Works matching IS 1553734X AND DT 2024 AND VI 20 AND IP 7

Results: 59

An integrative approach to protein sequence design through multiobjective optimization.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1011953

By:

Hong, Lu;
Kortemme, Tanja

Publication type:

Article

Probabilistic neural transfer function estimation with Bayesian system identification.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1012354

By:

Wu, Nan;
Valera, Isabel;
Sinz, Fabian;
Ecker, Alexander;
Euler, Thomas;
Qiu, Yongrong

Publication type:

Article

Parameter estimation in a whole-brain network model of epilepsy: Comparison of parallel global optimization solvers.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1011642

By:

Penas, David R.;
Hashemi, Meysam;
Jirsa, Viktor K.;
Banga, Julio R.

Publication type:

Article

Forecasting of influenza activity and associated hospital admission burden and estimating the impact of COVID-19 pandemic on 2019/20 winter season in Hong Kong.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1012311

By:

Lau, Yiu-Chung;
Shan, Songwei;
Wang, Dong;
Chen, Dongxuan;
Du, Zhanwei;
Lau, Eric H. Y.;
He, Daihai;
Tian, Linwei;
Wu, Peng;
Cowling, Benjamin J.;
Ali, Sheikh Taslim

Publication type:

Article

Population bursts in a modular neural network as a mechanism for synchronized activity in KNDy neurons.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1011820

By:

Blanco, Wilfredo;
Tabak, Joel;
Bertram, Richard

Publication type:

Article

Multitask learning of a biophysically-detailed neuron model.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1011728

By:

Verhellen, Jonas;
Beshkov, Kosio;
Amundsen, Sebastian;
Ness, Torbjørn V.;
Einevoll, Gaute T.

Publication type:

Article

Using deep learning to decipher the impact of telomerase promoter mutations on the dynamic metastatic morpholome.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1012271

By:

Nevarez, Andres J.;
Mudla, Anusorn;
Diaz, Sabrina A.;
Hao, Nan

Publication type:

Article

Detecting and quantifying heterogeneity in susceptibility using contact tracing data.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1012310

By:

Tuschhoff, Beth M.;
Kennedy, David A.

Publication type:

Article

Reassessing the modularity of gene co-expression networks using the Stochastic Block Model.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1012300

By:

Melo, Diogo;
Pallares, Luisa F.;
Ayroles, Julien F.

Publication type:

Article

Derivation and simulation of a computational model of active cell populations: How overlap avoidance, deformability, cell-cell junctions and cytoskeletal forces affect alignment.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1011879

By:

Leech, Vivienne;
Kenny, Fiona N.;
Marcotti, Stefania;
Shaw, Tanya J.;
Stramer, Brian M.;
Manhart, Angelika

Publication type:

Article

A rule-based multiscale model of hepatic stellate cell plasticity: Critical role of the inactivation loop in fibrosis progression.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1011858

By:

Bouguéon, Matthieu;
Legagneux, Vincent;
Hazard, Octave;
Bomo, Jérémy;
Siegel, Anne;
Feret, Jérôme;
Théret, Nathalie

Publication type:

Article

Spatial inequities in access to medications for treatment of opioid use disorder highlight scarcity of methadone providers under counterfactual scenarios.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1012307

By:

Tatara, Eric;
Lin, Qinyun;
Ozik, Jonathan;
Kolak, Marynia;
Collier, Nicholson;
Halpern, Dylan;
Anselin, Luc;
Dahari, Harel;
Boodram, Basmattee;
Schneider, John

Publication type:

Article

nf-core/airrflow: An adaptive immune receptor repertoire analysis workflow employing the Immcantation framework.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1012265

By:

Gabernet, Gisela;
Marquez, Susanna;
Bjornson, Robert;
Peltzer, Alexander;
Meng, Hailong;
Aron, Edel;
Lee, Noah Y.;
Jensen, Cole;
Ladd, David;
Polster, Mark;
Hanssen, Friederike;
Heumos, Simon;
Yaari, Gur;
Kowarik, Markus C.;
Nahnsen, Sven;
Kleinstein, Steven H.

Publication type:

Article

Improved protein complex prediction with AlphaFold-multimer by denoising the MSA profile.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1012253

By:

Bryant, Patrick;
Noé, Frank

Publication type:

Article

Nine quick tips for open meta-analyses.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1012252

By:

Moreau, David;
Wiebels, Kristina

Publication type:

Article

A comprehensive exploration of the druggable conformational space of protein kinases using AI-predicted structures.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1012302

By:

Herrington, Noah B.;
Li, Yan Chak;
Stein, David;
Pandey, Gaurav;
Schlessinger, Avner

Publication type:

Article

Generating information-dense promoter sequences with optimal string packing.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1012276

By:

Andreani, Virgile;
South, Eric J.;
Dunlop, Mary J.

Publication type:

Article

A low-dimensional approximation of optimal confidence.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1012273

By:

Le Denmat, Pierre;
Verguts, Tom;
Desender, Kobe

Publication type:

Article

FedGMMAT: Federated generalized linear mixed model association tests.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1012142

By:

Li, Wentao;
Chen, Han;
Jiang, Xiaoqian;
Harmanci, Arif

Publication type:

Article

Spatial information allows inference of the prevalence of direct cell–to–cell viral infection.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1012264

By:

Williams, Thomas;
McCaw, James M.;
Osborne, James M.

Publication type:

Article

Simulation of Soluble and Bound VEGF-stimulated in vitro Capillary-like Network Formation on Deformed Substrate.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1012281

By:

Chiang, Hsun;
Chung, Chih-Ang

Publication type:

Article

Protein stability prediction by fine-tuning a protein language model on a mega-scale dataset.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1012248

By:

Chu, Simon K. S.;
Narang, Kush;
Siegel, Justin B.

Publication type:

Article

Quantifying massively parallel microbial growth with spatially mediated interactions.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1011585

By:

Borse, Florian;
Kičiatovas, Dovydas;
Kuosmanen, Teemu;
Vidal, Mabel;
Cabrera-Vives, Guillermo;
Cairns, Johannes;
Warringer, Jonas;
Mustonen, Ville

Publication type:

Article

Emergent effects of synaptic connectivity on the dynamics of global and local slow waves in a large-scale thalamocortical network model of the human brain.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1012245

By:

Marsh, Brianna;
Navas-Zuloaga, M. Gabriela;
Rosen, Burke Q.;
Sokolov, Yury;
Delanois, Jean Erik;
Gonzalez, Oscar C.;
Krishnan, Giri P.;
Halgren, Eric;
Bazhenov, Maxim

Publication type:

Article

Fixation times on directed graphs.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1012299

By:

Brewster, David A.;
Nowak, Martin A.;
Tkadlec, Josef

Publication type:

Article

Achieving Occam's razor: Deep learning for optimal model reduction.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1012283

By:

Antal, Botond B.;
Chesebro, Anthony G.;
Strey, Helmut H.;
Mujica-Parodi, Lilianne R.;
Weistuch, Corey

Publication type:

Article

Ten simple rules for building and maintaining a responsible data science workflow.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1012232

By:

Stoudt, Sara;
Jernite, Yacine;
Marshall, Brandeis;
Marwick, Ben;
Sharan, Malvika;
Whitaker, Kirstie;
Danchev, Valentin

Publication type:

Article

When should lockdown be implemented? Devising cost-effective strategies for managing epidemics amid vaccine uncertainty.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1012010

By:

Doyle, Nathan J.;
Cumming, Fergus;
Thompson, Robin N.;
Tildesley, Michael J.

Publication type:

Article

Convergence, sampling and total order estimator effects on parameter orthogonality in global sensitivity analysis.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1011946

By:

Saxton, Harry;
Xu, Xu;
Schenkel, Torsten;
Clayton, Richard H.;
Halliday, Ian

Publication type:

Article

Identifying topologically associating domains using differential kernels.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1012221

By:

Maisuradze, Luka;
King, Megan C.;
Surovtsev, Ivan V.;
Mochrie, Simon G. J.;
Shattuck, Mark D.;
O'Hern, Corey S.

Publication type:

Article

Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1012180

By:

Hoff, Samuel E.;
Thomasen, F. Emil;
Lindorff-Larsen, Kresten;
Bonomi, Massimiliano

Publication type:

Article

Agent-based model predicts that layered structure and 3D movement work synergistically to reduce bacterial load in 3D in vitro models of tuberculosis granuloma.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1012266

By:

Petrucciani, Alexa;
Hoerter, Alexis;
Kotze, Leigh;
Du Plessis, Nelita;
Pienaar, Elsje

Publication type:

Article

Epidemiological modeling of SARS-CoV-2 in white-tailed deer (Odocoileus virginianus) reveals conditions for introduction and widespread transmission.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1012263

By:

Rosenblatt, Elias;
Cook, Jonathan D.;
DiRenzo, Graziella V.;
Grant, Evan H. Campbell;
Arce, Fernando;
Pepin, Kim M.;
Rudolph, F. Javiera;
Runge, Michael C.;
Shriner, Susan;
Walsh, Daniel P.;
Mosher, Brittany A.

Publication type:

Article

Identifying cell states in single-cell RNA-seq data at statistically maximal resolution.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1012224

By:

Grobecker, Pascal;
Sakoparnig, Thomas;
van Nimwegen, Erik

Publication type:

Article

NRV: An open framework for in silico evaluation of peripheral nerve electrical stimulation strategies.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1011826

By:

Couppey, Thomas;
Regnacq, Louis;
Giraud, Roland;
Romain, Olivier;
Bornat, Yannick;
Kolbl, Florian

Publication type:

Article

Reinforcement learning of altruistic punishment differs between cultures and across the lifespan.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1012274

By:

Guo, Ziyan;
Yu, Jialu;
Wang, Wenxin;
Lockwood, Patricia;
Wu, Zhen

Publication type:

Article

Role of diffusion and reaction of the constituents in spreading of histone modification marks.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1012235

By:

Manivannan, Vinoth;
Inamdar, Mandar M.;
Padinhateeri, Ranjith

Publication type:

Article

PARE: A framework for removal of confounding effects from any distance-based dimension reduction method.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1012241

By:

Chen, Andrew A.;
Clark, Kelly;
Dewey, Blake E.;
DuVal, Anna;
Pellegrini, Nicole;
Nair, Govind;
Jalkh, Youmna;
Khalil, Samar;
Zurawski, Jon;
Calabresi, Peter A.;
Reich, Daniel S.;
Bakshi, Rohit;
Shou, Haochang;
Shinohara, Russell T.

Publication type:

Article

Modeling soybean growth: A mixed model approach.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1011258

By:

Delattre, Maud;
Toda, Yusuke;
Tressou, Jessica;
Iwata, Hiroyoshi

Publication type:

Article

Jointly efficient encoding and decoding in neural populations.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1012240

By:

Blanco Malerba, Simone;
Micheli, Aurora;
Woodford, Michael;
Azeredo da Silveira, Rava

Publication type:

Article

Synaptic reorganization of synchronized neuronal networks with synaptic weight and structural plasticity.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1012261

By:

Chauhan, Kanishk;
Neiman, Alexander B.;
Tass, Peter A.

Publication type:

Article

Kernel Bayesian logistic tensor decomposition with automatic rank determination for predicting multiple types of miRNA-disease associations.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1012287

By:

Ma, Yingjun;
Ma, Yuanyuan

Publication type:

Article

Competitive advantages of T-even phage lysis inhibition in response to secondary infection.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1012242

By:

Hvid, Ulrik;
Mitarai, Namiko

Publication type:

Article

BCI Toolbox: An open-source python package for the Bayesian causal inference model.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1011791

By:

Zhu, Haocheng;
Beierholm, Ulrik;
Shams, Ladan

Publication type:

Article

Phenotypic memory in quorum sensing.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1011696

By:

Ostovar, Ghazaleh;
Boedicker, James Q.

Publication type:

Article

scBoolSeq: Linking scRNA-seq statistics and Boolean dynamics.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1011620

By:

Magaña-López, Gustavo;
Calzone, Laurence;
Zinovyev, Andrei;
Paulevé, Loïc

Publication type:

Article

Modeling the impact of neuromorphological alterations in Down syndrome on fast neural oscillations.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1012259

By:

Clusella, Pau;
Manubens-Gil, Linus;
Garcia-Ojalvo, Jordi;
Dierssen, Mara

Publication type:

Article

Elucidating the complex membrane binding of a protein with multiple anchoring domains using extHMMM.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1011421

By:

Madsen, Jesper J.;
Ohkubo, Y. Zenmei

Publication type:

Article

Estimating error rates for single molecule protein sequencing experiments.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1012258

By:

Smith, Matthew Beauregard;
VanderVelden, Kent;
Blom, Thomas;
Stout, Heather D.;
Mapes, James H.;
Folsom, Tucker M.;
Martin, Christopher;
Bardo, Angela M.;
Marcotte, Edward M.

Publication type:

Article

ArborSim: Articulated, branching, OpenSim routing for constructing models of multi-jointed appendages with complex muscle-tendon architecture.

Published in:

PLoS Computational Biology, 2024, v. 20, n. 7, p. 1, doi. 10.1371/journal.pcbi.1012243

By:

Fu, Xun;
Withers, Jack;
Miyamae, Juri A.;
Moore, Talia Y.

Publication type:

Article