Works matching IS 1553734X AND DT 2023 AND VI 19 AND IP 9

Results: 71

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

iCVS—Inferring Cardio-Vascular hidden States from physiological signals available at the bedside.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1010835

By:

Ravid Tannenbaum, Neta;
Gottesman, Omer;
Assadi, Azadeh;
Mazwi, Mjaye;
Shalit, Uri;
Eytan, Danny

Publication type:

Article

Trackplot: A flexible toolkit for combinatorial analysis of genomic data.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011477

By:

Zhang, Yiming;
Zhou, Ran;
Liu, Lunxu;
Chen, Lu;
Wang, Yuan

Publication type:

Article

An automated interface for sedimentation velocity analysis in SEDFIT.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011454

By:

Schuck, Peter;
To, Samuel C.;
Zhao, Huaying

Publication type:

Article

Controlling brain dynamics: Landscape and transition path for working memory.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011446

By:

Ye, Leijun;
Feng, Jianfeng;
Li, Chunhe

Publication type:

Article

Predicting the target landscape of kinase inhibitors using 3D convolutional neural networks.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011301

By:

Kanev, Georgi K.;
Zhang, Yaran;
Kooistra, Albert J.;
Bender, Andreas;
Leurs, Rob;
Bailey, David;
Würdinger, Thomas;
de Graaf, Chris;
de Esch, Iwan J. P.;
Westerman, Bart A.

Publication type:

Article

Age-differentiated incentives for adaptive behavior during epidemics produce oscillatory and chaotic dynamics.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011217

By:

Arthur, Ronan F.;
Levin, May;
Labrogere, Alexandre;
Feldman, Marcus W.

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

The inhibitory control of traveling waves in cortical networks.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1010697

By:

Palkar, Grishma;
Wu, Jian-young;
Ermentrout, Bard

Publication type:

Article

RSim: A reference-based normalization method via rank similarity.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011447

By:

Yuan, Bo;
Wang, Shulei

Publication type:

Article

A multi-layer mean-field model of the cerebellum embedding microstructure and population-specific dynamics.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011434

By:

Lorenzi, Roberta Maria;
Geminiani, Alice;
Zerlaut, Yann;
De Grazia, Marialaura;
Destexhe, Alain;
Gandini Wheeler-Kingshott, Claudia A. M.;
Palesi, Fulvia;
Casellato, Claudia;
D'Angelo, Egidio

Publication type:

Article

Evaluating the impact of test-trace-isolate for COVID-19 management and alternative strategies.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011423

By:

Zhang, Kun;
Xia, Zhichu;
Huang, Shudong;
Sun, Gui-Quan;
Lv, Jiancheng;
Ajelli, Marco;
Ejima, Keisuke;
Liu, Quan-Hui

Publication type:

Article

Bayesian inference for spatio-temporal stochastic transmission of plant disease in the presence of roguing: A case study to characterise the dispersal of Flavescence dorée.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011399

By:

Kwame Adrakey, Hola;
Gibson, Gavin J.;
Eveillard, Sandrine;
Malembic-Maher, Sylvie;
Fabre, Frederic

Publication type:

Article

Self-loops in evolutionary graph theory: Friends or foes?

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011387

By:

Sharma, Nikhil;
Yagoobi, Sedigheh;
Traulsen, Arne

Publication type:

Article

Dynamical modelling of viral infection and cooperative immune protection in COVID-19 patients.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011383

By:

Zhou, Zhengqing;
Li, Dianjie;
Zhao, Ziheng;
Shi, Shuyu;
Wu, Jianghua;
Li, Jianwei;
Zhang, Jingpeng;
Gui, Ke;
Zhang, Yu;
Ouyang, Qi;
Mei, Heng;
Hu, Yu;
Li, Fangting

Publication type:

Article

Nonlinear expression patterns and multiple shifts in gene network interactions underlie robust phenotypic change in Drosophila melanogaster selected for night sleep duration.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011389

By:

Souto-Maior, Caetano;
Serrano Negron, Yazmin L.;
Harbison, Susan T.

Publication type:

Article

SARS-CoV-2 infection perturbs enhancer mediated transcriptional regulation of key pathways.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 9, p. 1, doi. 10.1371/journal.pcbi.1011397

By:

Yedidya, Yahel;
Davis, Daniel;
Drier, Yotam

Publication type:

Article