Ten principles for machine-actionable data management plans

Tomasz Miksa, Stephanie Simms, Daniel Mietchen, Sarah Jones

PLOS Computational Biology: published March 28, 2019 | https://doi.org/10.1371/journal.pcbi.1006750

Agent-based modeling of morphogenetic systems: Advantages and challenges

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

PLOS Computational Biology: published March 28, 2019 | https://doi.org/10.1371/journal.pcbi.1006577

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

PLOS Computational Biology: published March 28, 2019 | https://doi.org/10.1371/journal.pcbi.1006658

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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

PLOS Computational Biology: published March 1, 2019 | https://doi.org/10.1371/journal.pcbi.1006213

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

PLOS Computational Biology: published March 1, 2019 | https://doi.org/10.1371/journal.pcbi.1006786

Soma-axon coupling configurations that enhance neuronal coincidence detection

Joshua H. Goldwyn, Michiel W. H. Remme, John Rinzel

PLOS Computational Biology: published March 4, 2019 | https://doi.org/10.1371/journal.pcbi.1006476

Computational geometry for modeling neural populations: From visualization to simulation

Marc de Kamps, Mikkel Lepperød, Yi Ming Lai

PLOS Computational Biology: published March 4, 2019 | https://doi.org/10.1371/journal.pcbi.1006729

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

PLOS Computational Biology: published March 4, 2019 | https://doi.org/10.1371/journal.pcbi.1006839

Genesis of the αβ T-cell receptor

Thomas Dupic, Quentin Marcou, Aleksandra M. Walczak, Thierry Mora

PLOS Computational Biology: published March 4, 2019 | https://doi.org/10.1371/journal.pcbi.1006874

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

PLOS Computational Biology: published March 5, 2019 | https://doi.org/10.1371/journal.pcbi.1006676

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

PLOS Computational Biology: published March 5, 2019 | https://doi.org/10.1371/journal.pcbi.1006701

Evolutionary model for the unequal segregation of high copy plasmids

Karin Münch, Richard Münch, Rebekka Biedendieck, Dieter Jahn, Johannes Müller

PLOS Computational Biology: published March 5, 2019 | https://doi.org/10.1371/journal.pcbi.1006724

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

PLOS Computational Biology: published March 5, 2019 | https://doi.org/10.1371/journal.pcbi.1006773

Bacterial surface colonization, preferential attachment and fitness under periodic stress

Maor Grinberg, Tomer Orevi, Nadav Kashtan

PLOS Computational Biology: published March 5, 2019 | https://doi.org/10.1371/journal.pcbi.1006815

Determination of effective synaptic conductances using somatic voltage clamp

Songting Li, Nan Liu, Li Yao, Xiaohui Zhang, Douglas Zhou, David Cai

PLOS Computational Biology: published March 5, 2019 | https://doi.org/10.1371/journal.pcbi.1006871

Tuft dendrites of pyramidal neurons operate as feedback-modulated functional subunits

Florian Eberhardt, Andreas V. M. Herz, Stefan Häusler

PLOS Computational Biology: published March 6, 2019 | https://doi.org/10.1371/journal.pcbi.1006757

Modeling individual time courses of thrombopoiesis during multi-cyclic chemotherapy

Yuri Kheifetz, Markus Scholz

PLOS Computational Biology: published March 6, 2019 | https://doi.org/10.1371/journal.pcbi.1006775

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Humans use multi-objective control to regulate lateral foot placement when walking

Jonathan B. Dingwell, Joseph P. Cusumano

PLOS Computational Biology: published March 6, 2019 | https://doi.org/10.1371/journal.pcbi.1006850

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

Robert John Holash, Brian R. MacIntosh

PLOS Computational Biology: published March 7, 2019 | https://doi.org/10.1371/journal.pcbi.1006712

A new clustering and nomenclature for beta turns derived from high-resolution protein structures

Maxim Shapovalov, Slobodan Vucetic, Roland L. Dunbrack Jr.

PLOS Computational Biology: published March 7, 2019 | https://doi.org/10.1371/journal.pcbi.1006844

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

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

PLOS Computational Biology: published March 7, 2019 | https://doi.org/10.1371/journal.pcbi.1006845

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

PLOS Computational Biology: published March 7, 2019 | https://doi.org/10.1371/journal.pcbi.1006848

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

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

PLOS Computational Biology: published March 7, 2019 | https://doi.org/10.1371/journal.pcbi.1006855

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

PLOS Computational Biology: published March 7, 2019 | https://doi.org/10.1371/journal.pcbi.1006879

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

PLOS Computational Biology: published March 7, 2019 | https://doi.org/10.1371/journal.pcbi.1006881

How adaptive plasticity evolves when selected against

Alfredo Rago, Kostas Kouvaris, Tobias Uller, Richard Watson

PLOS Computational Biology: published March 8, 2019 | https://doi.org/10.1371/journal.pcbi.1006260

Quantitative cell-based model predicts mechanical stress response of growing tumor spheroids over various growth conditions and cell lines

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

PLOS Computational Biology: published March 8, 2019 | https://doi.org/10.1371/journal.pcbi.1006273

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

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

PLOS Computational Biology: published March 8, 2019 | https://doi.org/10.1371/journal.pcbi.1006397

A dynamic power-law sexual network model of gonorrhoea outbreaks

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

PLOS Computational Biology: published March 8, 2019 | https://doi.org/10.1371/journal.pcbi.1006748

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

PLOS Computational Biology: published March 8, 2019 | https://doi.org/10.1371/journal.pcbi.1006831

A spectrum of routing strategies for brain networks

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

PLOS Computational Biology: published March 8, 2019 | https://doi.org/10.1371/journal.pcbi.1006833

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

PLOS Computational Biology: published March 8, 2019 | https://doi.org/10.1371/journal.pcbi.1006835

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

PLOS Computational Biology: published March 8, 2019 | https://doi.org/10.1371/journal.pcbi.1006856

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

PLOS Computational Biology: published March 11, 2019 | https://doi.org/10.1371/journal.pcbi.1006794

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

PLOS Computational Biology: published March 11, 2019 | https://doi.org/10.1371/journal.pcbi.1006832

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

PLOS Computational Biology: published March 11, 2019 | https://doi.org/10.1371/journal.pcbi.1006840

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Myopic control of neural dynamics

David Hocker, Il Memming Park

PLOS Computational Biology: published March 11, 2019 | https://doi.org/10.1371/journal.pcbi.1006854

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

PLOS Computational Biology: published March 11, 2019 | https://doi.org/10.1371/journal.pcbi.1006858

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

PLOS Computational Biology: published March 11, 2019 | https://doi.org/10.1371/journal.pcbi.1006895

Spike burst-pause dynamics of Purkinje cells regulate sensorimotor adaptation

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

PLOS Computational Biology: published March 12, 2019 | https://doi.org/10.1371/journal.pcbi.1006298

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

Can Eren Sezener, Amir Dezfouli, Mehdi Keramati

PLOS Computational Biology: published March 12, 2019 | https://doi.org/10.1371/journal.pcbi.1006827

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

Jacopo Bono, Claudia Clopath

PLOS Computational Biology: published March 12, 2019 | https://doi.org/10.1371/journal.pcbi.1006834

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

PLOS Computational Biology: published March 13, 2019 | https://doi.org/10.1371/journal.pcbi.1006875

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

PLOS Computational Biology: published March 14, 2019 | https://doi.org/10.1371/journal.pcbi.1006425

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

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

PLOS Computational Biology: published March 14, 2019 | https://doi.org/10.1371/journal.pcbi.1006894

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

PLOS Computational Biology: published March 15, 2019 | https://doi.org/10.1371/journal.pcbi.1006402

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

PLOS Computational Biology: published March 18, 2019 | https://doi.org/10.1371/journal.pcbi.1006597

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

Paul C. Bressloff

PLOS Computational Biology: published March 18, 2019 | https://doi.org/10.1371/journal.pcbi.1006755

Modeling second-order boundary perception: A machine learning approach

Christopher DiMattina, Curtis L. Baker Jr.

PLOS Computational Biology: published March 18, 2019 | https://doi.org/10.1371/journal.pcbi.1006829

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

Eugenio Valdano, Susanna Manrubia, Sergio Gómez, Alex Arenas

PLOS Computational Biology: published March 18, 2019 | https://doi.org/10.1371/journal.pcbi.1006876

Building a mechanistic mathematical model of hepatitis C virus entry

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

PLOS Computational Biology: published March 18, 2019 | https://doi.org/10.1371/journal.pcbi.1006905

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

T. Alex Perkins, Robert C. Reiner Jr., 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

PLOS Computational Biology: published March 20, 2019 | https://doi.org/10.1371/journal.pcbi.1006710

Identification of pathways associated with chemosensitivity through network embedding

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

PLOS Computational Biology: published March 20, 2019 | https://doi.org/10.1371/journal.pcbi.1006864

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

PLOS Computational Biology: published March 20, 2019 | https://doi.org/10.1371/journal.pcbi.1006882

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

Manuel Beiran, Srdjan Ostojic

PLOS Computational Biology: published March 21, 2019 | https://doi.org/10.1371/journal.pcbi.1006893

ChIPulate: A comprehensive ChIP-seq simulation pipeline

Vishaka Datta, Sridhar Hannenhalli, Rahul Siddharthan

PLOS Computational Biology: published March 21, 2019 | https://doi.org/10.1371/journal.pcbi.1006921

Rapid interpretation of small-angle X-ray scattering data

Marie Weiel, Ines Reinartz, Alexander Schug

PLOS Computational Biology: published March 22, 2019 | https://doi.org/10.1371/journal.pcbi.1006900

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

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

PLOS Computational Biology: published March 25, 2019 | https://doi.org/10.1371/journal.pcbi.1006828

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

PLOS Computational Biology: published March 25, 2019 | https://doi.org/10.1371/journal.pcbi.1006847

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

PLOS Computational Biology: published March 27, 2019 | https://doi.org/10.1371/journal.pcbi.1006269

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

PLOS Computational Biology: published March 27, 2019 | https://doi.org/10.1371/journal.pcbi.1006859

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

PLOS Computational Biology: published March 27, 2019 | https://doi.org/10.1371/journal.pcbi.1006865

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

PLOS Computational Biology: published March 28, 2019 | https://doi.org/10.1371/journal.pcbi.1006564

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

PLOS Computational Biology: published March 28, 2019 | https://doi.org/10.1371/journal.pcbi.1006744

Bayes-optimal estimation of overlap between populations of fixed size

Daniel B. Larremore

PLOS Computational Biology: published March 29, 2019 | https://doi.org/10.1371/journal.pcbi.1006898

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

Finlay Campbell, Anne Cori, Neil Ferguson, Thibaut Jombart

PLOS Computational Biology: published March 29, 2019 | https://doi.org/10.1371/journal.pcbi.1006930

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

PLOS Computational Biology: published March 4, 2019 | https://doi.org/10.1371/journal.pcbi.1006880

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