Expectations for papers performing Mendelian randomization analyses

Scott M. Williams, Hua Tang, Gregory M. Cooper, Anne O’Donnell-Luria, Santhosh Girirajan, Aimée M. Dudley, Anne Goriely, Zoltán Kutalik, Xiaofeng Zhu, Giorgio Sirugo, Michael P. Epstein

PLOS Genetics: published July 17, 2025 | https://doi.org/10.1371/journal.pgen.1011767

The length and strength of compartmental interactions are modulated by condensin II activity

Randi Isenhart, Son C. Nguyen, Leah Rosin, Weihuan Cao, Patrick Walsh, Haris Muzaffar, Christopher E. Ellison, Eric F. Joyce

PLOS Genetics: published July 1, 2025 | https://doi.org/10.1371/journal.pgen.1011724

Phenotypic tolerance for rDNA copy number variation within the natural range of C. elegans

Ashley N. Hall, Elizabeth A. Morton, Rebecca Walters, Josh T. Cuperus, Christine Queitsch

PLOS Genetics: published July 2, 2025 | https://doi.org/10.1371/journal.pgen.1011759

Cellular imbalance of specific RNA-binding proteins associates with harmful R-loops

José Antonio Mérida-Cerro, Guillaume Chevreux, Benoit Palancade, Ana G. Rondón, Andrés Aguilera

PLOS Genetics: published July 2, 2025 | https://doi.org/10.1371/journal.pgen.1011491

Ubp2 modulates DJ-1-mediated redox-dependent mitochondrial dynamics in Saccharomyces cerevisiae

Sananda Biswas, Patrick D’Silva

PLOS Genetics: published July 3, 2025 | https://doi.org/10.1371/journal.pgen.1011353

SpoIIIL is a forespore factor required for efficient cell-cell signalling during Bacillus subtilis sporulation

Danae Morales Angeles, Kaitlyn Coleman, Chimezie Progress Odika, Chris L. B. Graham, Helena Chan, Michael Gilmore, Najwa Taib, Elda Bauda, Christine Moriscot, Benoit Gallet, Hannah Fisher, Per A. Bullough, Cécile Morlot, Darius Köster, Simonetta Gribaldo, Felipe Cava, Christopher D. A. Rodrigues

PLOS Genetics: published July 3, 2025 | https://doi.org/10.1371/journal.pgen.1011768

Clonal interference and genomic repair during strain coexistence in the gut

Nelson Frazão, Elsa Seixas, Manolo Mischler, Jorge Moura-de-Sousa, Hugo C. Barreto, Isabel Gordo

PLOS Genetics: published July 7, 2025 | https://doi.org/10.1371/journal.pgen.1011777

Genomic organization, domain assortments, and nucleotide-binding domain diversity of NLR proteins in Sordariales fungi

Lucas Bonometti, Florian Charriat, Noah Hensen, Silvia Miñana-Posada, Hanna Johannesson, Pierre Gladieux

PLOS Genetics: published July 7, 2025 | https://doi.org/10.1371/journal.pgen.1011739

Protein sequence editing defines distinct and overlapping functions of SKN-1A/Nrf1 and SKN-1C/Nrf2

Briar Jochim, Irini Topalidou, Nicolas Lehrbach

PLOS Genetics: published July 7, 2025 | https://doi.org/10.1371/journal.pgen.1011780

Clu1/Clu form mitochondria-associated granules upon metabolic transitions and regulate mitochondrial protein translation via ribosome interactions

Leonor Miller-Fleming, Wing Hei Au, Laura Raik, Pedro Rebelo-Guiomar, Jasper Schmitz, Ha Yoon Cho, Aron Czako, Alexander J. Whitworth

PLOS Genetics: published July 7, 2025 | https://doi.org/10.1371/journal.pgen.1011773

Systematically identification of survival-associated eQTLs in a Japanese kidney cancer cohort

Xiya Song, Han Jin, Xiangyu Li, Meng Yuan, Hong Yang, Yusuke Sato, Haruki Kume, Seishi Ogawa, Cheng Zhang, Adil Mardinoglu

PLOS Genetics: published July 7, 2025 | https://doi.org/10.1371/journal.pgen.1011770

The foraging gene coordinates brain and heart networks to modulate socially cued interval timing in Drosophila

Hongyu Miao, Wengjing Li, Yongwen Huang, Woo Jae Kim

PLOS Genetics: published July 8, 2025 | https://doi.org/10.1371/journal.pgen.1011752

L-2-hydroxyglutarate regulates centromere and heterochromatin conformation in the male germline

Nina Mayorek, Miriam Schlossberg, Yousef Mansour, Nir Pillar, Ilan Stein, Fatima Mushasha, Guy Baziza Paz, Eleonora Medvedev, Zakhariya Manevitch, Julia Menzel, Elina Aizenshtein, Boris Sarvin, Nikita Sarvin, Erwin Goldberg, Bryan A. Niedenberger, Christopher B. Geyer, Tomer Shlomi, Michael Klutstein, Eli Pikarsky

PLOS Genetics: published July 10, 2025 | https://doi.org/10.1371/journal.pgen.1011785

Nuclear p62/SQSTM1 facilitates ubiquitin-independent proteasomal degradation of BMAL1

Chenliang Zhang, Quanyou Wu, Huan Zhang, Ruichen Liu, Liping Li

PLOS Genetics: published July 10, 2025 | https://doi.org/10.1371/journal.pgen.1011794

Experimental evolution partially restores functionality of bacterial chemotaxis network with reduced number of components

Manika Kargeti, Irina Kalita, Sarah Hoch, Maryia Ratnikava, Wenhao Xu, Bin Ni, Ron L. Dy, Remy Colin, Victor Sourjik

PLOS Genetics: published July 10, 2025 | https://doi.org/10.1371/journal.pgen.1011784

Doublesex and GATAβ4 synergistically regulate the sex-dimorphic expression of storage protein 1 in Bombyx mori

Jiamin Yan, Haonan Dong, Tingting Tian, Chunxia Xiao, Yuanyuan Sun, Jing Gong, Qingyou Xia, Yong Hou

PLOS Genetics: published July 11, 2025 | https://doi.org/10.1371/journal.pgen.1011762

Discovery of oligodendrocyte enhancers that regulate Sox10 expression

Hongjoo An, Chuandong Fan, Dongkyeong Kim, Huy Bui, Yungki Park

PLOS Genetics: published July 11, 2025 | https://doi.org/10.1371/journal.pgen.1011778

MYH11 rare variant augments aortic growth and induces cardiac hypertrophy and heart failure with pressure overload

Zhen Zhou, Kgosi Hughes, Nisha Saif, Hyoseon Kim, Michael P. Massett, Mingjie Zheng, Alana C. Cecchi, Dongchuan Guo, David R. Murdock, Ping Pan, Jelita S. Clinton, Jun Wang, John M. Greally, Dianna M. Milewicz

PLOS Genetics: published July 14, 2025 | https://doi.org/10.1371/journal.pgen.1011394

Semaphorin 3f and post-embryonic regulation of retinal progenitors

Amira Kalifa, Carrie L. Hehr, Katelyn L. Shewchuk, Risa Mori-Kreiner, Shaelene Standing, Rami Halabi, Sarah McFarlane

PLOS Genetics: published July 14, 2025 | https://doi.org/10.1371/journal.pgen.1011748

Shaping and interpretation of Dpp morphogen gradient by endocytic trafficking

Sheida Hadji Rasouliha, Gustavo Aguilar, Cindy Reinger, Shinya Matsuda

PLOS Genetics: published July 14, 2025 | https://doi.org/10.1371/journal.pgen.1011766

Bayesian network imputation methods applied to multi-omics data identify putative causal relationships in a type 2 diabetes dataset containing incomplete data: An IMI DIRECT Study

Richard Howey, Jonathan Adam, Jerzy Adamski, Natalie N. Atabaki, Søren Brunak, Piotr Jaroslaw Chmura, Federico De Masi, Emmanouil T. Dermitzakis, Juan J. Fernandez-Tajes, Ian M. Forgie, Paul W. Franks, Giuseppe N. Giordano, Mark Haid, Torben Hansen, Tue H. Hansen, Peter P. Harms, Andrew T. Hattersley, Mun-gwan Hong, Ulrik Plesner Jacobsen, Angus G. Jones, Robert W. Koivula, Tarja Kokkola, Anubha Mahajan, Andrea Mari, Mark I. McCarthy, Timothy J. McDonald, Petra B. Musholt, Imre Pavo, Ewan R. Pearson, Oluf Pedersen, Hartmut Ruetten, Femke Rutters, Jochen M. Schwenk, Sapna Sharma, Leen M. ’t Hart, Henrik Vestergaard, Mark Walker, The IMI DIRECT Consortium, Ana Viñuela, Heather J. Cordell

PLOS Genetics: published July 15, 2025 | https://doi.org/10.1371/journal.pgen.1011776

Four ZIPs contribute to Zn, Fe, Cu and Mn acquisition at the outer root domain

Kevin Robe, Linnka Lefebvre-Legendre, Fabienne Cleard, Marie Barberon

PLOS Genetics: published July 15, 2025 | https://doi.org/10.1371/journal.pgen.1011796

Genetic and environmental influences on the distributions of three chromosomal drive haplotypes in maize

Meghan J. Brady, R. Kelly Dawe

PLOS Genetics: published July 16, 2025 | https://doi.org/10.1371/journal.pgen.1011742

The heme-regulated inhibitor kinase Hri1 is activated in response to aminolevulinic acid deficiency in Schizosaccharomyces pombe

Samuel Plante, Ariane Brault, Mariano Avino, Hajer Sakouhi, Florie Lo Ying Ping, Tobias Vahsen, Simon Labbé

PLOS Genetics: published July 16, 2025 | https://doi.org/10.1371/journal.pgen.1011797

Genetic disruption of the baculum compromises the ability of male mice to copulate

Caleb R. Ghione, Nicholas G. Schultz, Sungdae Park, Douglas B. Menke, Matthew D. Dean

PLOS Genetics: published July 16, 2025 | https://doi.org/10.1371/journal.pgen.1011787

Molecular circuit between Aspergillus nidulans transcription factors MsnA and VelB to coordinate fungal stress and developmental responses

Emmanouil Bastakis, Jennifer Gerke, Seyma Özkan, Rebekka Harting, Tanja Lienard, Christoph Sasse, Emmanouil S. Xylakis, Merle Aden, Anja Strohdiek, Gabriele Heinrich, Verena Grosse, Gerhard H. Braus

PLOS Genetics: published July 17, 2025 | https://doi.org/10.1371/journal.pgen.1011578

The insulin-like peptide INS-27 mediates a muscle-to-neuron feedback signal coupling muscle activity with AMPA receptor trafficking

Bethany J. Rennich, Regina M. Powers, Samantha Moores, Molly Hodul, Peter Juo

PLOS Genetics: published July 18, 2025 | https://doi.org/10.1371/journal.pgen.1011786

Reversion of a RND transporter pseudogene reveals latent stress resistance potential in Brucella ovis

Thomas Kim, Bongjin Hong, Rosemary Northcote, Thomas V. O’Halloran, Erika Lisabeth, Richard R. Neubig, Aretha Fiebig, Sean Crosson

PLOS Genetics: published July 21, 2025 | https://doi.org/10.1371/journal.pgen.1011795

Refined CRISPR/Cas9 genome editing in the pea aphid uncovers the essential roles of Laccase2 in overwintering egg adaptation

Shuji Shigenobu, Shinichi Yoda, Sonoko Ohsawa, Miyuzu Suzuki

PLOS Genetics: published July 21, 2025 | https://doi.org/10.1371/journal.pgen.1011557

E-cadherin endocytosis promotes non-canonical EGFR:STAT signalling to induce cell death and inhibit heterochromatinisation

Miguel Ramirez Moreno, Amy Quinton, Eleanor Jacobsen, Przemyslaw A. Stempor, Martin P. Zeidler, Natalia A. Bulgakova

PLOS Genetics: published July 21, 2025 | https://doi.org/10.1371/journal.pgen.1011781

A novel expectation-maximization approach to infer general diploid selection from time-series genetic data

Adam G. Fine, Matthias Steinrücken

PLOS Genetics: published July 22, 2025 | https://doi.org/10.1371/journal.pgen.1011769

Single-cell analysis of gene regulatory networks in the mammary glands of P4HA1-knockout mice

Akshat Gupta, Lilin Huang, Jinpeng Liu, Ke Chen, Ren Xu, Wei Wu

PLOS Genetics: published July 22, 2025 | https://doi.org/10.1371/journal.pgen.1011505

Novel insights into post-myocardial infarction cardiac remodeling through algorithmic detection of cell-type composition shifts

Brian Gural, Logan Kirkland, Abigail Hockett, Peyton Sandroni, Jiandong Zhang, Manuel Rosa-Garrido, Samantha K. Swift, Douglas J. Chapski, Michael A. Flinn, Caitlin C. O’Meara, Thomas M. Vondriska, Michaela Patterson, Brian C. Jensen, Christoph D. Rau

PLOS Genetics: published July 24, 2025 | https://doi.org/10.1371/journal.pgen.1011807

Genetic inference of on-target and off-target side-effects of antipsychotic medications

Andrew R. Elmore, Aws Sadik, Lavinia Paternoster, Golam M. Khandaker, Tom R. Gaunt, Gibran Hemani

PLOS Genetics: published July 28, 2025 | https://doi.org/10.1371/journal.pgen.1011793

Identification of hub gene associated with colorectal cancer: Integrating Mendelian randomization, transcriptome analysis and experimental verification

Yu Zhang, Xu Han, Yichun Yang, Jiayan Ren, Zixi Zhang, Yanmin Zhang, Qi Su, Dake Chu

PLOS Genetics: published July 29, 2025 | https://doi.org/10.1371/journal.pgen.1011788

Enhanced genetic fine mapping accuracy with Bayesian Linear Regression models in diverse genetic architectures

Merina Shrestha, Zhonghao Bai, Tahereh Gholipourshahraki, Astrid J. Hjelholt, Sile Hu, Mads Kjolby, Palle Duun Rohde, Peter Sørensen

PLOS Genetics: published July 30, 2025 | https://doi.org/10.1371/journal.pgen.1011783

Activation of Pvt1b isoform contributes to local Pvt1 abundance to repress Myc during stress

Qiao Li, Christiane E. Olivero, Erin Floyd, Jane Ding, Emily Dangelmaier, James Knight, Nadya Dimitrova

PLOS Genetics: published July 31, 2025 | https://doi.org/10.1371/journal.pgen.1011790

Correction: Reduced crossover interference and increased ZMM-independent recombination in the absence of Tel1/ATM

Carol M. Anderson, Ashwini Oke, Phoebe Yam, Tangna Zhuge, Jennifer C. Fung

PLOS Genetics: published July 7, 2025 | https://doi.org/10.1371/journal.pgen.1011779

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1. Reduced Crossover Interference and Increased ZMM-Independent Recombination in the Absence of Tel1/ATM

Phenotype to genotype: A new and rapid approach using whole-genome sequencing

McKenna Feltes, Aleksey V. Zimin, Sofia Angel, Nainika Pansari, Monica R. Hensley, Jennifer L. Anderson, Meng-Chieh Shen, Mackenzie Klemek, Yi Shen, Vighnesh S. Ginde, Hannah Kozan, Nhan V. Le, Vivian P. Truong, Meredith H. Wilson, Steven L. Salzberg, Steven A. Farber

PLOS Genetics: published July 14, 2025 | https://doi.org/10.1371/journal.pgen.1011702