Works matching IS 1553734X AND DT 2025 AND VI 21 AND IP 2

Results: 41

A model of Notch signalling control of angiogenesis: Evidence of a role for Notch ligand heterodimerization.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 2, p. 1, doi. 10.1371/journal.pcbi.1012825

By:

Chen, Daipeng;
Liu, Xinxin;
Wang, Haijiang;
Merks, Roeland M.H.;
Baker, David A.

Publication type:

Article

ENQUIRE automatically reconstructs, expands, and drives enrichment analysis of gene and Mesh co-occurrence networks from context-specific biomedical literature.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 2, p. 1, doi. 10.1371/journal.pcbi.1012745

By:

Musella, Luca;
Afonso Castro, Alejandro;
Lai, Xin;
Widmann, Max;
Vera, Julio

Publication type:

Article

Decoding biomolecular condensate dynamics: an energy landscape approach.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 2, p. 1, doi. 10.1371/journal.pcbi.1012826

By:

Biswas, Subhadip;
Potoyan, Davit A

Publication type:

Article

Computational mechanism underlying switching of motor actions.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 2, p. 1, doi. 10.1371/journal.pcbi.1012811

By:

Zhong, Shan;
Pouratian, Nader;
Christopoulos, Vassilios

Publication type:

Article

Mapping the learning curves of deep learning networks.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 2, p. 1, doi. 10.1371/journal.pcbi.1012286

By:

Jiang, Yanru;
Dale, Rick

Publication type:

Article

Challenging a paradigm: Staggered versus single-pulse mass dog vaccination strategy for rabies elimination.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 2, p. 1, doi. 10.1371/journal.pcbi.1012780

By:

Bellotti, Brinkley Raynor;
Díaz, Elvis W.;
De la Puente-León, Micaela;
Rieders, Maria T.;
Recuenco, Sergio E.;
Levy, Michael Z.;
Castillo-Neyra, Ricardo

Publication type:

Article

Identifying patterns differing between high-dimensional datasets with generalized contrastive PCA.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 2, p. 1, doi. 10.1371/journal.pcbi.1012747

By:

Oliveira, Eliezyer Fermino de;
Garg, Pranjal;
Hjerling-Leffler, Jens;
Batista-Brito, Renata;
Sjulson, Lucas

Publication type:

Article

Identification of recurrent dynamics in distributed neural populations.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 2, p. 1, doi. 10.1371/journal.pcbi.1012816

By:

Osuna-Orozco, Rodrigo;
Castillo, Edward;
Harris, Kameron Decker;
Santacruz, Samantha R.

Publication type:

Article

A SuperLearner-based pipeline for the development of DNA methylation-derived predictors of phenotypic traits.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 2, p. 1, doi. 10.1371/journal.pcbi.1012768

By:

Khodasevich, Dennis;
Holland, Nina;
van der Laan, Lars;
Cardenas, Andres

Publication type:

Article

Structural prediction of chimeric immunogen candidates to elicit targeted antibodies against betacoronaviruses.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 2, p. 1, doi. 10.1371/journal.pcbi.1012812

By:

Simpson, Jamel;
Kasson, Peter M.

Publication type:

Article

Interpreting the CTCF-mediated sequence grammar of genome folding with AkitaV2.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 2, p. 1, doi. 10.1371/journal.pcbi.1012824

By:

Smaruj, Paulina N.;
Kamulegeya, Fahad;
Kelley, David R.;
Fudenberg, Geoffrey

Publication type:

Article

Repeated games with partner choice.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 2, p. 1, doi. 10.1371/journal.pcbi.1012810

By:

Graser, Christopher;
Fujiwara-Greve, Takako;
García, Julián;
van Veelen, Matthijs

Publication type:

Article

Contributions of action potentials to scalp EEG: Theory and biophysical simulations.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 2, p. 1, doi. 10.1371/journal.pcbi.1012794

By:

Brake, Niklas;
Khadra, Anmar

Publication type:

Article

Multi-strain phage induced clearance of bacterial infections.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 2, p. 1, doi. 10.1371/journal.pcbi.1012793

By:

Marchi, Jacopo;
Minh, Chau Nguyen Ngoc;
Debarbieux, Laurent;
Weitz, Joshua S

Publication type:

Article

Information transmission in a cell monolayer: A numerical study.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 2, p. 1, doi. 10.1371/journal.pcbi.1012846

By:

Nałęcz-Jawecki, Paweł;
Szyc, Przemysław;
Grabowski, Frederic;
Kochańczyk, Marek;
Lipniacki, Tomasz

Publication type:

Article

Resilience of mobility network to dynamic population response across COVID-19 interventions: Evidences from Chile.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 2, p. 1, doi. 10.1371/journal.pcbi.1012802

By:

Casaburi, Pasquale;
Dall'Amico, Lorenzo;
Gozzi, Nicolò;
Kalimeri, Kyriaki;
Sapienza, Anna;
Schifanella, Rossano;
Matteo, Tiziana Di;
Ferres, Leo;
Mazzoli, Mattia

Publication type:

Article

Impact of increased diagnosis of early HIV infection and immediate antiretroviral treatment initiation on HIV transmission among men who have sex with men in the Netherlands.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 2, p. 1, doi. 10.1371/journal.pcbi.1012055

By:

Teslya, Alexandra;
Heijne, Janneke Cornelia Maria;
van der Loeff, Maarten Franciscus Schim;
van Sighem, Ard;
Roberts, Jacob Aiden;
Dijkstra, Maartje;
de Bree, Godelieve J;
Schmidt, Axel Jeremias;
Jonas, Kai J;
Kretzschmar, Mirjam E;
Rozhnova, Ganna

Publication type:

Article

Noradrenergic and Dopaminergic modulation of meta-cognition and meta-control.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 2, p. 1, doi. 10.1371/journal.pcbi.1012675

By:

Ershadmanesh, Sara;
Rajabi, Sahar;
Rostami, Reza;
Moran, Rani;
Dayan, Peter

Publication type:

Article

An agent-based model to simulate the transmission dynamics of bloodborne pathogens within hospitals.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 2, p. 1, doi. 10.1371/journal.pcbi.1012850

By:

Henriot, Paul;
El-Kassas, Mohamed;
Anwar, Wagida;
Girgis, Samia A.;
El Gaafary, Maha;
Jean, Kévin;
Temime, Laura

Publication type:

Article

An application of nowcasting methods: Cases of norovirus during the winter 2023/2024 in England.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 2, p. 1, doi. 10.1371/journal.pcbi.1012849

By:

Mellor, Jonathon;
Tang, Maria L.;
Finch, Emilie;
Christie, Rachel;
Polhill, Oliver;
Overton, Christopher E.;
Hoban, Ann;
Douglas, Amy;
Deeny, Sarah R.;
Ward, Thomas

Publication type:

Article

Compression-enabled interpretability of voxelwise encoding models.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 2, p. 1, doi. 10.1371/journal.pcbi.1012822

By:

Kamali, Fatemeh;
Suratgar, Amir Abolfazl;
Menhaj, Mohammadbagher;
Abbasi-Asl, Reza

Publication type:

Article

Bayesian classification of OXPHOS deficient skeletal myofibres.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 2, p. 1, doi. 10.1371/journal.pcbi.1012770

By:

Childs, Jordan;
Gomes, Tiago Bernardino;
Vincent, Amy E;
Golightly, Andrew;
Lawless, Conor

Publication type:

Article

Quantifying infectious disease epidemic risks: A practical approach for seasonal pathogens.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 2, p. 1, doi. 10.1371/journal.pcbi.1012364

By:

Kaye, Alexander R;
Guzzetta, Giorgio;
Tildesley, Michael J;
Thompson, Robin N

Publication type:

Article

SpatialKNifeY (SKNY): Extending from spatial domain to surrounding area to identify microenvironment features with single-cell spatial omics data.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 2, p. 1, doi. 10.1371/journal.pcbi.1012854

By:

Sakai, Shunsuke A.;
Nomura, Ryosuke;
Nagasawa, Satoi;
Chi, SungGi;
Suzuki, Ayako;
Suzuki, Yutaka;
Imai, Mitsuho;
Nakamura, Yoshiaki;
Yoshino, Takayuki;
Ishikawa, Shumpei;
Tsuchihara, Katsuya;
Kageyama, Shun-Ichiro;
Yamashita, Riu

Publication type:

Article

ChromaFactor: Deconvolution of single-molecule chromatin organization with non-negative matrix factorization.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 2, p. 1, doi. 10.1371/journal.pcbi.1012841

By:

Gunsalus, Laura M.;
Keiser, Michael J.;
Pollard, Katherine S.

Publication type:

Article

NAVIP: Unraveling the influence of neighboring small sequence variants on functional impact prediction.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 2, p. 1, doi. 10.1371/journal.pcbi.1012732

By:

Baasner, Jan-Simon;
Rempel, Andreas;
Howard, Dakota;
Pucker, Boas

Publication type:

Article

Estimating Mycobacterium tuberculosis transmission in a South African clinic: Spatiotemporal model based on person movements.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 2, p. 1, doi. 10.1371/journal.pcbi.1012823

By:

Banholzer, Nicolas;
Middelkoop, Keren;
Leukes, Juane;
Weingartner, Ernest;
Schmutz, Remo;
Zürcher, Kathrin;
Egger, Matthias;
Wood, Robin;
Fenner, Lukas

Publication type:

Article

Optimal control prevents itself from eradicating stochastic disease epidemics.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 2, p. 1, doi. 10.1371/journal.pcbi.1012781

By:

Russell, Rachel;
Cunniffe, Nik J

Publication type:

Article

Nowcasting reported covid-19 hospitalizations using de-identified, aggregated medical insurance claims data.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 2, p. 1, doi. 10.1371/journal.pcbi.1012717

By:

Shen, Xueda;
Rumack, Aaron;
Wilder, Bryan;
Tibshirani, Ryan J

Publication type:

Article

Tumor-immune partitioning and clustering algorithm for identifying tumor-immune cell spatial interaction signatures within the tumor microenvironment.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 2, p. 1, doi. 10.1371/journal.pcbi.1012707

By:

Lau, Mai Chan;
Borowsky, Jennifer;
Väyrynen, Juha P.;
Haruki, Koichiro;
Zhao, Melissa;
Dias Costa, Andressa;
Gu, Simeng;
da Silva, Annacarolina;
Ugai, Tomotaka;
Arima, Kota;
Nguyen, Minh N.;
Takashima, Yasutoshi;
Yeong, Joe;
Tai, David;
Hamada, Tsuyoshi;
Lennerz, Jochen K.;
Fuchs, Charles S.;
Wu, Catherine J.;
Meyerhardt, Jeffrey A.;
Ogino, Shuji

Publication type:

Article

Integrating multiscale mathematical modeling and multidimensional data reveals the effects of epigenetic instability on acquired drug resistance in cancer.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 2, p. 1, doi. 10.1371/journal.pcbi.1012815

By:

Wang, Shun;
Lei, Jinzhi;
Zou, Xiufen;
Jin, Suoqin

Publication type:

Article

Ten simple rules for fostering creativity in research labs.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 2, p. 1, doi. 10.1371/journal.pcbi.1012788

By:

Rillig, Matthias C.

Publication type:

Article

Using a multi-strain infectious disease model with physical information neural networks to study the time dependence of SARS-CoV-2 variants of concern.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 2, p. 1, doi. 10.1371/journal.pcbi.1012778

By:

Li, Wenxuan;
Chen, Xu;
Liu, Suli;
Zhang, Chiyu;
Liu, Guyue

Publication type:

Article

An in silico framework for the rational design of vaginal probiotic therapy.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 2, p. 1, doi. 10.1371/journal.pcbi.1012064

By:

Lee, Christina Y.;
Bonakdar, Sina;
Arnold, Kelly B.

Publication type:

Article

Bimodality in E. coli gene expression: Sources and robustness to genome-wide stresses.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 2, p. 1, doi. 10.1371/journal.pcbi.1012817

By:

Baptista, Ines S. C.;
Dash, Suchintak;
Arsh, Amir M.;
Kandavalli, Vinodh;
Scandolo, Carlo Maria;
Sanders, Barry C.;
Ribeiro, Andre S.

Publication type:

Article

Hexagons all the way down: grid cells as a conformal isometric map of space.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 2, p. 1, doi. 10.1371/journal.pcbi.1012804

By:

Schøyen, Vemund Sigmundson;
Beshkov, Kosio;
Pettersen, Markus Borud;
Hermansen, Erik;
Holzhausen, Konstantin;
Malthe-Sørenssen, Anders;
Fyhn, Marianne;
Lepperød, Mikkel Elle

Publication type:

Article

Reliability-enhanced data cleaning in biomedical machine learning using inductive conformal prediction.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 2, p. 1, doi. 10.1371/journal.pcbi.1012803

By:

Zhan, Xianghao;
Xu, Qinmei;
Zheng, Yuanning;
Lu, Guangming;
Gevaert, Olivier

Publication type:

Article

Early detection of disease outbreaks and non-outbreaks using incidence data: A framework using feature-based time series classification and machine learning.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 2, p. 1, doi. 10.1371/journal.pcbi.1012782

By:

Gao, Shan;
Chakraborty, Amit K;
Greiner, Russell;
Lewis, Mark A;
Wang, Hao

Publication type:

Article

AWGE-ESPCA: An edge sparse PCA model based on adaptive noise elimination regularization and weighted gene network for Hermetia illucens genomic data analysis.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 2, p. 1, doi. 10.1371/journal.pcbi.1012773

By:

Miao, Rui;
Yu, Hao-Yang;
Zhong, Bing-Jie;
Sun, Hong-Xia;
Xia, Qiang

Publication type:

Article

Detection of latent brain states from spontaneous neural activity in the amygdala.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 2, p. 1, doi. 10.1371/journal.pcbi.1012247

By:

Aucoin, Alexa;
Lin, Kevin K.;
Gothard, Katalin M.

Publication type:

Article

Accurate Bayesian phylogenetic point estimation using a tree distribution parameterized by clade probabilities.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 2, p. 1, doi. 10.1371/journal.pcbi.1012789

By:

Berling, Lars;
Klawitter, Jonathan;
Bouckaert, Remco;
Xie, Dong;
Gavryushkin, Alex;
Drummond, Alexei J

Publication type:

Article