PLOS Genetics

2005 - 2025

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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

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

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

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

Volume 19, issue 10, 2023

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

Souvik Seal, Benjamin G Bitler and Debashis Ghosh

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

Volume 19, issue 9, 2023

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

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

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

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

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

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

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 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

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

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

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

Volume 19, issue 6, 2023

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

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

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

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

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

Volume 19, issue 1, 2023

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 Fletcher and Qiongshi Lu

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

Volume 18, issue 12, 2022

Leveraging pleiotropy to discover and interpret GWAS results for sleep-associated traits pp. 1-34

Sung Chun, Sebastian Akle, Athanasios Teodosiadis, Brian E Cade, Heming Wang, Tamar Sofer, Daniel S Evans, Katie L Stone, Sina A Gharib, Sutapa Mukherjee, Lyle J Palmer, David Hillman, Jerome I Rotter, Craig L Hanis, John A Stamatoyannopoulos, Susan Redline, Chris Cotsapas and Shamil R Sunyaev

Volume 18, issue 11, 2022

Leveraging pleiotropy for joint analysis of genome-wide association studies with per trait interpretations pp. 1-24

Kodi Taraszka, Noah Zaitlen and Eleazar Eskin

Exome-wide association study to identify rare variants influencing COVID-19 outcomes: Results from the Host Genetics Initiative pp. 1-26

Guillaume Butler-Laporte, Gundula Povysil, Jack A Kosmicki, Elizabeth T Cirulli, Theodore Drivas, Simone Furini, Chadi Saad, Axel Schmidt, Pawel Olszewski, Urszula Korotko, Mathieu Quinodoz, Elifnaz Çelik, Kousik Kundu, Klaudia Walter, Junghyun Jung, Amy D Stockwell, Laura G Sloofman, Daniel M Jordan, Ryan C Thompson, Diane Del Valle, Nicole Simons, Esther Cheng, Robert Sebra, Eric E Schadt, Seunghee Kim-Schulze, Sacha Gnjatic, Miriam Merad, Joseph D Buxbaum, Noam D Beckmann, Alexander W Charney, Bartlomiej Przychodzen, Timothy Chang, Tess D Pottinger, Ning Shang, Fabian Brand, Francesca Fava, Francesca Mari, Karolina Chwialkowska, Magdalena Niemira, Szymon Pula, J Kenneth Baillie, Alex Stuckey, Antonio Salas, Xabier Bello, Jacobo Pardo-Seco, Alberto Gómez-Carballa, Irene Rivero-Calle, Federico Martinón-Torres, Andrea Ganna, Konrad J Karczewski, Kumar Veerapen, Mathieu Bourgey, Guillaume Bourque, Robert JM Eveleigh, Vincenzo Forgetta, David Morrison, David Langlais, Mark Lathrop, Vincent Mooser, Tomoko Nakanishi, Robert Frithiof, Michael Hultström, Miklos Lipcsey, Yanara Marincevic-Zuniga, Jessica Nordlund, Kelly M Schiabor Barrett, William Lee, Alexandre Bolze, Simon White, Stephen Riffle, Francisco Tanudjaja, Efren Sandoval, Iva Neveux, Shaun Dabe, Nicolas Casadei, Susanne Motameny, Manal Alaamery, Salam Massadeh, Nora Aljawini, Mansour S Almutairi, Yaseen M Arabi, Saleh A Alqahtani, Fawz S Al Harthi, Amal Almutairi, Fatima Alqubaishi, Sarah Alotaibi, Albandari Binowayn, Ebtehal A Alsolm, Hadeel El Bardisy, Mohammad Fawzy, Fang Cai, Nicole Soranzo, Adam Butterworth, Host Genetics Initiative Covid-19, DeCOI Host Genetics Group, Multicenter Study (Italy) Gen-Covid, Mount Sinai Clinical Intelligence Center, consortium (Spain) Gen-Covid, GenOMICC Consortium, Japan COVID-19 Task Force, Regeneron Genetics Center, Daniel H Geschwind, Stephanie Arteaga, Alexis Stephens, Manish J Butte, Paul C Boutros, Takafumi N Yamaguchi, Shu Tao, Stefan Eng, Timothy Sanders, Paul J Tung, Michael E Broudy, Yu Pan, Alfredo Gonzalez, Nikhil Chavan, Ruth Johnson, Bogdan Pasaniuc, Brian Yaspan, Sandra Smieszek, Carlo Rivolta, Stephanie Bibert, Pierre-Yves Bochud, Maciej Dabrowski, Pawel Zawadzki, Mateusz Sypniewski, Elżbieta Kaja, Pajaree Chariyavilaskul, Voraphoj Nilaratanakul, Nattiya Hirankarn, Vorasuk Shotelersuk, Monnat Pongpanich, Chureerat Phokaew, Wanna Chetruengchai, Katsushi Tokunaga, Masaya Sugiyama, Yosuke Kawai, Takanori Hasegawa, Tatsuhiko Naito, Ho Namkoong, Ryuya Edahiro, Akinori Kimura, Seishi Ogawa, Takanori Kanai, Koichi Fukunaga, Yukinori Okada, Seiya Imoto, Satoru Miyano, Serghei Mangul, Malak S Abedalthagafi, Hugo Zeberg, Joseph J Grzymski, Nicole L Washington, Stephan Ossowski, Kerstin U Ludwig, Eva C Schulte, Olaf Riess, Marcin Moniuszko, Miroslaw Kwasniewski, Hamdi Mbarek, Said I Ismail, Anurag Verma, David B Goldstein, Krzysztof Kiryluk, Alessandra Renieri, Manuel A R Ferreira and J Brent Richards

COVID-19 and systemic lupus erythematosus genetics: A balance between autoimmune disease risk and protection against infection pp. 1-19

Yuxuan Wang, Suri Guga, Kejia Wu, Zoe Khaw, Konstantinos Tzoumkas, Phil Tombleson, Mary E Comeau, Carl D Langefeld, Deborah S Cunninghame Graham, David L Morris and Timothy J Vyse

A robust and adaptive framework for interaction testing in quantitative traits between multiple genetic loci and exposure variables pp. 1-19

Julian Hecker, Dmitry Prokopenko, Matthew Moll, Sanghun Lee, Wonji Kim, Dandi Qiao, Kirsten Voorhies, Woori Kim, Stijn Vansteelandt, Brian D Hobbs, Michael H Cho, Edwin K Silverman, Sharon M Lutz, Dawn L DeMeo, Scott T Weiss and Christoph Lange

Education interacts with genetic variants near GJD2, RBFOX1, LAMA2, KCNQ5 and LRRC4C to confer susceptibility to myopia pp. 1-20

Rosie Clark, Alfred Pozarickij, Pirro G Hysi, Kyoko Ohno-Matsui, Cathy Williams, Jeremy A Guggenheim and UK Biobank Eye and Vision Consortium

Volume 18, issue 10, 2022

A Prism Vote method for individualized risk prediction of traits in genotype data of Multi-population pp. 1-16

Xiaoxuan Xia, Yexian Zhang, Rui Sun, Yingying Wei, Qi Li, Marc Ka Chun Chong, William Ka Kei Wu, Benny Chung-Ying Zee, Hua Tang and Maggie Haitian Wang

Prioritized candidate causal haplotype blocks in plant genome-wide association studies pp. 1-25

Xing Wu, Wei Jiang, Christopher Fragoso, Jing Huang, Geyu Zhou, Hongyu Zhao and Stephen Dellaporta

Volume 18, issue 9, 2022

Localized variation in ancestral admixture identifies pilocytic astrocytoma risk loci among Latino children pp. 1-13

Shaobo Li, Charleston W K Chiang, Swe Swe Myint, Katti Arroyo, Tsz Fung Chan, Libby Morimoto, Catherine Metayer, Adam J de Smith, Kyle M Walsh and Joseph L Wiemels

Oocyte mitophagy is critical for extended reproductive longevity pp. 1-21

Vanessa Cota, Salman Sohrabi, Rachel Kaletsky and Coleen T Murphy

Neurocognitive trajectory and proteomic signature of inherited risk for Alzheimer’s disease pp. 1-20

Manish D Paranjpe, Mark Chaffin, Sohail Zahid, Scott Ritchie, Jerome I Rotter, Stephen S Rich, Robert Gerszten, Xiuqing Guo, Susan Heckbert, Russ Tracy, John Danesh, Eric S Lander, Michael Inouye, Sekar Kathiresan, Adam S Butterworth and Amit V Khera

Volume 18, issue 7, 2022

Evaluating indirect genetic effects of siblings using singletons pp. 1-16

Laurence J Howe, David M Evans, Gibran Hemani, George Davey Smith and Neil M Davies

Estimating the timing of multiple admixture events using 3-locus linkage disequilibrium pp. 1-17

Mason Liang, Mikhail Shishkin, Anastasia Mikhailova, Vladimir Shchur and Rasmus Nielsen

Fine-mapping from summary data with the “Sum of Single Effects” model pp. 1-24

Yuxin Zou, Peter Carbonetto, Gao Wang and Matthew Stephens

Volume 18, issue 6, 2022

Integrated analysis of direct and proxy genome wide association studies highlights polygenicity of Alzheimer’s disease outside of the APOE region pp. 1-28

Javier de la Fuente, Andrew D Grotzinger, Riccardo E Marioni, Michel G Nivard and Elliot M Tucker-Drob

EPIC: Inferring relevant cell types for complex traits by integrating genome-wide association studies and single-cell RNA sequencing pp. 1-22

Rujin Wang, Dan-Yu Lin and Yuchao Jiang

A multi-population phenome-wide association study of genetically-predicted height in the Million Veteran Program pp. 1-23

Sridharan Raghavan, Jie Huang, Catherine Tcheandjieu, Jennifer E Huffman, Elizabeth Litkowski, Chang Liu, Yuk-Lam A Ho, Haley Hunter-Zinck, Hongyu Zhao, Eirini Marouli, Kari E North, the VA Million Veteran Program, Ethan Lange, Leslie A Lange, Benjamin F Voight, J Michael Gaziano, Saiju Pyarajan, Elizabeth R Hauser, Philip S Tsao, Peter W F Wilson, Kyong-Mi Chang, Kelly Cho, Christopher J O’Donnell, Yan V Sun and Themistocles L Assimes

Volume 18, issue 5, 2022

Sex-heterogeneous SNPs disproportionately influence gene expression and health pp. 1-18

Michela Traglia, Margaux Bout and Lauren A Weiss

Robust inference of bi-directional causal relationships in presence of correlated pleiotropy with GWAS summary data pp. 1-28

Haoran Xue and Wei Pan

A Bayesian model selection approach to mediation analysis pp. 1-33

Wesley L Crouse, Gregory R Keele, Madeleine S Gastonguay, Gary A Churchill and William Valdar

A practical problem with Egger regression in Mendelian randomization pp. 1-19

Zhaotong Lin, Isaac Pan and Wei Pan

Genetic characterization of outbred Sprague Dawley rats and utility for genome-wide association studies pp. 1-29

Alexander F Gileta, Christopher J Fitzpatrick, Apurva S Chitre, Celine L St. Pierre, Elizabeth V Joyce, Rachael J Maguire, Africa M McLeod, Natalia M Gonzales, April E Williams, Jonathan D Morrow, Terry E Robinson, Shelly B Flagel and Abraham A Palmer

Major sex differences in allele frequencies for X chromosomal variants in both the 1000 Genomes Project and gnomAD pp. 1-35

Zhong Wang, Lei Sun and Andrew D Paterson

Volume 18, issue 4, 2022

MiR172-APETALA2-like genes integrate vernalization and plant age to control flowering time in wheat pp. 1-33

Juan M Debernardi, Daniel P Woods, Kun Li, Chengxia Li and Jorge Dubcovsky

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

Michael DeGiorgio and Zachary A Szpiech

Efficient estimation of SNP heritability using Gaussian predictive process in large scale cohort studies pp. 1-19

Souvik Seal, Abhirup Datta and Saonli Basu

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

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

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

Volume 18, issue 2, 2022

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

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

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

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

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

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