A how-to guide for code sharing in biology

Richard J. Abdill, Emma Talarico, Laura Grieneisen

PLOS Biology: published September 10, 2024 | https://doi.org/10.1371/journal.pbio.3002815

A new lineage nomenclature to aid genomic surveillance of dengue virus

Verity Hill, Sara Cleemput, James Siqueira Pereira, Robert J. Gifford, Vagner Fonseca, Houriiyah Tegally, Anderson F. Brito, Gabriela Ribeiro, Vinicius Carius de Souza, Isabela Carvalho Brcko, Igor Santana Ribeiro, Iago Trezena Tavares De Lima, Svetoslav Nanev Slavov, Sandra Coccuzzo Sampaio, Maria Carolina Elias, Vi Thuy Tran, Duong Thi Hue Kien, Tuyen Huynh, Sophie Yacoub, Idrissa Dieng, Richard Salvato, Gabriel Luz Wallau, Tatiana S. Gregianini, Fernanda M. S. Godinho, Chantal B. F. Vogels, Mallery I. Breban, Mariana Leguia, Suraj Jagtap, Rahul Roy, Chanditha Hapuarachchi, Gaspary Mwanyika, Marta Giovanetti, Luiz C. J. Alcantara, Nuno R. Faria, Christine V. F. Carrington, Kathryn A. Hanley, Edward C. Holmes, Wim Dumon, Alex Ranieri Jerônimo Lima, Tulio de Oliveira, Nathan D. Grubaugh

PLOS Biology: published September 16, 2024 | https://doi.org/10.1371/journal.pbio.3002834

Fixing science means an end to gaming the system

Nicholas J. L. Brown

PLOS Biology: published September 9, 2024 | https://doi.org/10.1371/journal.pbio.3002816

Promoting reusable and open methods and protocols (PRO-MaP) can improve methodological reporting in the life sciences

Sofia Batista Leite, Matthew A. Brooke, Annamaria Carusi, Andy Collings, Pierre Deceuninck, Jean-François Dechamp, Bronwen Dekker, Elisa De Ranieri, Emma Ganley, Annalisa Gastaldello, Fanglian He, Marcel LaFlamme, Ingrid Langezaal, James Morris, David Pamies, Monica Piergiovanni, Bernd Pulverer, David Sadler, Caroline Shamu, Vivian Siegel, Marco Straccia, Tracey L. Weissgerber

PLOS Biology: published September 19, 2024 | https://doi.org/10.1371/journal.pbio.3002835

Keeping time: How musical training may boost cognition

M. Florencia Assaneo, Fernando Lizcano-Cortés, Pablo Ripolles

PLOS Biology: published September 5, 2024 | https://doi.org/10.1371/journal.pbio.3002810

Little impact of new mutations on mammalian trait variation

Beth L. Dumont

PLOS Biology: published September 27, 2024 | https://doi.org/10.1371/journal.pbio.3002825

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Placebo effects beyond dopamine

Karin B. Jensen

PLOS Biology: published September 25, 2024 | https://doi.org/10.1371/journal.pbio.3002812

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Remember oligodendrocytes: Uncovering their overlooked role in Alzheimer’s disease

Lena Spieth, Mikael Simons

PLOS Biology: published September 12, 2024 | https://doi.org/10.1371/journal.pbio.3002798

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High temperatures increase the virulence of Vibrio bacteria towards their coral host and competing bacteria via type VI secretion systems

Weiquan Wang, Kaihao Tang, Xiaoxue Wang

PLOS Biology: published September 4, 2024 | https://doi.org/10.1371/journal.pbio.3002788

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Diverse signatures of convergent evolution in cactus-associated yeasts

Carla Gonçalves, Marie-Claire Harrison, Jacob L. Steenwyk, Dana A. Opulente, Abigail L. LaBella, John F. Wolters, Xiaofan Zhou, Xing-Xing Shen, Marizeth Groenewald, Chris Todd Hittinger, Antonis Rokas

PLOS Biology: published September 23, 2024 | https://doi.org/10.1371/journal.pbio.3002832

An estimate of fitness reduction from mutation accumulation in a mammal allows assessment of the consequences of relaxed selection

Jobran Chebib, Anika Jonas, Eugenio López-Cortegano, Sven Künzel, Diethard Tautz, Peter D. Keightley

PLOS Biology: published September 26, 2024 | https://doi.org/10.1371/journal.pbio.3002795

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Human brain state dynamics are highly reproducible and associated with neural and behavioral features

Kangjoo Lee, Jie Lisa Ji, Clara Fonteneau, Lucie Berkovitch, Masih Rahmati, Lining Pan, Grega Repovš, John H. Krystal, John D. Murray, Alan Anticevic

PLOS Biology: published September 24, 2024 | https://doi.org/10.1371/journal.pbio.3002808

Functional network modules overlap and are linked to interindividual connectome differences during human brain development

Tianyuan Lei, Xuhong Liao, Xinyuan Liang, Lianglong Sun, Mingrui Xia, Yunman Xia, Tengda Zhao, Xiaodan Chen, Weiwei Men, Yanpei Wang, Leilei Ma, Ningyu Liu, Jing Lu, Gai Zhao, Yuyin Ding, Yao Deng, Jiali Wang, Rui Chen, Haibo Zhang, Shuping Tan, Jia-Hong Gao, Shaozheng Qin, Sha Tao, Qi Dong, Yong He

PLOS Biology: published September 18, 2024 | https://doi.org/10.1371/journal.pbio.3002653

Beta-band neural variability reveals age-related dissociations in human working memory maintenance and deletion

Wen Wen, Shrey Grover, Douglas Hazel, Peyton Berning, Frederik Baumgardt, Vighnesh Viswanathan, Olivia Tween, Robert M. G. Reinhart

PLOS Biology: published September 11, 2024 | https://doi.org/10.1371/journal.pbio.3002784

Phosphorylation of the DNA damage repair factor 53BP1 by ATM kinase controls neurodevelopmental programs in cortical brain organoids

Bitna Lim, Yurika Matsui, Seunghyun Jung, Mohamed Nadhir Djekidel, Wenjie Qi, Zuo-Fei Yuan, Xusheng Wang, Xiaoyang Yang, Nina Connolly, Abbas Shirinifard Pilehroud, Haitao Pan, Fang Wang, Shondra M. Pruett-Miller, Kanisha Kavdia, Vishwajeeth Pagala, Yiping Fan, Junmin Peng, Beisi Xu, Jamy C. Peng

PLOS Biology: published September 3, 2024 | https://doi.org/10.1371/journal.pbio.3002760

A dystroglycan–laminin–integrin axis coordinates cell shape remodeling in the developing Drosophila retina

Rhian F. Walther, Courtney Lancaster, Jemima J. Burden, Franck Pichaud

PLOS Biology: published September 3, 2024 | https://doi.org/10.1371/journal.pbio.3002783

Polygenic scores for complex traits are associated with changes in concentration of circulating lipid species

Rubina Tabassum, Nina Mars, Pietro Della Briotta Parolo, Mathias J. Gerl, Christian Klose, FinnGen, Matti Pirinen, Kai Simons, Elisabeth Widén, Samuli Ripatti

PLOS Biology: published September 26, 2024 | https://doi.org/10.1371/journal.pbio.3002830

LXR-dependent enhancer activation regulates the temporal organization of the liver’s response to refeeding leading to lipogenic gene overshoot

Noga Korenfeld, Tali Gorbonos, Maria C. Romero Florian, Dan Rotaro, Dana Goldberg, Talia Radushkevitz-Frishman, Meital Charni-Natan, Meirav Bar-Shimon, Carolyn L. Cummins, Ido Goldstein

PLOS Biology: published September 12, 2024 | https://doi.org/10.1371/journal.pbio.3002735

The conserved protein adaptors CALM/AP180 and FCHo1/2 cooperatively recruit Eps15 to promote the initiation of clathrin-mediated endocytosis in yeast

Yidi Sun, Albert Yeam, Jonathan Kuo, Yuichiro Iwamoto, Gean Hu, David G. Drubin

PLOS Biology: published September 24, 2024 | https://doi.org/10.1371/journal.pbio.3002833

A genome-wide arrayed CRISPR screen identifies PLSCR1 as an intrinsic barrier to SARS-CoV-2 entry that recent virus variants have evolved to resist

Jérémie Le Pen, Gabrielle Paniccia, Volker Kinast, Marcela Moncada-Velez, Alison W. Ashbrook, Michael Bauer, H.-Heinrich Hoffmann, Ana Pinharanda, Inna Ricardo-Lax, Ansgar F. Stenzel, Edwin A. Rosado-Olivieri, Kenneth H. Dinnon III, William C. Doyle, Catherine A. Freije, Seon-Hui Hong, Danyel Lee, Tyler Lewy, Joseph M. Luna, Avery Peace, Carltin Schmidt, William M. Schneider, Roni Winkler, Elaine Z. Yip, Chloe Larson, Timothy McGinn, Miriam-Rose Menezes, Lavoisier Ramos-Espiritu, Priyam Banerjee, John T. Poirier, Francisco J. Sànchez-Rivera, Aurélie Cobat, Qian Zhang, Jean-Laurent Casanova, Thomas S. Carroll, J. Fraser Glickman, Eleftherios Michailidis, Brandon Razooky, Margaret R. MacDonald, Charles M. Rice

PLOS Biology: published September 24, 2024 | https://doi.org/10.1371/journal.pbio.3002767

Plasmodium RON11 triggers biogenesis of the merozoite rhoptry pair and is essential for erythrocyte invasion

David Anaguano, Opeoluwa Adewale-Fasoro, Grace W. Vick, Sean Yanik, James Blauwkamp, Manuel A. Fierro, Sabrina Absalon, Prakash Srinivasan, Vasant Muralidharan

PLOS Biology: published September 18, 2024 | https://doi.org/10.1371/journal.pbio.3002801

Plasmodium NEK1 coordinates MTOC organisation and kinetochore attachment during rapid mitosis in male gamete formation

Mohammad Zeeshan, Ravish Rashpa, David J. Ferguson, George Mckeown, Raushan Nugmanova, Amit K. Subudhi, Raphael Beyeler, Sarah L. Pashley, Robert Markus, Declan Brady, Magali Roques, Andrew R. Bottrill, Andrew M. Fry, Arnab Pain, Sue Vaughan, Anthony A. Holder, Eelco C. Tromer, Mathieu Brochet, Rita Tewari

PLOS Biology: published September 10, 2024 | https://doi.org/10.1371/journal.pbio.3002802

PP1 phosphatase controls both daughter cell formation and amylopectin levels in Toxoplasma gondii

Asma Sarah Khelifa, Maanasa Bhaskaran, Tom Boissavy, Thomas Mouveaux, Tatiana Araujo Silva, Cerina Chhuon, Marcia Attias, Ida Chiara Guerrera, Wanderley De Souza, David Dauvillee, Emmanuel Roger, Mathieu Gissot

PLOS Biology: published September 10, 2024 | https://doi.org/10.1371/journal.pbio.3002791

Alveolin proteins in the Toxoplasma inner membrane complex form a highly interconnected structure that maintains parasite shape and replication

Peter S. Back, Vignesh Senthilkumar, Charles P. Choi, Justin J. Quan, Qing Lou, Anne K. Snyder, Andrew M. Ly, Justin G. Lau, Z. Hong Zhou, Gary E. Ward, Peter J. Bradley

PLOS Biology: published September 12, 2024 | https://doi.org/10.1371/journal.pbio.3002809

Wnt target gene activation requires β-catenin separation into biomolecular condensates

Richard A. Stewart, Zhihao Ding, Ung Seop Jeon, Lauren B. Goodman, Jeannine J. Tran, John P. Zientko, Malavika Sabu, Ken M. Cadigan

PLOS Biology: published September 24, 2024 | https://doi.org/10.1371/journal.pbio.3002368

Changes in DNA methylation contribute to rapid adaptation in bacterial plant pathogen evolution

Rekha Gopalan-Nair, Aurore Coissac, Ludovic Legrand, Céline Lopez-Roques, Yann Pécrix, Céline Vandecasteele, Olivier Bouchez, Xavier Barlet, Anne Lanois, Alain Givaudan, Julien Brillard, Stéphane Genin, Alice Guidot

PLOS Biology: published September 20, 2024 | https://doi.org/10.1371/journal.pbio.3002792

Mycobacteria that cause tuberculosis have retained ancestrally acquired genes for the biosynthesis of chemically diverse terpene nucleosides

Jacob A. Mayfield, Sahadevan Raman, Alexandrea K. Ramnarine, Vivek K. Mishra, Annie D. Huang, Sandrine Dudoit, Jeffrey Buter, Tan-Yun Cheng, David C. Young, Yashodhan M. Nair, Isobel G. Ouellet, Braden T. Griebel, Shuyi Ma, David R. Sherman, Ludovic Mallet, Kyu Y. Rhee, Adriaan J. Minnaard, D. Branch Moody

PLOS Biology: published September 30, 2024 | https://doi.org/10.1371/journal.pbio.3002813

The coral pathogen Vibrio coralliilyticus uses a T6SS to secrete a group of novel anti-eukaryotic effectors that contribute to virulence

Shir Mass, Hadar Cohen, Ram Podicheti, Douglas B. Rusch, Motti Gerlic, Blake Ushijima, Julia C. van Kessel, Eran Bosis, Dor Salomon

PLOS Biology: published September 3, 2024 | https://doi.org/10.1371/journal.pbio.3002734

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The genetic basis of the kākāpō structural color polymorphism suggests balancing selection by an extinct apex predator

Lara Urban, Anna W. Santure, Lydia Uddstrom, Andrew Digby, Deidre Vercoe, Daryl Eason, Jodie Crane, Kākāpō Recovery Team, Matthew J. Wylie, Tāne Davis, Marissa F. LeLec, Joseph Guhlin, Simon Poulton, Jon Slate, Alana Alexander, Patricia Fuentes-Cross, Peter K. Dearden, Neil J. Gemmell, Farhan Azeem, Marvin Weyland, Harald G. L. Schwefel, Cock van Oosterhout, Hernán E. Morales

PLOS Biology: published September 10, 2024 | https://doi.org/10.1371/journal.pbio.3002755

Syllable processing is organized in discrete subregions of the human superior temporal gyrus

Daniel R. Cleary, Youngbin Tchoe, Andrew Bourhis, Charles W. Dickey, Brittany Stedelin, Mehran Ganji, Sang Heon Lee, Jihwan Lee, Dominic A. Siler, Erik C. Brown, Burke Q. Rosen, Erik Kaestner, Jimmy C. Yang, Daniel J. Soper, Seunggu Jude Han, Angelique C. Paulk, Sydney S. Cash, Ahmed M. Raslan, Shadi A. Dayeh, Eric Halgren

PLOS Biology: published September 6, 2024 | https://doi.org/10.1371/journal.pbio.3002774

Bats generate lower affinity but higher diversity antibody responses than those of mice, but pathogen-binding capacity increases if protein is restricted in their diet

Daniel E. Crowley, Caylee A. Falvo, Evelyn Benson, Jodi Hedges, Mark Jutila, Shahrzad Ezzatpour, Hector C. Aguilar, Manuel Ruiz-Aravena, Wenjun Ma, Tony Schountz, Agnieszka Rynda-Apple, Raina K. Plowright

PLOS Biology: published September 24, 2024 | https://doi.org/10.1371/journal.pbio.3002800

Centrosome amplification primes ovarian cancer cells for apoptosis and potentiates the response to chemotherapy

Frances Edwards, Giulia Fantozzi, Anthony Y. Simon, Jean-Philippe Morretton, Aurelie Herbette, Andrea E. Tijhuis, Rene Wardenaar, Stacy Foulane, Simon Gemble, Diana C.J. Spierings, Floris Foijer, Odette Mariani, Anne Vincent-Salomon, Sergio Roman-Roman, Xavier Sastre-Garau, Oumou Goundiam, Renata Basto

PLOS Biology: published September 5, 2024 | https://doi.org/10.1371/journal.pbio.3002759

Structure of the Nmd4-Upf1 complex supports conservation of the nonsense-mediated mRNA decay pathway between yeast and humans

Irène Barbarin-Bocahu, Nathalie Ulryck, Amandine Rigobert, Nadia Ruiz Gutierrez, Laurence Decourty, Mouna Raji, Bhumika Garkhal, Hervé Le Hir, Cosmin Saveanu, Marc Graille

PLOS Biology: published September 27, 2024 | https://doi.org/10.1371/journal.pbio.3002821

A flexible loop in the paxillin LIM3 domain mediates its direct binding to integrin β subunits

Timo Baade, Marcus Michaelis, Andreas Prestel, Christoph Paone, Nikolai Klishin, Marleen Herbinger, Laura Scheinost, Ruslan Nedielkov, Christof R. Hauck, Heiko M. Möller

PLOS Biology: published September 4, 2024 | https://doi.org/10.1371/journal.pbio.3002757

A taxon-rich and genome-scale phylogeny of Opisthokonta

Hongyue Liu, Jacob L. Steenwyk, Xiaofan Zhou, Darrin T. Schultz, Kevin M. Kocot, Xing-Xing Shen, Antonis Rokas, Yuanning Li

PLOS Biology: published September 16, 2024 | https://doi.org/10.1371/journal.pbio.3002794

Integration of estimated regional gene expression with neuroimaging and clinical phenotypes at biobank scale

Nhung Hoang, Neda Sardaripour, Grace D. Ramey, Kurt Schilling, Emily Liao, Yiting Chen, Jee Hyun Park, Xavier Bledsoe, Bennett A. Landman, Eric R. Gamazon, Mary Lauren Benton, John A. Capra, Mikail Rubinov

PLOS Biology: published September 13, 2024 | https://doi.org/10.1371/journal.pbio.3002782

Identification of a highly efficient chloroplast-targeting peptide for plastid engineering

Chonprakun Thagun, Masaki Odahara, Yutaka Kodama, Keiji Numata

PLOS Biology: published September 19, 2024 | https://doi.org/10.1371/journal.pbio.3002785

Organelle landscape analysis using a multiparametric particle-based method

Yoshitaka Kurikawa, Ikuko Koyama-Honda, Norito Tamura, Seiichi Koike, Noboru Mizushima

PLOS Biology: published September 17, 2024 | https://doi.org/10.1371/journal.pbio.3002777

SPOT: A machine learning model that predicts specific substrates for transport proteins

Alexander Kroll, Nico Niebuhr, Gregory Butler, Martin J. Lercher

PLOS Biology: published September 26, 2024 | https://doi.org/10.1371/journal.pbio.3002807

Dopamine has no direct causal role in the formation of treatment expectations and placebo analgesia in humans

Angelika Kunkel, Livia Asan, Isabel Krüger, Clara Erfurt, Laura Ruhnau, Elif Buse Caliskan, Jana Hackert, Katja Wiech, Katharina Schmidt, Ulrike Bingel

PLOS Biology: published September 24, 2024 | https://doi.org/10.1371/journal.pbio.3002772

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Multisensory perceptual and causal inference is largely preserved in medicated post-acute individuals with schizophrenia

Tim Rohe, Klaus Hesse, Ann-Christine Ehlis, Uta Noppeney

PLOS Biology: published September 10, 2024 | https://doi.org/10.1371/journal.pbio.3002790

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