Works matching IS 1553734X AND DT 2025 AND VI 21 AND IP 4

Results: 99

Foraging animals use dynamic Bayesian updating to model meta-uncertainty in environment representations.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1012989

By:

Webb, James;
Steffan, Paul;
Hayden, Benjamin Y.;
Lee, Daeyeol;
Kemere, Caleb;
McGinley, Matthew

Publication type:

Article

Falsifying computational models of endothelial cell network formation through quantitative comparison with in vitro models.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1012965

By:

Vergroesen, Tessa M.;
Vermeulen, Vincent;
Merks, Roeland M. H.

Publication type:

Article

Heuristic energy-based cyclic peptide design.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1012290

By:

Zhu, Qiyao;
Mulligan, Vikram Khipple;
Shasha, Dennis

Publication type:

Article

Behavior-driven forecasts of neighborhood-level COVID-19 spread in New York City.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1012979

By:

Zhang, Renquan;
Tai, Jilei;
Yao, Qing;
Yang, Wan;
Ruggeri, Kai;
Shaman, Jeffrey;
Pei, Sen

Publication type:

Article

Structure-based mechanism of RyR channel operation by calcium and magnesium ions.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1012950

By:

Zahradníková, Alexandra;
Pavelková, Jana;
Sabo, Miroslav;
Baday, Sefer;
Zahradník, Ivan

Publication type:

Article

Unlocking the soundscape of coral reefs with artificial intelligence: pretrained networks and unsupervised learning win out.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1013029

By:

Williams, Ben;
Balvanera, Santiago M.;
Sethi, Sarab S.;
Lamont, Timothy A.C.;
Jompa, Jamaluddin;
Prasetya, Mochyudho;
Richardson, Laura;
Chapuis, Lucille;
Weschke, Emma;
Hoey, Andrew;
Beldade, Ricardo;
Mills, Suzanne C.;
Haguenauer, Anne;
Zuberer, Frederic;
Simpson, Stephen D.;
Curnick, David;
Jones, Kate E.

Publication type:

Article

Dynamic modeling of EEG responses to natural speech reveals earlier processing of predictable words.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1013006

By:

Dou, Jin;
Anderson, Andrew J.;
White, Aaron S.;
Norman-Haignere, Samuel V.;
Lalor, Edmund C.

Publication type:

Article

Simulating dynamic insecticide selection pressures for resistance management in mosquitoes assuming polygenic resistance.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1012944

By:

Hobbs, Neil Philip;
Hastings, Ian

Publication type:

Article

Computational modeling of frequency-dependent neocortical response to thalamic neurostimulation in epilepsy.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1012943

By:

Joseph Tomy, Linda Iris;
Köksal-Ersöz, Elif;
Nica, Anca;
Yochum, Maxime;
Benquet, Pascal;
Wendling, Fabrice

Publication type:

Article

scPEDSSC: proximity enhanced deep sparse subspace clustering method for scRNA-seq data.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1012924

By:

Wei, Xiaopeng;
Wu, Jingli;
Li, Gaoshi;
Liu, Jiafei;
Wu, Xi;
He, Chang

Publication type:

Article

Correction: Mathematical modeling suggests heterogeneous replication of Mycobacterium tuberculosis in rabbits.

Published in:

2025

By:

Ganusov, Vitaly V.;
Kolloli, Afsal;
Subbian, Selvakumar

Publication type:

Correction Notice

Complexity reduction by symmetry: Uncovering the minimal regulatory network for logical computation in bacteria.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1013005

By:

Álvarez-García, Luis A.;
Liebermeister, Wolfram;
Leifer, Ian;
Makse, Hernán A.

Publication type:

Article

Balancing complexity, performance and plausibility to meta learn plasticity rules in recurrent spiking networks.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1012910

By:

Confavreux, Basile;
Agnes, Everton J.;
Zenke, Friedemann;
Sprekeler, Henning;
Vogels, Tim P.

Publication type:

Article

Efficient discovery of frequently co-occurring mutations in a sequence database with matrix factorization.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1012391

By:

Robert Kolar, Michael;
Mitra, Debasis;
Kobzarenko, Valerie

Publication type:

Article

An evolutionary model of rhythmic accelerando in animal vocal signalling.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1013011

By:

Jadoul, Yannick;
Hersh, Taylor A.;
Fernández Domingos, Elias;
Gamba, Marco;
Favaro, Livio;
Ravignani, Andrea

Publication type:

Article

Resource competition-driven bistability and stochastic switching amplify gene expression noise.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1012931

By:

Goetz, Hanah;
Zhang, Rong;
Wang, Xiao;
Tian, Xiao-Jun

Publication type:

Article

Cell-type-specific firing patterns in a V1 cortical column model depend on feedforward and feedback-driven states.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1012036

By:

Moreni, Giulia;
Dorcioman, Rares A.;
Pennartz, Cyriel M. A.;
Mejias, Jorge F.

Publication type:

Article

Repetitive training enhances the pattern recognition capability of cultured neural networks.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1013043

By:

Shao, Wen-Wei;
Shao, Qi;
Xu, Hai-Huan;
Qiao, Guan-Ji;
Wang, Run-Xuan;
Ma, Zhi-Yun;
Meng, Wei-Wei;
Yang, Zhuo-Bin;
Zang, Yun-Liang;
Li, Xiao-Hong

Publication type:

Article

Meta-Reinforcement Learning reconciles surprise, value, and control in the anterior cingulate cortex.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1013025

By:

Vriens, Tim;
Vassena, Eliana;
Pezzulo, Giovanni;
Baldassarre, Gianluca;
Silvetti, Massimo

Publication type:

Article

TGF-M: Topology-augmented geometric features enhance molecular property prediction.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1013004

By:

He, Wei;
Tian, Xu;
Li, Xue;
Han, Peifu;
Wang, Shuang;
Liu, Lin;
Song, Tao

Publication type:

Article

Editorial Note: Mathematical modeling of the molecular switch of TNFR1-mediated signaling pathways applying Petri net formalism and in silico knockout analysis.

Published in:: PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1013003
Publication type:: Article

Emergence and maintenance of modularity in neural networks with Hebbian and anti-Hebbian inhibitory STDP.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1012973

By:

Bergoin, Raphaël;
Torcini, Alessandro;
Deco, Gustavo;
Quoy, Mathias;
Zamora-López, Gorka

Publication type:

Article

Learning and teaching biological data science in the Bioconductor community.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1012925

By:

Drnevich, Jenny;
Tan, Frederick J.;
Almeida-Silva, Fabricio;
Castelo, Robert;
Culhane, Aedin C.;
Davis, Sean;
Doyle, Maria A.;
Geistlinger, Ludwig;
Ghazi, Andrew R.;
Holmes, Susan;
Lahti, Leo;
Mahmoud, Alexandru;
Nishida, Kozo;
Ramos, Marcel;
Rue-Albrecht, Kevin;
Shih, David J. H.;
Gatto, Laurent;
Soneson, Charlotte

Publication type:

Article

Mechanism of Arrhythmogenesis Driven by Early After Depolarizations in Cardiac Tissue.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1012635

By:

Stein, Jack;
Greene, D'Artagnan;
Fenton, Flavio;
Shiferaw, Yohannes

Publication type:

Article

Theory of axo-axonic inhibition.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1013047

By:

Brette, Romain

Publication type:

Article

A computational account of multiple motives guiding context-dependent prosocial behavior.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1013032

By:

Lugrin, Claire;
Hu, Jie;
Ruff, Christian C.

Publication type:

Article

Modelling transmission thresholds and hypoendemic stability for onchocerciasis elimination.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1013026

By:

Stapley, Jacob N.;
Hamley, Jonathan I.D.;
Basáñez, Maria-Gloria;
Walker, Martin

Publication type:

Article

Revealing cancer driver genes through integrative transcriptomic and epigenomic analyses with Moonlight.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1012999

By:

Nourbakhsh, Mona;
Zheng, Yuanning;
Noor, Humaira;
Chen, Hongjin;
Akhuli, Subhayan;
Tiberti, Matteo;
Gevaert, Olivier;
Papaleo, Elena

Publication type:

Article

Bayesian Inference of Pathogen Phylogeography using the Structured Coalescent Model.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1012995

By:

Roberts, Ian;
Everitt, Richard G.;
Koskela, Jere;
Didelot, Xavier

Publication type:

Article

Transfer learning of multicellular organization via single-cell and spatial transcriptomics.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1012991

By:

Tan, Yecheng;
Wang, Ai;
Wang, Zezhou;
Lin, Wei;
Yan, Yan;
Nie, Qing;
Shi, Jifan

Publication type:

Article

Statistical signature of subtle behavioral changes in large-scale assays.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1012990

By:

Blanc, Alexandre;
Laurent, François;
Barbier-Chebbah, Alex;
Van Assel, Hugues;
Cocanougher, Benjamin T.;
Jones, Benjamin M.W.;
Hague, Peter;
Zlatic, Marta;
Chikhi, Rayan;
Vestergaard, Christian L.;
Jovanic, Tihana;
Masson, Jean-Baptiste;
Barré, Chloé

Publication type:

Article

A Discretized Overlap Resolution Algorithm (DORA) for resolving spatial overlaps in individual-based models of microbes.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1012974

By:

Hashem, Ihab;
Wang, Jian;
Van Impe, Jan F.M.

Publication type:

Article

Temporal resolution of spike coding in feedforward networks with signal convergence and divergence.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1012971

By:

Mobille, Zach;
Sikandar, Usama Bin;
Sponberg, Simon;
Choi, Hannah

Publication type:

Article

Identifying reproducible transcription regulator coexpression patterns with single cell transcriptomics.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1012962

By:

Morin, Alexander;
Chu, Ching Pan;
Pavlidis, Paul

Publication type:

Article

The NOSTRA model: Coherent estimation of infection sources in the case of possible nosocomial transmission.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1012949

By:

Pascall, David J.;
Jackson, Christopher;
Evans, Stephanie;
Gouliouris, Theodore;
Illingworth, Christopher J.R.;
Piatek, Stefan G.;
Robotham, Julie V.;
Stirrup, Oliver;
Warne, Ben;
Breuer, Judith;
De Angelis, Daniela

Publication type:

Article

Fluid and solute transport by cells and a model of systemic circulation.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1012935

By:

Wu, Yufei;
Benson, Morgan A.;
Sun, Sean X.

Publication type:

Article

An expandable synthetic library of human paired antibody sequences.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1012932

By:

Marinov, Toma M.;
Wasdin, Perry T.;
Jordaan, Gwen;
Janke, Alexis K.;
Abu-Shmais, Alexandra A.;
Georgiev, Ivelin S.

Publication type:

Article

Design of nanobody targeting SARS-CoV-2 spike glycoprotein using CDR-grafting assisted by molecular simulation and machine learning.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1012921

By:

Ferraz, Matheus VF;
Adan, W Camilla S;
Lima, Tayná E;
Santos, Adriele JC;
Paula, Sérgio O de;
Dhalia, Rafael;
Wallau, Gabriel L;
Wade, Rebecca C;
Viana, Isabelle FT;
Lins, Roberto D

Publication type:

Article

mdciao: Accessible Analysis and Visualization of Molecular Dynamics Simulation Data.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1012837

By:

Pérez-Hernández, Guillermo;
Hildebrand, Peter W.

Publication type:

Article

The confidence-noise confidence-boost (CNCB) model of confidence rating data.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1012451

By:

Mamassian, Pascal;
de Gardelle, Vincent

Publication type:

Article

A new paradigm considering multicellular adhesion, repulsion and attraction represent diverse cellular tile patterns.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1011909

By:

Carrillo, Jose A.;
Murakawa, Hideki;
Sato, Makoto;
Wang, Miaoxing

Publication type:

Article

Expression of Concern: HiSV: A control-free method for structural variation detection from Hi-C data.

Published in:: 2025
Publication type:: Correction Notice

Traveling waves in the human visual cortex: An MEG-EEG model-based approach.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1013007

By:

Grabot, Laetitia;
Merholz, Garance;
Winawer, Jonathan;
Heeger, David J.;
Dugué, Laura

Publication type:

Article

Joint estimation of hand-foot-mouth disease model and prediction in korea using the ensemble kalman filter.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1012996

By:

Abbas, Wasim;
Lee, Sieun;
Kim, Sangil

Publication type:

Article

A spectral framework to map QTLs affecting joint differential networks of gene co-expression.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1012953

By:

Hu, Jiaxin;
Weber, Jesse N.;
Fuess, Lauren E.;
Steinel, Natalie C.;
Bolnick, Daniel I.;
Wang, Miaoyan

Publication type:

Article

Eleven quick tips to unlock the power of in vivo data science.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1012947

By:

Kieran, Troy J.;
Maines, Taronna R.;
Belser, Jessica A.

Publication type:

Article

Contributions of mechanical loading and hormonal changes to eccentric hypertrophy during volume overload: A Bayesian analysis using logic-based network models.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1012390

By:

Bracamonte, Johane H.;
Watkins, Lionel;
Pat, Betty;
Dell'Italia, Louis J.;
Saucerman, Jeffrey J.;
Holmes, Jeffrey W.

Publication type:

Article

Modeling diffusive search by non-adaptive sperm: Empirical and computational insights.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1012865

By:

Brisard, Benjamin M.;
Cashwell, Kylie D.;
Stewart, Stephanie M.;
Harrison, Logan M.;
Charles, Aidan C.;
Dennis, Chelsea V.;
Henslee, Ivie R.;
Carrow, Ethan L.;
Belcher, Heather A.;
Bhowmick, Debajit;
Vos, Paul W.;
Majka, Maciej;
Bier, Martin;
Hart, David M.;
Schmidt, Cameron A.

Publication type:

Article

RMPJ: An ImageJ plugin for morphological information processing in biomedical images.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1012992

By:

Kimori, Yoshitaka

Publication type:

Article

Fitting dynamic measles models to subnational case notification data from Ethiopia: Methodological challenges and key considerations.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1012922

By:

Sbarra, Alyssa N.;
Haeuser, Emily;
Kidane, Samuel;
Abate, Andargie;
Abebe, Ayele M.;
Ahmed, Muktar;
Alemayehu, Tsegaye;
Amsalu, Erkihun;
Aravkin, Aleksandr Y.;
Asgedom, Akeza A.;
Bayleyegn, Nebiyou;
Dagnew, Mulat;
Demisse, Biniyam;
Etafa, Werku;
Fetensa, Getahun;
Gebremeskel, Teferi G.;
Geremew, Habtamu;
Gizaw, Abraham T.;
Hunde, Gamechu A.;
Meles, Hadush N.

Publication type:

Article