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Table of Contents: January 2016

COVER

Social Norms of Cooperation in Small-Scale Societies

Image Credit: Pacheco et al.
Issue Image

Indirect reciprocity, besides providing a convenient framework to address the evolution of moral systems, offers a simple and plausible explanation for the prevalence of cooperation among unrelated individuals. By helping someone, an individual may increase her/his reputation, which may change the pre-disposition of others to help her/him in the future. This, however, depends on what is reckoned as a good or a bad action. Pacheco et al.

Editorial

Ten Simple Rules for a Bioinformatics Journal Club

Andrew Lonsdale, Jocelyn Sietsma Penington, Timothy Rice, Michael Walker, Harriet Dashnow

Education

A Quick Introduction to Version Control with Git and GitHub

John D. Blischak, Emily R. Davenport, Greg Wilson

Review

Research Articles

NINJA-OPS: Fast Accurate Marker Gene Alignment Using Concatenated Ribosomes

Gabriel A. Al-Ghalith, Emmanuel Montassier, Henry N. Ward, Dan Knights

Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5’-Phosphate Production in E. coli

Matthew A. Oberhardt, Raphy Zarecki, Leah Reshef, Fangfang Xia, Miquel Duran-Frigola, Rachel Schreiber, Christopher S. Henry, Nir Ben-Tal, Daniel J. Dwyer, Uri Gophna, Eytan Ruppin

Fluctuating Nonlinear Spring Model of Mechanical Deformation of Biological Particles

Olga Kononova, Joost Snijder, Yaroslav Kholodov, Kenneth A. Marx, Gijs J. L. Wuite, Wouter H. Roos, Valeri Barsegov

A Thermodynamic Model of Monovalent Cation Homeostasis in the Yeast Saccharomyces cerevisiae

Susanne Gerber, Martina Fröhlich, Hella Lichtenberg-Fraté, Sergey Shabala, Lana Shabala, Edda Klipp

Probing the Limits to MicroRNA-Mediated Control of Gene Expression

Araks Martirosyan, Matteo Figliuzzi, Enzo Marinari, Andrea De Martino

Coenzyme Q Biosynthesis: Evidence for a Substrate Access Channel in the FAD-Dependent Monooxygenase Coq6

Alexandre Ismail, Vincent Leroux, Myriam Smadja, Lucie Gonzalez, Murielle Lombard, Fabien Pierrel, Caroline Mellot-Draznieks, Marc Fontecave

Social Norms of Cooperation in Small-Scale Societies

Fernando P. Santos, Francisco C. Santos, Jorge M. Pacheco

Adaptive Landscape by Environment Interactions Dictate Evolutionary Dynamics in Models of Drug Resistance

C. Brandon Ogbunugafor, C. Scott Wylie, Ibrahim Diakite, Daniel M. Weinreich, Daniel L. Hartl

Fast and Rigorous Computation of Gene and Pathway Scores from SNP-Based Summary Statistics

David Lamparter, Daniel Marbach, Rico Rueedi, Zoltán Kutalik, Sven Bergmann

Spatial Metrics of Tumour Vascular Organisation Predict Radiation Efficacy in a Computational Model

Jacob G. Scott, Alexander G. Fletcher, Alexander R. A. Anderson, Philip K. Maini

Measuring Integrated Information from the Decoding Perspective

Masafumi Oizumi, Shun-ichi Amari, Toru Yanagawa, Naotaka Fujii, Naotsugu Tsuchiya

Model-Based Comprehensive Analysis of School Closure Policies for Mitigating Influenza Epidemics and Pandemics

Laura Fumanelli, Marco Ajelli, Stefano Merler, Neil M. Ferguson, Simon Cauchemez

Evolutionary and Functional Relationships in the Truncated Hemoglobin Family

Juan P. Bustamante, Leandro Radusky, Leonardo Boechi, Darío A. Estrin, Arjen ten Have, Marcelo A. Martí

Discovery of Influenza A Virus Sequence Pairs and Their Combinations for Simultaneous Heterosubtypic Targeting that Hedge against Antiviral Resistance

Keng Boon Wee, Raphael Tze Chuen Lee, Jing Lin, Zacharias Aloysius Dwi Pramono, Sebastian Maurer-Stroh

Brain Connectivity Dissociates Responsiveness from Drug Exposure during Propofol-Induced Transitions of Consciousness

Srivas Chennu, Stuart O’Connor, Ram Adapa, David K. Menon, Tristan A. Bekinschtein

Optimal Population-Level Infection Detection Strategies for Malaria Control and Elimination in a Spatial Model of Malaria Transmission

Jaline Gerardin, Caitlin A. Bever, Busiku Hamainza, John M. Miller, Philip A. Eckhoff, Edward A. Wenger

The Molecular Basis of Polyunsaturated Fatty Acid Interactions with the Shaker Voltage-Gated Potassium Channel

Samira Yazdi, Matthias Stein, Fredrik Elinder, Magnus Andersson, Erik Lindahl

Evidence for Functional Groupings of Vibrissae across the Rodent Mystacial Pad

Jennifer A. Hobbs, R. Blythe Towal, Mitra J. Z. Hartmann

Josephin Domain Structural Conformations Explored by Metadynamics in Essential Coordinates

Marco A. Deriu, Gianvito Grasso, Jack A. Tuszynski, Diego Gallo, Umberto Morbiducci, Andrea Danani

Residual Viremia in Treated HIV+ Individuals

Jessica M. Conway, Alan S. Perelson

Neurally Encoding Time for Olfactory Navigation

In Jun Park, Andrew M. Hein, Yuriy V. Bobkov, Matthew A. Reidenbach, Barry W. Ache, Jose C. Principe

Coordinating Role of RXRα in Downregulating Hepatic Detoxification during Inflammation Revealed by Fuzzy-Logic Modeling

Roland Keller, Marcus Klein, Maria Thomas, Andreas Dräger, Ute Metzger, Markus F. Templin, Thomas O. Joos, Wolfgang E. Thasler, Andreas Zell, Ulrich M. Zanger

K+ Block Is the Mechanism of Functional Asymmetry in Bacterial Nav Channels

Van Ngo, Yibo Wang, Stephan Haas, Sergei Y. Noskov, Robert A. Farley

Pore Structure and Synergy in Antimicrobial Peptides of the Magainin Family

Almudena Pino-Angeles, John M. Leveritt III, Themis Lazaridis