Works matching IS 1553734X AND DT 2019 AND VI 15 AND IP 3

Results: 67

Bayes-optimal estimation of overlap between populations of fixed size.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006898

By:

Larremore, Daniel B.

Publication type:

Article

Bayesian inference of transmission chains using timing of symptoms, pathogen genomes and contact data.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006930

By:

Campbell, Finlay;
Cori, Anne;
Ferguson, Neil;
Jombart, Thibaut

Publication type:

Article

Agent-based modeling of morphogenetic systems: Advantages and challenges.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006577

By:

Glen, Chad M.;
Kemp, Melissa L.;
Voit, Eberhard O.

Publication type:

Article

Ten principles for machine-actionable data management plans.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006750

By:

Miksa, Tomasz;
Simms, Stephanie;
Mietchen, Daniel;
Jones, Sarah

Publication type:

Article

A computational framework To assess genome-wide distribution Of polymorphic human endogenous retrovirus-K In human populations.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006564

By:

Li, Weiling;
Lin, Lin;
Malhotra, Raunaq;
Yang, Lei;
Acharya, Raj;
Poss, Mary

Publication type:

Article

Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006658

By:

Nussinov, Ruth;
Jang, Hyunbum;
Tsai, Chung-Jung;
Cheng, Feixiong

Publication type:

Article

Synchrony is more than its top-down and climatic parts: interacting Moran effects on phytoplankton in British seas.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006744

By:

Sheppard, Lawrence W.;
Defriez, Emma J.;
Reid, Philip C.;
Reuman, Daniel C.

Publication type:

Article

Evaluating reproducibility of AI algorithms in digital pathology with DAPPER.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006269

By:

Bizzego, Andrea;
Bussola, Nicole;
Chierici, Marco;
Maggio, Valerio;
Francescatto, Margherita;
Cima, Luca;
Cristoforetti, Marco;
Jurman, Giuseppe;
Furlanello, Cesare

Publication type:

Article

LMTRDA: Using logistic model tree to predict MiRNA-disease associations by fusing multi-source information of sequences and similarities.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006865

By:

Wang, Lei;
You, Zhu-Hong;
Chen, Xing;
Li, Yang-Ming;
Dong, Ya-Nan;
Li, Li-Ping;
Zheng, Kai

Publication type:

Article

Conformational ensemble of native α-synuclein in solution as determined by short-distance crosslinking constraint-guided discrete molecular dynamics simulations.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006859

By:

Brodie, Nicholas I.;
Popov, Konstantin I.;
Petrotchenko, Evgeniy V.;
Dokholyan, Nikolay V.;
Borchers, Christoph H.

Publication type:

Article

Searching algorithm for Type IV effector proteins (S4TE) 2.0: Improved tools for Type IV effector prediction, analysis and comparison in proteobacteria.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006847

By:

Noroy, Christophe;
Lefrançois, Thierry;
Meyer, Damien F.

Publication type:

Article

Scalable nonlinear programming framework for parameter estimation in dynamic biological system models.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006828

By:

Shin, Sungho;
Venturelli, Ophelia S.;
Zavala, Victor M.

Publication type:

Article

Identification of pathways associated with chemosensitivity through network embedding.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006864

By:

Wang, Sheng;
Huang, Edward;
Cairns, Junmei;
Peng, Jian;
Wang, Liewei;
Sinha, Saurabh

Publication type:

Article

ChIPulate: A comprehensive ChIP-seq simulation pipeline.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006921

By:

Datta, Vishaka;
Hannenhalli, Sridhar;
Siddharthan, Rahul

Publication type:

Article

ZnT2 is an electroneutral proton-coupled vesicular antiporter displaying an apparent stoichiometry of two protons per zinc ion.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006882

By:

Golan, Yarden;
Alhadeff, Raphael;
Warshel, Arieh;
Assaraf, Yehuda G.

Publication type:

Article

An agent-based model of dengue virus transmission shows how uncertainty about breakthrough infections influences vaccination impact projections.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006710

By:

Perkins, T. Alex;
Reiner, Robert C.;
España, Guido;
ten Bosch, Quirine A.;
Verma, Amit;
Liebman, Kelly A.;
Paz-Soldan, Valerie A.;
Elder, John P.;
Morrison, Amy C.;
Stoddard, Steven T.;
Kitron, Uriel;
Vazquez-Prokopec, Gonzalo M.;
Scott, Thomas W.;
Smith, David L.

Publication type:

Article

Contrasting the effects of adaptation and synaptic filtering on the timescales of dynamics in recurrent networks.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006893

By:

Beiran, Manuel;
Ostojic, Srdjan

Publication type:

Article

Rapid interpretation of small-angle X-ray scattering data.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006900

By:

Weiel, Marie;
Reinartz, Ines;
Schug, Alexander

Publication type:

Article

Modeling second-order boundary perception: A machine learning approach.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006829

By:

DiMattina, Christopher;
Baker, Curtis L.

Publication type:

Article

Endemicity and prevalence of multipartite viruses under heterogeneous between-host transmission.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006876

By:

Valdano, Eugenio;
Manrubia, Susanna;
Gómez, Sergio;
Arenas, Alex

Publication type:

Article

Stochastic neural field model of stimulus-dependent variability in cortical neurons.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006755

By:

Bressloff, Paul C.

Publication type:

Article

Self-organization of conducting pathways explains electrical wave propagation in cardiac tissues with high fraction of non-conducting cells.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006597

By:

Kudryashova, Nina;
Nizamieva, Aygul;
Tsvelaya, Valeriya;
Panfilov, Alexander V.;
Agladze, Konstantin I.

Publication type:

Article

Building a mechanistic mathematical model of hepatitis C virus entry.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006905

By:

Kalemera, Mphatso;
Mincheva, Dilyana;
Grove, Joe;
Illingworth, Christopher J. R.

Publication type:

Article

Boolean model of growth signaling, cell cycle and apoptosis predicts the molecular mechanism of aberrant cell cycle progression driven by hyperactive PI3K.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006402

By:

Sizek, Herbert;
Hamel, Andrew;
Deritei, Dávid;
Campbell, Sarah;
Ravasz Regan, Erzsébet

Publication type:

Article

Understanding narwhal diving behaviour using Hidden Markov Models with dependent state distributions and long range dependence.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006425

By:

Ngô, Manh Cuong;
Heide-Jørgensen, Mads Peter;
Ditlevsen, Susanne

Publication type:

Article

The logic of ionic homeostasis: Cations are for voltage, but not for volume.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006894

By:

Dmitriev, Andrey V.;
Dmitriev, Alexander A.;
Linsenmeier, Robert A.

Publication type:

Article

A spatio-temporal individual-based network framework for West Nile virus in the USA: Spreading pattern of West Nile virus.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006875

By:

Moon, Sifat A.;
Cohnstaedt, Lee W.;
McVey, D. Scott;
Scoglio, Caterina M.

Publication type:

Article

Optimizing the depth and the direction of prospective planning using information values.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006827

By:

Sezener, Can Eren;
Dezfouli, Amir;
Keramati, Mehdi

Publication type:

Article

Synaptic plasticity onto inhibitory neurons as a mechanism for ocular dominance plasticity.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006834

By:

Bono, Jacopo;
Clopath, Claudia

Publication type:

Article

Spike burst-pause dynamics of Purkinje cells regulate sensorimotor adaptation.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006298

By:

Luque, Niceto R.;
Naveros, Francisco;
Carrillo, Richard R.;
Ros, Eduardo;
Arleo, Angelo

Publication type:

Article

Myopic control of neural dynamics.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006854

By:

Hocker, David;
Park, Il Memming

Publication type:

Article

Pan-cancer association of a centrosome amplification gene expression signature with genomic alterations and clinical outcome.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006832

By:

de Almeida, Bernardo P.;
Vieira, André F.;
Paredes, Joana;
Bettencourt-Dias, Mónica;
Barbosa-Morais, Nuno L.

Publication type:

Article

The number of active metabolic pathways is bounded by the number of cellular constraints at maximal metabolic rates.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006858

By:

de Groot, Daan H.;
van Boxtel, Coco;
Planqué, Robert;
Bruggeman, Frank J.;
Teusink, Bas

Publication type:

Article

A complete statistical model for calibration of RNA-seq counts using external spike-ins and maximum likelihood theory.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006794

By:

Athanasiadou, Rodoniki;
Neymotin, Benjamin;
Brandt, Nathan;
Wang, Wei;
Christiaen, Lionel;
Gresham, David;
Tranchina, Daniel

Publication type:

Article

Latent goal models for dynamic strategic interaction.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006895

By:

Iqbal, Shariq N.;
Yin, Lun;
Drucker, Caroline B.;
Kuang, Qian;
Gariépy, Jean-François;
Platt, Michael L.;
Pearson, John M.

Publication type:

Article

Modeling differentiation-state transitions linked to therapeutic escape in triple-negative breast cancer.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006840

By:

Chapman, Margaret P.;
Risom, Tyler;
Aswani, Anil J.;
Langer, Ellen M.;
Sears, Rosalie C.;
Tomlin, Claire J.

Publication type:

Article

Effectiveness of Ultra-Low Volume insecticide spraying to prevent dengue in a non-endemic metropolitan area of Brazil.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006831

By:

Marini, Giovanni;
Guzzetta, Giorgio;
Marques Toledo, Cecilia A.;
Teixeira, Mauro;
Rosà, Roberto;
Merler, Stefano

Publication type:

Article

Quantitative agent-based modeling reveals mechanical stress response of growing tumor spheroids is predictable over various growth conditions and cell lines.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006273

By:

Van Liedekerke, Paul;
Neitsch, Johannes;
Johann, Tim;
Alessandri, Kevin;
Nassoy, Pierre;
Drasdo, Dirk

Publication type:

Article

A spectrum of routing strategies for brain networks.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006833

By:

Avena-Koenigsberger, Andrea;
Yan, Xiaoran;
Kolchinsky, Artemy;
van den Heuvel, Martijn;
Hagmann, Patric;
Sporns, Olaf

Publication type:

Article

Methods for computing the maximum performance of computational models of fMRI responses.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006397

By:

Lage-Castellanos, Agustin;
Valente, Giancarlo;
Formisano, Elia;
De Martino, Federico

Publication type:

Article

A dynamic power-law sexual network model of gonorrhoea outbreaks.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006748

By:

Whittles, Lilith K.;
White, Peter J.;
Didelot, Xavier

Publication type:

Article

OptRAM: In-silico strain design via integrative regulatory-metabolic network modeling.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006835

By:

Shen, Fangzhou;
Sun, Renliang;
Yao, Jie;
Li, Jian;
Liu, Qian;
Price, Nathan D.;
Liu, Chenguang;
Wang, Zhuo

Publication type:

Article

How adaptive plasticity evolves when selected against.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006260

By:

Rago, Alfredo;
Kouvaris, Kostas;
Uller, Tobias;
Watson, Richard

Publication type:

Article

A demonstration of modularity, reuse, reproducibility, portability and scalability for modeling and simulation of cardiac electrophysiology using Kepler Workflows.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006856

By:

Yang, Pei-Chi;
Purawat, Shweta;
Ieong, Pek U.;
Jeng, Mao-Tsuen;
DeMarco, Kevin R.;
Vorobyov, Igor;
McCulloch, Andrew D.;
Altinas, Ilkay;
Amaro, Rommie E.;
Clancy, Colleen E.

Publication type:

Article

A stochastic simulation of skeletal muscle calcium transients in a structurally realistic sarcomere model using MCell.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006712

By:

Holash, Robert John;
MacIntosh, Brian R.

Publication type:

Article

Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006848

By:

Liu, Joanne K.;
Lloyd, Colton;
Al-Bassam, Mahmoud;
Ebrahim, Ali;
Kim, Ji-Nu;
Olson, Connor;
Aksenov, Alexander;
Dorrestein, Pieter;
Zengler, Karsten

Publication type:

Article

Estimating the number of genetic mutations (hits) required for carcinogenesis based on the distribution of somatic mutations.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006881

By:

Anandakrishnan, Ramu;
Varghese, Robin T.;
Kinney, Nicholas A.;
Garner, Harold R.

Publication type:

Article

Predicting the mechanism and rate of H-NS binding to AT-rich DNA.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006845

By:

Riccardi, Enrico;
van Mastbergen, Eva C.;
Navarre, William Wiley;
Vreede, Jocelyne

Publication type:

Article

A theoretical single-parameter model for urbanisation to study infectious disease spread and interventions.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006879

By:

Engebretsen, Solveig;
Engø-Monsen, Kenth;
Frigessi, Arnoldo;
Freiesleben de Blasio, Birgitte

Publication type:

Article

An enriched network motif family regulates multistep cell fate transitions with restricted reversibility.

Published in:

PLoS Computational Biology, 2019, v. 15, n. 3, p. 1, doi. 10.1371/journal.pcbi.1006855

By:

Ye, Yujie;
Kang, Xin;
Bailey, Jordan;
Li, Chunhe;
Hong, Tian

Publication type:

Article