Works matching IS 1553734X AND DT 2024 AND VI 20 AND IP 3

Results: 50

Amplifiers of selection for the Moran process with both Birth-death and death-Birth updating.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1012008

By:

Svoboda, Jakub;
Joshi, Soham;
Tkadlec, Josef;
Chatterjee, Krishnendu

Publication type:

Article

Parameter estimation in behavioral epidemic models with endogenous societal risk-response.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011992

By:

Osi, Ann;
Ghaffarzadegan, Navid

Publication type:

Article

Active reinforcement learning versus action bias and hysteresis: control with a mixture of experts and nonexperts.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011950

By:

Colas, Jaron T.;
O'Doherty, John P.;
Grafton, Scott T.

Publication type:

Article

Scalable gradients enable Hamiltonian Monte Carlo sampling for phylodynamic inference under episodic birth-death-sampling models.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011640

By:

Shao, Yucai;
Magee, Andrew F.;
Vasylyeva, Tetyana I.;
Suchard, Marc A.

Publication type:

Article

Modeling resistance to the broadly neutralizing antibody PGT121 in people living with HIV-1.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011518

By:

Cassidy, Tyler;
Stephenson, Kathryn E.;
Barouch, Dan H.;
Perelson, Alan S.

Publication type:

Article

A dual computational and experimental strategy to enhance TSLP antibody affinity for improved asthma treatment.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011984

By:

Lv, Yitong;
Gong, He;
Liu, Xuechao;
Hao, Jia;
Xu, Lei;
Sun, Zhiwei;
Yu, Changyuan;
Xu, Lida

Publication type:

Article

Bias in the arrival of variation can dominate over natural selection in Richard Dawkins's biomorphs.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011893

By:

Martin, Nora S.;
Camargo, Chico Q.;
Louis, Ard A.

Publication type:

Article

Enrichment on steps, not genes, improves inference of differentially expressed pathways.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011968

By:

Markarian, Nicholas;
Van Auken, Kimberly M.;
Ebert, Dustin;
Sternberg, Paul W.

Publication type:

Article

PathIntegrate: Multivariate modelling approaches for pathway-based multi-omics data integration.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011814

By:

Wieder, Cecilia;
Cooke, Juliette;
Frainay, Clement;
Poupin, Nathalie;
Bowler, Russell;
Jourdan, Fabien;
Kechris, Katerina J.;
Lai, Rachel PJ;
Ebbels, Timothy

Publication type:

Article

Learning environment-specific learning rates.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011978

By:

Simoens, Jonas;
Verguts, Tom;
Braem, Senne

Publication type:

Article

Detecting changes in generation and serial intervals under varying pathogen biology, contact patterns and outbreak response.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011967

By:

Pung, Rachael;
Russell, Timothy W.;
Kucharski, Adam J.

Publication type:

Article

Modelling and analysis of cAMP-induced mixed-mode oscillations in cortical neurons: Critical roles of HCN and M-type potassium channels.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011559

By:

Martin, Matteo;
Pedersen, Morten Gram

Publication type:

Article

A machine-learning method for biobank-scale genetic prediction of blood group antigens.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011977

By:

Hyvärinen, Kati;
Haimila, Katri;
Moslemi, Camous;
Biobank, Blood Service;
Olsson, Martin L.;
Ostrowski, Sisse R.;
Pedersen, Ole B.;
Erikstrup, Christian;
Partanen, Jukka;
Ritari, Jarmo

Publication type:

Article

Ethical frameworks should be applied to computational modelling of infectious disease interventions.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011933

By:

Zachreson, Cameron;
Savulescu, Julian;
Shearer, Freya M.;
Plank, Michael J.;
Coghlan, Simon;
Miller, Joel C.;
Ainslie, Kylie E. C.;
Geard, Nicholas

Publication type:

Article

Continuous evaluation of denoising strategies in resting-state fMRI connectivity using fMRIPrep and Nilearn.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011942

By:

Wang, Hao-Ting;
Meisler, Steven L.;
Sharmarke, Hanad;
Clarke, Natasha;
Gensollen, Nicolas;
Markiewicz, Christopher J.;
Paugam, François;
Thirion, Bertrand;
Bellec, Pierre

Publication type:

Article

Impact on backpropagation of the spatial heterogeneity of sodium channel kinetics in the axon initial segment.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011846

By:

Barlow, Benjamin S. M.;
Longtin, André;
Joós, Béla

Publication type:

Article

The condition for dynamic stability in humans walking with feedback control.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011861

By:

Reimann, Hendrik;
Bruijn, Sjoerd M.

Publication type:

Article

Metabolic symbiosis between oxygenated and hypoxic tumour cells: An agent-based modelling study.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011944

By:

Jayathilake, Pahala Gedara;
Victori, Pedro;
Pavillet, Clara E.;
Lee, Chang Heon;
Voukantsis, Dimitrios;
Miar, Ana;
Arora, Anjali;
Harris, Adrian L.;
Morten, Karl J.;
Buffa, Francesca M.

Publication type:

Article

Unlocking ensemble ecosystem modelling for large and complex networks.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011976

By:

Vollert, Sarah A.;
Drovandi, Christopher;
Adams, Matthew P.

Publication type:

Article

Bayesian inference of relative fitness on high-throughput pooled competition assays.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011937

By:

Razo-Mejia, Manuel;
Mani, Madhav;
Petrov, Dmitri

Publication type:

Article

Ensemble dynamics and information flow deduction from whole-brain imaging data.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011848

By:

Toyoshima, Yu;
Sato, Hirofumi;
Nagata, Daiki;
Kanamori, Manami;
Jang, Moon Sun;
Kuze, Koyo;
Oe, Suzu;
Teramoto, Takayuki;
Iwasaki, Yuishi;
Yoshida, Ryo;
Ishihara, Takeshi;
Iino, Yuichi

Publication type:

Article

Bayesian inference is facilitated by modular neural networks with different time scales.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011897

By:

Ichikawa, Kohei;
Kaneko, Kunihiko

Publication type:

Article

Evolutionary graph theory beyond pairwise interactions: Higher-order network motifs shape times to fixation in structured populations.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011905

By:

Kuo, Yang Ping;
Carja, Oana

Publication type:

Article

For long-term sustainable software in bioinformatics.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011920

By:

Coelho, Luis Pedro

Publication type:

Article

End-to-end deep learning approach to mouse behavior classification from cortex-wide calcium imaging.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011074

By:

Ajioka, Takehiro;
Nakai, Nobuhiro;
Yamashita, Okito;
Takumi, Toru

Publication type:

Article

CRISPR-M: Predicting sgRNA off-target effect using a multi-view deep learning network.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011972

By:

Sun, Jialiang;
Guo, Jun;
Liu, Jian

Publication type:

Article

kCSD-python, reliable current source density estimation with quality control.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011941

By:

Chintaluri, Chaitanya;
Bejtka, Marta;
Średniawa, Władysław;
Czerwiński, Michał;
Dzik, Jakub M.;
Jędrzejewska-Szmek, Joanna;
Wójcik, Daniel K.

Publication type:

Article

Computational prediction of protein interactions in single cells by proximity sequencing.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011915

By:

Xia, Junjie;
Phan, Hoang Van;
Vistain, Luke;
Chen, Mengjie;
Khan, Aly A.;
Tay, Savaş

Publication type:

Article

An analytically tractable, age-structured model of the impact of vector control on mosquito-transmitted infections.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011440

By:

Davis, Emma L.;
Hollingsworth, T. Déirdre;
Keeling, Matt J.

Publication type:

Article

Mathematical models of Plasmodium vivax transmission: A scoping review.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011931

By:

Anwar, Md Nurul;
Smith, Lauren;
Devine, Angela;
Mehra, Somya;
Walker, Camelia R.;
Ivory, Elizabeth;
Conway, Eamon;
Mueller, Ivo;
McCaw, James M.;
Flegg, Jennifer A.;
Hickson, Roslyn I.

Publication type:

Article

Combining machine learning with structure-based protein design to predict and engineer post-translational modifications of proteins.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011939

By:

Ertelt, Moritz;
Mulligan, Vikram Khipple;
Maguire, Jack B.;
Lyskov, Sergey;
Moretti, Rocco;
Schiffner, Torben;
Meiler, Jens;
Schoeder, Clara T.

Publication type:

Article

AI-Aristotle: A physics-informed framework for systems biology gray-box identification.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011916

By:

Ahmadi Daryakenari, Nazanin;
De Florio, Mario;
Shukla, Khemraj;
Karniadakis, George Em

Publication type:

Article

It is theoretically possible to avoid misfolding into non-covalent lasso entanglements using small molecule drugs.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011901

By:

Jiang, Yang;
Deane, Charlotte M.;
Morris, Garrett M.;
O'Brien, Edward P.

Publication type:

Article

Mechanistic insights into ligand dissociation from the SARS-CoV-2 spike glycoprotein.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011955

By:

Hasse, Timothy;
Mantei, Esra;
Shahoei, Rezvan;
Pawnikar, Shristi;
Wang, Jinan;
Miao, Yinglong;
Huang, Yu-ming M.

Publication type:

Article

Multiscale modeling of HBV infection integrating intra- and intercellular viral propagation to analyze extracellular viral markers.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011238

By:

Kitagawa, Kosaku;
Kim, Kwang Su;
Iwamoto, Masashi;
Hayashi, Sanae;
Park, Hyeongki;
Nishiyama, Takara;
Nakamura, Naotoshi;
Fujita, Yasuhisa;
Nakaoka, Shinji;
Aihara, Kazuyuki;
Perelson, Alan S.;
Allweiss, Lena;
Dandri, Maura;
Watashi, Koichi;
Tanaka, Yasuhito;
Iwami, Shingo

Publication type:

Article

Using early detection data to estimate the date of emergence of an epidemic outbreak.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011934

By:

Jijón, Sofía;
Czuppon, Peter;
Blanquart, François;
Débarre, Florence

Publication type:

Article

teemi: An open-source literate programming approach for iterative design-build-test-learn cycles in bioengineering.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011929

By:

Petersen, Søren D.;
Levassor, Lucas;
Pedersen, Christine M.;
Madsen, Jan;
Hansen, Lea G.;
Zhang, Jie;
Haidar, Ahmad K.;
Frandsen, Rasmus J. N.;
Keasling, Jay D.;
Weber, Tilmann;
Sonnenschein, Nikolaus;
K. Jensen, Michael

Publication type:

Article

Model design choices impact biological insight: Unpacking the broad landscape of spatial-temporal model development decisions.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011917

By:

Yu, Jessica S.;
Bagheri, Neda

Publication type:

Article

Cortical cell assemblies and their underlying connectivity: An in silico study.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011891

By:

Ecker, András;
Egas Santander, Daniela;
Bolaños-Puchet, Sirio;
Isbister, James B.;
Reimann, Michael W.

Publication type:

Article

Modeling circuit mechanisms of opposing cortical responses to visual flow perturbations.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011921

By:

Galván Fraile, J.;
Scherr, Franz;
Ramasco, José J.;
Arkhipov, Anton;
Maass, Wolfgang;
Mirasso, Claudio R.

Publication type:

Article

Bifurcations and bursting in the Epileptor.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011903

By:

Saggio, Maria Luisa;
Jirsa, Viktor

Publication type:

Article

Using birth-death processes to infer tumor subpopulation structure from live-cell imaging drug screening data.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011888

By:

Wu, Chenyu;
Gunnarsson, Einar Bjarki;
Myklebust, Even Moa;
Köhn-Luque, Alvaro;
Tadele, Dagim Shiferaw;
Enserink, Jorrit Martijn;
Frigessi, Arnoldo;
Foo, Jasmine;
Leder, Kevin

Publication type:

Article

Unsupervised learning of perceptual feature combinations.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011926

By:

Tamosiunaite, Minija;
Tetzlaff, Christian;
Wörgötter, Florentin

Publication type:

Article

Decomposing bulk signals to reveal hidden information in processive enzyme reactions: A case study in mRNA translation.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011918

By:

Haase, Nadin;
Holtkamp, Wolf;
Christ, Simon;
Heinemann, Dag;
Rodnina, Marina V.;
Rudorf, Sophia

Publication type:

Article

LAP: Liability Antibody Profiler by sequence & structural mapping of natural and therapeutic antibodies.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011881

By:

Satława, Tadeusz;
Tarkowski, Mateusz;
Wróbel, Sonia;
Dudzic, Paweł;
Gawłowski, Tomasz;
Klaus, Tomasz;
Orłowski, Marek;
Kostyn, Anna;
Kumar, Sandeep;
Buchanan, Andrew;
Krawczyk, Konrad

Publication type:

Article

Tipping points emerge from weak mutualism in metacommunities.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011899

By:

Denk, Jonas;
Hallatschek, Oskar

Publication type:

Article

Dimensionality of locomotor behaviors in developing C. elegans.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011906

By:

Hassinan, Cera W.;
Sterrett, Scott C.;
Summy, Brennan;
Khera, Arnav;
Wang, Angie;
Bai, Jihong

Publication type:

Article

How neuronal morphology impacts the synchronisation state of neuronal networks.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011874

By:

Gowers, Robert P.;
Schreiber, Susanne

Publication type:

Article

Linear motifs regulating protein secretion, sorting and autophagy in Leishmania parasites are diverged with respect to their host equivalents.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011902

By:

Zeke, Andras;
Gibson, Toby J.;
Dobson, Laszlo

Publication type:

Article

Enhanced perfusion following exposure to radiotherapy: A theoretical investigation.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 3, p. 1, doi. 10.1371/journal.pcbi.1011252

By:

Köry, Jakub;
Narain, Vedang;
Stolz, Bernadette J.;
Kaeppler, Jakob;
Markelc, Bostjan;
Muschel, Ruth J.;
Maini, Philip K.;
Pitt-Francis, Joe M.;
Byrne, Helen M.

Publication type:

Article