Sailesh Kotecha

Volume 16, issue 11, 2020

Genetic compensation prevents myopathy and heart failure in an in vivo model of Bag3 deficiency pp. 1-24

Federica Diofano, Karolina Weinmann, Isabelle Schneider, Kevin D Thiessen, Wolfgang Rottbauer and Steffen Just

Multivariable G-E interplay in the prediction of educational achievement pp. 1-20

Andrea G Allegrini, Ville Karhunen, Jonathan R I Coleman, Saskia Selzam, Kaili Rimfeld, Sophie von Stumm, Jean-Baptiste Pingault and Robert Plomin

LabWAS: Novel findings and study design recommendations from a meta-analysis of clinical labs in two independent biobanks pp. 1-23

Jeffery A Goldstein, Joshua S Weinstock, Lisa A Bastarache, Daniel B Larach, Lars G Fritsche, Ellen M Schmidt, Chad M Brummett, Sachin Kheterpal, Goncalo R Abecasis, Joshua C Denny and Matthew Zawistowski

Inferring causal direction between two traits in the presence of horizontal pleiotropy with GWAS summary data pp. 1-30

Haoran Xue and Wei Pan

Genotype imputation using the Positional Burrows Wheeler Transform pp. 1-19

Simone Rubinacci, Olivier Delaneau and Jonathan Marchini

Volume 16, issue 10, 2020

Transcriptome and epigenome diversity and plasticity of muscle stem cells following transplantation pp. 1-21

Brendan Evano, Diljeet Gill, Irene Hernando-Herraez, Glenda Comai, Thomas M Stubbs, Pierre-Henri Commere, Wolf Reik and Shahragim Tajbakhsh

AKH-FOXO pathway regulates starvation-induced sleep loss through remodeling of the small ventral lateral neuron dorsal projections pp. 1-21

Qiankun He, Juan Du, Liya Wei and Zhangwu Zhao

Selection for ancient periodic motifs that do not impart DNA bending pp. 1-25

Aletheia Atzinger and Jeffrey G Lawrence

A fast and scalable framework for large-scale and ultrahigh-dimensional sparse regression with application to the UK Biobank pp. 1-30

Junyang Qian, Yosuke Tanigawa, Wenfei Du, Matthew Aguirre, Chris Chang, Robert Tibshirani, Manuel A Rivas and Trevor Hastie

A cautionary note on the use of unsupervised machine learning algorithms to characterise malaria parasite population structure from genetic distance matrices pp. 1-23

James A Watson, Aimee R Taylor, Elizabeth A Ashley, Arjen Dondorp, Caroline O Buckee, Nicholas J White and Chris C Holmes

By what name shall I call thee? pp. 1-2

Gregory S Barsh and Gregory P Copenhaver

Estimating indirect parental genetic effects on offspring phenotypes using virtual parental genotypes derived from sibling and half sibling pairs pp. 1-29

Liang-Dar Hwang, Justin D Tubbs, Justin Luong, Mischa Lundberg, Gunn-Helen Moen, Geng Wang, Nicole M Warrington, Pak C Sham, Gabriel Cuellar-Partida and David M Evans

Exploring the Complexity of Protein-Level Dosage Compensation that Fine-Tunes Stoichiometry of Multiprotein Complexes pp. 1-20

Koji Ishikawa, Akari Ishihara and Hisao Moriya

Automated feature extraction from population wearable device data identified novel loci associated with sleep and circadian rhythms pp. 1-22

Xinyue Li and Hongyu Zhao

Novel loci for childhood body mass index and shared heritability with adult cardiometabolic traits pp. 1-26

Suzanne Vogelezang, Jonathan P Bradfield, Tarunveer S Ahluwalia, John A Curtin, Timo A Lakka, Niels Grarup, Markus Scholz, Peter J van der Most, Claire Monnereau, Evie Stergiakouli, Anni Heiskala, Momoko Horikoshi, Iryna O Fedko, Natalia Vilor-Tejedor, Diana L Cousminer, Marie Standl, Carol A Wang, Jorma Viikari, Frank Geller, Carmen Íñiguez, Niina Pitkänen, Alessandra Chesi, Jonas Bacelis, Loic Yengo, Maties Torrent, Ioanna Ntalla, Øyvind Helgeland, Saskia Selzam, Judith M Vonk, Mohammed H Zafarmand, Barbara Heude, Ismaa Sadaf Farooqi, Akram Alyass, Robin N Beaumont, Christian T Have, Peter Rzehak, Jose Ramon Bilbao, Theresia M Schnurr, Inês Barroso, Klaus Bønnelykke, Lawrence J Beilin, Lisbeth Carstensen, Marie-Aline Charles, Bo Chawes, Karine Clément, Ricardo Closa-Monasterolo, Adnan Custovic, Johan G Eriksson, Joaquin Escribano, Maria Groen-Blokhuis, Veit Grote, Dariusz Gruszfeld, Hakon Hakonarson, Torben Hansen, Andrew T Hattersley, Mette Hollensted, Jouke-Jan Hottenga, Elina Hyppönen, Stefan Johansson, Raimo Joro, Mika Kähönen, Ville Karhunen, Wieland Kiess, Bridget A Knight, Berthold Koletzko, Andreas Kühnapfel, Kathrin Landgraf, Jean-Paul Langhendries, Terho Lehtimäki, Jaakko T Leinonen, Aihuali Li, Virpi Lindi, Estelle Lowry, Mariona Bustamante, Carolina Medina-Gomez, Mads Melbye, Kim F Michaelsen, Camilla S Morgen, Trevor A Mori, Tenna R H Nielsen, Harri Niinikoski, Albertine J Oldehinkel, Katja Pahkala, Kalliope Panoutsopoulou, Oluf Pedersen, Craig E Pennell, Christine Power, Sijmen A Reijneveld, Fernando Rivadeneira, Angela Simpson, Peter D Sly, Jakob Stokholm, Kook K Teo, Elisabeth Thiering, Nicholas J Timpson, André G Uitterlinden, Catharina E M van Beijsterveldt, Barbera D C van Schaik, Marc Vaudel, Elvira Verduci, Rebecca K Vinding, Mandy Vogel, Eleftheria Zeggini, Sylvain Sebert, Mads V Lind, Christopher D Brown, Loreto Santa-Marina, Eva Reischl, Christine Frithioff-Bøjsøe, David Meyre, Eleanor Wheeler, Ken Ong, Ellen A Nohr, Tanja G M Vrijkotte, Gerard H Koppelman, Robert Plomin, Pål R Njølstad, George D Dedoussis, Philippe Froguel, Thorkild I A Sørensen, Bo Jacobsson, Rachel M Freathy, Babette S Zemel, Olli Raitakari, Martine Vrijheid, Bjarke Feenstra, Leo-Pekka Lyytikäinen, Harold Snieder, Holger Kirsten, Patrick G Holt, Joachim Heinrich, Elisabeth Widén, Jordi Sunyer, Dorret I Boomsma, Marjo-Riitta Järvelin, Antje Körner, George Davey Smith, Jens-Christian Holm, Mustafa Atalay, Clare Murray, Hans Bisgaard, Mark I McCarthy, Early Growth Genetics Consortium, Vincent W V Jaddoe, Struan F A Grant and Janine F Felix

Volume 16, issue 9, 2020

The causal effect of obesity on prediabetes and insulin resistance reveals the important role of adipose tissue in insulin resistance pp. 1-23

Zong Miao, Marcus Alvarez, Arthur Ko, Yash Bhagat, Elior Rahmani, Brandon Jew, Sini Heinonen, Linda Liliana Muñoz-Hernandez, Miguel Herrera-Hernandez, Carlos Aguilar-Salinas, Teresa Tusie-Luna, Karen L Mohlke, Markku Laakso, Kirsi H Pietiläinen, Eran Halperin and Päivi Pajukanta

Leveraging correlations between variants in polygenic risk scores to detect heterogeneity in GWAS cohorts pp. 1-35

Jie Yuan, Henry Xing, Alexandre Louis Lamy, The Schizophrenia Working Group of the Psychiatric Genomics Consortium, Todd Lencz and Itsik Pe’er

Restriction on self-renewing asymmetric division is coupled to terminal asymmetric division in the Drosophila CNS pp. 1-27

Ivana Gaziova, Michael Gazi, Jordan Mar and Krishna Moorthi Bhat

Volume 16, issue 8, 2020

On the cross-population generalizability of gene expression prediction models pp. 1-28

Kevin L Keys, Angel C Y Mak, Marquitta J White, Walter L Eckalbar, Andrew W Dahl, Joel Mefford, Anna V Mikhaylova, María G Contreras, Jennifer R Elhawary, Celeste Eng, Donglei Hu, Scott Huntsman, Sam S Oh, Sandra Salazar, Michael A Lenoir, Jimmie C Ye, Timothy A Thornton, Noah Zaitlen, Esteban G Burchard and Christopher R Gignoux

Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph pp. 1-24

Melissa J Hubisz, Amy L Williams and Adam Siepel

Learning the properties of adaptive regions with functional data analysis pp. 1-44

Mehreen R Mughal, Hillary Koch, Jinguo Huang, Francesca Chiaromonte and Michael DeGiorgio

A general framework for functionally informed set-based analysis: Application to a large-scale colorectal cancer study pp. 1-21

Xinyuan Dong, Yu-Ru Su, Richard Barfield, Stephanie A Bien, Qianchuan He, Tabitha A Harrison, Jeroen R Huyghe, Temitope O Keku, Noralane M Lindor, Clemens Schafmayer, Andrew T Chan, Stephen B Gruber, Mark A Jenkins, Charles Kooperberg, Ulrike Peters and Li Hsu

Cryptic genetic variation enhances primate L1 retrotransposon survival by enlarging the functional coiled coil sequence space of ORF1p pp. 1-19

Anthony V Furano, Charlie E Jones, Vipul Periwal, Kathryn E Callahan, Jean-Claude Walser and Pamela R Cook

Pan-genomic open reading frames: A potential supplement of single nucleotide polymorphisms in estimation of heritability and genomic prediction pp. 1-19

Zhengcao Li and Henner Simianer

Volume 16, issue 7, 2020

Mixed methods pp. 1-2

David J Balding, Gregory S Barsh, Gregory P Copenhaver and Chengqi Yi

Linking protein to phenotype with Mendelian Randomization detects 38 proteins with causal roles in human diseases and traits pp. 1-24

Andrew D Bretherick, Oriol Canela-Xandri, Peter K Joshi, David W Clark, Konrad Rawlik, Thibaud S Boutin, Yanni Zeng, Carmen Amador, Pau Navarro, Igor Rudan, Alan F Wright, Harry Campbell, Veronique Vitart, Caroline Hayward, James F Wilson, Albert Tenesa, Chris P Ponting, J Kenneth Baillie and Chris Haley

Unified inference of missense variant effects and gene constraints in the human genome pp. 1-24

Yi-Fei Huang

Volume 16, issue 6, 2020

Estimation of non-null SNP effect size distributions enables the detection of enriched genes underlying complex traits pp. 1-48

Wei Cheng, Sohini Ramachandran and Lorin Crawford

A Bayesian method to estimate variant-induced disease penetrance pp. 1-16

Brett M Kroncke, Derek K Smith, Yi Zuo, Andrew M Glazer, Dan M Roden and Jeffrey D Blume

Super-resolution imaging of RAD51 and DMC1 in DNA repair foci reveals dynamic distribution patterns in meiotic prophase pp. 1-30

Johan A Slotman, Maarten W Paul, Fabrizia Carofiglio, H Martijn de Gruiter, Tessa Vergroesen, Lieke Koornneef, Wiggert A van Cappellen, Adriaan B Houtsmuller and Willy M Baarends

Protein-protein interaction network controlling establishment and maintenance of switchable cell polarity pp. 1-30

Luís António Menezes Carreira, Filipe Tostevin, Ulrich Gerland and Lotte Søgaard-Andersen

Volume 16, issue 5, 2020

Trans-ethnic meta-analysis of genome-wide association studies identifies maternal ITPR1 as a novel locus influencing fetal growth during sensitive periods in pregnancy pp. 1-20

Fasil Tekola-Ayele, Cuilin Zhang, Jing Wu, Katherine L Grantz, Mohammad L Rahman, Deepika Shrestha, Marion Ouidir, Tsegaselassie Workalemahu and Michael Y Tsai

Population genetic models of GERP scores suggest pervasive turnover of constrained sites across mammalian evolution pp. 1-26

Christian D Huber, Bernard Y Kim and Kirk E Lohmueller

ASEP: Gene-based detection of allele-specific expression cross individuals in a population by RNA sequencing pp. 1-23

Jiaxin Fan, Jian Hu, Chenyi Xue, Hanrui Zhang, Katalin Susztak, Muredach P Reilly, Rui Xiao and Mingyao Li

A high-fat diet induces a microbiota-dependent increase in stem cell activity in the Drosophila intestine pp. 1-23

Jakob von Frieling, Muhammed Naeem Faisal, Femke Sporn, Roxana Pfefferkorn, Stella Solveig Nolte, Felix Sommer, Philip Rosenstiel and Thomas Roeder

Accounting for long-range correlations in genome-wide simulations of large cohorts pp. 1-12

Dominic Nelson, Jerome Kelleher, Aaron P Ragsdale, Claudia Moreau, Gil McVean and Simon Gravel

Bidirectional crosstalk between Hypoxia-Inducible Factor and glucocorticoid signalling in zebrafish larvae pp. 1-28

Davide Marchi, Kirankumar Santhakumar, Eleanor Markham, Nan Li, Karl-Heinz Storbeck, Nils Krone, Vincent T Cunliffe and Fredericus J M van Eeden

Beyond SNP heritability: Polygenicity and discoverability of phenotypes estimated with a univariate Gaussian mixture model pp. 1-30

Dominic Holland, Oleksandr Frei, Rahul Desikan, Chun-Chieh Fan, Alexey A Shadrin, Olav B Smeland, V S Sundar, Paul Thompson, Ole A Andreassen and Anders M Dale

Simultaneous SNP selection and adjustment for population structure in high dimensional prediction models pp. 1-25

Sahir R Bhatnagar, Yi Yang, Tianyuan Lu, Erwin Schurr, Loredo-Osti Jc, Marie Forest, Karim Oualkacha and Celia M T Greenwood

Scalable probabilistic PCA for large-scale genetic variation data pp. 1-19

Aman Agrawal, Alec M Chiu, Minh Le, Eran Halperin and Sriram Sankararaman

Volume 16, issue 4, 2020

Eliciting priors and relaxing the single causal variant assumption in colocalisation analyses pp. 1-20

Chris Wallace

Technical and social issues influencing the adoption of preprints in the life sciences pp. 1-16

Naomi C Penfold and Jessica K Polka

Leveraging gene co-expression patterns to infer trait-relevant tissues in genome-wide association studies pp. 1-30

Lulu Shang, Jennifer A Smith and Xiang Zhou

Volume 16, issue 3, 2020

Bayesian network analysis incorporating genetic anchors complements conventional Mendelian randomization approaches for exploratory analysis of causal relationships in complex data pp. 1-35

Richard Howey, So-Youn Shin, Caroline Relton, George Davey Smith and Heather J Cordell

Tracking human population structure through time from whole genome sequences pp. 1-23

Ke Wang, Iain Mathieson, Jared O’Connell and Stephan Schiffels

Pleiotropy facilitates local adaptation to distant optima in common ragweed (Ambrosia artemisiifolia) pp. 1-23

Tuomas Hämälä, Amanda J Gorton, David A Moeller and Peter Tiffin

Drosophila insulin-like peptide 2 mediates dietary regulation of sleep intensity pp. 1-26

Elizabeth B Brown, Kreesha D Shah, Richard Faville, Benjamin Kottler and Alex C Keene

A Snf1-related nutrient-responsive kinase antagonizes endocytosis in yeast pp. 1-40

Jessica M Tumolo, Nathaniel L Hepowit, Samika S Joshi and Jason A MacGurn

What is ancestry? pp. 1-6

Iain Mathieson and Aylwyn Scally

The influence of rare variants in circulating metabolic biomarkers pp. 1-19

Fernando Riveros-Mckay, Clare Oliver-Williams, Savita Karthikeyan, Klaudia Walter, Kousik Kundu, Willem H Ouwehand, David Roberts, Emanuele Di Angelantonio, Nicole Soranzo, John Danesh, Study Interval, Eleanor Wheeler, Eleftheria Zeggini, Adam S Butterworth and Inês Barroso

Minority-centric meta-analyses of blood lipid levels identify novel loci in the Population Architecture using Genomics and Epidemiology (PAGE) study pp. 1-19

Yao Hu, Mariaelisa Graff, Jeffrey Haessler, Steven Buyske, Stephanie A Bien, Ran Tao, Heather M Highland, Katherine K Nishimura, Niha Zubair, Yingchang Lu, Marie Verbanck, Austin T Hilliard, Derek Klarin, Scott M Damrauer, Yuk-Lam Ho, the VA Million Veteran Program, Peter W F Wilson, Kyong-Mi Chang, Philip S Tsao, Kelly Cho, Christopher J O’Donnell, Themistocles L Assimes, Lauren E Petty, Jennifer E Below, Ozan Dikilitas, Daniel J Schaid, Matthew L Kosel, Iftikhar J Kullo, Laura J Rasmussen-Torvik, Gail P Jarvik, Qiping Feng, Wei-Qi Wei, Eric B Larson, Frank D Mentch, Berta Almoguera, Patrick M Sleiman, Laura M Raffield, Adolfo Correa, Lisa W Martin, Martha Daviglus, Tara C Matise, Jose Luis Ambite, Christopher S Carlson, Ron Do, Ruth J F Loos, Lynne R Wilkens, Loic Le Marchand, Chris Haiman, Daniel O Stram, Lucia A Hindorff, Kari E North, Charles Kooperberg, Iona Cheng and Ulrike Peters

Volume 16, issue 2, 2020

A molecular barcode to inform the geographical origin and transmission dynamics of Plasmodium vivax malaria pp. 1-19

Ernest Diez Benavente, Monica Campos, Jody Phelan, Debbie Nolder, Jamille G Dombrowski, Claudio R F Marinho, Kanlaya Sriprawat, Aimee R Taylor, James Watson, Cally Roper, Francois Nosten, Colin J Sutherland, Susana Campino and Taane G Clark

Volume 16, issue 1, 2020

The derived allele of a novel intergenic variant at chromosome 11 associates with lower body mass index and a favorable metabolic phenotype in Greenlanders pp. 1-17

Mette K Andersen, Emil Jørsboe, Line Skotte, Kristian Hanghøj, Camilla H Sandholt, Ida Moltke, Niels Grarup, Timo Kern, Yuvaraj Mahendran, Bolette Søborg, Peter Bjerregaard, Christina V L Larsen, Inger K Dahl-Petersen, Hemant K Tiwari, Bjarke Feenstra, Anders Koch, Howard W Wiener, Scarlett E Hopkins, Oluf Pedersen, Mads Melbye, Bert B Boyer, Marit E Jørgensen, Anders Albrechtsen and Torben Hansen

High-throughput discovery of genetic determinants of circadian misalignment pp. 1-25

Tao Zhang, Pancheng Xie, Yingying Dong, Zhiwei Liu, Fei Zhou, Dejing Pan, Zhengyun Huang, Qiaocheng Zhai, Yue Gu, Qingyu Wu, Nobuhiko Tanaka, Yuichi Obata, Allan Bradley, Christopher J Lelliott, Sanger Institute Mouse Genetics Project, Lauryl M J Nutter, Colin McKerlie, Ann M Flenniken, Marie-France Champy, Tania Sorg, Yann Herault, Martin Hrabe De Angelis, Valerie Gailus Durner, Ann-Marie Mallon, Steve D M Brown, Terry Meehan, Helen E Parkinson, Damian Smedley, K C Kent Lloyd, Jun Yan, Xiang Gao, Je Kyung Seong, Chi-Kuang Leo Wang, Radislav Sedlacek, Yi Liu, Jan Rozman, Ling Yang and Ying Xu