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Table of Contents

February 2018

Cortical microtubule array pattern in a Nicotiana benthamiana leaf pavement cell, visualized using 35S::TUB-mCherry. Instances of the formation of ordered band-like structures around the necks of protrusions are highlighted by the dashed arrows. Simulation of microtubule dynamics on the reconstructed surface of such cells, extracted by segmenting the confocal microscopy images, showed occurrence of similar microtubule band formation around the necks of protrusions. This study shows that cell geometry strongly influences the location and orientation of patterns in the cortical microtubule array of plants. Chakrabortty et al.

Image Credit: Ikram Blilou (KAUST)

Editorial

Ten simple rules for writing a popular science book

Adam J. Kucharski

Message from ISCB

The development and application of bioinformatics core competencies to improve bioinformatics training and education

Nicola Mulder, Russell Schwartz, Michelle D. Brazas, Cath Brooksbank, Bruno Gaeta, Sarah L. Morgan, Mark A. Pauley, Anne Rosenwald, Gabriella Rustici, Michael Sierk, Tandy Warnow, Lonnie Welch

Education

Quick tips for creating effective and impactful biological pathways using the Systems Biology Graphical Notation

Vasundra Touré, Nicolas Le Novère, Dagmar Waltemath, Olaf Wolkenhauer

Research Articles

Ligand-induced perturbation of the HIF-2α:ARNT dimer dynamics

Stefano Motta, Claudia Minici, Dario Corrada, Laura Bonati, Alessandro Pandini

Genetic programming based models in plant tissue culture: An addendum to traditional statistical approach

Meenu R. Mridula, Ashalatha S. Nair, K. Satheesh Kumar

Mathematical modelling of the antibiotic-induced morphological transition of Pseudomonas aeruginosa

Chloe Spalding, Emma Keen, David J. Smith, Anne-Marie Krachler, Sara Jabbari

Multiscale modeling of layer formation in epidermis

Huijing Du, Yangyang Wang, Daniel Haensel, Briana Lee, Xing Dai, Qing Nie

Differential tissue growth and cell adhesion alone drive early tooth morphogenesis: An ex vivo and in silico study

Miquel Marin-Riera, Jacqueline Moustakas-Verho, Yoland Savriama, Jukka Jernvall, Isaac Salazar-Ciudad

A biophysical model of dynamic balancing of excitation and inhibition in fast oscillatory large-scale networks

Romesh G. Abeysuriya, Jonathan Hadida, Stamatios N. Sotiropoulos, Saad Jbabdi, Robert Becker, Benjamin A. E. Hunt, Matthew J. Brookes, Mark W. Woolrich

PhysiCell: An open source physics-based cell simulator for 3-D multicellular systems

Ahmadreza Ghaffarizadeh, Randy Heiland, Samuel H. Friedman, Shannon M. Mumenthaler, Paul Macklin

Systems-level computational modeling demonstrates fuel selection switching in high capacity running and low capacity running rats

Michael A. Moxley, Kalyan C. Vinnakota, Jason N. Bazil, Nathan R. Qi, Daniel A. Beard

Memory functions reveal structural properties of gene regulatory networks

Edgar Herrera-Delgado, Ruben Perez-Carrasco, James Briscoe, Peter Sollich

Exploiting the geometry of the solution space to reduce sensitivity to neuromotor noise

Zhaoran Zhang, Dena Guo, Meghan E. Huber, Se-Woong Park, Dagmar Sternad

The self-organization of plant microtubules inside the cell volume yields their cortical localization, stable alignment, and sensitivity to external cues

Vincent Mirabet, Pawel Krupinski, Olivier Hamant, Elliot M. Meyerowitz, Henrik Jönsson, Arezki Boudaoud

Prediction of infectious disease epidemics via weighted density ensembles

Evan L. Ray, Nicholas G. Reich

Control fast or control smart: When should invading pathogens be controlled?

Robin N. Thompson, Christopher A. Gilligan, Nik J. Cunniffe

Metabolic enzyme cost explains variable trade-offs between microbial growth rate and yield

Meike T. Wortel, Elad Noor, Michael Ferris, Frank J. Bruggeman, Wolfram Liebermeister

Trade-off between synergy and efficacy in combinations of HIV-1 latency-reversing agents

Vipul Gupta, Narendra M. Dixit

A stochastic and dynamical view of pluripotency in mouse embryonic stem cells

Yen Ting Lin, Peter G. Hufton, Esther J. Lee, Davit A. Potoyan

Integrating linear optimization with structural modeling to increase HIV neutralization breadth

Alexander M. Sevy, Swetasudha Panda, James E. Crowe Jr, Jens Meiler, Yevgeniy Vorobeychik

A multiscale modelling approach to assess the impact of metabolic zonation and microperfusion on the hepatic carbohydrate metabolism

Nikolaus Berndt, Marius Stefan Horger, Sascha Bulik, Hermann-Georg Holzhütter

Optimizing homeostatic cell renewal in hierarchical tissues

Cesar Alvarado, Nicole A. Fider, Helen J. Wearing, Natalia L. Komarova

A comprehensive and quantitative comparison of text-mining in 15 million full-text articles versus their corresponding abstracts

David Westergaard, Hans-Henrik Stærfeldt, Christian Tønsberg, Lars Juhl Jensen, Søren Brunak

Modeling the interactions of sense and antisense Period transcripts in the mammalian circadian clock network

Dorjsuren Battogtokh, Shihoko Kojima, John J. Tyson

Life cycle synchronization is a viral drug resistance mechanism

Iulia A. Neagu, Jason Olejarz, Mark Freeman, Daniel I.S. Rosenbloom, Martin A. Nowak, Alison L. Hill

A model of risk and mental state shifts during social interaction

Andreas Hula, Iris Vilares, Terry Lohrenz, Peter Dayan, P. Read Montague

Recognition of sites of functional specialisation in all known eukaryotic protein kinase families

Raju Kalaivani, Raju Reema, Narayanaswamy Srinivasan

Same but not alike: Structure, flexibility and energetics of domains in multi-domain proteins are influenced by the presence of other domains

Sneha Vishwanath, Alexandre G. de Brevern, Narayanaswamy Srinivasan

Electrical receptive fields of retinal ganglion cells: Influence of presynaptic neurons

Matias I. Maturana, Nicholas V. Apollo, David J. Garrett, Tatiana Kameneva, Shaun L. Cloherty, David B. Grayden, Anthony N. Burkitt, Michael R. Ibbotson, Hamish Meffin

Hub connectivity, neuronal diversity, and gene expression in the Caenorhabditis elegans connectome

Aurina Arnatkevic̆iūtė, Ben D. Fulcher, Roger Pocock, Alex Fornito

History dependence in insect flight decisions during odor tracking

Rich Pang, Floris van Breugel, Michael Dickinson, Jeffrey A. Riffell, Adrienne Fairhall

Spike and burst coding in thalamocortical relay cells

Fleur Zeldenrust, Pascal Chameau, Wytse J. Wadman

Heritable tumor cell division rate heterogeneity induces clonal dominance

Margriet M. Palm, Marjet Elemans, Joost B. Beltman

The feasibility of equilibria in large ecosystems: A primary but neglected concept in the complexity-stability debate

Michaël Dougoud, Laura Vinckenbosch, Rudolf P. Rohr, Louis-Félix Bersier, Christian Mazza

A computational approach to distinguish somatic vs. germline origin of genomic alterations from deep sequencing of cancer specimens without a matched normal

James X. Sun, Yuting He, Eric Sanford, Meagan Montesion, Garrett M. Frampton, Stéphane Vignot, Jean-Charles Soria, Jeffrey S. Ross, Vincent A. Miller, Phil J. Stephens, Doron Lipson, Roman Yelensky

Imaging of neural oscillations with embedded inferential and group prevalence statistics

Peter W. Donhauser, Esther Florin, Sylvain Baillet

Interpretation of correlated neural variability from models of feed-forward and recurrent circuits

Volker Pernice, Rava Azeredo da Silveira

Membrane perturbing properties of toxin mycolactone from Mycobacterium ulcerans

Cesar A. López, Clifford J. Unkefer, Basil I. Swanson, Jessica M. J. Swanson, S. Gnanakaran

A maximum-entropy model for predicting chromatin contacts

Pau Farré, Eldon Emberly

Simulation enabled search for explanatory mechanisms of the fracture healing process

Ryan C. Kennedy, Meir Marmor, Ralph Marcucio, C. Anthony Hunt

A computational framework for cortical microtubule dynamics in realistically shaped plant cells

Bandan Chakrabortty, Ikram Blilou, Ben Scheres, Bela M. Mulder

Evolutionary analysis of polyproline motifs in Escherichia coli reveals their regulatory role in translation

Fei Qi, Magdalena Motz, Kirsten Jung, Jürgen Lassak, Dmitrij Frishman