Works matching IS 1553734X AND DT 2023 AND VI 19 AND IP 8

Results: 71

E(3) equivariant graph neural networks for robust and accurate protein-protein interaction site prediction.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011435

By:

Roche, Rahmatullah;
Moussad, Bernard;
Shuvo, Md Hossain;
Bhattacharya, Debswapna

Publication type:

Article

Phylogenetic inference of the emergence of sequence modules and protein-protein interactions in the ADAMTS-TSL family.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011404

By:

Dennler, Olivier;
Coste, François;
Blanquart, Samuel;
Belleannée, Catherine;
Théret, Nathalie

Publication type:

Article

iCircDA-NEAE: Accelerated attribute network embedding and dynamic convolutional autoencoder for circRNA-disease associations prediction.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011344

By:

Yuan, Lin;
Zhao, Jiawang;
Shen, Zhen;
Zhang, Qinhu;
Geng, Yushui;
Zheng, Chun-Hou;
Huang, De-Shuang

Publication type:

Article

Automatic extraction of actin networks in plants.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011407

By:

Hembrow, Jordan;
Deeks, Michael J.;
Richards, David M.

Publication type:

Article

Steady-state approximations for Hodgkin-Huxley cell models: Reduction of order for uterine smooth muscle cell model.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011359

By:

Means, Shawn A.;
Roesler, Mathias W.;
Garrett, Amy S.;
Cheng, Leo;
Clark, Alys R.

Publication type:

Article

Modulation of antigen discrimination by duration of immune contacts in a kinetic proofreading model of T cell activation with extreme statistics.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011216

By:

Morgan, Jonathan;
Lindsay, Alan E.

Publication type:

Article

Switching state-space modeling of neural signal dynamics.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011395

By:

He, Mingjian;
Das, Proloy;
Hotan, Gladia;
Purdon, Patrick L.

Publication type:

Article

Estimating the epidemic reproduction number from temporally aggregated incidence data: A statistical modelling approach and software tool.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011439

By:

Nash, Rebecca K.;
Bhatt, Samir;
Cori, Anne;
Nouvellet, Pierre

Publication type:

Article

VIRify: An integrated detection, annotation and taxonomic classification pipeline using virus-specific protein profile hidden Markov models.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011422

By:

Rangel-Pineros, Guillermo;
Almeida, Alexandre;
Beracochea, Martin;
Sakharova, Ekaterina;
Marz, Manja;
Reyes Muñoz, Alejandro;
Hölzer, Martin;
Finn, Robert D.

Publication type:

Article

Accelerating Bayesian inference of dependency between mixed-type biological traits.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011419

By:

Zhang, Zhenyu;
Nishimura, Akihiko;
Trovão, Nídia S.;
Cherry, Joshua L.;
Holbrook, Andrew J.;
Ji, Xiang;
Lemey, Philippe;
Suchard, Marc A.

Publication type:

Article

Structural identifiability of biomolecular controller motifs with and without flow measurements as model output.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011398

By:

Haus, Eivind S.;
Drengstig, Tormod;
Thorsen, Kristian

Publication type:

Article

Scoring epidemiological forecasts on transformed scales.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011393

By:

Bosse, Nikos I.;
Abbott, Sam;
Cori, Anne;
van Leeuwen, Edwin;
Bracher, Johannes;
Funk, Sebastian

Publication type:

Article

Neural network models for influenza forecasting with associated uncertainty using Web search activity trends.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011392

By:

Morris, Michael;
Hayes, Peter;
Cox, Ingemar J.;
Lampos, Vasileios

Publication type:

Article

Prediction of DNA Methylation based on Multi-dimensional feature encoding and double convolutional fully connected convolutional neural network.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011370

By:

Hu, Wenxing;
Guan, Lixin;
Li, Mengshan

Publication type:

Article

TFOFinder: Python program for identifying purine-only double-stranded stretches in the predicted secondary structure(s) of RNA targets.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011418

By:

Neugroschl, Atara;
Catrina, Irina E.

Publication type:

Article

Curated single cell multimodal landmark datasets for R/Bioconductor.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011324

By:

Eckenrode, Kelly B.;
Righelli, Dario;
Ramos, Marcel;
Argelaguet, Ricard;
Vanderaa, Christophe;
Geistlinger, Ludwig;
Culhane, Aedin C.;
Gatto, Laurent;
Carey, Vincent;
Morgan, Martin;
Risso, Davide;
Waldron, Levi

Publication type:

Article

Disentangling Abstraction from Statistical Pattern Matching in Human and Machine Learning.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011316

By:

Kumar, Sreejan;
Dasgupta, Ishita;
Daw, Nathaniel D.;
Cohen, Jonathan. D.;
Griffiths, Thomas L.

Publication type:

Article

Rapid memory encoding in a recurrent network model with behavioral time scale synaptic plasticity.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011139

By:

Li, Pan Ye;
Roxin, Alex

Publication type:

Article

Mathematical modeling indicates that regulatory inhibition of CD8<sup>+</sup> T cell cytotoxicity can limit efficacy of IL-15 immunotherapy in cases of high pre-treatment SIV viral load.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011425

By:

Cody, Jonathan W.;
Ellis-Connell, Amy L.;
O'Connor, Shelby L.;
Pienaar, Elsje

Publication type:

Article

When does humoral memory enhance infection?

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011377

By:

Nikas, Ariel;
Ahmed, Hasan;
Moore, Mia R.;
Zarnitsyna, Veronika I.;
Antia, Rustom

Publication type:

Article

Inferring gene regulatory networks using transcriptional profiles as dynamical attractors.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1010991

By:

Li, Ruihao;
Rozum, Jordan C.;
Quail, Morgan M.;
Qasim, Mohammad N.;
Sindi, Suzanne S.;
Nobile, Clarissa J.;
Albert, Réka;
Hernday, Aaron D.

Publication type:

Article

STREAK: A supervised cell surface receptor abundance estimation strategy for single cell RNA-sequencing data using feature selection and thresholded gene set scoring.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011413

By:

Javaid, Azka;
Frost, Hildreth Robert

Publication type:

Article

Regulated bacterial interaction networks: A mathematical framework to describe competitive growth under inclusion of metabolite cross-feeding.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011402

By:

Guex, Isaline;
Mazza, Christian;
Dubey, Manupriyam;
Batsch, Maxime;
Li, Renyi;
van der Meer, Jan Roelof

Publication type:

Article

A subcomponent-guided deep learning method for interpretable cancer drug response prediction.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011382

By:

Liu, Xuan;
Zhang, Wen

Publication type:

Article

Flux balance analysis-based metabolic modeling of microbial secondary metabolism: Current status and outlook.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011391

By:

Qiu, Sizhe;
Yang, Aidong;
Zeng, Hong

Publication type:

Article

Efficient sampling-based Bayesian Active Learning for synaptic characterization.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011342

By:

Gontier, Camille;
Surace, Simone Carlo;
Delvendahl, Igor;
Müller, Martin;
Pfister, Jean-Pascal

Publication type:

Article

Metabolic modeling of sex-specific liver tissue suggests mechanism of differences in toxicological responses.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1010927

By:

Moore, Connor J.;
Holstege, Christopher P.;
Papin, Jason A.

Publication type:

Article

Enhancing reinforcement learning models by including direct and indirect pathways improves performance on striatal dependent tasks.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011385

By:

Blackwell, Kim T.;
Doya, Kenji

Publication type:

Article

BALDR: A Web-based platform for informed comparison and prioritization of biomarker candidates for type 2 diabetes mellitus.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011403

By:

Lundgaard, Agnete T.;
Burdet, Frédéric;
Siggaard, Troels;
Westergaard, David;
Vagiaki, Danai;
Cantwell, Lisa;
Röder, Timo;
Vistisen, Dorte;
Sparsø, Thomas;
Giordano, Giuseppe N.;
Ibberson, Mark;
Banasik, Karina;
Brunak, Søren

Publication type:

Article

The blossoming of methods and software in computational biology.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011390

By:

Mac Gabhann, Feilim;
Pitzer, Virginia E.;
Papin, Jason A.

Publication type:

Article

The specious art of single-cell genomics.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011288

By:

Chari, Tara;
Pachter, Lior

Publication type:

Article

Elucidation of genome-wide understudied proteins targeted by PROTAC-induced degradation using interpretable machine learning.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1010974

By:

Xie, Li;
Xie, Lei

Publication type:

Article

A physiologically based pharmacokinetic model to optimize the dosage regimen and withdrawal time of cefquinome in pigs.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011331

By:

Mi, Kun;
Sun, Lei;
Hou, Yixuan;
Cai, Xin;
Zhou, Kaixiang;
Ma, Wenjin;
Xu, Xiangyue;
Pan, Yuanhu;
Liu, Zhenli;
Huang, Lingli

Publication type:

Article

An objective criterion to evaluate sequence-similarity networks helps in dividing the protein family sequence space.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1010881

By:

Hornung, Bastian Volker Helmut;
Terrapon, Nicolas

Publication type:

Article

Non-asymptotic transients away from steady states determine cellular responsiveness to dynamic spatial-temporal signals.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011388

By:

Nandan, Akhilesh;
Koseska, Aneta

Publication type:

Article

In-silico and in-vitro morphometric analysis of intestinal organoids.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011386

By:

Montes-Olivas, Sandra;
Legge, Danny;
Lund, Abbie;
Fletcher, Alexander G.;
Williams, Ann C.;
Marucci, Lucia;
Homer, Martin

Publication type:

Article

serosim: An R package for simulating serological data arising from vaccination, epidemiological and antibody kinetics processes.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011384

By:

Menezes, Arthur;
Takahashi, Saki;
Routledge, Isobel;
Metcalf, C. Jessica E.;
Graham, Andrea L.;
Hay, James A.

Publication type:

Article

Practical sampling of constraint-based models: Optimized thinning boosts CHRR performance.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011378

By:

Jadebeck, Johann F.;
Wiechert, Wolfgang;
Nöh, Katharina

Publication type:

Article

Prediction of opioid-related outcomes in a medicaid surgical population: Evidence to guide postoperative opiate therapy and monitoring.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011376

By:

El Hajouji, Oualid;
Sun, Ran S.;
Zammit, Alban;
Humphreys, Keith;
Asch, Steven M.;
Carroll, Ian;
Curtin, Catherine M.;
Hernandez-Boussard, Tina

Publication type:

Article

A stochastic analysis of the interplay between antibiotic dose, mode of action, and bacterial competition in the evolution of antibiotic resistance.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011364

By:

Czuppon, Peter;
Day, Troy;
Débarre, Florence;
Blanquart, François

Publication type:

Article

A structured evaluation of genome-scale constraint-based modeling tools for microbial consortia.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011363

By:

Scott Jr., William T.;
Benito-Vaquerizo, Sara;
Zimmermann, Johannes;
Bajić, Djordje;
Heinken, Almut;
Suarez-Diez, Maria;
Schaap, Peter J.

Publication type:

Article

The shape of cancer relapse: Topological data analysis predicts recurrence in paediatric acute lymphoblastic leukaemia.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011329

By:

Chulián, Salvador;
Stolz, Bernadette J.;
Martínez-Rubio, Álvaro;
Blázquez Goñi, Cristina;
Rodríguez Gutiérrez, Juan F.;
Caballero Velázquez, Teresa;
Molinos Quintana, Águeda;
Ramírez Orellana, Manuel;
Castillo Robleda, Ana;
Fuster Soler, José Luis;
Minguela Puras, Alfredo;
Martínez Sánchez, María V.;
Rosa, María;
Pérez-García, Víctor M.;
Byrne, Helen M.

Publication type:

Article

Collaborative nowcasting of COVID-19 hospitalization incidences in Germany.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011394

By:

Wolffram, Daniel;
Abbott, Sam;
an der Heiden, Matthias;
Funk, Sebastian;
Günther, Felix;
Hailer, Davide;
Heyder, Stefan;
Hotz, Thomas;
van de Kassteele, Jan;
Küchenhoff, Helmut;
Müller-Hansen, Sören;
Syliqi, Diellë;
Ullrich, Alexander;
Weigert, Maximilian;
Schienle, Melanie;
Bracher, Johannes

Publication type:

Article

Deconvolution of cancer cell states by the XDec-SM method.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011365

By:

Murillo, Oscar D.;
Petrosyan, Varduhi;
LaPlante, Emily L.;
Dobrolecki, Lacey E.;
Lewis, Michael T.;
Milosavljevic, Aleksandar

Publication type:

Article

Influence of cell type specific infectivity and tissue composition on SARS-CoV-2 infection dynamics within human airway epithelium.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011356

By:

Raach, Benjamin;
Bundgaard, Nils;
Haase, Marika J.;
Starruß, Jörn;
Sotillo, Rocio;
Stanifer, Megan L.;
Graw, Frederik

Publication type:

Article

Functional and spatial rewiring principles jointly regulate context-sensitive computation.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011325

By:

Li, Jia;
Rentzeperis, Ilias;
van Leeuwen, Cees

Publication type:

Article

Evaluation of vaginal microbiome equilibrium states identifies microbial parameters linked to resilience after menses and antibiotic therapy.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1011295

By:

Lee, Christina Y.;
Diegel, Jenna;
France, Michael T.;
Ravel, Jacques;
Arnold, Kelly B.

Publication type:

Article

Receptive field sizes and neuronal encoding bandwidth are constrained by axonal conduction delays.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1010871

By:

Hladnik, Tim C.;
Grewe, Jan

Publication type:

Article

VarSCAT: A computational tool for sequence context annotations of genomic variants.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1010727

By:

Wang, Ning;
Khan, Sofia;
Elo, Laura L.

Publication type:

Article

Intrinsic motivation for choice varies with individual risk attitudes and the controllability of the environment.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 8, p. 1, doi. 10.1371/journal.pcbi.1010551

By:

Munuera, Jérôme;
Ribes Agost, Marta;
Bendetowicz, David;
Kerebel, Adrien;
Chambon, Valérian;
Lau, Brian

Publication type:

Article