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Table of Contents: 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

Ten simple rules for writing a career development award proposal

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

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

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

Genetic drift and selection in many-allele range expansions

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

Olfactory coding in the turbulent realm

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

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

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

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

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

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

pSSAlib: The partial-propensity stochastic chemical network simulator

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

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

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

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

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

Stabilizing patterns in time: Neural network approach

Nadav Ben-Shushan, Misha Tsodyks

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

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

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

Xinxin Wang, Anders E. Carlsson

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

Optimal occlusion uniformly partitions red blood cells fluxes within a microvascular network

Shyr-Shea Chang, Shenyinying Tu, Kyung In Baek, Andrew Pietersen, Yu-Hsiu Liu, Van M. Savage, Sheng-Ping L. Hwang, Tzung K. Hsiai, Marcus Roper

MAGPIE: Simplifying access and execution of computational models in the life sciences

Christoph Baldow, Sebastian Salentin, Michael Schroeder, Ingo Roeder, Ingmar Glauche

Filament turnover tunes both force generation and dissipation to control long-range flows in a model actomyosin cortex

William M. McFadden, Patrick M. McCall, Margaret L. Gardel, Edwin M. Munro

Invariant recognition drives neural representations of action sequences

Andrea Tacchetti, Leyla Isik, Tomaso Poggio

An error-tuned model for sensorimotor learning

James N. Ingram, Mohsen Sadeghi, J. Randall Flanagan, Daniel M. Wolpert

Complete hazard ranking to analyze right-censored data: An ALS survival study

Zhengnan Huang, Hongjiu Zhang, Jonathan Boss, Stephen A. Goutman, Bhramar Mukherjee, Ivo D. Dinov, Yuanfang Guan, for the Pooled Resource Open-Access ALS Clinical Trials Consortium

Optimal number of spacers in CRISPR arrays

Alexander Martynov, Konstantin Severinov, Iaroslav Ispolatov

Molecular recognition and packing frustration in a helical protein

Loan Huynh, Chris Neale, Régis Pomès, Hue Sun Chan

Theoretical perspectives on central chemosensitivity: CO2/H+-sensitive neurons in the locus coeruleus

Maria C. Quintero, Robert W. Putnam, Juan M. Cordovez

Mechanistic modeling quantifies the influence of tumor growth kinetics on the response to anti-angiogenic treatment

Thomas D. Gaddy, Qianhui Wu, Alyssa D. Arnheim, Stacey D. Finley

Scalable multi-sample single-cell data analysis by Partition-Assisted Clustering and Multiple Alignments of Networks

Ye Henry Li, Dangna Li, Nikolay Samusik, Xiaowei Wang, Leying Guan, Garry P. Nolan, Wing Hung Wong

Physiological models of the lateral superior olive

Go Ashida, Daniel J. Tollin, Jutta Kretzberg

High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock

Nawsad Alam, Oriel Goldstein, Bing Xia, Kathryn A. Porter, Dima Kozakov, Ora Schueler-Furman

System identification of signaling dependent gene expression with different time-scale data

Takaho Tsuchiya, Masashi Fujii, Naoki Matsuda, Katsuyuki Kunida, Shinsuke Uda, Hiroyuki Kubota, Katsumi Konishi, Shinya Kuroda

MPLasso: Inferring microbial association networks using prior microbial knowledge

Chieh Lo, Radu Marculescu

Local motion adaptation enhances the representation of spatial structure at EMD arrays

Jinglin Li, Jens P. Lindemann, Martin Egelhaaf

Corrections

Correction: Identifying influential neighbors in animal flocking

The PLOS Computational Biology Staff

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