PLOS Computational Biology Volume 15(3) March 2019

[Virtual Post Bioclues]

 

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Manage Preferences > New Articles in PLOS Computational Biology PUBLISHED: March 01, 2019 to March 29, 2019 EDUCATION Ten principles for machine-actionable data management plans Tomasz Miksa, Stephanie Simms, Daniel Mietchen, Sarah Jones REVIEWS Agent-based modeling of morphogenetic systems: Advantages and challenges Chad M. Glen, Melissa L. Kemp, Eberhard O. Voit Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers Ruth Nussinov, Hyunbum Jang, Chung-Jung Tsai, Feixiong Cheng RESEARCH ARTICLES Spatial clustering and common regulatory elements correlate with coordinated gene expression Jingyu Zhang, Hengyu Chen, Ruoyan Li, David A. Taft, Guang Yao, Fan Bai, Jianhua Xing The genetic basis for adaptation of model-designed syntrophic co-cultures Colton J. Lloyd, Zachary A. King, Troy E. Sandberg, Ying Hefner, Connor A. Olson, Patrick V. Phaneuf, Edward J. O’Brien, Jon G. Sanders, Rodolfo A. Salido, Karenina Sanders, Caitriona Brennan, Gregory Humphrey, Rob Knight, Adam M. Feist Soma-axon coupling configurations that enhance neuronal coincidence detection Joshua H. Goldwyn, Michiel W. H. Remme, John Rinzel The gradient of the reinforcement landscape influences sensorimotor learning Joshua G. A. Cashaback, Christopher K. Lao, Dimitrios J. Palidis, Susan K. Coltman, Heather R. McGregor, Paul L. Gribble Genesis of the αβ T-cell receptor Thomas Dupic, Quentin Marcou, Aleksandra M. Walczak, Thierry Mora Computational geometry for modeling neural populations: From visualization to simulation Marc de Kamps, Mikkel Lepperød, Yi Ming Lai In vitro and in silico multidimensional modeling of oncolytic tumor virotherapy dynamics David R. Berg, Chetan P. Offord, Iris Kemler, Matthew K. Ennis, Lawrence Chang, George Paulik, Zeljko Bajzer, Claudia Neuhauser, David Dingli Determination of effective synaptic conductances using somatic voltage clamp Songting Li, Nan Liu, Li Yao, Xiaohui Zhang, Douglas Zhou, David Cai New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx Mohamed Mounir, Marta Lucchetta, Tiago C. Silva, Catharina Olsen, Gianluca Bontempi, Xi Chen, Houtan Noushmehr, Antonio Colaprico, Elena Papaleo Goal-related feedback guides motor exploration and redundancy resolution in human motor skill acquisition Marieke Rohde, Kenichi Narioka, Jochen J. Steil, Lina K. Klein, Marc O. Ernst Bacterial surface colonization, preferential attachment and fitness under periodic stress Maor Grinberg, Tomer Orevi, Nadav Kashtan Evolutionary model for the unequal segregation of high copy plasmids Karin Münch, Richard Münch, Rebekka Biedendieck, Dieter Jahn, Johannes Müller Tuft dendrites of pyramidal neurons operate as feedback-modulated functional subunits Florian Eberhardt, Andreas V. M. Herz, Stefan Häusler Modeling individual time courses of thrombopoiesis during multi-cyclic chemotherapy Yuri Kheifetz, Markus Scholz Humans use multi-objective control to regulate lateral foot placement when walking Jonathan B. Dingwell, Joseph P. Cusumano Estimating the number of genetic mutations (hits) required for carcinogenesis based on the distribution of somatic mutations Ramu Anandakrishnan, Robin T. Varghese, Nicholas A. Kinney, Harold R. Garner Predicting the mechanism and rate of H-NS binding to AT-rich DNA Enrico Riccardi, Eva C. van Mastbergen, William Wiley Navarre, Jocelyne Vreede A theoretical single-parameter model for urbanisation to study infectious disease spread and interventions Solveig Engebretsen, Kenth Engø-Monsen, Arnoldo Frigessi, Birgitte Freiesleben de Blasio A new clustering and nomenclature for beta turns derived from high-resolution protein structures Maxim Shapovalov, Slobodan Vucetic, Roland L. Dunbrack Jr. A stochastic simulation of skeletal muscle calcium transients in a structurally realistic sarcomere model using MCell Robert John Holash, Brian R. MacIntosh An enriched network motif family regulates multistep cell fate transitions with restricted reversibility Yujie Ye, Xin Kang, Jordan Bailey, Chunhe Li, Tian Hong Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen Joanne K. Liu, Colton Lloyd, Mahmoud M. Al-Bassam, Ali Ebrahim, Ji-Nu Kim, Connor Olson, Alexander Aksenov, Pieter Dorrestein, Karsten Zengler Quantitative agent-based modeling reveals mechanical stress response of growing tumor spheroids is predictable over various growth conditions and cell lines Paul Van Liedekerke, Johannes Neitsch, Tim Johann, Kevin Alessandri, Pierre Nassoy, Dirk Drasdo Methods for computing the maximum performance of computational models of fMRI responses Agustin Lage-Castellanos, Giancarlo Valente, Elia Formisano, Federico De Martino A demonstration of modularity, reuse, reproducibility, portability and scalability for modeling and simulation of cardiac electrophysiology using Kepler Workflows Pei-Chi Yang, Shweta Purawat, Pek U. Ieong, Mao-Tsuen Jeng, Kevin R. DeMarco, Igor Vorobyov, Andrew D. McCulloch, Ilkay Altintas, Rommie E. Amaro, Colleen E. Clancy OptRAM: In-silico strain design via integrative regulatory-metabolic network modeling Fangzhou Shen, Renliang Sun, Jie Yao, Jian Li, Qian Liu, Nathan D. Price, Chenguang Liu, Zhuo Wang Effectiveness of Ultra-Low Volume insecticide spraying to prevent dengue in a non-endemic metropolitan area of Brazil Giovanni Marini, Giorgio Guzzetta, Cecilia A. Marques Toledo, Mauro Teixeira, Roberto Rosà, Stefano Merler A spectrum of routing strategies for brain networks Andrea Avena-Koenigsberger, Xiaoran Yan, Artemy Kolchinsky, Martijn P. van den Heuvel, Patric Hagmann, Olaf Sporns How adaptive plasticity evolves when selected against Alfredo Rago, Kostas Kouvaris, Tobias Uller, Richard Watson A dynamic power-law sexual network model of gonorrhoea outbreaks Lilith K. Whittles, Peter J. White, Xavier Didelot Latent goal models for dynamic strategic interaction Shariq N. Iqbal, Lun Yin, Caroline B. Drucker, Qian Kuang, Jean-François Gariépy, Michael L. Platt, John M. Pearson Pan-cancer association of a centrosome amplification gene expression signature with genomic alterations and clinical outcome Bernardo P. de Almeida, André F. Vieira, Joana Paredes, Mónica Bettencourt-Dias, Nuno L. Barbosa-Morais Modeling differentiation-state transitions linked to therapeutic escape in triple-negative breast cancer Margaret P. Chapman, Tyler Risom, Anil J. Aswani, Ellen M. Langer, Rosalie C. Sears, Claire J. Tomlin The number of active metabolic pathways is bounded by the number of cellular constraints at maximal metabolic rates Daan H. de Groot, Coco van Boxtel, Robert Planqué, Frank J. Bruggeman, Bas Teusink Myopic control of neural dynamics David Hocker, Il Memming Park A complete statistical model for calibration of RNA-seq counts using external spike-ins and maximum likelihood theory Rodoniki Athanasiadou, Benjamin Neymotin, Nathan Brandt, Wei Wang, Lionel Christiaen, David Gresham, Daniel Tranchina Synaptic plasticity onto inhibitory neurons as a mechanism for ocular dominance plasticity Jacopo Bono, Claudia Clopath Spike burst-pause dynamics of Purkinje cells regulate sensorimotor adaptation Niceto R. Luque, Francisco Naveros, Richard R. Carrillo, Eduardo Ros, Angelo Arleo Optimizing the depth and the direction of prospective planning using information values Can Eren Sezener, Amir Dezfouli, Mehdi Keramati A spatio-temporal individual-based network framework for West Nile virus in the USA: Spreading pattern of West Nile virus Sifat A. Moon, Lee W. Cohnstaedt, D. Scott McVey, Caterina M. Scoglio Understanding narwhal diving behaviour using Hidden Markov Models with dependent state distributions and long range dependence Manh Cuong Ngô, Mads Peter Heide-Jørgensen, Susanne Ditlevsen The logic of ionic homeostasis: Cations are for voltage, but not for volume Andrey V. Dmitriev, Alexander A. Dmitriev, Robert A. Linsenmeier Boolean model of growth signaling, cell cycle and apoptosis predicts the molecular mechanism of aberrant cell cycle progression driven by hyperactive PI3K Herbert Sizek, Andrew Hamel, Dávid Deritei, Sarah Campbell, Erzsébet Ravasz Regan Building a mechanistic mathematical model of hepatitis C virus entry Mphatso Kalemera, Dilyana Mincheva, Joe Grove, Christopher J. R. Illingworth Stochastic neural field model of stimulus-dependent variability in cortical neurons Paul C. Bressloff Endemicity and prevalence of multipartite viruses under heterogeneous between-host transmission Eugenio Valdano, Susanna Manrubia, Sergio Gómez, Alex Arenas Self-organization of conducting pathways explains electrical wave propagation in cardiac tissues with high fraction of non-conducting cells Nina Kudryashova, Aygul Nizamieva, Valeriya Tsvelaya, Alexander V. Panfilov, Konstantin I. Agladze Modeling second-order boundary perception: A machine learning approach Christopher DiMattina, Curtis L. Baker Jr. An agent-based model of dengue virus transmission shows how uncertainty about breakthrough infections influences vaccination impact projections T. Alex Perkins, Robert C. Reiner, Guido España, Quirine A. ten Bosch, Amit Verma, Kelly A. Liebman, Valerie A. Paz-Soldan, John P. Elder, Amy C. Morrison, Steven T. Stoddard, Uriel Kitron, Gonzalo M. Vazquez-Prokopec, Thomas W. Scott, David L. Smith ZnT2 is an electroneutral proton-coupled vesicular antiporter displaying an apparent stoichiometry of two protons per zinc ion Yarden Golan, Raphael Alhadeff, Arieh Warshel, Yehuda G. Assaraf Identification of pathways associated with chemosensitivity through network embedding Sheng Wang, Edward Huang, Junmei Cairns, Jian Peng, Liewei Wang, Saurabh Sinha Contrasting the effects of adaptation and synaptic filtering on the timescales of dynamics in recurrent networks Manuel Beiran, Srdjan Ostojic ChIPulate: A comprehensive ChIP-seq simulation pipeline Vishaka Datta, Sridhar Hannenhalli, Rahul Siddharthan Rapid interpretation of small-angle X-ray scattering data Marie Weiel, Ines Reinartz, Alexander Schug Scalable nonlinear programming framework for parameter estimation in dynamic biological system models Sungho Shin, Ophelia S. Venturelli, Victor M. Zavala Searching algorithm for Type IV effector proteins (S4TE) 2.0: Improved tools for Type IV effector prediction, analysis and comparison in proteobacteria Christophe Noroy, Thierry Lefrançois, Damien F. Meyer LMTRDA: Using logistic model tree to predict MiRNA-disease associations by fusing multi-source information of sequences and similarities Lei Wang, Zhu-Hong You, Xing Chen, Yang-Ming Li, Ya-Nan Dong, Li-Ping Li, Kai Zheng Conformational ensemble of native α-synuclein in solution as determined by short-distance crosslinking constraint-guided discrete molecular dynamics simulations Nicholas I. Brodie, Konstantin I. Popov, Evgeniy V. Petrotchenko, Nikolay V. Dokholyan, Christoph H. Borchers Evaluating reproducibility of AI algorithms in digital pathology with DAPPER Andrea Bizzego, Nicole Bussola, Marco Chierici, Valerio Maggio, Margherita Francescatto, Luca Cima, Marco Cristoforetti, Giuseppe Jurman, Cesare Furlanello Synchrony is more than its top-down and climatic parts: interacting Moran effects on phytoplankton in British seas Lawrence W. Sheppard, Emma J. Defriez, Philip C. Reid, Daniel C. Reuman A computational framework To assess genome-wide distribution Of polymorphic human endogenous retrovirus-K In human populations Weiling Li, Lin Lin, Raunaq Malhotra, Lei Yang, Raj Acharya, Mary Poss Bayesian inference of transmission chains using timing of symptoms, pathogen genomes and contact data Finlay Campbell, Anne Cori, Neil Ferguson, Thibaut Jombart Bayes-optimal estimation of overlap between populations of fixed size Daniel B. Larremore CORRECTION Correction: In-silico dynamic analysis of cytotoxic drug administration to solid tumours: Effect of binding affinity and vessel permeability Vasileios Vavourakis, Triantafyllos Stylianopoulos, Peter A. Wijeratne