Ten quick tips to SNIFF out sustainable and secure scientific software

V. P. Nagraj, Karsten H. Siller, Thomas Stewart, Neal Magee, Stephen D. Turner

PLOS Computational Biology: published July 15, 2026 | https://doi.org/10.1371/journal.pcbi.1014510

Eight quick tips for data-model integration in ecology

Laurinne J. Balstad, Joe Brennan, Marissa L. Baskett, Mattea K. Berglund, Mei Z. Blundell, Jessica A. Bolin, Amy A. Briggs, Mary C. Fisher, Christopher M. Heggerud, Madeline Jarvis-Cross, Lauren Mossman, Andrea N. Odell, Jennifer Paige, Sophia Pelletier, Mikaela M. Provost

PLOS Computational Biology: published July 20, 2026 | https://doi.org/10.1371/journal.pcbi.1014524

Twelve quick tips for AI-assisted coding in science

Eric W. Bridgeford, Iain Declan Campbell, Zijiao Chen, Zhicheng Lin, Harrison Ritz, Joachim Vandekerckhove, Russell A. Poldrack

PLOS Computational Biology: published July 27, 2026 | https://doi.org/10.1371/journal.pcbi.1014428

Another 10 years of PLOS Computational Biology: A data-driven reflection on trends in genomics research

Jean Fan

PLOS Computational Biology: published July 2, 2026 | https://doi.org/10.1371/journal.pcbi.1014471

A brief overview of 20 years of neuroscience in PLoS Computational Biology

Hugues Berry, Lyle J. Graham, Kim T. Blackwell

PLOS Computational Biology: published July 6, 2026 | https://doi.org/10.1371/journal.pcbi.1014468

What will be the future of computational biology for macromolecules in the era of AI?

Arne Elofsson, Nir Ben-Tal

PLOS Computational Biology: published July 8, 2026 | https://doi.org/10.1371/journal.pcbi.1014467

Systems biology during 20 years of PLoS Computational Biology

Mark Alber, Marc R. Birtwistle, Stacey D. Finley, Pedro Mendes

PLOS Computational Biology: published July 10, 2026 | https://doi.org/10.1371/journal.pcbi.1014465

Optimized phenotype definitions boost GWAS power

Michael Zietz, Kathleen LaRow Brown, Undina Gisladottir, Nicholas P. Tatonetti

PLOS Computational Biology: published July 1, 2026 | https://doi.org/10.1371/journal.pcbi.1014431

Redefining and estimating the early-phase reproduction ratio for epidemic outbreaks in spatially structured populations

Boxuan Wang, Eugenio Valdano

PLOS Computational Biology: published July 1, 2026 | https://doi.org/10.1371/journal.pcbi.1014425

Mobility data resolution needed to inform predictive models of spatial epidemic spread from mobile phone data

Giulia Pullano, Shweta Bansal, Stefania Rubrichi, Vittoria Colizza

PLOS Computational Biology: published July 2, 2026 | https://doi.org/10.1371/journal.pcbi.1014427

Extracting host-specific developmental signatures from longitudinal microbiome data

Balázs Erdős, Christos Chatzis, Jonathan Thorsen, Jakob Stokholm, Age K. Smilde, Morten A. Rasmussen, Evrim Acar

PLOS Computational Biology: published July 6, 2026 | https://doi.org/10.1371/journal.pcbi.1014486

Combinatorial multiomic analysis from a pedigree of Sox10^Dom Hirschsprung mice identifies multiple high confidence candidate modifiers of Enteric Nervous System development

Joseph T. Benthal, Justin A. Avila, Jeffrey R. Smith, E. Michelle Southard-Smith

PLOS Computational Biology: published July 6, 2026 | https://doi.org/10.1371/journal.pcbi.1014424

Zooplankton feeding behavioral signatures in the morphology of macroscale prey spatial distribution

Eduardo H. Colombo, Corina E. Tarnita, Juan A. Bonachela

PLOS Computational Biology: published July 6, 2026 | https://doi.org/10.1371/journal.pcbi.1014411

Predictive coding explains asymmetric connectivity in the brain: A neural network study

Romesa Khan, Hongsheng Zhong, Shuvam Das, Jack Cai, Matthias Niemeier

PLOS Computational Biology: published July 6, 2026 | https://doi.org/10.1371/journal.pcbi.1014435

Population sparseness determines strength of Hebbian plasticity for maximal memory lifetime in associative networks

Naomi Auer, Lars Chen, Jakob Stubenrauch, Benjamin Lindner, Richard Kempter

PLOS Computational Biology: published July 6, 2026 | https://doi.org/10.1371/journal.pcbi.1013235

The energetic cost of human standing balance and gait initiation over a range of natural postures

Matto Leeuwis, Nikki van Aerts, Ajay Seth, Patrick A. Forbes

PLOS Computational Biology: published July 7, 2026 | https://doi.org/10.1371/journal.pcbi.1013522

Development of whole-limb skeletal patterning through the coordination of growth and self-organization models

Soha Ben Tahar, Ester Comellas, Timothy Duerr, Dareen Bakr, James Monaghan, Jose J. Muñoz, Sandra J. Shefelbine

PLOS Computational Biology: published July 7, 2026 | https://doi.org/10.1371/journal.pcbi.1014348

Analysis and design of disordered polypeptides with optimized sequence patterning properties

Arjun Singh, Ali I. Ukperaj, Gabriel F. Porto, Gregory L. Dignon

PLOS Computational Biology: published July 8, 2026 | https://doi.org/10.1371/journal.pcbi.1014462

Spiking neurons as predictive controllers of linear systems

Paolo Agliati, André Urbano, Pablo Lanillos, Nasir Ahmad, Marcel van Gerven, Sander Keemink

PLOS Computational Biology: published July 9, 2026 | https://doi.org/10.1371/journal.pcbi.1014432

Mind the gap: An embedding guide to safely travel in sequence space

Adam Wu, Jakub Lála, Quentin Trolliet, Abhinav Rajendran, Stefano Angioletti-Uberti

PLOS Computational Biology: published July 9, 2026 | https://doi.org/10.1371/journal.pcbi.1014433

Panorama: A robust pangenome-based method for predicting and comparing biological systems across species

Jérôme Arnoux, Jean Mainguy, Laura Bry, Quentin Fernandez de Grado, Yazid Hoblos, David Vallenet, Alexandra Calteau

PLOS Computational Biology: published July 10, 2026 | https://doi.org/10.1371/journal.pcbi.1013856

Quartet: Disentangling positive and negative components of microbial interactions

Aamir Faisal Ansari, Gayathri Sambamoorthy, Thrisha C. Alexander, Yugandhar B. S. Reddy, Janhavi Raut, Narendra M. Dixit

PLOS Computational Biology: published July 10, 2026 | https://doi.org/10.1371/journal.pcbi.1014502

AI-guided identification of natural CTSL inhibitors with therapeutic potential for renal injury

Feier Ma, Qi Li, Sirui Zhou, Xiaoya Li, Jin-Kui Yang

PLOS Computational Biology: published July 10, 2026 | https://doi.org/10.1371/journal.pcbi.1014464

CPP2Vec: A representation learning approach for cell-penetrating peptides prediction

Stavroula Svolou, Vasileios Konstantakos, Anastasia Krithara, Georgios Paliouras

PLOS Computational Biology: published July 13, 2026 | https://doi.org/10.1371/journal.pcbi.1014118

Mutual inhibition model of pattern formation: The role of Wnt-Dickkopf interactions in driving Hydra body axis formation

Moritz Mercker, Alexey Kazarnikov, Anja Tursch, Thomas Richter, Suat Özbek, Thomas Holstein, Anna Marciniak-Czochra

PLOS Computational Biology: published July 13, 2026 | https://doi.org/10.1371/journal.pcbi.1014416

Integrating multi-type features and knowledge graph for graded prediction of drug-induced liver injury in humans

Ying Liu, Kaimiao Hu, Jie Geng, Qi Dai, Leyi Wei, Ran Su

PLOS Computational Biology: published July 14, 2026 | https://doi.org/10.1371/journal.pcbi.1013640

Early reduction in aversive Pavlovian bias as a mediator of anhedonia improvement during Behavioural Activation in realistic treatment settings

Lioba C. S. Berndt, Daisy Crawley, Ruslana Tymchyk, Anna Hall, Jakub Onysk, Tore Erdmann, Elliott Wimmer, Isabel M. Berwian, Agnes Norbury, Quentin J. M. Huys

PLOS Computational Biology: published July 14, 2026 | https://doi.org/10.1371/journal.pcbi.1014439

Application of a uniaxial force by pulling the skin around the mammary gland may affect the orientation of the ducts and the length of the mammary ductal network: Findings from computational modeling and laboratory experiments

Daisy Ulloa, Kelsey M. Teeple, Sara B. Scinto, Wonders O. Ogundare, Deloris D. Franklin, Theresa M. Casey, Uduak Z. George

PLOS Computational Biology: published July 14, 2026 | https://doi.org/10.1371/journal.pcbi.1014421

Popformer: Learning general signatures of positive selection with a self-supervised transformer

Leon Zong, Sorelle A. Friedler, Sara Mathieson

PLOS Computational Biology: published July 15, 2026 | https://doi.org/10.1371/journal.pcbi.1014492

Representational capacity shapes both the “whether” and “how” of social learning

Max Taylor-Davies

PLOS Computational Biology: published July 15, 2026 | https://doi.org/10.1371/journal.pcbi.1014504

Screening of core targets for Di(2-ethylhexyl) Phthalate-related gastric cancer based on machine learning, molecular docking, and SHAP analysis

Shenghao Li, Qing Peng, Liyuan Hao, Jingyu Mao, Bingjie Huo

PLOS Computational Biology: published July 16, 2026 | https://doi.org/10.1371/journal.pcbi.1014514

Accounting for Defective Viral Genomes in viral consensus genome reconstruction, application to influenza virus

Kévin Da Silva, Nadia Naffakh, Marie-Anne Rameix-Welti, Frédéric Lemoine

PLOS Computational Biology: published July 16, 2026 | https://doi.org/10.1371/journal.pcbi.1014115

Targeting stiffness-dependent YAP/TAZ restores angiogenesis dynamics impaired by ALK1 knockout in silico

Margot Passier, Sandra Loerakker, Tommaso Ristori

PLOS Computational Biology: published July 16, 2026 | https://doi.org/10.1371/journal.pcbi.1013561

Dynamics-enhanced molecular property prediction guided by deep learning

Qiang Liu, Debby Dan Wang, Weiqing Guo, Yuting Huang, Xizhao Wang

PLOS Computational Biology: published July 16, 2026 | https://doi.org/10.1371/journal.pcbi.1014515

Molecular surveillance of multiplicity of infection, haplotype frequencies, and prevalence in infectious diseases

Henri Christian Junior Tsoungui Obama, Kristan Alexander Schneider

PLOS Computational Biology: published July 17, 2026 | https://doi.org/10.1371/journal.pcbi.1012955

PumpKin: A machine-learning pipeline for automatically tracking localized kinematics in freely moving C. elegans

Erin Shappell, Debra Buggs, Jennah Walcott, Hang Lu

PLOS Computational Biology: published July 17, 2026 | https://doi.org/10.1371/journal.pcbi.1014489

HNPP: Higher-order network-based personalized PageRank for detecting critical phase in complex biological systems

Jiayuan Zhong, Xuerong Gu, Dandan Ding, Qiao Wei, Bowen Niu, Ting Tao, Pei Chen, Rui Liu

PLOS Computational Biology: published July 17, 2026 | https://doi.org/10.1371/journal.pcbi.1014475

Pathways for glomerular macromolecule filtration: A mathematical model for transport across glomerular filtration surface, mesangium and shear-induced shunts

Numpong Punyaratabandhu, Thapakorn Pankoh, Yuttana Roongthumskul, Panadda Dechadilok, Pisut Katavetin

PLOS Computational Biology: published July 20, 2026 | https://doi.org/10.1371/journal.pcbi.1014503

Multi-class, unsupervised detection and classification of biological and anthropogenic sounds in coral reefs

Daniel Duane, Matthew T. Duggan, Erika Berlik, Marc S. Dantzker, Aaron N. Rice, Lauren A. Freeman

PLOS Computational Biology: published July 20, 2026 | https://doi.org/10.1371/journal.pcbi.1014516

Position-dependent codon occurrence is associated with patterns of translational efficiency and ribosomal occupancy in the human transcriptome

Kaavya Subramanian, Nathan Waugh, Cole Shanks, David A. Hendrix

PLOS Computational Biology: published July 20, 2026 | https://doi.org/10.1371/journal.pcbi.1014501

Quantifying the spatiotemporal mechanical dynamics of engineered cardiac microbundles

Hiba Kobeissi, Samuel J. DePalma, Javiera Jilberto, David Nordsletten, Brendon M. Baker, Emma Lejeune

PLOS Computational Biology: published July 20, 2026 | https://doi.org/10.1371/journal.pcbi.1014522

Ergodicity transformations predict human decision-making under risk

Benjamin Skjold, Simon Richard Steinkamp, Colm Connaughton, Oliver James Hulme, Ole Peters

PLOS Computational Biology: published July 20, 2026 | https://doi.org/10.1371/journal.pcbi.1014409

Beyond memory capacity: A probabilistic, dual store model of visuospatial working memory

Eduardo A. Aponte, Thanneer M. Perumal, Francesca Cormack, Christopher H. Chatham

PLOS Computational Biology: published July 20, 2026 | https://doi.org/10.1371/journal.pcbi.1014535

Population-level behavioral and structural drivers of COVID-19 vaccine uptake in the US

Ran Xu, Navid Ghaffarzadegan, Gaofei Zhang, Goshi Aoki, Hazhir Rahmandad

PLOS Computational Biology: published July 20, 2026 | https://doi.org/10.1371/journal.pcbi.1013988

Eco-evolutionary dynamics lead to functionally robust and redundant communities

Lorenzo Fant, Iuri Macocco, Jacopo Grilli

PLOS Computational Biology: published July 21, 2026 | https://doi.org/10.1371/journal.pcbi.1014437

Coordinative structures as scale-free networks: Cascade and percolation dynamics in motor learning with empirical validation

Chulwook Park

PLOS Computational Biology: published July 21, 2026 | https://doi.org/10.1371/journal.pcbi.1014523

Large vision model framework for automated C. elegans analysis: From static morphometry to dynamic neural activity

Aurélie Guisnet, Michael Hendricks

PLOS Computational Biology: published July 22, 2026 | https://doi.org/10.1371/journal.pcbi.1013441

A cost-optimized 5-protein panel revolutionizes systemic lupus erythematosus diagnosis

Wenhua Lv, Zhenwei Shang, Chen Sun, Yuping Zou, Siyu Wei, Haiyan Chen, Junxian Tao, Hongsheng Tian, Yu Dong, Chen Zhang, Mingming Zhang, Hongchao Lv, Yongshuai Jiang

PLOS Computational Biology: published July 23, 2026 | https://doi.org/10.1371/journal.pcbi.1014513

Catheter configuration for mapping micro-anatomic reentries sustaining atrial fibrillation: A simulation study

Miguel Rodrigo, Giada S. Romitti, María Termenón-Rivas, Ning Li, Vadim V. Fedorov

PLOS Computational Biology: published July 24, 2026 | https://doi.org/10.1371/journal.pcbi.1014493

Whisker stimulation reinforces a resting-state network in the barrel cortex: Nested oscillations and avalanches

Benedetta Mariani, Ramón Guevara, Mattia Tambaro, Marta Maschietto, Alessandro Leparulo, Stefano Vassanelli, Samir Suweis

PLOS Computational Biology: published July 24, 2026 | https://doi.org/10.1371/journal.pcbi.1014521

Cell-type-specific m¹A dynamics are associated with microglial phenotypic transition and neuronal metabolic adaptation during spinal cord injury

Chi Zhang, Shaolong Li, Ruizhi Jiang, Heng Duan, Chuang Li, Enlin Qi, Mingxin Wu, Xueying Li, Shiqing Feng, Hengxing Zhou

PLOS Computational Biology: published July 24, 2026 | https://doi.org/10.1371/journal.pcbi.1014573

The curriculum effect in visual learning: The role of readout dimensionality

Charlotte Volk, Christopher C. Pack, Shahab Bakhtiari

PLOS Computational Biology: published July 24, 2026 | https://doi.org/10.1371/journal.pcbi.1014553

Network analysis of surface deformation reveals trunk modularity and synchronization during gait

Zilu Wang, Jingbang Yang, Yong Wang, Tiantong Wang, Heran Zhong, Fengchen Liu, Chenxi Zhang, Jiangtian Li, Rongli Wang, Ximing Xu, Jiangang Shi, Sunil K. Agrawal, Qining Wang

PLOS Computational Biology: published July 24, 2026 | https://doi.org/10.1371/journal.pcbi.1014388

Single pulse electrical stimulation in white matter modulates iEEG visual responses in human early visual cortex

Harvey Huang, Kendrick N. Kay, Nicholas M. Gregg, Gabriela Ojeda Valencia, Myung-Ho In, Christoph Kapeller, Yunhong Shu, Gregory A. Worrell, Kai J. Miller, Dora Hermes

PLOS Computational Biology: published July 24, 2026 | https://doi.org/10.1371/journal.pcbi.1014563

ALFAssay: A feed‑forward neural network for quantitative fragmentomics‑based ctDNA profiling in breast cancer

Alexandra Stanciu, Andrea Gombos, Elisa Agostinetto, Delphine Vincent, Laurence Buisseret, Andreas Papagiannis, Francoise Rothe, Nicola Occelli, Christos Sotiriou, David Venet, Michail Ignatiadis

PLOS Computational Biology: published July 27, 2026 | https://doi.org/10.1371/journal.pcbi.1014505

Quantitative analysis of massive SARS-CoV-2 testing in the community in France in 2021–2022 reveals the associations of variant, vaccination, and age with viral dynamics in symptomatic individuals

Maxime Beaulieu, Nathanaël Hozé, Vincent Vieillefond, Timothée Goetschy, Gina Cosentino, François Blanquart, Florence Débarre, Jérémie Guedj

PLOS Computational Biology: published July 27, 2026 | https://doi.org/10.1371/journal.pcbi.1013811

Revealing dichotomous prior biases in social anxiety through a social prism model

Yuxi Wang, Qianqian Ju, Renhe Jia, Minghao Yuan, Yujia Peng

PLOS Computational Biology: published July 27, 2026 | https://doi.org/10.1371/journal.pcbi.1014509

Deciphering chromatin architecture and dynamics in Plasmodium falciparum using the nucDetective pipeline

Simon Holzinger, Leo Schmutterer, Victoria Marie Rothe, Maria Theresia Watzlowik, Uwe Schwartz, Gernot Längst

PLOS Computational Biology: published July 27, 2026 | https://doi.org/10.1371/journal.pcbi.1014557

Reconstruction of historical malaria transmission in Senegal using multiplex serocatalytic models

Gaëlle Baudemont, Thomas Obadia, Laura Garcia, Camille Lambert, Françoise Donnadieu, Fatoumata Diene Sarr, Joseph Faye, Cheikh Sokhna, Inès Vigan-Womas, Aissatou Toure-Balde, Chris Drakeley, Makhtar Niang, Michael T. White

PLOS Computational Biology: published July 27, 2026 | https://doi.org/10.1371/journal.pcbi.1013630

Body surface potential driven personalisation of electrophysiological digital twins in hypertrophic cardiomyopathy

Shambhavi Malik, Ludovica Cicci, Abdul Qayyum, Rahul Ghelani, Ji-jian Chow, Jagdeep Singh Mohal, Zachary I. Whinnett, Amanda Varnava, Gernot Plank, Prapa Kanagaratnam, Steven A. Niederer

PLOS Computational Biology: published July 27, 2026 | https://doi.org/10.1371/journal.pcbi.1014555

Can neural networks model the human perception of geometric shapes?

Maxence Pajot, Théo Morfoisse, Mathias Sablé-Meyer, Yair Lakretz, Stanislas Dehaene

PLOS Computational Biology: published July 27, 2026 | https://doi.org/10.1371/journal.pcbi.1014554

Remembering the “when”: Hebbian memory models for the time of past events

Johanni Brea, Alireza Modirshanechi, Georgios Iatropoulos, Wulfram Gerstner

PLOS Computational Biology: published July 28, 2026 | https://doi.org/10.1371/journal.pcbi.1014575

Flexible navigation with neuromodulated cognitive maps

Krubeal Danieli, Mikkel Elle Lepperød

PLOS Computational Biology: published July 28, 2026 | https://doi.org/10.1371/journal.pcbi.1013487

Inward rectifier potassium channels interact with calcium channels to promote robust and physiological bistability

Anaëlle De Worm, Guillaume Drion, Pierre Sacré

PLOS Computational Biology: published July 28, 2026 | https://doi.org/10.1371/journal.pcbi.1014549

Necking of epithelial tissues with cellular topological transition

Yuan He, Shi-Lei Xue

PLOS Computational Biology: published July 29, 2026 | https://doi.org/10.1371/journal.pcbi.1014565

Integrating chemical structures as treatments improves representations of microscopy images for morphological profiling

Yemin Yu, Emre Hayir, Neil Tenenholtz, Lester Mackey, Ying Wei, David Alvarez-Melis, Ava P. Amini, Alex X. Lu

PLOS Computational Biology: published July 29, 2026 | https://doi.org/10.1371/journal.pcbi.1014483

Sleep slow oscillation emergence on the scalp as a renewal point process

Mahmoud Alipour, Sara C. Mednick, Paola Malerba

PLOS Computational Biology: published July 29, 2026 | https://doi.org/10.1371/journal.pcbi.1014572

Computational insights on the interplay between electrotaxis and mechanotaxis

Pablo Sáez, Shardool Kulkarni, Custodio O. Nunes, Min Zhao, Elias H. Barriga

PLOS Computational Biology: published July 30, 2026 | https://doi.org/10.1371/journal.pcbi.1014511

A parallel dual-stream state-space module for reliable and efficient biomedical relation extraction

Yaxun Jia, Zhu Yuan, Lian Zhu, Bing Han, Li Ren, Zuo-lin Xiang

PLOS Computational Biology: published July 30, 2026 | https://doi.org/10.1371/journal.pcbi.1014480

Quantitative modelling of P-TEFb mediated CTD phosphorylation identifies local cooperativity

Aaron Callenbach, Domagoj Dorešić, Robert Düster, Vanessa Nakonecnij, Erika Dudkin, Matthias Geyer, Jan Hasenauer

PLOS Computational Biology: published July 30, 2026 | https://doi.org/10.1371/journal.pcbi.1014531

Combining sampling and attractor dynamics in spiking models of head direction systems

Vojko Pjanovic, Jacob A. Zavatone-Veth, Paul Masset, Sander W. Keemink, Michele Nardin

PLOS Computational Biology: published July 30, 2026 | https://doi.org/10.1371/journal.pcbi.1014577

Assessing scale and predictive diversity in models for single-cell transcriptomics based on Geneformer

Junfan Chen, Fabian Schmidt, Ricardo Henao

PLOS Computational Biology: published July 30, 2026 | https://doi.org/10.1371/journal.pcbi.1013701

A geometric-surface PDE model for cell-nucleus translocation through confinement

Francesca Ballatore, Anotida Madzvamuse, Cécile Jebane, Emmanuèle Helfer, Rachele Allena

PLOS Computational Biology: published July 30, 2026 | https://doi.org/10.1371/journal.pcbi.1014569

In silico clinical trials of BiTE expression by oncolytic viruses reveal the impact of patient heterogeneity on dosage protocol

Adrianne L. Jenner, Robyn P. Araujo, Noa L. Levi, Guy Ungerechts, Christine E. Engeland, Johannes P. W. Heidbuechel

PLOS Computational Biology: published July 30, 2026 | https://doi.org/10.1371/journal.pcbi.1014533

NLCD: A method to discover nonlinear causal relations among genes

Aravind Easwar, Manikandan Narayanan

PLOS Computational Biology: published July 31, 2026 | https://doi.org/10.1371/journal.pcbi.1014570

Prolines in linkers of multi-domain proteins: Intrinsic regulators of misfolding and aggregation

Simona Manasra, Yaakov Levy

PLOS Computational Biology: published July 31, 2026 | https://doi.org/10.1371/journal.pcbi.1014588

Correction: Identifying essential factors for energy-efficient walking control across a wide range of velocities in reflex-based musculoskeletal systems

The PLOS Computational Biology Staff

PLOS Computational Biology: published July 6, 2026 | https://doi.org/10.1371/journal.pcbi.1014482

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