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

PLOS Computational Biology: published February 1, 2018 | https://doi.org/10.1371/journal.pcbi.1005808

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

PLOS Computational Biology: published February 1, 2018 | https://doi.org/10.1371/journal.pcbi.1005772

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

PLOS Computational Biology: published February 15, 2018 | https://doi.org/10.1371/journal.pcbi.1005740

Research Articles

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

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

PLOS Computational Biology: published February 28, 2018 | https://doi.org/10.1371/journal.pcbi.1006021

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

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

PLOS Computational Biology: published February 27, 2018 | https://doi.org/10.1371/journal.pcbi.1005976

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

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

PLOS Computational Biology: published February 26, 2018 | https://doi.org/10.1371/journal.pcbi.1006012

Multiscale modeling of layer formation in epidermis

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

PLOS Computational Biology: published February 26, 2018 | https://doi.org/10.1371/journal.pcbi.1006006

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

PLOS Computational Biology: published February 26, 2018 | https://doi.org/10.1371/journal.pcbi.1005981

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

PLOS Computational Biology: published February 23, 2018 | https://doi.org/10.1371/journal.pcbi.1006007

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

PLOS Computational Biology: published February 23, 2018 | https://doi.org/10.1371/journal.pcbi.1005991

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

PLOS Computational Biology: published February 23, 2018 | https://doi.org/10.1371/journal.pcbi.1005982

Association between expression of random gene sets and survival is evident in multiple cancer types and may be explained by sub-classification

Yishai Shimoni

PLOS Computational Biology: published February 22, 2018 | https://doi.org/10.1371/journal.pcbi.1006026

Memory functions reveal structural properties of gene regulatory networks

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

PLOS Computational Biology: published February 22, 2018 | https://doi.org/10.1371/journal.pcbi.1006003

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

PLOS Computational Biology: published February 20, 2018 | https://doi.org/10.1371/journal.pcbi.1006013

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

PLOS Computational Biology: published February 20, 2018 | https://doi.org/10.1371/journal.pcbi.1006011

Prediction of infectious disease epidemics via weighted density ensembles

Evan L. Ray, Nicholas G. Reich

PLOS Computational Biology: published February 20, 2018 | https://doi.org/10.1371/journal.pcbi.1005910

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

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

PLOS Computational Biology: published February 16, 2018 | https://doi.org/10.1371/journal.pcbi.1006014

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

PLOS Computational Biology: published February 16, 2018 | https://doi.org/10.1371/journal.pcbi.1006010

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

Vipul Gupta, Narendra M. Dixit

PLOS Computational Biology: published February 16, 2018 | https://doi.org/10.1371/journal.pcbi.1006004

In silico analysis of antibiotic-induced Clostridium difficile infection: Remediation techniques and biological adaptations

Eric W. Jones, Jean M. Carlson

PLOS Computational Biology: published February 16, 2018 | https://doi.org/10.1371/journal.pcbi.1006001

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

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

PLOS Computational Biology: published February 16, 2018 | https://doi.org/10.1371/journal.pcbi.1006000

Integrating linear optimization with structural modeling to increase HIV neutralization breadth

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

PLOS Computational Biology: published February 16, 2018 | https://doi.org/10.1371/journal.pcbi.1005999

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

PLOS Computational Biology: published February 15, 2018 | https://doi.org/10.1371/journal.pcbi.1006005

Optimizing homeostatic cell renewal in hierarchical tissues

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

PLOS Computational Biology: published February 15, 2018 | https://doi.org/10.1371/journal.pcbi.1005967

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

PLOS Computational Biology: published February 15, 2018 | https://doi.org/10.1371/journal.pcbi.1005962

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

Dorjsuren Battogtokh, Shihoko Kojima, John J. Tyson

PLOS Computational Biology: published February 15, 2018 | https://doi.org/10.1371/journal.pcbi.1005957

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

PLOS Computational Biology: published February 15, 2018 | https://doi.org/10.1371/journal.pcbi.1005947

A model of risk and mental state shifts during social interaction

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

PLOS Computational Biology: published February 15, 2018 | https://doi.org/10.1371/journal.pcbi.1005935

Examining the controllability of sepsis using genetic algorithms on an agent-based model of systemic inflammation

Robert Chase Cockrell, Gary An

PLOS Computational Biology: published February 15, 2018 | https://doi.org/10.1371/journal.pcbi.1005876

Self-crowding of AMPA receptors in the excitatory postsynaptic density can effectuate anomalous receptor sub-diffusion

Rahul Gupta

PLOS Computational Biology: published February 14, 2018 | https://doi.org/10.1371/journal.pcbi.1005984

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

Raju Kalaivani, Raju Reema, Narayanaswamy Srinivasan

PLOS Computational Biology: published February 13, 2018 | https://doi.org/10.1371/journal.pcbi.1005975

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

PLOS Computational Biology: published February 12, 2018 | https://doi.org/10.1371/journal.pcbi.1006008

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

PLOS Computational Biology: published February 7, 2018 | https://doi.org/10.1371/journal.pcbi.1005965

A phylogenetic method to perform genome-wide association studies in microbes that accounts for population structure and recombination

Caitlin Collins, Xavier Didelot

PLOS Computational Biology: published February 5, 2018 | https://doi.org/10.1371/journal.pcbi.1005958

Cover

Simulation of microtubule dynamics reveals strong influence of cell shape on the formation cortical array in plants.

Editorial

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Education

Research Articles