December 2017

To quantitatively study the dynamics of competing genotypes in a population growing into new territory (a range expansion), four strains of E. coli, differing only by a heritable fluorescent marker, were mixed and inoculated onto a nutrient-rich agar plate. Over the course of eight days, cells at the front divided and formed a dense colony. The resulting image, which can be analyzed and understood quantitatively, depicts the formation of monoclonal sectors and provides insight into the evolutionary consequences of population expansions. Weinstein et al.

Image Credit: Bryan T. Weinstein

Editorials

Ten simple rules for international short-term research stays

Diego A. Forero, Sandra Lopez-Leon, George P. Patrinos

PLOS Computational Biology: published December 7, 2017 | https://doi.org/10.1371/journal.pcbi.1005832

Ten simple rules for writing a career development award proposal

Crystal M. Botham, Joshua A. Arribere, Sky W. Brubaker, Kevin T. Beier

PLOS Computational Biology: published December 14, 2017 | https://doi.org/10.1371/journal.pcbi.1005863

Education

A cyber-linked undergraduate research experience in computational biomolecular structure prediction and design

Rebecca F. Alford, Andrew Leaver-Fay, Lynda Gonzales, Erin L. Dolan, Jeffrey J. Gray

PLOS Computational Biology: published December 7, 2017 | https://doi.org/10.1371/journal.pcbi.1005837

Research Articles

Metabomatching: Using genetic association to identify metabolites in proton NMR spectroscopy

Rico Rueedi, Roger Mallol, Johannes Raffler, David Lamparter, Nele Friedrich, Peter Vollenweider, Gérard Waeber, Gabi Kastenmüller, Zoltán Kutalik, Sven Bergmann

PLOS Computational Biology: published December 1, 2017 | https://doi.org/10.1371/journal.pcbi.1005839

Genetic drift and selection in many-allele range expansions

Bryan T. Weinstein, Maxim O. Lavrentovich, Wolfram Möbius, Andrew W. Murray, David R. Nelson

PLOS Computational Biology: published December 1, 2017 | https://doi.org/10.1371/journal.pcbi.1005866

Olfactory coding in the turbulent realm

Vincent Jacob, Christelle Monsempès, Jean-Pierre Rospars, Jean-Baptiste Masson, Philippe Lucas

PLOS Computational Biology: published December 1, 2017 | https://doi.org/10.1371/journal.pcbi.1005870

Sequence-dependent nucleosome sliding in rotation-coupled and uncoupled modes revealed by molecular simulations

Toru Niina, Giovanni B. Brandani, Cheng Tan, Shoji Takada

PLOS Computational Biology: published December 1, 2017 | https://doi.org/10.1371/journal.pcbi.1005880

A model of the onset of the senescence associated secretory phenotype after DNA damage induced senescence

Patrick Meyer, Pallab Maity, Andre Burkovski, Julian Schwab, Christoph Müssel, Karmveer Singh, Filipa F. Ferreira, Linda Krug, Harald J. Maier, Meinhard Wlaschek, Thomas Wirth, Hans A. Kestler, Karin Scharffetter-Kochanek

PLOS Computational Biology: published December 4, 2017 | https://doi.org/10.1371/journal.pcbi.1005741

Efficient encoding of motion is mediated by gap junctions in the fly visual system

Siwei Wang, Alexander Borst, Noga Zaslavsky, Naftali Tishby, Idan Segev

PLOS Computational Biology: published December 4, 2017 | https://doi.org/10.1371/journal.pcbi.1005846

pSSAlib: The partial-propensity stochastic chemical network simulator

Oleksandr Ostrenko, Pietro Incardona, Rajesh Ramaswamy, Lutz Brusch, Ivo F. Sbalzarini

PLOS Computational Biology: published December 4, 2017 | https://doi.org/10.1371/journal.pcbi.1005865

Automated classification of dolphin echolocation click types from the Gulf of Mexico

Kaitlin E. Frasier, Marie A. Roch, Melissa S. Soldevilla, Sean M. Wiggins, Lance P. Garrison, John A. Hildebrand

PLOS Computational Biology: published December 7, 2017 | https://doi.org/10.1371/journal.pcbi.1005823

Predicting the pathogenicity of novel variants in mitochondrial tRNA with MitoTIP

Sanjay Sonney, Jeremy Leipzig, Marie T. Lott, Shiping Zhang, Vincent Procaccio, Douglas C. Wallace, Neal Sondheimer

PLOS Computational Biology: published December 11, 2017 | https://doi.org/10.1371/journal.pcbi.1005867

Thalamocortical control of propofol phase-amplitude coupling

Austin E. Soplata, Michelle M. McCarthy, Jason Sherfey, Shane Lee, Patrick L. Purdon, Emery N. Brown, Nancy Kopell

PLOS Computational Biology: published December 11, 2017 | https://doi.org/10.1371/journal.pcbi.1005879

Non-linear auto-regressive models for cross-frequency coupling in neural time series

Tom Dupré la Tour, Lucille Tallot, Laetitia Grabot, Valérie Doyère, Virginie van Wassenhove, Yves Grenier, Alexandre Gramfort

PLOS Computational Biology: published December 11, 2017 | https://doi.org/10.1371/journal.pcbi.1005893

Stabilizing patterns in time: Neural network approach

Nadav Ben-Shushan, Misha Tsodyks

PLOS Computational Biology: published December 12, 2017 | https://doi.org/10.1371/journal.pcbi.1005861

Feature reliability determines specificity and transfer of perceptual learning in orientation search

Amit Yashar, Rachel N. Denison

PLOS Computational Biology: published December 14, 2017 | https://doi.org/10.1371/journal.pcbi.1005882

Novel linear motif filtering protocol reveals the role of the LC8 dynein light chain in the Hippo pathway

Gábor Erdős, Tamás Szaniszló, Mátyás Pajkos, Borbála Hajdu-Soltész, Bence Kiss, Gábor Pál, László Nyitray, Zsuzsanna Dosztányi

PLOS Computational Biology: published December 14, 2017 | https://doi.org/10.1371/journal.pcbi.1005885

Specific excitatory connectivity for feature integration in mouse primary visual cortex

Dylan R. Muir, Patricia Molina-Luna, Morgane M. Roth, Fritjof Helmchen, Björn M. Kampa

PLOS Computational Biology: published December 14, 2017 | https://doi.org/10.1371/journal.pcbi.1005888

A master equation approach to actin polymerization applied to endocytosis in yeast

Xinxin Wang, Anders E. Carlsson

PLOS Computational Biology: published December 14, 2017 | https://doi.org/10.1371/journal.pcbi.1005901

Costs of task allocation with local feedback: Effects of colony size and extra workers in social insects and other multi-agent systems

Tsvetomira Radeva, Anna Dornhaus, Nancy Lynch, Radhika Nagpal, Hsin-Hao Su

PLOS Computational Biology: published December 14, 2017 | https://doi.org/10.1371/journal.pcbi.1005904