Works matching IS 1553-734X AND VI 19 AND IP 9 AND DT 2023

Results: 71

Transcription factor competition facilitates self-sustained oscillations in single gene genetic circuits.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011525

By:

Landman, Jasper;
Verduyn Lunel, Sjoerd M.;
Kegel, Willem K.

Publication type:

Article

Profile-Wise Analysis: A profile likelihood-based workflow for identifiability analysis, estimation, and prediction with mechanistic mathematical models.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011515

By:

Simpson, Matthew J.;
Maclaren, Oliver J.

Publication type:

Article

Integrating a tailored recurrent neural network with Bayesian experimental design to optimize microbial community functions.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011436

By:

Thompson, Jaron C.;
Zavala, Victor M.;
Venturelli, Ophelia S.

Publication type:

Article

Evaluating a large language model's ability to solve programming exercises from an introductory bioinformatics course.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011511

By:

Piccolo, Stephen R.;
Denny, Paul;
Luxton-Reilly, Andrew;
Payne, Samuel H.;
Ridge, Perry G.

Publication type:

Article

CIRCUST: A novel methodology for temporal order reconstruction of molecular rhythms; validation and application towards a daily rhythm gene expression atlas in humans.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011510

By:

Larriba, Yolanda;
Mason, Ivy C.;
Saxena, Richa;
Scheer, Frank A. J. L.;
Rueda, Cristina

Publication type:

Article

A role for cortical interneurons as adversarial discriminators.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011484

By:

Benjamin, Ari S.;
Kording, Konrad P.

Publication type:

Article

Ten simple rules for interpreting and evaluating a meta-analysis.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011461

By:

Carlson, Rebecca B.;
Martin, Jennifer R.;
Beckett, Robert D.

Publication type:

Article

Measuring uncertainty in human visual segmentation.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011483

By:

Vacher, Jonathan;
Launay, Claire;
Mamassian, Pascal;
Coen-Cagli, Ruben

Publication type:

Article

Generalizing biological surround suppression based on center surround similarity via deep neural network models.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011486

By:

Pan, Xu;
DeForge, Annie;
Schwartz, Odelia

Publication type:

Article

FunSpace: A functional and spatial analytic approach to cell imaging data using entropy measures.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011490

By:

Vu, Thao;
Seal, Souvik;
Ghosh, Tusharkanti;
Ahmadian, Mansooreh;
Wrobel, Julia;
Ghosh, Debashis

Publication type:

Article

Exploring tumor-normal cross-talk with TranNet: Role of the environment in tumor progression.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011472

By:

Amgalan, Bayarbaatar;
Day, Chi-Ping;
Przytycka, Teresa M.

Publication type:

Article

Nowcasting the 2022 mpox outbreak in England.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011463

By:

Overton, Christopher E.;
Abbott, Sam;
Christie, Rachel;
Cumming, Fergus;
Day, Julie;
Jones, Owen;
Paton, Rob;
Turner, Charlie;
Ward, Thomas

Publication type:

Article

Ten quick tips for building FAIR workflows.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011369

By:

de Visser, Casper;
Johansson, Lennart F.;
Kulkarni, Purva;
Mei, Hailiang;
Neerincx, Pieter;
Joeri van der Velde, K.;
Horvatovich, Péter;
van Gool, Alain J.;
Swertz, Morris A.;
Hoen, Peter A. C. 't;
Niehues, Anna

Publication type:

Article

Continuous evaluation of cost-to-go for flexible reaching control and online decisions.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011493

By:

De Comite, Antoine;
Lefèvre, Philippe;
Crevecoeur, Frédéric

Publication type:

Article

Maximizing multi-reaction dependencies provides more accurate and precise predictions of intracellular fluxes than the principle of parsimony.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011489

By:

Hashemi, Seirana;
Razaghi-Moghadam, Zahra;
Nikoloski, Zoran

Publication type:

Article

Fixation dynamics on hypergraphs.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011494

By:

Liu, Ruodan;
Masuda, Naoki

Publication type:

Article

Recombulator-X: A fast and user-friendly tool for estimating X chromosome recombination rates in forensic genetics.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011474

By:

Aneli, Serena;
Fariselli, Piero;
Chierto, Elena;
Bini, Carla;
Robino, Carlo;
Birolo, Giovanni

Publication type:

Article

Simulation-based inference for efficient identification of generative models in computational connectomics.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011406

By:

Boelts, Jan;
Harth, Philipp;
Gao, Richard;
Udvary, Daniel;
Yáñez, Felipe;
Baum, Daniel;
Hege, Hans-Christian;
Oberlaender, Marcel;
Macke, Jakob H.

Publication type:

Article

Likelihood-ratio test statistic for the finite-sample case in nonlinear ordinary differential equation models.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011417

By:

Tönsing, Christian;
Steiert, Bernhard;
Timmer, Jens;
Kreutz, Clemens

Publication type:

Article

A platform-independent framework for phenotyping of multiplex tissue imaging data.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011432

By:

Ahmadian, Mansooreh;
Rickert, Christian;
Minic, Angela;
Wrobel, Julia;
Bitler, Benjamin G.;
Xing, Fuyong;
Angelo, Michael;
Hsieh, Elena W. Y.;
Ghosh, Debashis;
Jordan, Kimberly R.

Publication type:

Article

Human-environment feedback and the consistency of proenvironmental behavior.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011429

By:

Ecotière, Claire;
Billiard, Sylvain;
André, Jean-Baptiste;
Collet, Pierre;
Ferrière, Régis;
Méléard, Sylvie

Publication type:

Article

Personalized prediction for multiple chronic diseases by developing the multi-task Cox learning model.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011396

By:

Zhang, Shuaijie;
Yang, Fan;
Wang, Lijie;
Si, Shucheng;
Zhang, Jianmei;
Xue, Fuzhong

Publication type:

Article

Fourteen quick tips for crowdsourcing geographically linked data for public health advocacy.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011285

By:

Atienza, Joshua;
Benedict, Anjalee;
Stein, Lincoln D.;
Pirzada, Kashif;
White, Cheryl;
Pai, Shraddha

Publication type:

Article

Identifying a developmental transition in honey bees using gene expression data.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1010704

By:

Daniels, Bryan C.;
Wang, Ying;
Page Jr, Robert E.;
Amdam, Gro V.

Publication type:

Article

The first multi-tissue genome-scale metabolic model of a woody plant highlights suberin biosynthesis pathways in Quercus suber.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011499

By:

Cunha, Emanuel;
Silva, Miguel;
Chaves, Inês;
Demirci, Huseyin;
Lagoa, Davide Rafael;
Lima, Diogo;
Rocha, Miguel;
Rocha, Isabel;
Dias, Oscar

Publication type:

Article

Mechanistic multiscale modelling of energy metabolism in human astrocytes reveals the impact of morphology changes in Alzheimer's Disease.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011464

By:

Farina, Sofia;
Voorsluijs, Valérie;
Fixemer, Sonja;
Bouvier, David;
Claus, Susanne;
Ellisman, Mark;
Bordas, Stéphane P. A.;
Skupin, Alexander

Publication type:

Article

Marginal effects of public health measures and COVID-19 disease burden in China: A large-scale modelling study.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011492

By:

Wang, Zengmiao;
Wu, Peiyi;
Wang, Lin;
Li, Bingying;
Liu, Yonghong;
Ge, Yuxi;
Wang, Ruixue;
Wang, Ligui;
Tan, Hua;
Wu, Chieh-Hsi;
Laine, Marko;
Salje, Henrik;
Song, Hongbin

Publication type:

Article

Incorporating physics to overcome data scarcity in predictive modeling of protein function: A case study of BK channels.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011460

By:

Nordquist, Erik;
Zhang, Guohui;
Barethiya, Shrishti;
Ji, Nathan;
White, Kelli M.;
Han, Lu;
Jia, Zhiguang;
Shi, Jingyi;
Cui, Jianmin;
Chen, Jianhan

Publication type:

Article

Mathematical reconstruction of the metabolic network in an in-vitro multiple myeloma model.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011374

By:

Vera-Siguenza, Elias;
Escribano-Gonzalez, Cristina;
Serrano-Gonzalo, Irene;
Eskla, Kattri-Liis;
Spill, Fabian;
Tennant, Daniel

Publication type:

Article

Excalibur: A new ensemble method based on an optimal combination of aggregation tests for rare-variant association testing for sequencing data.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011488

By:

Boutry, Simon;
Helaers, Raphaël;
Lenaerts, Tom;
Vikkula, Miikka

Publication type:

Article

Mixtures of strategies underlie rodent behavior during reversal learning.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011430

By:

Le, Nhat Minh;
Yildirim, Murat;
Wang, Yizhi;
Sugihara, Hiroki;
Jazayeri, Mehrdad;
Sur, Mriganka

Publication type:

Article

Uncovering specific mechanisms across cell types in dynamical models.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1010867

By:

Hauber, Adrian L.;
Rosenblatt, Marcus;
Timmer, Jens

Publication type:

Article

Beyond ℓ<sub>1</sub> sparse coding in V1.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011459

By:

Rentzeperis, Ilias;
Calatroni, Luca;
Perrinet, Laurent U.;
Prandi, Dario

Publication type:

Article

Evaluating the use of social contact data to produce age-specific short-term forecasts of SARS-CoV-2 incidence in England.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011453

By:

Munday, James D.;
Abbott, Sam;
Meakin, Sophie;
Funk, Sebastian

Publication type:

Article

Testing predictive coding theories of autism spectrum disorder using models of active inference.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011473

By:

Arthur, Tom;
Vine, Sam;
Buckingham, Gavin;
Brosnan, Mark;
Wilson, Mark;
Harris, David

Publication type:

Article

Classification of T lymphocyte motility behaviors using a machine learning approach.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011449

By:

Solorio, Yves Carpentier;
Lemaître, Florent;
Jabbour, Bassam;
Tastet, Olivier;
Arbour, Nathalie;
Assi, Elie Bou

Publication type:

Article

iHerd: an integrative hierarchical graph representation learning framework to quantify network changes and prioritize risk genes in disease.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011444

By:

Duan, Ziheng;
Dai, Yi;
Hwang, Ahyeon;
Lee, Cheyu;
Xie, Kaichi;
Xiao, Chutong;
Xu, Min;
Girgenti, Matthew J.;
Zhang, Jing

Publication type:

Article

OpenABC enables flexible, simplified, and efficient GPU accelerated simulations of biomolecular condensates.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011442

By:

Liu, Shuming;
Wang, Cong;
Latham, Andrew P.;
Ding, Xinqiang;
Zhang, Bin

Publication type:

Article

Pathfinder: Protein folding pathway prediction based on conformational sampling.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011438

By:

Huang, Zhaohong;
Cui, Xinyue;
Xia, Yuhao;
Zhao, Kailong;
Zhang, Guijun

Publication type:

Article

Simulation-based Reconstructed Diffusion unveils the effect of aging on protein diffusion in Escherichia coli.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011093

By:

Mantovanelli, Luca;
Linnik, Dmitrii S.;
Punter, Michiel;
Kojakhmetov, Hildeberto Jardón;
Śmigiel, Wojciech M.;
Poolman, Bert

Publication type:

Article

Emergence of belief-like representations through reinforcement learning.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011067

By:

Hennig, Jay A.;
Romero Pinto, Sandra A.;
Yamaguchi, Takahiro;
Linderman, Scott W.;
Uchida, Naoshige;
Gershman, Samuel J.

Publication type:

Article

Computational modeling of multiscale collateral blood supply in a whole-brain-scale arterial network.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011452

By:

Otani, Tomohiro;
Nishimura, Nozomi;
Yamashita, Hiroshi;
Ii, Satoshi;
Yamada, Shigeki;
Watanabe, Yoshiyuki;
Oshima, Marie;
Wada, Shigeo

Publication type:

Article

Mate selection: A useful approach to maximize genetic gain and control inbreeding in genomic and conventional oil palm (Elaeis guineensis Jacq.) hybrid breeding.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1010290

By:

Tchounke, Billy;
Sanchez, Leopoldo;
Bell, Joseph Martin;
Cros, David

Publication type:

Article

Spike-timing dependent plasticity partially compensates for neural delays in a multi-layered network of motion-sensitive neurons.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011457

By:

Sexton, Charlie M.;
Burkitt, Anthony N.;
Hogendoorn, Hinze

Publication type:

Article

A whole-task brain model of associative recognition that accounts for human behavior and neuroimaging data.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011427

By:

Borst, Jelmer P.;
Aubin, Sean;
Stewart, Terrence C.

Publication type:

Article

Error-independent effect of sensory uncertainty on motor learning when both feedforward and feedback control processes are engaged.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1010526

By:

Hewitson, Christopher L.;
Kaplan, David M.;
Crossley, Matthew J.

Publication type:

Article

Modelling African horse sickness emergence and transmission in the South African control area using a deterministic metapopulation approach.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011448

By:

de Klerk, Joanna N.;
Gorsich, Erin E.;
Grewar, John D.;
Atkins, Benjamin D.;
Tennant, Warren S. D.;
Labuschagne, Karien;
Tildesley, Michael J.

Publication type:

Article

What constrains food webs? A maximum entropy framework for predicting their structure with minimal biases.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011458

By:

Banville, Francis;
Gravel, Dominique;
Poisot, Timothée

Publication type:

Article

Predictive modeling of antibiotic eradication therapy success for new-onset Pseudomonas aeruginosa pulmonary infections in children with cystic fibrosis.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011424

By:

Graña-Miraglia, Lucía;
Morales-Lizcano, Nadia;
Wang, Pauline W.;
Hwang, David M.;
Yau, Yvonne C. W.;
Waters, Valerie J.;
Guttman, David S.

Publication type:

Article

Structure-based prediction of nucleic acid binding residues by merging deep learning- and template-based approaches.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011428

By:

Jiang, Zheng;
Shen, Yue-Yue;
Liu, Rong

Publication type:

Article