Works in PLoS Computational Biology, 2025, Vol 21, Issue 6

Results: 64

Optimal sampling frequency and site selection for wastewater and environmental surveillance of infectious pathogens: A value of information assessment.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1013190

By:

Impalli, Isabella;
Bergland, Erik;
Saad-Roy, Chadi M.;
Grenfell, Bryan T.;
Levin, Simon A.;
Larsson, D. G. Joakim;
Laxminarayan, Ramanan

Publication type:

Article

The roles of feedback loops in the Caenorhabditis elegans rhythmic forward locomotion.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1013171

By:

Zhao, Peng;
Wang, Boyang;
Rong, Yi;
Yuan, Ye;
Liu, Jian;
Huo, Hong;
Liu, Zhuyong;
Li, Zhaoyu;
Fang, Tao

Publication type:

Article

Studying gastrulation by invagination: The bending of a cell sheet by mechanical cell properties using 3D deformable cell based simulations.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1013151

By:

Dries, Roland M.;
Renders, Kim Y.;
Kaandorp, Jaap A.

Publication type:

Article

Evolutionary divergence of induced versus constitutive antiviral gene expression levels between primates and rodents.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1013165

By:

Schneor, Lilach;
Tussia-Cohen, Dafna;
Fraimovitch, Evgeny;
Friedman, Sivan;
Hagai, Tzachi

Publication type:

Article

A mammalian inferior colliculus model for sound source separation using interaural time differences.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1013243

By:

Leibold, Christian;
Groß, Sebastian

Publication type:

Article

Ten simple rules for effectively assessing lab environments.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1013223

By:

Naegle, Kristen M.;
Saucerman, Jeffrey J.;
Leonard-Duke, Julie;
Rariden, Michael;
Aberra, Yonathan Tamrat

Publication type:

Article

Identifiability of phenotypic adaptation from low-cell-count experiments and a stochastic model.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1013202

By:

Browning, Alexander P.;
Crossley, Rebecca M.;
Villa, Chiara;
Maini, Philip K.;
Jenner, Adrianne L.;
Cassidy, Tyler;
Hamis, Sara

Publication type:

Article

Synthetic method of analogues for emerging infectious disease forecasting.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1013203

By:

Murph, Alexander C.;
Gibson, G. Casey;
Amona, Elizabeth B.;
Beesley, Lauren J.;
Castro, Lauren A.;
Del Valle, Sara Y.;
Osthus, Dave

Publication type:

Article

MitoTracer facilitates the identification of informative mitochondrial mutations for precise lineage reconstruction.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1013090

By:

Yu, Xuexin;
Hu, Jing;
Tan, Yuhao;
Pan, Mingyao;
Zhang, Hongyi;
Li, Bo

Publication type:

Article

Impact of symmetry in local learning rules on predictive neural representations and generalization in spatial navigation.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1013056

By:

Keck, Janis;
Barry, Caswell;
Doeller, Christian F.;
Jost, Jürgen

Publication type:

Article

Lateralised memory networks may explain the use of higher-order visual features in navigating insects.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1012670

By:

Filippi, Giulio;
Knight, James;
Philippides, Andrew;
Graham, Paul

Publication type:

Article

Computations that sustain neural feature selectivity across processing stages.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1013075

By:

Rowekamp, Ryan J.;
Sharpee, Tatyana O.

Publication type:

Article

MVHGCN: Predicting circRNA-disease associations with multi-view heterogeneous graph convolutional neural networks.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1013225

By:

Miao, Yan;
Tang, Xuan;
Wang, Chunyu;
Sun, Zhenyuan;
Wang, Guohua;
Huang, Shan

Publication type:

Article

Predicting neuronal firing from calcium imaging using a control theoretic approach.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1012603

By:

Rondoni, Nicholas A.;
Lu, Fan;
Turner-Evans, Daniel B.;
Gomez, Marcella

Publication type:

Article

Correction: A disordered encounter complex is central to the yeast Abp1p SH3 domain binding pathway.

Published in:

2025

By:

Gerlach, Gabriella J.;
Carrock, Rachel;
Stix, Robyn;
Stollar, Elliott J.;
Ball, K. Aurelia

Publication type:

Correction Notice

Predicting antibody kinetics and duration of protection against SARS-CoV-2 following vaccination from sparse serological data.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1013192

By:

Deichmann, Julia;
Barda, Noam;
Canetti, Michal;
Peretz, Yovel;
Weiss-Ottolenghi, Yael;
Lustig, Yaniv;
Regev-Yochay, Gili;
Lipsitch, Marc

Publication type:

Article

Embodied decisions as active inference.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1013180

By:

Priorelli, Matteo;
Stoianov, Ivilin Peev;
Pezzulo, Giovanni

Publication type:

Article

Proteostasis signatures in human diseases.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1013155

By:

Lim, Christine M.;
Vendruscolo, Michele

Publication type:

Article

Parameterization of intraoperative human microelectrode recordings: Linking action potential morphology to brain anatomy.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1013184

By:

Baker, Matthew R.;
Klassen, Bryan T.;
Jensen, Michael A.;
Ojeda Valencia, Gabriela;
Heydari, Hossein;
Ince, Nuri F.;
Müller, Klaus-Robert;
Miller, Kai J.

Publication type:

Article

The role of learned song in the evolution and speciation of Eastern and Spotted towhees.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1013135

By:

Du'Mottuchi, Ximena León;
Creanza, Nicole

Publication type:

Article

Cholinergic modulation of neural networks supports sequential and complementary roles for NREM and REM states in memory consolidation.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1013097

By:

Satchell, Michael;
Butel-Fry, Edith;
Noureddine, Zahraa;
Simmons, Alexis;
Ognjanovski, Nicolette N.;
Aton, Sara J.;
Zochowski, Michal R.

Publication type:

Article

Multimodal CustOmics: A unified and interpretable multi-task deep learning framework for multimodal integrative data analysis in oncology.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1013012

By:

Benkirane, Hakim;
Vakalopoulou, Maria;
Planchard, David;
Adam, Julien;
Olaussen, Ken;
Michiels, Stefan;
Cournède, Paul-Henry

Publication type:

Article

RIDDEN: Data-driven inference of receptor activity from transcriptomic data.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1013188

By:

Barsi, Szilvia;
Varga, Eszter;
Dimitrov, Daniel;
Saez-Rodriguez, Julio;
Hunyady, László;
Szalai, Bence

Publication type:

Article

Uncovering the impact of randomness in HIV hotspot formation: A mathematical modeling study.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1013178

By:

Yamamoto, Nao;
Citron, Daniel T.;
Mwalili, Samuel M.;
Gathungu, Duncan K.;
Cuadros, Diego F.;
Bershteyn, Anna

Publication type:

Article

iPAR: A framework for modelling and inferring information about disease spread when the populations at risk are unknown.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1012622

By:

Catterall, Stephen;
Porphyre, Thibaud;
Marion, Glenn

Publication type:

Article

Correction: Catalyst: Fast and flexible modeling of reaction networks.

Published in:

2025

By:

Loman, Torkel E.;
Ma, Yingbo;
Ilin, Vasily;
Gowda, Shashi;
Korsbo, Niklas;
Yewale, Nikhil;
Rackauckas, Chris;
Isaacson, Samuel A.

Publication type:

Correction Notice

Sparse deconvolution of cell type medleys in spatial transcriptomics.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1013169

By:

Erdogan, Nuray Sogunmez;
Eroglu, Deniz

Publication type:

Article

Biomarkers of mRNA vaccine efficacy derived from mechanistic modeling of tumor-immune interactions.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1013163

By:

Voutouri, Chrysovalantis;
Munn, Lance L.;
Stylianopoulos, Triantafyllos;
Jain, Rakesh K.

Publication type:

Article

Electrodiffusion dynamics in the cardiomyocyte dyad at nano-scale resolution using the Poisson-Nernst-Planck (PNP) equations.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1013149

By:

Jæger, Karoline Horgmo;
Tveito, Aslak

Publication type:

Article

Uncertainty-aware traction force microscopy.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1013079

By:

Kandasamy, Adithan;
Yeh, Yi-Ting;
Serrano, Ricardo;
Mercola, Mark;
del Alamo, Juan C.

Publication type:

Article

Network architecture of transcriptomic stress responses in zebrafish embryos.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1013164

By:

Beine, Kaylee;
Feugere, Lauric;
Turner, Alexander P.;
Wollenberg Valero, Katharina C.

Publication type:

Article

Balanced state of networks of winner-take-all units.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1013081

By:

Pang, Rich

Publication type:

Article

Semantic influences on object detection: Drift diffusion modeling provides insights regarding mechanism.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1012269

By:

Xue, Jingming;
Wilson, Robert C.;
Peterson, Mary A.

Publication type:

Article

Using virtual patient cohorts to uncover immune response differences in cancer and immunosuppressed COVID-19 patients.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1013170

By:

Gazeau, Sonia T.;
Deng, Xiaoyan;
Brunet-Ratnasingham, Elsa;
Kaufmann, Daniel E.;
Larochelle, Catherine;
Morel, Penelope A.;
Heffernan, Jane M.;
Davis, Courtney L.;
Smith, Amber M.;
Jenner, Adrianne L.;
Craig, Morgan

Publication type:

Article

Correction: cytoNet: Spatiotemporal network analysis of cell communities.

Published in:

2025

By:

Mahadevan, Arun S.;
Long, Byron L.;
Hu, Chenyue W.;
Ryan, David T.;
Grandel, Nicolas E.;
Britton, George L.;
Bustos, Marisol;
Gonzalez Porras, Maria A.;
Stojkova, Katerina;
Ligeralde, Andrew;
Son, Hyeonwi;
Shannonhouse, John;
Robinson, Jacob T.;
Warmflash, Aryeh;
Brey, Eric M.;
Kim, Yu Shin;
Qutub, Amina A.

Publication type:

Correction Notice

Redox poise in R. rubrum phototrophic growth drives large-scale changes in macromolecular pathways.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1013015

By:

Cannon, William R.;
King, Ethan;
Huening, Katherine A.;
North, Justin A.

Publication type:

Article

Sensorimotor integration enhances temperature stimulus processing.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1013134

By:

Anderson, Lindsay S.;
Costabile, Jamie D.;
Schwinn, Sina;
Calderon, Delia;
Haesemeyer, Martin

Publication type:

Article

Correction: Including population and environmental dynamic heterogeneities in continuum models of collective behaviour with applications to locust foraging and group structure.

Published in:: 2025
Publication type:: Correction Notice

Energy optimization induces predictive-coding properties in a multi-compartment spiking neural network model.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1013112

By:

Zhang, Mingfang;
Chitic, Raluca;
Bohté, Sander M.

Publication type:

Article

Predicting potential recovery of the endangered bromeliad Tillandsia utriculata: An agent-based modeling approach.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1013157

By:

Campbell, Alexandra M.;
Kula, Anna C.;
Jabaily, Rachel S.;
Oberle, Brad;
Sidoti, Brian;
Capaldi, Alex;
Bodine, Erin N.

Publication type:

Article

Stochastic gene expression in proliferating cells: Differing noise intensity in single-cell and population perspectives.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1013014

By:

Zhang, Zhanhao;
Zabaikina, Iryna;
Nieto, Cesar;
Vahdat, Zahra;
Bokes, Pavol;
Singh, Abhyudai

Publication type:

Article

ScITree: Scalable Bayesian inference of transmission tree from epidemiological and genomic data.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1012657

By:

Waddel, Hannah;
Koelle, Katia;
Lau, Max S. Y.

Publication type:

Article

Computing generalized cophenetic distances under all L<sub>p</sub> norms: A near-linear time algorithmic framework.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1013069

By:

Górecki, Paweł;
Markin, Alexey;
Vijendran, Sriram;
Eulenstein, Oliver

Publication type:

Article

F-BIAS: Towards a distributed national core facility for bioimage analysis.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1013058

By:

Ambroset, Mélodie;
Marie, Anselmet;
Clément, Benedetti;
Arthur, Meslin;
Aurélien, Maillot;
Christian, Rouvière;
Guillaume, Maucort;
Marine, Breuilly;
Marvin, Albert;
Gaëlle, Letort;
Antonio, Trullo;
Volker, Bäcker;
Jérôme, Mutterer;
Fabrice, Cordelières;
Thierry, Pécot;
Minh-Son, Phan;
Stéphane, Rigaud;
Magali, Feyeux;
Perrine, Paul-Gilloteaux;
Anne-Sophie, Macé

Publication type:

Article

History-dependent switch-like differentiation of keratinocytes in response to skin barrier damage.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1013162

By:

Domíguez-Hüttinger, Elisa;
Flores-Garza, Eliezer;
Caldú-Primo, José Luis;
Day, Harley;
Roque Ramírez, Abihail;
Tanaka, Reiko J.

Publication type:

Article

A linear perception-action mapping accounts for response range-dependent biases in heading estimation from optic flow.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1013147

By:

Sun, Qi;
Xu, Ling-Hao;
Stocker, Alan A.

Publication type:

Article

Computational modeling of ketamine-induced changes in gamma-band oscillations: The contribution of parvalbumin and somatostatin interneurons.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1013118

By:

Rademacher, Jessie;
Grent-'t-Jong, Tineke;
Rivolta, Davide;
Sauer, Andreas;
Scheller, Bertram;
Gonzalez-Burgos, Guillermo;
Metzner, Christoph;
Uhlhaas, Peter J.

Publication type:

Article

Variance in C. elegans gut bacterial load suggests complex host-microbe dynamics.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1013110

By:

Boddu, Satya Spandana;
Martini, K. Michael;
Nemenman, Ilya;
Vega, Nic M.

Publication type:

Article

Nonequilibrium brain dynamics elicited as the origin of perturbative complexity.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1013150

By:

Stikvoort, Wiep;
Pérez-Ordoyo, Eider;
Mindlin, Iván;
Escrichs, Anira;
Sitt, Jacobo D.;
Kringelbach, Morten L.;
Deco, Gustavo;
Sanz Perl, Yonatan

Publication type:

Article

Resource acquisition in diel cycles and the cost of growing quickly.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 6, p. 1, doi. 10.1371/journal.pcbi.1013132

By:

Flynn, Kevin J.;
Morozov, Andrew Yu.

Publication type:

Article