PLOS Genetics

2005 - 2022

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Volume 15, issue 12, 2019

Leveraging allelic imbalance to refine fine-mapping for eQTL studies pp. 1-24

Jennifer Zou, Farhad Hormozdiari, Brandon Jew, Stephane E Castel, Tuuli Lappalainen, Jason Ernst, Jae Hoon Sul and Eleazar Eskin

An autism-causing calcium channel variant functions with selective autophagy to alter axon targeting and behavior pp. 1-20

Tyler Buddell, Vladislav Friedman, Cody J Drozd and Christopher C Quinn

Correction: Large-scale genome-wide meta-analysis of polycystic ovary syndrome suggests shared genetic architecture for different diagnosis criteria pp. 1-2

Felix Day, Tugce Karaderi, Michelle R Jones, Cindy Meun, Chunyan He, Alex Drong, Peter Kraft, Nan Lin, Hongyan Huang, Linda Broer, Reedik Magi, Richa Saxena, Triin Laisk, Margrit Urbanek, M Geoffrey Hayes, Gudmar Thorleifsson, Juan Fernandez-Tajes, Anubha Mahajan, Benjamin H Mullin, Bronwyn G A Stuckey, Timothy D Spector, Scott G Wilson, Mark O Goodarzi, Lea Davis, Barbara Obermayer-Pietsch, André G Uitterlinden, Verneri Anttila, Benjamin M Neale, Marjo-Riitta Jarvelin, Bart Fauser, Irina Kowalska, Jenny A Visser, Marianne Andersen, Ken Ong, Elisabet Stener-Victorin, David Ehrmann, Richard S Legro, Andres Salumets, Mark I McCarthy, Laure Morin-Papunen, Unnur Thorsteinsdottir, Kari Stefansson, the 23andMe Research Team, Unnur Styrkarsdottir, John R B Perry, Andrea Dunaif, Joop Laven, Steve Franks, Cecilia M Lindgren and Corrine K Welt

Crossover interference and sex-specific genetic maps shape identical by descent sharing in close relatives pp. 1-29

Madison Caballero, Daniel N Seidman, Ying Qiao, Jens Sannerud, Thomas D Dyer, Donna M Lehman, Joanne E Curran, Ravindranath Duggirala, John Blangero, Shai Carmi and Amy L Williams

Common gardens in teosintes reveal the establishment of a syndrome of adaptation to altitude pp. 1-34

Margaux-Alison Fustier, Natalia E Martínez-Ainsworth, Jonás A Aguirre-Liguori, Anthony Venon, Hélène Corti, Agnès Rousselet, Fabrice Dumas, Hannes Dittberner, María G Camarena, Daniel Grimanelli, Otso Ovaskainen, Matthieu Falque, Laurence Moreau, Juliette de Meaux, Salvador Montes-Hernández, Luis E Eguiarte, Yves Vigouroux, Domenica Manicacci and Maud I Tenaillon

Volume 15, issue 11, 2019

Microbial phenotypic heterogeneity in response to a metabolic toxin: Continuous, dynamically shifting distribution of formaldehyde tolerance in Methylobacterium extorquens populations pp. 1-38

Jessica A Lee, Siavash Riazi, Shahla Nemati, Jannell V Bazurto, Andreas E Vasdekis, Benjamin J Ridenhour, Christopher H Remien and Christopher J Marx

UMAP reveals cryptic population structure and phenotype heterogeneity in large genomic cohorts pp. 1-24

Alex Diaz-Papkovich, Luke Anderson-Trocmé, Chief Ben-Eghan and Simon Gravel

Contribution of Common Genetic Variants to Familial Aggregation of Disease and Implications for Sequencing Studies pp. 1-15

Andrew Schlafly, Ruth M Pfeiffer, Eduardo Nagore, Susana Puig, Donato Calista, Paola Ghiorzo, Chiara Menin, Maria Concetta Fargnoli, Ketty Peris, Lei Song, Tongwu Zhang, Jianxin Shi, Maria Teresa Landi and Joshua Neil Sampson

A meta-analysis of genome-wide association studies of epigenetic age acceleration pp. 1-30

Jude Gibson, Tom C Russ, Toni-Kim Clarke, David M Howard, Robert F Hillary, Kathryn L Evans, Rosie M Walker, Mairead L Bermingham, Stewart W Morris, Archie Campbell, Caroline Hayward, Alison D Murray, David J Porteous, Steve Horvath, Ake T Lu, Andrew M McIntosh, Heather C Whalley and Riccardo E Marioni

Inference of recombination maps from a single pair of genomes and its application to ancient samples pp. 1-21

Gustavo V. Barroso, Nataša Puzović and Julien Y Dutheil

Volume 15, issue 10, 2019

Differential Requirements for the RAD51 Paralogs in Genome Repair and Maintenance in Human Cells pp. 1-29

Edwige B Garcin, Stéphanie Gon, Meghan R Sullivan, Gregory J Brunette, Anne De Cian, Jean-Paul Concordet, Carine Giovannangeli, Wilhelm G Dirks, Sonja Eberth, Kara A Bernstein, Rohit Prakash, Maria Jasin and Mauro Modesti

Bayesian multivariate reanalysis of large genetic studies identifies many new associations pp. 1-18

Michael C Turchin and Matthew Stephens

Volume 15, issue 9, 2019

Native American admixture recapitulates population-specific migration and settlement of the continental United States pp. 1-23

I King Jordan, Lavanya Rishishwar and Andrew B Conley

Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development pp. 1-20

Jian Zhou, Ignacio E Schor, Victoria Yao, Chandra L Theesfeld, Raquel Marco-Ferreres, Alicja Tadych, Eileen E M Furlong and Olga G Troyanskaya

Correction: Suicidal Autointegration of Sleeping Beauty and piggyBac Transposons in Eukaryotic Cells pp. 1-1

Yongming Wang, Jichang Wang, Anatharam Devaraj, Manvendra Singh, Ana Jimenez Orgaz, Jia-Xuan Chen, Matthias Selbach, Zoltán Ivics and Zsuzsanna Izsvák

The inference of sex-biased human demography from whole-genome data pp. 1-25

Shaila Musharoff, Suyash Shringarpure, Carlos D Bustamante and Sohini Ramachandran

An approximate full-likelihood method for inferring selection and allele frequency trajectories from DNA sequence data pp. 1-32

Aaron J Stern, Peter R Wilton and Rasmus Nielsen

Volume 15, issue 8, 2019

A region-based gene association study combined with a leave-one-out sensitivity analysis identifies SMG1 as a pancreatic cancer susceptibility gene pp. 1-20

Cavin Wong, Fei Chen, Najmeh Alirezaie, Yifan Wang, Adeline Cuggia, Ayelet Borgida, Spring Holter, Tatiana Lenko, Celine Domecq, Alzheimer’s Disease Neuroimaging Initiative, Gloria M Petersen, Sapna Syngal, Randall Brand, Anil K Rustgi, Michele L Cote, Elena Stoffel, Sara H Olson, Nicholas J Roberts, Mohammad R Akbari, Jacek Majewski, Alison P Klein, Celia M T Greenwood, Steven Gallinger and George Zogopoulos

An estimator of first coalescent time reveals selection on young variants and large heterogeneity in rare allele ages among human populations pp. 1-25

Alexander Platt, Alyssa Pivirotto, Jared Knoblauch and Jody Hey

Volume 15, issue 7, 2019

Novel protective and risk loci in hip dysplasia in German Shepherds pp. 1-30

Lea I Mikkola, Saila Holopainen, Anu K Lappalainen, Tiina Pessa-Morikawa, Thomas J P Augustine, Meharji Arumilli, Marjo K Hytönen, Osmo Hakosalo, Hannes Lohi and Antti Iivanainen

Correction: Quorum sensing and stress-activated MAPK signaling repress yeast to hypha transition in the fission yeast Schizosaccharomyces japonicus pp. 1-1

Elisa Gómez-Gil, Alejandro Franco, Marisa Madrid, Beatriz Vázquez-Marín, Mariano Gacto, Jesualdo Fernández-Breis, Jero Vicente-Soler, Teresa Soto and José Cansado

Volume 15, issue 6, 2019

Solving the missing heritability problem pp. 1-7

Alexander I Young

Host-dependent nitrogen recycling as a mechanism of symbiont control in Aiptasia pp. 1-19

Guoxin Cui, Yi Jin Liew, Yong Li, Najeh Kharbatia, Noura I Zahran, Abdul-Hamid Emwas, Victor M Eguiluz and Manuel Aranda

Volume 15, issue 5, 2019

An integrative association method for omics data based on a modified Fisher’s method with application to childhood asthma pp. 1-18

Qi Yan, Nianjun Liu, Erick Forno, Glorisa Canino, Juan C Celedón and Wei Chen

A statistical model for reference-free inference of archaic local ancestry pp. 1-18

Arun Durvasula and Sriram Sankararaman

Estimating variance components in population scale family trees pp. 1-22

Tal Shor, Iris Kalka, Dan Geiger, Yaniv Erlich and Omer Weissbrod

The evolution of hybrid fitness during speciation pp. 1-21

Andrius J Dagilis, Mark Kirkpatrick and Daniel I Bolnick

Volume 15, issue 4, 2019

Associations of variants In the hexokinase 1 and interleukin 18 receptor regions with oxyhemoglobin saturation during sleep pp. 1-31

Brian E Cade, Han Chen, Adrienne M Stilp, Tin Louie, Sonia Ancoli-Israel, Raanan Arens, Richard Barfield, Jennifer E Below, Jianwen Cai, Matthew P Conomos, Daniel S Evans, Alexis C Frazier-Wood, Sina A Gharib, Kevin J Gleason, Daniel J Gottlieb, David R Hillman, W Craig Johnson, David J Lederer, Jiwon Lee, Jose S Loredo, Hao Mei, Sutapa Mukherjee, Sanjay R Patel, Wendy S Post, Shaun M Purcell, Alberto R Ramos, Kathryn J Reid, Ken Rice, Neomi A Shah, Tamar Sofer, Kent D Taylor, Timothy A Thornton, Heming Wang, Kristine Yaffe, Phyllis C Zee, Craig L Hanis, Lyle J Palmer, Jerome I Rotter, Katie L Stone, Gregory J Tranah, James G Wilson, Shamil R Sunyaev, Cathy C Laurie, Xiaofeng Zhu, Richa Saxena, Xihong Lin and Susan Redline

Reverse GWAS: Using genetics to identify and model phenotypic subtypes pp. 1-22

Andy Dahl, Na Cai, Arthur Ko, Markku Laakso, Päivi Pajukanta, Jonathan Flint and Noah Zaitlen

Genome-wide association study reveals sex-specific genetic architecture of facial attractiveness pp. 1-18

Bowen Hu, Ning Shen, James J Li, Hyunseung Kang, Jinkuk Hong, Jason Fletcher, Jan Greenberg, Marsha R Mailick and Qiongshi Lu

Genome-wide association study in Turkish and Iranian populations identify rare familial Mediterranean fever gene (MEFV) polymorphisms associated with ankylosing spondylitis pp. 1-18

Zhixiu Li, Servet Akar, Handan Yarkan, Sau Kuen Lee, Pınar Çetin, Gerçek Can, Gökce Kenar, Fernur Çapa, Omer Nuri Pamuk, Yavuz Pehlivan, Katie Cremin, Erika De Guzman, Jessica Harris, Lawrie Wheeler, Ahmadreza Jamshidi, Mahdi Vojdanian, Elham Farhadi, Nooshin Ahmadzadeh, Zeynep Yüce, Ediz Dalkılıç, Dilek Solmaz, Berrin Akın, Salim Dönmez, İsmail Sarı, Paul J Leo, Tony J Kenna, Fatos Önen, Mahdi Mahmoudi, Matthew A Brown and Nurullah Akkoc

FunSPU: A versatile and adaptive multiple functional annotation-based association test of whole-genome sequencing data pp. 1-21

Yiding Ma and Peng Wei

Correction: Genetic variants influence on the placenta regulatory landscape pp. 1-1

Fabien Delahaye, Catherine Do, Yu Kong, Remi Ashkar, Martha Salas, Ben Tycko, Ronald Wapner and Francine Hughes

Discovery and characterization of variance QTLs in human induced pluripotent stem cells pp. 1-16

Abhishek K Sarkar, Po-Yuan Tung, John D Blischak, Jonathan E Burnett, Yang I Li, Matthew Stephens and Yoav Gilad

Volume 15, issue 3, 2019

Powerful gene set analysis in GWAS with the Generalized Berk-Jones statistic pp. 1-27

Ryan Sun, Shirley Hui, Gary D Bader, Xihong Lin and Peter Kraft

Genetic effects on the commensal microbiota in inflammatory bowel disease patients pp. 1-25

Hugues Aschard, Vincent Laville, Eric Tchetgen Tchetgen, Dan Knights, Floris Imhann, Philippe Seksik, Noah Zaitlen, Mark S Silverberg, Jacques Cosnes, Rinse K Weersma, Ramnik Xavier, Laurent Beaugerie, David Skurnik and Harry Sokol

Volume 15, issue 2, 2019

Searching for the causal effects of body mass index in over 300 000 participants in UK Biobank, using Mendelian randomization pp. 1-20

Louise A C Millard, Neil M Davies, Kate Tilling, Tom R Gaunt and George Davey Smith

Fast and flexible linear mixed models for genome-wide genetics pp. 1-24

Daniel E Runcie and Lorin Crawford

Transcription-dependent spreading of the Dal80 yeast GATA factor across the body of highly expressed genes pp. 1-31

Aria Ronsmans, Maxime Wery, Ugo Szachnowski, Camille Gautier, Marc Descrimes, Evelyne Dubois, Antonin Morillon and Isabelle Georis

Spatial soft sweeps: Patterns of adaptation in populations with long-range dispersal pp. 1-29

Jayson Paulose, Joachim Hermisson and Oskar Hallatschek

Genetic association and transcriptome integration identify contributing genes and tissues at cystic fibrosis modifier loci pp. 1-36

Jiafen Gong, Fan Wang, Bowei Xiao, Naim Panjwani, Fan Lin, Katherine Keenan, Julie Avolio, Mohsen Esmaeili, Lin Zhang, Gengming He, David Soave, Scott Mastromatteo, Zeynep Baskurt, Sangook Kim, Wanda K O’Neal, Deepika Polineni, Scott M Blackman, Harriet Corvol, Garry R Cutting, Mitchell Drumm, Michael R Knowles, Johanna M Rommens, Lei Sun and Lisa J Strug

Stress response, behavior, and development are shaped by transposable element-induced mutations in Drosophila pp. 1-33

Gabriel E Rech, María Bogaerts-Márquez, Maite G Barrón, Miriam Merenciano, José Luis Villanueva-Cañas, Vivien Horváth, Anna-Sophie Fiston-Lavier, Isabelle Luyten, Sandeep Venkataram, Hadi Quesneville, Dmitri A Petrov and Josefa González

Volume 15, issue 1, 2019

Diapause induces functional axonal regeneration after necrotic insult in C. elegans pp. 1-32

Mauricio Caneo, Victoria Julian, Alexandra B Byrne, Mark J Alkema and Andrea Calixto

Correction: Human demographic history has amplified the effects of background selection across the genome pp. 1-1

Raul Torres, Zachary A Szpiech and Ryan D Hernandez

Correction: Loss of the Mia40a oxidoreductase leads to hepato-pancreatic insufficiency in zebrafish pp. 1-1

Anna M Sokol, Barbara Uszczynska-Ratajczak, Michelle M Collins, Michal Bazala, Ulrike Topf, Pia R Lundegaard, Sreedevi Sugunan, Stefan Guenther, Carsten Kuenne, Johannes Graumann, Sherine S L Chan, Didier Y R Stainier and Agnieszka Chacinska

Estimating recent migration and population-size surfaces pp. 1-21

Hussein Al-Asadi, Desislava Petkova, Matthew Stephens and John Novembre

Genetic architecture of human thinness compared to severe obesity pp. 1-25

Fernando Riveros-McKay, Vanisha Mistry, Rebecca Bounds, Audrey Hendricks, Julia M Keogh, Hannah Thomas, Elana Henning, Laura J Corbin, Understanding Society Scientific Group, Stephen O’Rahilly, Eleftheria Zeggini, Eleanor Wheeler, Inês Barroso and I Sadaf Farooqi

Integrating predicted transcriptome from multiple tissues improves association detection pp. 1-20

Alvaro N Barbeira, Milton Pividori, Jiamao Zheng, Heather E Wheeler, Dan L Nicolae and Hae Kyung Im

Admixture mapping reveals evidence of differential multiple sclerosis risk by genetic ancestry pp. 1-27

Calvin Chi, Xiaorong Shao, Brooke Rhead, Edlin Gonzales, Jessica B Smith, Anny H Xiang, Jennifer Graves, Amy Waldman, Timothy Lotze, Teri Schreiner, Bianca Weinstock-Guttman, Gregory Aaen, Jan-Mendelt Tillema, Jayne Ness, Meghan Candee, Lauren Krupp, Mark Gorman, Leslie Benson, Tanuja Chitnis, Soe Mar, Anita Belman, Theron Charles Casper, John Rose, Manikum Moodley, Mary Rensel, Moses Rodriguez, Benjamin Greenberg, Llana Kahn, Jennifer Rubin, Catherine Schaefer, Emmanuelle Waubant, Annette Langer-Gould and Lisa F Barcellos

Allele-specific RNA imaging shows that allelic imbalances can arise in tissues through transcriptional bursting pp. 1-29

Orsolya Symmons, Marcello Chang, Ian A Mellis, Jennifer M Kalish, Jihwan Park, Katalin Suszták, Marisa S Bartolomei and Arjun Raj