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.

Editorial

Ten Simple Rules for a Bioinformatics Journal Club

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

PLOS Computational Biology: published January 28, 2016 | https://doi.org/10.1371/journal.pcbi.1004526

Education

A Quick Introduction to Version Control with Git and GitHub

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

PLOS Computational Biology: published January 19, 2016 | https://doi.org/10.1371/journal.pcbi.1004668

Review

Computational Modeling, Formal Analysis, and Tools for Systems Biology

Ezio Bartocci, Pietro Lió

PLOS Computational Biology: published January 21, 2016 | https://doi.org/10.1371/journal.pcbi.1004591

Research Articles

Modelling Feedback Excitation, Pacemaker Properties and Sensory Switching of Electrically Coupled Brainstem Neurons Controlling Rhythmic Activity

Michael J. Hull, Stephen R. Soffe, David J. Willshaw, Alan Roberts

PLOS Computational Biology: published January 29, 2016 | https://doi.org/10.1371/journal.pcbi.1004702

A Biophysical Model of CRISPR/Cas9 Activity for Rational Design of Genome Editing and Gene Regulation

Iman Farasat, Howard M. Salis

PLOS Computational Biology: published January 29, 2016 | https://doi.org/10.1371/journal.pcbi.1004724

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

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

PLOS Computational Biology: published January 28, 2016 | https://doi.org/10.1371/journal.pcbi.1004658

Spontaneous Decoding of the Timing and Content of Human Object Perception from Cortical Surface Recordings Reveals Complementary Information in the Event-Related Potential and Broadband Spectral Change

Kai J. Miller, Gerwin Schalk, Dora Hermes, Jeffrey G. Ojemann, Rajesh P. N. Rao

PLOS Computational Biology: published January 28, 2016 | https://doi.org/10.1371/journal.pcbi.1004660

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

Troy Day, Andrew F. Read

PLOS Computational Biology: published January 28, 2016 | https://doi.org/10.1371/journal.pcbi.1004689

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

PLOS Computational Biology: published January 28, 2016 | https://doi.org/10.1371/journal.pcbi.1004705

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

PLOS Computational Biology: published January 28, 2016 | https://doi.org/10.1371/journal.pcbi.1004729

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

PLOS Computational Biology: published January 27, 2016 | https://doi.org/10.1371/journal.pcbi.1004697

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

PLOS Computational Biology: published January 27, 2016 | https://doi.org/10.1371/journal.pcbi.1004703

Probing the Limits to MicroRNA-Mediated Control of Gene Expression

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

PLOS Computational Biology: published January 26, 2016 | https://doi.org/10.1371/journal.pcbi.1004715

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

PLOS Computational Biology: published January 25, 2016 | https://doi.org/10.1371/journal.pcbi.1004664

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

PLOS Computational Biology: published January 25, 2016 | https://doi.org/10.1371/journal.pcbi.1004690

Social Norms of Cooperation in Small-Scale Societies

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

PLOS Computational Biology: published January 25, 2016 | https://doi.org/10.1371/journal.pcbi.1004709

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

PLOS Computational Biology: published January 25, 2016 | https://doi.org/10.1371/journal.pcbi.1004710

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

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

PLOS Computational Biology: published January 25, 2016 | https://doi.org/10.1371/journal.pcbi.1004714

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

PLOS Computational Biology: published January 22, 2016 | https://doi.org/10.1371/journal.pcbi.1004712

Measuring Integrated Information from the Decoding Perspective

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

PLOS Computational Biology: published January 21, 2016 | https://doi.org/10.1371/journal.pcbi.1004654

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

PLOS Computational Biology: published January 21, 2016 | https://doi.org/10.1371/journal.pcbi.1004681

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

PLOS Computational Biology: published January 20, 2016 | https://doi.org/10.1371/journal.pcbi.1004701

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

PLOS Computational Biology: published January 15, 2016 | https://doi.org/10.1371/journal.pcbi.1004663

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

PLOS Computational Biology: published January 14, 2016 | https://doi.org/10.1371/journal.pcbi.1004669

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

PLOS Computational Biology: published January 14, 2016 | https://doi.org/10.1371/journal.pcbi.1004707

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

PLOS Computational Biology: published January 13, 2016 | https://doi.org/10.1371/journal.pcbi.1004700

Consistency of VDJ Rearrangement and Substitution Parameters Enables Accurate B Cell Receptor Sequence Annotation

Duncan K. Ralph, Frederick A. Matsen IV

PLOS Computational Biology: published January 11, 2016 | https://doi.org/10.1371/journal.pcbi.1004409

A Network Model to Describe the Terminal Differentiation of B Cells

Akram Méndez, Luis Mendoza

PLOS Computational Biology: published January 11, 2016 | https://doi.org/10.1371/journal.pcbi.1004696

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

PLOS Computational Biology: published January 11, 2016 | https://doi.org/10.1371/journal.pcbi.1004704

Evidence for Functional Groupings of Vibrissae across the Rodent Mystacial Pad

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

PLOS Computational Biology: published January 8, 2016 | https://doi.org/10.1371/journal.pcbi.1004109

Josephin Domain Structural Conformations Explored by Metadynamics in Essential Coordinates

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

PLOS Computational Biology: published January 8, 2016 | https://doi.org/10.1371/journal.pcbi.1004699

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

Daniel D Seaton, J Krishnan

PLOS Computational Biology: published January 7, 2016 | https://doi.org/10.1371/journal.pcbi.1004604

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

Jayna Raghwani, Samir Bhatt, Oliver G. Pybus

PLOS Computational Biology: published January 7, 2016 | https://doi.org/10.1371/journal.pcbi.1004694

Coarse-Grained Simulations of Topology-Dependent Mechanisms of Protein Unfolding and Translocation Mediated by ClpY ATPase Nanomachines

Andrea N. Kravats, Sam Tonddast-Navaei, George Stan

PLOS Computational Biology: published January 6, 2016 | https://doi.org/10.1371/journal.pcbi.1004675

Residual Viremia in Treated HIV⁺ Individuals

Jessica M. Conway, Alan S. Perelson

PLOS Computational Biology: published January 6, 2016 | https://doi.org/10.1371/journal.pcbi.1004677

Transient Accumulation of NO₂^- and N₂O during Denitrification Explained by Assuming Cell Diversification by Stochastic Transcription of Denitrification Genes

Junaid Hassan, Zhi Qu, Linda L. Bergaust, Lars R. Bakken

PLOS Computational Biology: published January 5, 2016 | https://doi.org/10.1371/journal.pcbi.1004621

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Social Norms of Cooperation in Small-Scale Societies

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