Works matching IS 1553734X AND DT 2025 AND VI 21 AND IP 3

Results: 35

GeneCOCOA: Detecting context-specific functions of individual genes using co-expression data.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 3, p. 1, doi. 10.1371/journal.pcbi.1012278

By:

Zehr, Simonida;
Wolf, Sebastian;
Oellerich, Thomas;
Leisegang, Matthias S.;
Brandes, Ralf P.;
Schulz, Marcel H.;
Warwick, Timothy

Publication type:

Article

Uncovering temperature sensitivity of West Nile virus transmission: Novel computational approaches to mosquito-pathogen trait responses.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 3, p. 1, doi. 10.1371/journal.pcbi.1012866

By:

Heidecke, Julian;
Wallin, Jonas;
Fransson, Peter;
Singh, Pratik;
Sjödin, Henrik;
Stiles, Pascale Claire;
Treskova, Marina;
Rocklöv, Joacim

Publication type:

Article

Supervised fine-tuning of pre-trained antibody language models improves antigen specificity prediction.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 3, p. 1, doi. 10.1371/journal.pcbi.1012153

By:

Wang, Meng;
Patsenker, Jonathan;
Li, Henry;
Kluger, Yuval;
Kleinstein, Steven H.

Publication type:

Article

An integrative network approach for longitudinal stratification in Parkinson's disease.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 3, p. 1, doi. 10.1371/journal.pcbi.1012857

By:

Ryan, Barry;
Marioni, Riccardo;
Simpson, T. Ian

Publication type:

Article

Putting computational models of immunity to the test—An invited challenge to predict B.pertussis vaccination responses.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 3, p. 1, doi. 10.1371/journal.pcbi.1012927

By:

Shinde, Pramod;
Willemsen, Lisa;
Anderson, Michael;
Aoki, Minori;
Basu, Saonli;
Burel, Julie G.;
Cheng, Peng;
Ghosh Dastidar, Souradipto;
Dunleavy, Aidan;
Einav, Tal;
Forschmiedt, Jamie;
Fourati, Slim;
Garcia, Javier;
Gibson, William;
Greenbaum, Jason A.;
Guan, Leying;
Guan, Weikang;
Gygi, Jeremy P.;
Ha, Brendan;
Hou, Joe

Publication type:

Article

Anticancer drug response prediction integrating multi-omics pathway-based difference features and multiple deep learning techniques.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 3, p. 1, doi. 10.1371/journal.pcbi.1012905

By:

Wu, Yang;
Chen, Ming;
Qin, Yufang

Publication type:

Article

Computational studies reveal structural characterization and novel families of Puccinia striiformis f. sp. tritici effectors.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 3, p. 1, doi. 10.1371/journal.pcbi.1012503

By:

Asghar, Raheel;
Wu, Nan;
Ali, Noman;
Wang, Yulei;
Akkaya, Mahinur

Publication type:

Article

Analysis of systemic effects of dioxin on human health through template-and-anchor modeling.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 3, p. 1, doi. 10.1371/journal.pcbi.1012840

By:

Kumbale, Carla M.;
Zhang, Qiang;
Voit, Eberhard O.

Publication type:

Article

Investigation of hemodynamic bulk flow patterns caused by aortic stenosis using a combined 4D Flow MRI-CFD framework.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 3, p. 1, doi. 10.1371/journal.pcbi.1012467

By:

Wang, Tianai;
Quast, Christine;
Bönner, Florian;
Kelm, Malte;
Zeus, Tobias;
Lemainque, Teresa;
Steinseifer, Ulrich;
Neidlin, Michael

Publication type:

Article

How immunity shapes the long-term dynamics of influenza H3N2.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 3, p. 1, doi. 10.1371/journal.pcbi.1012893

By:

Eales, Oliver;
Shearer, Freya M.;
McCaw, James M.

Publication type:

Article

Unknotting RNA: A method to resolve computational artifacts.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 3, p. 1, doi. 10.1371/journal.pcbi.1012843

By:

Poblete, Simón;
Mlynarczyk, Mikolaj;
Szachniuk, Marta

Publication type:

Article

Gauge fixing for sequence-function relationships.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 3, p. 1, doi. 10.1371/journal.pcbi.1012818

By:

Posfai, Anna;
Zhou, Juannan;
McCandlish, David M.;
Kinney, Justin B.

Publication type:

Article

lncreased risk of slippage upon disengagement of the mitotic checkpoint.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 3, p. 1, doi. 10.1371/journal.pcbi.1012879

By:

Stier, Alma Beatrix;
Bonaiuti, Paolo;
Juhász, János;
Gross, Fridolin;
Ciliberto, Andrea

Publication type:

Article

Eleven quick tips for writing a Bioconductor package.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 3, p. 1, doi. 10.1371/journal.pcbi.1012856

By:

Soneson, Charlotte;
Shepherd, Lori;
Ramos, Marcel;
Rue-Albrecht, Kevin;
Rainer, Johannes;
Pagès, Hervé;
Carey, Vincent J.

Publication type:

Article

Machine learning-based prediction reveals kinase MAP4K4 regulates neutrophil differentiation through phosphorylating apoptosis-related proteins.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 3, p. 1, doi. 10.1371/journal.pcbi.1012877

By:

Wang, Guihua;
Zhang, Dan;
He, Zhifeng;
Mao, Bin;
Hu, Xiao;
Chen, Li;
Yang, Qingxin;
Zhou, Zhen;
Zhang, Yating;
Linghu, Kepan;
Tang, Chao;
Xu, Zijie;
Liu, Defu;
Song, Junwei;
Wang, Huiying;
Lin, Yishan;
Li, Ruihan;
Lin, Jing-Wen;
Chen, Lu

Publication type:

Article

RBC-GEM: A genome-scale metabolic model for systems biology of the human red blood cell.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 3, p. 1, doi. 10.1371/journal.pcbi.1012109

By:

Haiman, Zachary B.;
Key, Alicia;
D'Alessandro, Angelo;
Palsson, Bernhard O.

Publication type:

Article

Predictive reward-prediction errors of climbing fiber inputs integrate modular reinforcement learning with supervised learning.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 3, p. 1, doi. 10.1371/journal.pcbi.1012899

By:

Hoang, Huu;
Tsutsumi, Shinichiro;
Matsuzaki, Masanori;
Kano, Masanobu;
Toyama, Keisuke;
Kitamura, Kazuo;
Kawato, Mitsuo

Publication type:

Article

Pre-training artificial neural networks with spontaneous retinal activity improves motion prediction in natural scenes.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 3, p. 1, doi. 10.1371/journal.pcbi.1012830

By:

May, Lilly;
Dauphin, Alice;
Gjorgjieva, Julijana

Publication type:

Article

Synthetic population generation with public health characteristics for spatial agent-based models.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 3, p. 1, doi. 10.1371/journal.pcbi.1012439

By:

Von Hoene, Emma;
Roess, Amira;
Kavak, Hamdi;
Anderson, Taylor

Publication type:

Article

Generative AI helps extract ecological meaning from the complex three dimensional shapes of bird bills.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 3, p. 1, doi. 10.1371/journal.pcbi.1012887

By:

Dinnage, Russell;
Kleineberg, Marian

Publication type:

Article

Metabolic network reconstruction as a resource for analyzing Salmonella Typhimurium SL1344 growth in the mouse intestine.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 3, p. 1, doi. 10.1371/journal.pcbi.1012869

By:

Vayena, Evangelia;
Fuchs, Lea;
Peyhani, Homa Mohammadi;
Lagoda, Konrad;
Nguyen, Bidong;
Hardt, Wolf-Dietrich;
Hatzimanikatis, Vassily

Publication type:

Article

Mixed recurrent connectivity in primate prefrontal cortex.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 3, p. 1, doi. 10.1371/journal.pcbi.1012867

By:

Sigalas, Evangelos;
Libedinsky, Camilo

Publication type:

Article

TphPMF: A microbiome data imputation method using hierarchical Bayesian Probabilistic Matrix Factorization.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 3, p. 1, doi. 10.1371/journal.pcbi.1012858

By:

Han, Xinyu;
Song, Kai

Publication type:

Article

Predicting the diversity of photosynthetic light-harvesting using thermodynamics and machine learning.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 3, p. 1, doi. 10.1371/journal.pcbi.1012845

By:

Gray, Callum;
Chitnavis, Samir;
Buja, Tamara;
Duffy, Christopher D P

Publication type:

Article

Computational modelling identifies primary mediators of crosstalk between DNA damage and oxidative stress responses.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 3, p. 1, doi. 10.1371/journal.pcbi.1012844

By:

Burgers, Elsje J;
Sharma, Raju P;
Eugenio, Carl Joshua S;
Heldring, Muriel M;
Wijaya, Lukas S;
van de Water, Bob;
Beltman, Joost B

Publication type:

Article

Internal cohesion gradient as a novel mechanism of collective cell migration.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 3, p. 1, doi. 10.1371/journal.pcbi.1012769

By:

Oprysk, Larissa M.;
Vazquez, Maribel;
Shinbrot, Troy

Publication type:

Article

Exploring the transmission of cognitive task information through optimal brain pathways.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 3, p. 1, doi. 10.1371/journal.pcbi.1012870

By:

Wang, Zhengdong;
Yang, Yifeixue;
Huang, Ziyi;
Zhao, Wanyun;
Su, Kaiqiang;
Zhu, Hengcheng;
Yin, Dazhi

Publication type:

Article

Penalised regression improves imputation of cell-type specific expression using RNA-seq data from mixed cell populations compared to domain-specific methods.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 3, p. 1, doi. 10.1371/journal.pcbi.1012859

By:

Lin, Wei-Yu;
Kartawinata, Melissa;
Jebson, Bethany R.;
Restuadi, Restuadi;
Peckham, Hannah;
Radziszewska, Anna;
Deakin, Claire;
Ciurtin, Coziana;
Wedderburn, Lucy R.;
Wallace, Chris

Publication type:

Article

iSoMAs: Finding isoform expression and somatic mutation associations in human cancers.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 3, p. 1, doi. 10.1371/journal.pcbi.1012847

By:

Tan, Hua;
Gotea, Valer;
Jaiswal, Sushil K.;
Seidel, Nancy E.;
Holland, David O.;
Fedkenheuer, Kevin;
Elkahloun, Abdel G.;
Bang-Christensen, Sara R.;
Elnitski, Laura

Publication type:

Article

DySCo: A general framework for dynamic functional connectivity.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 3, p. 1, doi. 10.1371/journal.pcbi.1012795

By:

Alteriis, Giuseppe de;
Sherwood, Oliver;
Ciaramella, Alessandro;
Leech, Robert;
Cabral, Joana;
Turkheimer, Federico E;
Expert, Paul

Publication type:

Article

Efficient numerosity estimation under limited time.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 3, p. 1, doi. 10.1371/journal.pcbi.1012790

By:

Heng, Joseph A;
Woodford, Michael;
Polania, Rafael

Publication type:

Article

Mathematical modeling reveals ferritin as the strongest cellular driver of dietary iron transfer block in enterocytes.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 3, p. 1, doi. 10.1371/journal.pcbi.1012374

By:

Masison, Joseph;
Mendes, Pedro

Publication type:

Article

Suprachiasmatic nucleus-wide estimation of oscillatory temporal dynamics.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 3, p. 1, doi. 10.1371/journal.pcbi.1012855

By:

Yao, Yifan;
Pauls, Scott;
Foley, Duncan;
Yoshikawa, Tomoko;
Honma, Sato;
Honma, Ken-Ichi;
McVeigh, Ellie;
Foley, Nicolas C.;
Silver, Rae

Publication type:

Article

Post-processing and weighted combination of infectious disease nowcasts.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 3, p. 1, doi. 10.1371/journal.pcbi.1012836

By:

Amaral, André Victor Ribeiro;
Wolffram, Daniel;
Moraga, Paula;
Bracher, Johannes

Publication type:

Article

Modeling decision-making under uncertainty with qualitative outcomes.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 3, p. 1, doi. 10.1371/journal.pcbi.1012440

By:

Korem, Nachshon;
Duek, Or;
Jia, Ruonan;
Wertheimer, Emily;
Metviner, Sierra;
Grubb, Michael;
Levy, Ifat

Publication type:

Article