May 2018

We investigate the dynamics of cooperative transport, where the motion of the ants is frustrated by an obstacle that contains a narrow opening that serves as the only available passage to the nest, and through which single ants can pass but not the cargo. A theoretical model for this frustrated motion predicts a bi-stable dynamic behavior that stochastically switches between large amplitude oscillations along the obstacle and extended lingering near the opening. These predictions are experimentally confirmed: The bi-stability provides two possible problem solving strategies, whereby the ants attempt to fit small objects through the opening, but guide large objects away from the opening and around the obstacle. Ron et al.

Image Credit: Ehud Fonio

Editorials

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Daniel Mietchen, Shoshana Wodak, Szymon Wasik, Natalia Szostak, Christophe Dessimoz

PLOS Computational Biology: published May 31, 2018 | https://doi.org/10.1371/journal.pcbi.1006137

Ten simple rules for writing a cover letter to accompany a job application for an academic position

Lubomir Tomaska, Jozef Nosek

PLOS Computational Biology: published May 31, 2018 | https://doi.org/10.1371/journal.pcbi.1006132

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2018 outstanding contributions to ISCB award: Russ Altman

Christiana N. Fogg, Diane E. Kovats, Ron Shamir

PLOS Computational Biology: published May 17, 2018 | https://doi.org/10.1371/journal.pcbi.1006140

2018 ISCB accomplishments by a senior scientist award

Christiana N. Fogg, Diane E. Kovats, Ron Shamir

PLOS Computational Biology: published May 17, 2018 | https://doi.org/10.1371/journal.pcbi.1006138

Art in Science Competition invites artworks to the annual exhibition on ISMB 2018 in Chicago

Milana Frenkel-Morgenstern, Lonnie Welch, Bruno Gaeta, Diane E. Kovats

PLOS Computational Biology: published May 7, 2018 | https://doi.org/10.1371/journal.pcbi.1006139

Research Articles

Minimal model of interictal and ictal discharges “Epileptor-2”

Anton V. Chizhov, Artyom V. Zefirov, Dmitry V. Amakhin, Elena Yu. Smirnova, Aleksey V. Zaitsev

PLOS Computational Biology: published May 31, 2018 | https://doi.org/10.1371/journal.pcbi.1006186

Quantitative theory of deep brain stimulation of the subthalamic nucleus for the suppression of pathological rhythms in Parkinson’s disease

Eli J. Müller, Peter A. Robinson

PLOS Computational Biology: published May 29, 2018 | https://doi.org/10.1371/journal.pcbi.1006217

Simulations to benchmark time-varying connectivity methods for fMRI

William Hedley Thompson, Craig Geoffrey Richter, Pontus Plavén-Sigray, Peter Fransson

PLOS Computational Biology: published May 29, 2018 | https://doi.org/10.1371/journal.pcbi.1006196

Parameter uncertainty quantification using surrogate models applied to a spatial model of yeast mating polarization

Marissa Renardy, Tau-Mu Yi, Dongbin Xiu, Ching-Shan Chou

PLOS Computational Biology: published May 29, 2018 | https://doi.org/10.1371/journal.pcbi.1006181

Optimizing the learning rate for adaptive estimation of neural encoding models

Han-Lin Hsieh, Maryam M. Shanechi

PLOS Computational Biology: published May 29, 2018 | https://doi.org/10.1371/journal.pcbi.1006168

Detecting change in stochastic sound sequences

Benjamin Skerritt-Davis, Mounya Elhilali

PLOS Computational Biology: published May 29, 2018 | https://doi.org/10.1371/journal.pcbi.1006162

How epigenome drives chromatin folding and dynamics, insights from efficient coarse-grained models of chromosomes

Surya K. Ghosh, Daniel Jost

PLOS Computational Biology: published May 29, 2018 | https://doi.org/10.1371/journal.pcbi.1006159

Structural organization and energy storage in crosslinked actin assemblies

Rui Ma, Julien Berro

PLOS Computational Biology: published May 29, 2018 | https://doi.org/10.1371/journal.pcbi.1006150

Coupled feedback loops maintain synaptic long-term potentiation: A computational model of PKMzeta synthesis and AMPA receptor trafficking

Peter Helfer, Thomas R. Shultz

PLOS Computational Biology: published May 29, 2018 | https://doi.org/10.1371/journal.pcbi.1006147

Can a time varying external drive give rise to apparent criticality in neural systems?

Viola Priesemann, Oren Shriki

PLOS Computational Biology: published May 29, 2018 | https://doi.org/10.1371/journal.pcbi.1006081

Variability in pulmonary vein electrophysiology and fibrosis determines arrhythmia susceptibility and dynamics

Caroline H. Roney, Jason D. Bayer, Hubert Cochet, Marianna Meo, Rémi Dubois, Pierre Jaïs, Edward J. Vigmond

PLOS Computational Biology: published May 24, 2018 | https://doi.org/10.1371/journal.pcbi.1006166

Design of optimal nonlinear network controllers for Alzheimer's disease

Lazaro M. Sanchez-Rodriguez, Yasser Iturria-Medina, Erica A. Baines, Sabela C. Mallo, Mehdy Dousty, Roberto C. Sotero, on behalf of The Alzheimer’s Disease Neuroimaging Initiative

PLOS Computational Biology: published May 24, 2018 | https://doi.org/10.1371/journal.pcbi.1006136

The complex ecosystem in non small cell lung cancer invasion

Seth Haney, Jessica Konen, Adam I. Marcus, Maxim Bazhenov

PLOS Computational Biology: published May 24, 2018 | https://doi.org/10.1371/journal.pcbi.1006131

Logistical constraints lead to an intermediate optimum in outbreak response vaccination

Yun Tao, Katriona Shea, Matthew Ferrari

PLOS Computational Biology: published May 23, 2018 | https://doi.org/10.1371/journal.pcbi.1006161

Traceability, reproducibility and wiki-exploration for “à-la-carte” reconstructions of genome-scale metabolic models

Méziane Aite, Marie Chevallier, Clémence Frioux, Camille Trottier, Jeanne Got, María Paz Cortés, Sebastián N. Mendoza, Grégory Carrier, Olivier Dameron, Nicolas Guillaudeux, Mauricio Latorre, Nicolás Loira, Gabriel V. Markov, Alejandro Maass, Anne Siegel

PLOS Computational Biology: published May 23, 2018 | https://doi.org/10.1371/journal.pcbi.1006146

Polymorphic sites preferentially avoid co-evolving residues in MHC class I proteins

Linda Dib, Nicolas Salamin, David Gfeller

PLOS Computational Biology: published May 21, 2018 | https://doi.org/10.1371/journal.pcbi.1006188

Implications for human odor sensing revealed from the statistics of odorant-receptor interactions

Ji Hyun Bak, Seogjoo J. Jang, Changbong Hyeon

PLOS Computational Biology: published May 21, 2018 | https://doi.org/10.1371/journal.pcbi.1006175

Community-based benchmarking improves spike rate inference from two-photon calcium imaging data

Philipp Berens, Jeremy Freeman, Thomas Deneux, Nikolay Chenkov, Thomas McColgan, Artur Speiser, Jakob H. Macke, Srinivas C. Turaga, Patrick Mineault, Peter Rupprecht, Stephan Gerhard, Rainer W. Friedrich, Johannes Friedrich, Liam Paninski, Marius Pachitariu, Kenneth D. Harris, Ben Bolte, Timothy A. Machado, Dario Ringach, Jasmine Stone, Luke E. Rogerson, Nicolas J. Sofroniew, Jacob Reimer, Emmanouil Froudarakis, Thomas Euler, Miroslav Román Rosón, Lucas Theis, Andreas S. Tolias, Matthias Bethge

PLOS Computational Biology: published May 21, 2018 | https://doi.org/10.1371/journal.pcbi.1006157

Systematic interrogation of diverse Omic data reveals interpretable, robust, and generalizable transcriptomic features of clinically successful therapeutic targets

Andrew D. Rouillard, Mark R. Hurle, Pankaj Agarwal

PLOS Computational Biology: published May 21, 2018 | https://doi.org/10.1371/journal.pcbi.1006142

Atomic resolution mechanism of ligand binding to a solvent inaccessible cavity in T4 lysozyme

Jagannath Mondal, Navjeet Ahalawat, Subhendu Pandit, Lewis E. Kay, Pramodh Vallurupalli

PLOS Computational Biology: published May 18, 2018 | https://doi.org/10.1371/journal.pcbi.1006180

On the role of sparseness in the evolution of modularity in gene regulatory networks

Carlos Espinosa-Soto

PLOS Computational Biology: published May 18, 2018 | https://doi.org/10.1371/journal.pcbi.1006172

Potassium and sodium microdomains in thin astroglial processes: A computational model study

Kevin Breslin, John Joseph Wade, KongFatt Wong-Lin, Jim Harkin, Bronac Flanagan, Harm Van Zalinge, Steve Hall, Matthew Walker, Alexei Verkhratsky, Liam McDaid

PLOS Computational Biology: published May 18, 2018 | https://doi.org/10.1371/journal.pcbi.1006151

Firing-rate based network modeling of the dLGN circuit: Effects of cortical feedback on spatiotemporal response properties of relay cells

Milad Hobbi Mobarhan, Geir Halnes, Pablo Martínez-Cañada, Torkel Hafting, Marianne Fyhn, Gaute T. Einevoll

PLOS Computational Biology: published May 17, 2018 | https://doi.org/10.1371/journal.pcbi.1006156

Enzyme sequestration by the substrate: An analysis in the deterministic and stochastic domains

Andreas Petrides, Glenn Vinnicombe

PLOS Computational Biology: published May 17, 2018 | https://doi.org/10.1371/journal.pcbi.1006107

Near real-time forecasting for cholera decision making in Haiti after Hurricane Matthew

Damiano Pasetto, Flavio Finger, Anton Camacho, Francesco Grandesso, Sandra Cohuet, Joseph C. Lemaitre, Andrew S. Azman, Francisco J. Luquero, Enrico Bertuzzo, Andrea Rinaldo

PLOS Computational Biology: published May 16, 2018 | https://doi.org/10.1371/journal.pcbi.1006127

A loop-counting method for covariate-corrected low-rank biclustering of gene-expression and genome-wide association study data

Aaditya V. Rangan, Caroline C. McGrouther, John Kelsoe, Nicholas Schork, Eli Stahl, Qian Zhu, Arjun Krishnan, Vicky Yao, Olga Troyanskaya, Seda Bilaloglu, Preeti Raghavan, Sarah Bergen, Anders Jureus, Mikael Landen, Bipolar Disorders Working Group of the Psychiatric Genomics Consortium

PLOS Computational Biology: published May 14, 2018 | https://doi.org/10.1371/journal.pcbi.1006105

Functional triplet motifs underlie accurate predictions of single-trial responses in populations of tuned and untuned V1 neurons

Joseph B. Dechery, Jason N. MacLean

PLOS Computational Biology: published May 4, 2018 | https://doi.org/10.1371/journal.pcbi.1006153

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Bi-stable collective states provide ants with multiple problem-solving strategies during cooperative transport

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