Works matching IS 1553734X AND DT 2022 AND VI 18 AND IP 1

Results: 68

Criticality enhances the multilevel reliability of stimulus responses in cortical neural networks.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009848

By:

Liang, Junhao;
Zhou, Changsong

Publication type:

Article

Identification of dynamic mass-action biochemical reaction networks using sparse Bayesian methods.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009830

By:

Jiang, Richard;
Singh, Prashant;
Wrede, Fredrik;
Hellander, Andreas;
Petzold, Linda

Publication type:

Article

Analytical kinetic model of native tandem promoters in E. coli.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009824

By:

Chauhan, Vatsala;
Bahrudeen, Mohamed N. M.;
Palma, Cristina S. D.;
Baptista, Ines S. C.;
Almeida, Bilena L. B.;
Dash, Suchintak;
Kandavalli, Vinodh;
Ribeiro, Andre S.

Publication type:

Article

Sparse connectivity for MAP inference in linear models using sister mitral cells.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009808

By:

Tootoonian, Sina;
Schaefer, Andreas T.;
Latham, Peter E.

Publication type:

Article

Nurturing diversity and inclusion in AI in Biomedicine through a virtual summer program for high school students.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009719

By:

Oskotsky, Tomiko;
Bajaj, Ruchika;
Burchard, Jillian;
Cavazos, Taylor;
Chen, Ina;
Connell, Will;
Eaneff, Stephanie;
Grant, Tianna;
Kanungo, Ishan;
Lindquist, Karla;
Myers-Turnbull, Douglas;
Naing, Zun Zar Chi;
Tang, Alice;
Vora, Bianca;
Wang, Jon;
Karim, Isha;
Swadling, Claire;
Yang, Janice;
Lindstaedt, Bill;
Sirota, Marina

Publication type:

Article

Fast and accurate influenza forecasting in the United States with Inferno.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1008651

By:

Osthus, Dave

Publication type:

Article

A three-dimensional multiscale model for the prediction of thrombus growth under flow with single-platelet resolution.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009850

By:

Shankar, Kaushik N.;
Zhang, Yiyuan;
Sinno, Talid;
Diamond, Scott L.

Publication type:

Article

Modeling the temporal dynamics of master regulators and CtrA proteolysis in Caulobacter crescentus cell cycle.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009847

By:

Xu, Chunrui;
Watson, Layne T.;
Hollis, Henry;
Dai, Michelle;
Yao, Xiangyu;
Cao, Yang;
Chen, Minghan

Publication type:

Article

Traveling waves in the prefrontal cortex during working memory.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009827

By:

Bhattacharya, Sayak;
Brincat, Scott L.;
Lundqvist, Mikael;
Miller, Earl K.

Publication type:

Article

From complete cross-docking to partners identification and binding sites predictions.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009825

By:

Dequeker, Chloé;
Mohseni Behbahani, Yasser;
David, Laurent;
Laine, Elodie;
Carbone, Alessandra

Publication type:

Article

Adhesion-regulated junction slippage controls cell intercalation dynamics in an Apposed-Cortex Adhesion Model.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009812

By:

Nestor-Bergmann, Alexander;
Blanchard, Guy B.;
Hervieux, Nathan;
Fletcher, Alexander G.;
Étienne, Jocelyn;
Sanson, Bénédicte

Publication type:

Article

Parametric Copula-GP model for analyzing multidimensional neuronal and behavioral relationships.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009799

By:

Kudryashova, Nina;
Amvrosiadis, Theoklitos;
Dupuy, Nathalie;
Rochefort, Nathalie;
Onken, Arno

Publication type:

Article

Positional SHAP (PoSHAP) for Interpretation of machine learning models trained from biological sequences.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009736

By:

Dickinson, Quinn;
Meyer, Jesse G.

Publication type:

Article

Project-based learning course on metabolic network modelling in computational systems biology.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009711

By:

Sauter, Thomas;
Bintener, Tamara;
Kishk, Ali;
Presta, Luana;
Prohaska, Tessy;
Guignard, Daniel;
Zeng, Ni;
Cipriani, Claudia;
Arshad, Sundas;
Pfau, Thomas;
Martins Conde, Patricia;
Pires Pacheco, Maria

Publication type:

Article

AIME: Autoencoder-based integrative multi-omics data embedding that allows for confounder adjustments.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009826

By:

Yu, Tianwei

Publication type:

Article

Machine learning-driven identification of drugs inhibiting cytochrome P450 2C9.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009820

By:

Goldwaser, Elodie;
Laurent, Catherine;
Lagarde, Nathalie;
Fabrega, Sylvie;
Nay, Laure;
Villoutreix, Bruno O.;
Jelsch, Christian;
Nicot, Arnaud B.;
Loriot, Marie-Anne;
Miteva, Maria A.

Publication type:

Article

Dose-dependent thresholds of dexamethasone destabilize CAR T-cell treatment efficacy.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009504

By:

Brummer, Alexander B.;
Yang, Xin;
Ma, Eric;
Gutova, Margarita;
Brown, Christine E.;
Rockne, Russell C.

Publication type:

Article

Dynamic inference of cell developmental complex energy landscape from time series single-cell transcriptomic data.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009821

By:

Jiang, Qi;
Zhang, Shuo;
Wan, Lin

Publication type:

Article

The structural coverage of the human proteome before and after AlphaFold.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009818

By:

Porta-Pardo, Eduard;
Ruiz-Serra, Victoria;
Valentini, Samuel;
Valencia, Alfonso

Publication type:

Article

Foraging as sampling without replacement: A Bayesian statistical model for estimating biases in target selection.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009813

By:

Clarke, Alasdair D. F.;
Hunt, Amelia R.;
Hughes, Anna E.

Publication type:

Article

Polypolish: Short-read polishing of long-read bacterial genome assemblies.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009802

By:

Wick, Ryan R.;
Holt, Kathryn E.

Publication type:

Article

McComedy: A user-friendly tool for next-generation individual-based modeling of microbial consumer-resource systems.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009777

By:

Bogdanowski, André;
Frank, Karin;
Banitz, Thomas;
Muhsal, Linea Katharina;
Kost, Christian

Publication type:

Article

Efficient ReML inference in variance component mixed models using a Min-Max algorithm.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009659

By:

Laporte, Fabien;
Charcosset, Alain;
Mary-Huard, Tristan

Publication type:

Article

Discovering adaptation-capable biological network structures using control-theoretic approaches.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009769

By:

Bhattacharya, Priyan;
Raman, Karthik;
Tangirala, Arun K.

Publication type:

Article

Constrained brain volume in an efficient coding model explains the fraction of excitatory and inhibitory neurons in sensory cortices.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009642

By:

Alreja, Arish;
Nemenman, Ilya;
Rozell, Christopher J.

Publication type:

Article

CRBPDL: Identification of circRNA-RBP interaction sites using an ensemble neural network approach.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009798

By:

Niu, Mengting;
Zou, Quan;
Lin, Chen

Publication type:

Article

Fine-scale estimation of effective reproduction numbers for dengue surveillance.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009791

By:

Ong, Janet;
Soh, Stacy;
Ho, Soon Hoe;
Seah, Annabel;
Dickens, Borame Sue;
Tan, Ken Wei;
Koo, Joel Ruihan;
Cook, Alex R.;
Richards, Daniel R.;
Gaw, Leon Yan-Feng;
Ng, Lee Ching;
Lim, Jue Tao

Publication type:

Article

Bringing bioinformatics to schools with the 4273pi project.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009705

By:

Bain, Stevie A.;
Plaisier, Heleen;
Anderson, Felicity;
Cook, Nicola;
Crouch, Kathryn;
Meagher, Thomas R.;
Ritchie, Michael G.;
Wallace, Edward W. J.;
Barker, Daniel

Publication type:

Article

Use of Raman and Raman optical activity to extract atomistic details of saccharides in aqueous solution.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009678

By:

Palivec, Vladimír;
Johannessen, Christian;
Kaminský, Jakub;
Martinez-Seara, Hector

Publication type:

Article

Extended ensemble simulations of a SARS-CoV-2 nsp1–5'-UTR complex.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009804

By:

Sakuraba, Shun;
Xie, Qilin;
Kasahara, Kota;
Iwakiri, Junichi;
Kono, Hidetoshi

Publication type:

Article

Evolution enhances mutational robustness and suppresses the emergence of a new phenotype: A new computational approach for studying evolution.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009796

By:

Kaneko, Tadamune;
Kikuchi, Macoto

Publication type:

Article

DeLTA 2.0: A deep learning pipeline for quantifying single-cell spatial and temporal dynamics.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009797

By:

O'Connor, Owen M.;
Alnahhas, Razan N.;
Lugagne, Jean-Baptiste;
Dunlop, Mary J.

Publication type:

Article

Characterizing non-exponential growth and bimodal cell size distributions in fission yeast: An analytical approach.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009793

By:

Jia, Chen;
Singh, Abhyudai;
Grima, Ramon

Publication type:

Article

Simulated poaching affects global connectivity and efficiency in social networks of African savanna elephants—An exemplar of how human disturbance impacts group-living species.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009792

By:

Wiśniewska, Maggie;
Puga-Gonzalez, Ivan;
Lee, Phyllis;
Moss, Cynthia;
Russell, Gareth;
Garnier, Simon;
Sueur, Cédric

Publication type:

Article

Ictal wavefront propagation in slices and simulations with conductance-based refractory density model.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009782

By:

Chizhov, Anton V.;
Amakhin, Dmitry V.;
Smirnova, Elena Yu.;
Zaitsev, Aleksey V.

Publication type:

Article

Full scale structural, mechanical and dynamical properties of HIV-1 liposomes.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009781

By:

Bryer, Alexander J.;
Reddy, Tyler;
Lyman, Edward;
Perilla, Juan R.

Publication type:

Article

Longitudinally monitored immune biomarkers predict the timing of COVID-19 outcomes.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009778

By:

Lasso, Gorka;
Khan, Saad;
Allen, Stephanie A.;
Mariano, Margarette;
Florez, Catalina;
Orner, Erika P.;
Quiroz, Jose A.;
Quevedo, Gregory;
Massimi, Aldo;
Hegde, Aditi;
Wirchnianski, Ariel S.;
Bortz III, Robert H.;
Malonis, Ryan J.;
Georgiev, George I.;
Tong, Karen;
Herrera, Natalia G.;
Morano, Nicholas C.;
Garforth, Scott J.;
Malaviya, Avinash;
Khokhar, Ahmed

Publication type:

Article

Ultrafast population coding and axo-somatic compartmentalization.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009775

By:

Zhang, Chenfei;
Hofmann, David;
Neef, Andreas;
Wolf, Fred

Publication type:

Article

Diversity of synaptic protein complexes as a function of the abundance of their constituent proteins: A modeling approach.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009758

By:

Miski, Marcell;
Keömley-Horváth, Bence Márk;
Rákóczi Megyeriné, Dorina;
Csikász-Nagy, Attila;
Gáspári, Zoltán

Publication type:

Article

Controlling gene expression timing through gene regulatory architecture.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009745

By:

Ali, Md Zulfikar;
Brewster, Robert C.

Publication type:

Article

The evolutionary maintenance of Lévy flight foraging.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009490

By:

Campeau, Winston;
Simons, Andrew M.;
Stevens, Brett

Publication type:

Article

A deep generative model of 3D single-cell organization.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009155

By:

Donovan-Maiye, Rory M.;
Brown, Jackson M.;
Chan, Caleb K.;
Ding, Liya;
Yan, Calysta;
Gaudreault, Nathalie;
Theriot, Julie A.;
Maleckar, Mary M.;
Knijnenburg, Theo A.;
Johnson, Gregory R.

Publication type:

Article

Data-driven modeling predicts gene regulatory network dynamics during the differentiation of multipotential hematopoietic progenitors.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009779

By:

Handzlik, Joanna E.;
Manu

Publication type:

Article

Computable early Caenorhabditis elegans embryo with a phase field model.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009755

By:

Kuang, Xiangyu;
Guan, Guoye;
Wong, Ming-Kin;
Chan, Lu-Yan;
Zhao, Zhongying;
Tang, Chao;
Zhang, Lei

Publication type:

Article

A Bayesian approach to modeling phytoplankton population dynamics from size distribution time series.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009733

By:

Mattern, Jann Paul;
Glauninger, Kristof;
Britten, Gregory L.;
Casey, John R.;
Hyun, Sangwon;
Wu, Zhen;
Armbrust, E. Virginia;
Harchaoui, Zaid;
Ribalet, François

Publication type:

Article

Identification of periodic attractors in Boolean networks using a priori information.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009702

By:

Münzner, Ulrike;
Mori, Tomoya;
Krantz, Marcus;
Klipp, Edda;
Akutsu, Tatsuya

Publication type:

Article

An initial 'snapshot' of sensory information biases the likelihood and speed of subsequent changes of mind.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009738

By:

Turner, William;
Feuerriegel, Daniel;
Hester, Robert;
Bode, Stefan

Publication type:

Article

Using population-specific add-on polymorphisms to improve genotype imputation in underrepresented populations.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009628

By:

Xu, Zhi Ming;
Rüeger, Sina;
Zwyer, Michaela;
Brites, Daniela;
Hiza, Hellen;
Reinhard, Miriam;
Rutaihwa, Liliana;
Borrell, Sonia;
Isihaka, Faima;
Temba, Hosiana;
Maroa, Thomas;
Naftari, Rastard;
Hella, Jerry;
Sasamalo, Mohamed;
Reither, Klaus;
Portevin, Damien;
Gagneux, Sebastien;
Fellay, Jacques

Publication type:

Article

Dominating lengthscales of zebrafish collective behaviour.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009394

By:

Yang, Yushi;
Turci, Francesco;
Kague, Erika;
Hammond, Chrissy L.;
Russo, John;
Royall, C. Patrick

Publication type:

Article

Hybrid simulation modelling of networks of heterogeneous care homes and the inter-facility spread of Covid-19 by sharing staff.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 1, p. 1, doi. 10.1371/journal.pcbi.1009780

By:

Nguyen, Le Khanh Ngan;
Megiddo, Itamar;
Howick, Susan

Publication type:

Article