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Table of Contents

January 2016

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.

Image Credit: Pacheco et al.


Ten Simple Rules for a Bioinformatics Journal Club

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


A Quick Introduction to Version Control with Git and GitHub

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


Computational Modeling, Formal Analysis, and Tools for Systems Biology

Ezio Bartocci, Pietro Lió

Research Articles

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

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

Does High-Dose Antimicrobial Chemotherapy Prevent the Evolution of Resistance?

Troy Day, Andrew F. Read

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

Binding Site Identification and Flexible Docking of Single Stranded RNA to Proteins Using a Fragment-Based Approach

Isaure Chauvot de Beauchene, Sjoerd J. de Vries, Martin Zacharias

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

A Computational Model for the AMPA Receptor Phosphorylation Master Switch Regulating Cerebellar Long-Term Depression

Andrew R. Gallimore, A. Radu Aricescu, Michisuke Yuzaki, Radu Calinescu

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

Asymmetrical Damage Partitioning in Bacteria: A Model for the Evolution of Stochasticity, Determinism, and Genetic Assimilation

Lin Chao, Camilla Ulla Rang, Audrey Menegaz Proenca, Jasper Ubirajara Chao

A Network Model to Describe the Terminal Differentiation of B Cells

Akram Méndez, Luis Mendoza

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

Model-Based Analysis of Cell Cycle Responses to Dynamically Changing Environments

Daniel D Seaton, J Krishnan

Faster Adaptation in Smaller Populations: Counterintuitive Evolution of HIV during Childhood Infection

Jayna Raghwani, Samir Bhatt, Oliver G. Pybus

Residual Viremia in Treated HIV+ Individuals

Jessica M. Conway, Alan S. Perelson

Long-Lasting Sparks: Multi-Metastability and Release Competition in the Calcium Release Unit Network

Zhen Song, Alain Karma, James N. Weiss, Zhilin Qu

Neurally Encoding Time for Olfactory Navigation

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

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