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Table of Contents

March 2019

This image is an immunocytochemical confocal tile scan of cardiac cell culture with a high fraction of non-conducting cells (69%), where conducting cardiac cells are labelled with anti-α-actinin antibody and coloured in pink. Kudryashova et al. show in this issue that cardiac cells can form a conductive pathway (pink cells outlined in white), which enables electrical wave propagation despite a paradoxically small number of conducting cells. Such self-organisation into a connected branching network can be explained by alignment of cytoskeletons in the neighbouring cells, as demonstrated in a computer model.

Image Credit: Aygul Nizamieva

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

Research Articles

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

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

Soma-axon coupling configurations that enhance neuronal coincidence detection

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

Computational geometry for modeling neural populations: From visualization to simulation

Marc de Kamps, Mikkel Lepperød, Yi Ming Lai

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

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

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

Evolutionary model for the unequal segregation of high copy plasmids

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

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

Bacterial surface colonization, preferential attachment and fitness under periodic stress

Maor Grinberg, Tomer Orevi, Nadav Kashtan

Determination of effective synaptic conductances using somatic voltage clamp

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

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

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

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

Jonathan B. Dingwell, Joseph P. Cusumano

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

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

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

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

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

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

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

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

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

How adaptive plasticity evolves when selected against

Alfredo Rago, Kostas Kouvaris, Tobias Uller, Richard Watson

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 dynamic power-law sexual network model of gonorrhoea outbreaks

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

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

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

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

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

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

Myopic control of neural dynamics

David Hocker, Il Memming Park

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

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

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

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.

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

Eugenio Valdano, Susanna Manrubia, Sergio Gómez, Alex Arenas

Building a mechanistic mathematical model of hepatitis C virus entry

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

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

Identification of pathways associated with chemosensitivity through network embedding

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

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

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

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

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

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

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

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

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

Finlay Campbell, Anne Cori, Neil Ferguson, Thibaut Jombart