Strategies to investigate and mitigate collider bias in genetic and Mendelian randomisation studies of disease progression

Ruth E. Mitchell, April E. Hartley, Venexia M. Walker, Apostolos Gkatzionis, James Yarmolinsky, Joshua A. Bell, Amanda H. W. Chong, Lavinia Paternoster, Kate Tilling, George Davey Smith

PLOS Genetics: published February 23, 2023 | https://doi.org/10.1371/journal.pgen.1010596

QTL study reveals candidate genes underlying host resistance in a Red Queen model system

Maridel Fredericksen, Peter D. Fields, Louis Du Pasquier, Virginie Ricci, Dieter Ebert

PLOS Genetics: published February 2, 2023 | https://doi.org/10.1371/journal.pgen.1010570

Buffered EGFR signaling regulated by spitz-to-argos expression ratio is a critical factor for patterning the Drosophila eye

Nikhita Pasnuri, Manish Jaiswal, Krishanu Ray, Aprotim Mazumder

PLOS Genetics: published February 2, 2023 | https://doi.org/10.1371/journal.pgen.1010622

A genetic strategy to measure insulin signaling regulation and physiology in Drosophila

Deborah D. Tsao, Kathleen R. Chang, Lutz Kockel, Sangbin Park, Seung K. Kim

PLOS Genetics: published February 2, 2023 | https://doi.org/10.1371/journal.pgen.1010619

Assembly of the 81.6 Mb centromere of pea chromosome 6 elucidates the structure and evolution of metapolycentric chromosomes

Jiří Macas, Laura Ávila Robledillo, Jonathan Kreplak, Petr Novák, Andrea Koblížková, Iva Vrbová, Judith Burstin, Pavel Neumann

PLOS Genetics: published February 3, 2023 | https://doi.org/10.1371/journal.pgen.1010633

RPG interacts with E3-ligase CERBERUS to mediate rhizobial infection in Lotus japonicus

Xiaolin Li, Miaoxia Liu, Min Cai, David Chiasson, Martin Groth, Anne B. Heckmann, Trevor L. Wang, Martin Parniske, J. Allan Downie, Fang Xie

PLOS Genetics: published February 3, 2023 | https://doi.org/10.1371/journal.pgen.1010621

Termination factor Rho mediates transcriptional reprogramming of Bacillus subtilis stationary phase

Vladimir Bidnenko, Pierre Nicolas, Cyprien Guérin, Sandra Dérozier, Arnaud Chastanet, Julien Dairou, Yulia Redko-Hamel, Matthieu Jules, Elena Bidnenko

PLOS Genetics: published February 3, 2023 | https://doi.org/10.1371/journal.pgen.1010618

Spinal cord extracts of amyotrophic lateral sclerosis spread TDP-43 pathology in cerebral organoids

Yoshitaka Tamaki, Jay P. Ross, Paria Alipour, Charles-Étienne Castonguay, Boting Li, Helene Catoire, Daniel Rochefort, Makoto Urushitani, Ryosuke Takahashi, Joshua A. Sonnen, Stefano Stifani, Patrick A. Dion, Guy A. Rouleau

PLOS Genetics: published February 6, 2023 | https://doi.org/10.1371/journal.pgen.1010606

Differential modularity of the mammalian Engrailed 1 enhancer network directs sweat gland development

Daniel Aldea, Blerina Kokalari, Yuji Atsuta, Heather L. Dingwall, Ying Zheng, Arben Nace, George Cotsarelis, Yana G. Kamberov

PLOS Genetics: published February 6, 2023 | https://doi.org/10.1371/journal.pgen.1010614

Rad51 filaments assembled in the absence of the complex formed by the Rad51 paralogs Rad55 and Rad57 are outcompeted by translesion DNA polymerases on UV-induced ssDNA gaps

Laurent Maloisel, Emilie Ma, Jamie Phipps, Alice Deshayes, Stefano Mattarocci, Stéphane Marcand, Karine Dubrana, Eric Coïc

PLOS Genetics: published February 7, 2023 | https://doi.org/10.1371/journal.pgen.1010639

PRSet: Pathway-based polygenic risk score analyses and software

Shing Wan Choi, Judit García-González, Yunfeng Ruan, Hei Man Wu, Christian Porras, Jessica Johnson, Bipolar Disorder Working group of the Psychiatric Genomics Consortium, Clive J. Hoggart, Paul F. O’Reilly

PLOS Genetics: published February 7, 2023 | https://doi.org/10.1371/journal.pgen.1010624

GWAS on retinal vasculometry phenotypes

Xiaofan Jiang, Pirro G. Hysi, Anthony P. Khawaja, Omar A. Mahroo, Zihe Xu, Christopher J. Hammond, Paul J. Foster, Roshan A. Welikala, Sarah A. Barman, Peter H. Whincup, Alicja R. Rudnicka, Christopher G. Owen, David P. Strachan, The UK Biobank Eye and Vision Consortium

PLOS Genetics: published February 9, 2023 | https://doi.org/10.1371/journal.pgen.1010583

The piRNA cluster torimochi is an expanding transposon in cultured silkworm cells

Keisuke Shoji, Yusuke Umemura, Susumu Katsuma, Yukihide Tomari

PLOS Genetics: published February 9, 2023 | https://doi.org/10.1371/journal.pgen.1010632

Stepwise recombination suppression around the mating-type locus in an ascomycete fungus with self-fertile spores

Nina Vittorelli, Ricardo C. Rodríguez de la Vega, Alodie Snirc, Emilie Levert, Valérie Gautier, Christophe Lalanne, Elsa De Filippo, Pierre Gladieux, Sonia Guillou, Yu Zhang, Sravanthi Tejomurthula, Igor V. Grigoriev, Robert Debuchy, Philippe Silar, Tatiana Giraud, Fanny E. Hartmann

PLOS Genetics: published February 10, 2023 | https://doi.org/10.1371/journal.pgen.1010347

A ZTF-7/RPS-2 complex mediates the cold-warm response in C. elegans

Ting Xu, Shimiao Liao, Meng Huang, Chengming Zhu, Xiaona Huang, Qile Jin, Demin Xu, Chuanhai Fu, Xiangyang Chen, Xuezhu Feng, Shouhong Guang

PLOS Genetics: published February 10, 2023 | https://doi.org/10.1371/journal.pgen.1010628

Copy number footprints of platinum-based anticancer therapies

Santiago Gonzalez, Nuria Lopez-Bigas, Abel Gonzalez-Perez

PLOS Genetics: published February 13, 2023 | https://doi.org/10.1371/journal.pgen.1010634

Bayesian inference of admixture graphs on Native American and Arctic populations

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

PLOS Genetics: published February 13, 2023 | https://doi.org/10.1371/journal.pgen.1010410

Timing of integration into the chromosome is critical for the fitness of an integrative and conjugative element and its bacterial host

Saria A. McKeithen-Mead, Alan D. Grossman

PLOS Genetics: published February 13, 2023 | https://doi.org/10.1371/journal.pgen.1010524

Biosynthetic constraints on amino acid synthesis at the base of the food chain may determine their use in higher-order consumer genomes

Javier Gómez Ortega, David Raubenheimer, Sonika Tyagi, Christen K. Mirth, Matthew D. W. Piper

PLOS Genetics: published February 13, 2023 | https://doi.org/10.1371/journal.pgen.1010635

Pharmacological vitamin C inhibits mTOR signaling and tumor growth by degrading Rictor and inducing HMOX1 expression

Senlin Qin, Guoyan Wang, Lei Chen, Huijun Geng, Yining Zheng, Chao Xia, Shengru Wu, Junhu Yao, Lu Deng

PLOS Genetics: published February 14, 2023 | https://doi.org/10.1371/journal.pgen.1010629

The nutrient-responsive CDK Pho85 primes the Sch9 kinase for its activation by TORC1

Marie-Anne Deprez, Marco Caligaris, Joëlle Rosseels, Riko Hatakeyama, Ruben Ghillebert, Belém Sampaio-Marques, Kaivalya Mudholkar, Elja Eskes, Els Meert, Christian Ungermann, Paula Ludovico, Sabine Rospert, Claudio De Virgilio, Joris Winderickx

PLOS Genetics: published February 15, 2023 | https://doi.org/10.1371/journal.pgen.1010641

Germline protein, Cup, non-cell autonomously limits migratory cell fate in Drosophila oogenesis

Banhisikha Saha, Sayan Acharjee, Gaurab Ghosh, Purbasa Dasgupta, Mohit Prasad

PLOS Genetics: published February 15, 2023 | https://doi.org/10.1371/journal.pgen.1010631

Functional impact of subunit composition and compensation on Drosophila melanogaster nicotinic receptors–targets of neonicotinoids

Yuma Komori, Koichi Takayama, Naoki Okamoto, Masaki Kamiya, Wataru Koizumi, Makoto Ihara, Daitaro Misawa, Kotaro Kamiya, Yuto Yoshinari, Kazuki Seike, Shu Kondo, Hiromu Tanimoto, Ryusuke Niwa, David B. Sattelle, Kazuhiko Matsuda

PLOS Genetics: published February 16, 2023 | https://doi.org/10.1371/journal.pgen.1010522

A novel role for trithorax in the gene regulatory network for a rapidly evolving fruit fly pigmentation trait

Michael L. Weinstein, Chad M. Jaenke, Hasiba Asma, Matthew Spangler, Katherine A. Kohnen, Claire C. Konys, Melissa E. Williams, Ashley V. Williams, Mark Rebeiz, Marc S. Halfon, Thomas M. Williams

PLOS Genetics: published February 16, 2023 | https://doi.org/10.1371/journal.pgen.1010653

Escape from X-inactivation in twins exhibits intra- and inter-individual variability across tissues and is heritable

Antonino Zito, Amy L. Roberts, Alessia Visconti, Niccolo’ Rossi, Rosa Andres-Ejarque, Stefano Nardone, Julia S. El-Sayed Moustafa, Mario Falchi, Kerrin S. Small

PLOS Genetics: published February 21, 2023 | https://doi.org/10.1371/journal.pgen.1010556

GRAS-1 is a novel regulator of early meiotic chromosome dynamics in C. elegans

Marina Martinez-Garcia, Pedro Robles Naharro, Marnie W. Skinner, Kerstin A. Baran, Laura I. Lascarez-Lagunas, Saravanapriah Nadarajan, Nara Shin, Carlos G. Silva-García, Takamune T. Saito, Sara Beese-Sims, Brianna N. Diaz-Pacheco, Elizaveta Berson, Ana B. Castañer, Sarai Pacheco, Enrique Martinez-Perez, Philip W. Jordan, Monica P. Colaiácovo

PLOS Genetics: published February 21, 2023 | https://doi.org/10.1371/journal.pgen.1010666

ARHGAP15 promotes metastatic colonization in gastric cancer by suppressing RAC1-ROS pathway

Fei-fei Zhang, Chen Jiang, Dong-ping Jiang, Yu-zhu Cui, Xin-yue Wang, Liang-zhan Sun, Miao Chen, Ka-On Lam, Sha-yi Wu, Krista Verhoeft, Dora Lai-wan Kwong, Xin-Yuan Guan

PLOS Genetics: published February 21, 2023 | https://doi.org/10.1371/journal.pgen.1010640

Off-target piRNA gene silencing in Drosophila melanogaster rescued by a transposable element insertion

Danny E. Miller, Ana P. Dorador, Kelley Van Vaerenberghe, Angela Li, Emily K. Grantham, Stefan Cerbin, Celeste Cummings, Marilyn Barragan, Rhonda R. Egidy, Allison R. Scott, Kate E. Hall, Anoja Perera, William D. Gilliland, R. Scott Hawley, Justin P. Blumenstiel

PLOS Genetics: published February 21, 2023 | https://doi.org/10.1371/journal.pgen.1010598

CLOCK and TIMELESS regulate rhythmic occupancy of the BRAHMA chromatin-remodeling protein at clock gene promoters

Christine A. Tabuloc, Yao D. Cai, Rosanna S. Kwok, Elizabeth C. Chan, Sergio Hidalgo, Joanna C. Chiu

PLOS Genetics: published February 21, 2023 | https://doi.org/10.1371/journal.pgen.1010649

Long-read sequencing identifies novel structural variations in colorectal cancer

Luming Xu, Xingyue Wang, Xiaohuan Lu, Fan Liang, Zhibo Liu, Hongyan Zhang, Xiaoqiong Li, ShaoBo Tian, Lin Wang, Zheng Wang

PLOS Genetics: published February 22, 2023 | https://doi.org/10.1371/journal.pgen.1010514

Long divergent haplotypes introgressed from wild sheep are associated with distinct morphological and adaptive characteristics in domestic sheep

Hong Cheng, Zhuangbiao Zhang, Jiayue Wen, Johannes A. Lenstra, Rasmus Heller, Yudong Cai, Yingwei Guo, Ming Li, Ran Li, Wenrong Li, Sangang He, Jintao Wang, Junjie Shao, Yuxuan Song, Lei Zhang, Masum Billah, Xihong Wang, Mingjun Liu, Yu Jiang

PLOS Genetics: published February 23, 2023 | https://doi.org/10.1371/journal.pgen.1010615

Modeling and predicting the overlap of B- and T-cell receptor repertoires in healthy and SARS-CoV-2 infected individuals

María Ruiz Ortega, Natanael Spisak, Thierry Mora, Aleksandra M. Walczak

PLOS Genetics: published February 24, 2023 | https://doi.org/10.1371/journal.pgen.1010652

Why does the X chromosome lag behind autosomes in GWAS findings?

Ivan P. Gorlov, Christopher I. Amos

PLOS Genetics: published February 27, 2023 | https://doi.org/10.1371/journal.pgen.1010472

Allelic contribution of Nrxn1α to autism-relevant behavioral phenotypes in mice

Bing Xu, Yugong Ho, Maria Fasolino, Joanna Medina, William Timothy O’Brien, Janine M. Lamonica, Erin Nugent, Edward S. Brodkin, Marc V. Fuccillo, Maja Bucan, Zhaolan Zhou

PLOS Genetics: published February 27, 2023 | https://doi.org/10.1371/journal.pgen.1010659

Sub-cellular level resolution of common genetic variation in the photoreceptor layer identifies continuum between rare disease and common variation

Hannah Currant, Tomas W. Fitzgerald, Praveen J. Patel, Anthony P. Khawaja, UK Biobank Eye and Vision Consortium, Andrew R. Webster, Omar A. Mahroo, Ewan Birney

PLOS Genetics: published February 27, 2023 | https://doi.org/10.1371/journal.pgen.1010587

Genetic prevalence and clinical relevance of canine Mendelian disease variants in over one million dogs

Jonas Donner, Jamie Freyer, Stephen Davison, Heidi Anderson, Matthew Blades, Leena Honkanen, Laura Inman, Casey A. Brookhart-Knox, Annette Louviere, Oliver P. Forman, Rebecca Chodroff Foran

PLOS Genetics: published February 27, 2023 | https://doi.org/10.1371/journal.pgen.1010651

Correction: A modified TurboID approach identifies tissue-specific centriolar components in C. elegans

Elisabeth Holzer, Cornelia Rumpf-Kienzl, Sebastian Falk, Alexander Dammermann

PLOS Genetics: published February 13, 2023 | https://doi.org/10.1371/journal.pgen.1010645

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PLOS Genetics: published February 9, 2023 | https://doi.org/10.1371/journal.pgen.1010612

The identification of mediating effects using genome-based restricted maximum likelihood estimation

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

PLOS Genetics: published February 21, 2023 | https://doi.org/10.1371/journal.pgen.1010638