Works matching IS 1553734X AND DT 2025 AND VI 21 AND IP 1

Results: 58

Simulation-based validation of a method to detect changes in SARS-CoV-2 reinfection risk.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012792

By:

Lombard, Belinda;
Moultrie, Harry;
Pulliam, Juliet R.C.;
van Schalkwyk, Cari

Publication type:

Article

Design of field trials for the evaluation of transmissible vaccines in animal populations.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012779

By:

Sheen, Justin K.;
Kennedy-Shaffer, Lee;
Levy, Michael Z.;
Metcalf, Charlotte Jessica E.

Publication type:

Article

RSero: A user-friendly R package to reconstruct pathogen circulation history from seroprevalence studies.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012777

By:

Hozé, Nathanaël;
Pons-Salort, Margarita;
Metcalf, C. Jessica E.;
White, Michael;
Salje, Henrik;
Cauchemez, Simon

Publication type:

Article

Capturing continuous, long timescale behavioral changes in Drosophila melanogaster postural data.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012753

By:

McKenzie-Smith, Grace C.;
Wolf, Scott W.;
Ayroles, Julien F.;
Shaevitz, Joshua W.

Publication type:

Article

Ten quick tips to build a Model Life Cycle.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012731

By:

Poisot, Timothée;
Becker, Daniel J.;
Brookson, Cole B.;
Graeden, Ellie;
Ryan, Sadie J.;
Turon, Gemma;
Carlson, Colin

Publication type:

Article

Bayesian identification of differentially expressed isoforms using a novel joint model of RNA-seq data.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012750

By:

Shi, Xu;
Wang, Xiao;
Jin, Lu;
Halakivi-Clarke, Leena;
Clarke, Robert;
Neuwald, Andrew F.;
Xuan, Jianhua

Publication type:

Article

ASGCL: Adaptive Sparse Mapping-based graph contrastive learning network for cancer drug response prediction.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012748

By:

Dong, Yunyun;
Zhang, Yuanrong;
Qian, Yuhua;
Zhao, Yiming;
Yang, Ziting;
Feng, Xiufang

Publication type:

Article

Correction: Epidemiological and health economic implications of symptom propagation in respiratory pathogens: A mathematical modelling investigation.

Published in:

2025

By:

Asplin, Phoebe;
Keeling, Matt J.;
Mancy, Rebecca;
Hill, Edward M.

Publication type:

Correction Notice

The role of oscillations in grid cells' toroidal topology.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012776

By:

Sarra, Giovanni di;
Jha, Siddharth;
Roudi, Yasser

Publication type:

Article

The calcitron: A simple neuron model that implements many learning rules via the calcium control hypothesis.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012754

By:

Moldwin, Toviah;
Azran, Li Shay;
Segev, Idan

Publication type:

Article

Spherical harmonics texture extraction for versatile analysis of biological objects.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012349

By:

Gros, Oane;
Passmore, Josiah B.;
Borst, Noa O.;
Kutra, Dominik;
Nijenhuis, Wilco;
Fuqua, Timothy;
Kapitein, Lukas C.;
Crocker, Justin M.;
Kreshuk, Anna;
Köhler, Simone

Publication type:

Article

Ten simple rules to complete successfully a computational MSc thesis project.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012756

By:

Saccenti, Edoardo;
Furlan, Cristina

Publication type:

Article

DNA spontaneously wrapping around a histone core prefers negative supercoiling: A Brownian dynamics study.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012362

By:

Long, Chunhong;
Liang, Hongqiong;
Wan, Biao

Publication type:

Article

Specificity and tunability of efflux pumps: A new role for the proton gradient?

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012772

By:

Gerry, Matthew;
Kirby, Duncan;
Alexandrov, Boian S;
Segal, Dvira;
Zilman, Anton

Publication type:

Article

Human-like face pareidolia emerges in deep neural networks optimized for face and object recognition.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012751

By:

Gupta, Pranjul;
Dobs, Katharina

Publication type:

Article

Biophysical modeling and experimental analysis of the dynamics of C. elegans body-wall muscle cells.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012318

By:

Du, Xuexing;
Crodelle, Jennifer;
Barranca, Victor James;
Li, Songting;
Shi, Yunzhu;
Gao, Shangbang;
Zhou, Douglas

Publication type:

Article

Social mates dynamically coordinate aggressive behavior to produce strategic territorial defense.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012740

By:

Moody, Nicole M.;
Williams, Cole M.;
Ramachandran, Sohini;
Fuxjager, Matthew J.

Publication type:

Article

Exploiting the similarity of dissimilarities for biomedical applications and enhanced machine learning.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012716

By:

Kabir, Mohammad Neamul;
Wang, Li Rong;
Goh, Wilson Wen Bin

Publication type:

Article

The tumour histopathology "glossary" for AI developers.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012708

By:

Mandal, Soham;
Baker, Ann-Marie;
Graham, Trevor A.;
Bräutigam, Konstantin

Publication type:

Article

Data-driven discovery and parameter estimation of mathematical models in biological pattern formation.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012689

By:

Hishinuma, Hidekazu;
Takigawa-Imamura, Hisako;
Miura, Takashi

Publication type:

Article

Physiology-informed regularisation enables training of universal differential equation systems for biological applications.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012198

By:

de Rooij, Max;
Erdős, Balázs;
van Riel, Natal A. W.;
O'Donovan, Shauna D.

Publication type:

Article

Extracting the fingerprints of sequences of random rhythmic auditory stimuli from electrophysiological data.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012765

By:

Najman, Fernando A.;
Galves, Antonio;
Svarc, Marcela;
Vargas, Claudia D.

Publication type:

Article

Data-driven model discovery and model selection for noisy biological systems.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012762

By:

Wu, Xiaojun;
McDermott, MeiLu;
MacLean, Adam L

Publication type:

Article

Trajectory inference from single-cell genomics data with a process time model.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012752

By:

Fang, Meichen;
Gorin, Gennady;
Pachter, Lior

Publication type:

Article

Connectome-based biophysical models of pathological protein spreading in neurodegenerative diseases.

Published in:

2025

By:

Ren, Peng;
Cui, Xuehua;
Liang, Xia

Publication type:

Literature Review

A Structural Model of Truncated Gaussia princeps Luciferase Elucidating the Crucial Catalytic Function of No.76 Arginine towards Coelenterazine Oxidation.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012722

By:

Wu, Nan;
Xu, Zhi-Chao;
Du, Kai-Dong;
Huang, Shen;
Kobayashi, Naohiro;
Kuroda, Yutaka;
Bai, Yan-Hong

Publication type:

Article

Balancing central control and sensory feedback produces adaptable and robust locomotor patterns in a spiking, neuromechanical model of the salamander spinal cord.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012101

By:

Pazzaglia, Alessandro;
Bicanski, Andrej;
Ferrario, Andrea;
Arreguit, Jonathan;
Ryczko, Dimitri;
Ijspeert, Auke

Publication type:

Article

Adaptation optimizes sensory encoding for future stimuli.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012746

By:

Mao, Jiang;
Rothkopf, Constantin A;
Stocker, Alan A

Publication type:

Article

BuDDI: Bulk Deconvolution with Domain Invariance to predict cell-type-specific perturbations from bulk.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012742

By:

Davidson, Natalie R.;
Zhang, Fan;
Greene, Casey S.

Publication type:

Article

Integration of unpaired single cell omics data by deep transfer graph convolutional network.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012625

By:

Kan, Yulong;
Qi, Yunjing;
Zhang, Zhongxiao;
Liang, Xikeng;
Wang, Weihao;
Jin, Shuilin

Publication type:

Article

Mechanisms for dysregulation of excitatory-inhibitory balance underlying allodynia in dorsal horn neural subcircuits.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012234

By:

Ginsberg, Alexander G.;
Lempka, Scott F.;
Duan, Bo;
Booth, Victoria;
Crodelle, Jennifer

Publication type:

Article

Optimal control of agent-based models via surrogate modeling.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012138

By:

Fonseca, Luis L.;
Böttcher, Lucas;
Mehrad, Borna;
Laubenbacher, Reinhard C.

Publication type:

Article

Benchmarking residue-resolution protein coarse-grained models for simulations of biomolecular condensates.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012737

By:

Feito, Alejandro;
Sanchez-Burgos, Ignacio;
Tejero, Ignacio;
Sanz, Eduardo;
Rey, Antonio;
Collepardo-Guevara, Rosana;
Tejedor, Andrés R.;
Espinosa, Jorge R.

Publication type:

Article

Dialogue mechanisms between astrocytic and neuronal networks: A whole-brain modelling approach.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012683

By:

Ali, Obaï Bin Ka'b;
Vidal, Alexandre;
Grova, Christophe;
Benali, Habib

Publication type:

Article

Towards constructing a generalized structural 3D breathing human lung model based on experimental volumes, pressures, and strains.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012680

By:

Badrou, Arif;
Mariano, Crystal A.;
Ramirez, Gustavo O.;
Shankel, Matthew;
Rebelo, Nuno;
Eskandari, Mona

Publication type:

Article

HighDimMixedModels.jl: Robust high-dimensional mixed-effects models across omics data.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012143

By:

Gorstein, Evan;
Aghdam, Rosa;
Solís-Lemus, Claudia

Publication type:

Article

The role of chromatin state in intron retention: A case study in leveraging large scale deep learning models.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012755

By:

Daoud, Ahmed;
Ben-Hur, Asa

Publication type:

Article

A robust transfer learning approach for high-dimensional linear regression to support integration of multi-source gene expression data.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012739

By:

Pan, Lulu;
Gao, Qian;
Wei, Kecheng;
Yu, Yongfu;
Qin, Guoyou;
Wang, Tong

Publication type:

Article

Ten simple rules for good model-sharing practices.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012702

By:

Kherroubi Garcia, Ismael;
Erdmann, Christopher;
Gesing, Sandra;
Barton, Michael;
Cadwallader, Lauren;
Hengeveld, Geerten;
Kirkpatrick, Christine R.;
Knight, Kathryn;
Lemmen, Carsten;
Ringuette, Rebecca;
Zhan, Qing;
Harrison, Melissa;
Mac Gabhann, Feilim;
Meyers, Natalie;
Osborne, Cailean;
Till, Charlotte;
Brenner, Paul;
Buys, Matt;
Chen, Min;
Lee, Allen

Publication type:

Article

Deciphering the interplay between biology and physics with a finite element method-implemented vertex organoid model: A tool for the mechanical analysis of cell behavior on a spherical organoid shell.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012681

By:

Laussu, Julien;
Michel, Deborah;
Magne, Léa;
Segonds, Stephane;
Marguet, Steven;
Hamel, Dimitri;
Quaranta-Nicaise, Muriel;
Barreau, Frederick;
Mas, Emmanuel;
Velay, Vincent;
Bugarin, Florian;
Ferrand, Audrey

Publication type:

Article

Multi-region infectious disease prediction modeling based on spatio-temporal graph neural network and the dynamic model.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012738

By:

Wang, Xiaoyi;
Jin, Zhen

Publication type:

Article

Eight quick tips for biologically and medically informed machine learning.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012711

By:

Oneto, Luca;
Chicco, Davide

Publication type:

Article

Fast yet force-effective mode of supracellular collective cell migration due to extracellular force transmission.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012664

By:

Bagchi, Amrit;
Sarker, Bapi;
Zhang, Jialiang;
Foston, Marcus;
Pathak, Amit

Publication type:

Article

Prediction of cccDNA dynamics in hepatitis B patients by a combination of serum surrogate markers.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012615

By:

Kim, Kwang Su;
Iwamoto, Masashi;
Kitagawa, Kosaku;
Park, Hyeongki;
Hayashi, Sanae;
Tsukuda, Senko;
Matsui, Takeshi;
Atsukawa, Masanori;
Matsuura, Kentaro;
Chuaypen, Natthaya;
Tangkijvanich, Pisit;
Allweiss, Lena;
Nishiyama, Takara;
Nakamura, Naotoshi;
Fujita, Yasuhisa;
Kawakami, Eiryo;
Nakaoka, Shinji;
Muramatsu, Masamichi;
Aihara, Kazuyuki;
Wakita, Takaji

Publication type:

Article

Aggregating multiple test results to improve medical decision-making.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012749

By:

Böttcher, Lucas;
D'Orsogna, Maria R.;
Chou, Tom

Publication type:

Article

A genome-scale metabolic model for the denitrifying bacterium Thauera sp. MZ1T accurately predicts degradation of pollutants and production of polymers.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012736

By:

Tec-Campos, Diego;
Tibocha-Bonilla, Juan D.;
Jiang, Celina;
Passi, Anurag;
Thiruppathy, Deepan;
Zuñiga, Cristal;
Posadas, Camila;
Zepeda, Alejandro;
Zengler, Karsten

Publication type:

Article

Prioritization of causal genes from genome-wide association studies by Bayesian data integration across loci.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012725

By:

Mousavi, Zeinab;
Arvanitis, Marios;
Duong, ThuyVy;
Brody, Jennifer A.;
Battle, Alexis;
Sotoodehnia, Nona;
Shojaie, Ali;
Arking, Dan E.;
Bader, Joel S.

Publication type:

Article

Intraneuronal binding of amyloid beta with reelin—Implications for the onset of Alzheimer's disease.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012709

By:

Kobro-Flatmoen, Asgeir;
Omholt, Stig W.

Publication type:

Article

Low-dimensional controllability of brain networks.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012691

By:

Ben Messaoud, Remy;
Le Du, Vincent;
Bousfiha, Camile;
Corsi, Marie-Constance;
Gonzalez-Astudillo, Juliana;
Kaufmann, Brigitte Charlotte;
Venot, Tristan;
Couvy-Duchesne, Baptiste;
Migliaccio, Lara;
Rosso, Charlotte;
Bartolomeo, Paolo;
Chavez, Mario;
De Vico Fallani, Fabrizio

Publication type:

Article

Benchmarking uncertainty quantification for protein engineering.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 1, p. 1, doi. 10.1371/journal.pcbi.1012639

By:

Greenman, Kevin P.;
Amini, Ava P.;
Yang, Kevin K.

Publication type:

Article