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Table of Contents: November 2013

The yellow boundaries separate the capsid's mechanical units, which were identified with the algorithm of Polles et al. The partitioning involves 32 units, which are further grouped in two distinct types: pentamers (blue) and hexamers (red).

Image Credit: Guido Polles

Editorials

Ten Simple Rules for Starting a Regional Student Group

Avinash Kumar Shanmugam, Geoff Macintyre, Magali Michaut, Thomas Abeel

Learning How to Run a Lab: Interviews with Principal Investigators

Theodore Alexandrov, Philip E. Bourne

Messages from ISCB

Breaking the Ice and Forging Links: The Importance of Socializing in Research

Miranda Stobbe, Tarun Mishra, Geoff Macintyre

Education Articles

Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data

Timothy Bailey, Pawel Krajewski, Istvan Ladunga, Celine Lefebvre, Qunhua Li, Tao Liu, Pedro Madrigal, Cenny Taslim, Jie Zhang

Ten Quick Tips for Using the Gene Ontology

Judith A. Blake

Perspectives

The Young PI Buzz: Learning from the Organizers of the Junior Principal Investigator Meeting at ISMB-ECCB 2013

Jeroen de Ridder, Yana Bromberg, Magali Michaut, Venkata P. Satagopam, Manuel Corpas, Geoff Macintyre, Theodore Alexandrov

Research Articles

Identification of Key Hinge Residues Important for Nucleotide-Dependent Allostery in E. coli Hsp70/DnaK

Peter Man-Un Ung, Andrea D. Thompson, Lyra Chang, Jason E. Gestwicki, Heather A. Carlson

Cell-Based Multi-Parametric Model of Cleft Progression during Submandibular Salivary Gland Branching Morphogenesis

Shayoni Ray, Daniel Yuan, Nimit Dhulekar, Basak Oztan, Bülent Yener, Melinda Larsen

Exploring the Composition of Protein-Ligand Binding Sites on a Large Scale

Nickolay A. Khazanov, Heather A. Carlson

A Petri Net Model of Granulomatous Inflammation: Implications for IL-10 Mediated Control of Leishmania donovani Infection

Luca Albergante, Jon Timmis, Lynette Beattie, Paul M. Kaye

Dread and the Disvalue of Future Pain

Giles W. Story, Ivaylo Vlaev, Ben Seymour, Joel S. Winston, Ara Darzi, Raymond J. Dolan

Related Articles

  1. Correction: Dread and the Disvalue of Future Pain

Genetic Architecture Promotes the Evolution and Maintenance of Cooperation

Antoine Frénoy, François Taddei, Dusan Misevic

Assessing Computational Methods for Transcription Factor Target Gene Identification Based on ChIP-seq Data

Weronika Sikora-Wohlfeld, Marit Ackermann, Eleni G. Christodoulou, Kalaimathy Singaravelu, Andreas Beyer

Understanding the Connection between Epigenetic DNA Methylation and Nucleosome Positioning from Computer Simulations

Guillem Portella, Federica Battistini, Modesto Orozco

Beyond GLMs: A Generative Mixture Modeling Approach to Neural System Identification

Lucas Theis, Andrè Maia Chagas, Daniel Arnstein, Cornelius Schwarz, Matthias Bethge

Harnessing Diversity towards the Reconstructing of Large Scale Gene Regulatory Networks

Takeshi Hase, Samik Ghosh, Ryota Yamanaka, Hiroaki Kitano

Multiscale Modeling of Influenza A Virus Infection Supports the Development of Direct-Acting Antivirals

Frank S. Heldt, Timo Frensing, Antje Pflugmacher, Robin Gröpler, Britta Peschel, Udo Reichl

Conserved Substitution Patterns around Nucleosome Footprints in Eukaryotes and Archaea Derive from Frequent Nucleosome Repositioning through Evolution

Tobias Warnecke, Erin A. Becker, Marc T. Facciotti, Corey Nislow, Ben Lehner

Predictive Coding of Dynamical Variables in Balanced Spiking Networks

Martin Boerlin, Christian K. Machens, Sophie Denève

A Tunable Coarse-Grained Model for Ligand-Receptor Interaction

Teresa Ruiz-Herrero, Javier Estrada, Raúl Guantes, David G. Miguez

Related Articles

  1. New Methods Section in PLOS Computational Biology

Evidence for Finely-Regulated Asynchronous Growth of Toxoplasma gondii Cysts Based on Data-Driven Model Selection

Adam M. Sullivan, Xiaopeng Zhao, Yasuhiro Suzuki, Eri Ochiai, Stephen Crutcher, Michael A. Gilchrist

Dynamical Adaptation in Photoreceptors

Damon A. Clark, Raphael Benichou, Markus Meister, Rava Azeredo da Silveira

In Silico Analysis of Cell Cycle Synchronisation Effects in Radiotherapy of Tumour Spheroids

Harald Kempf, Haralampos Hatzikirou, Marcus Bleicher, Michael Meyer-Hermann

Comparing Algorithms That Reconstruct Cell Lineage Trees Utilizing Information on Microsatellite Mutations

Noa Chapal-Ilani, Yosef E. Maruvka, Adam Spiro, Yitzhak Reizel, Rivka Adar, Liran I. Shlush, Ehud Shapiro

Receptor Concentration and Diffusivity Control Multivalent Binding of Sv40 to Membrane Bilayers

Oliwia M. Szklarczyk, Nélido González-Segredo, Philipp Kukura, Ariella Oppenheim, Daniel Choquet, Vahid Sandoghdar, Ari Helenius, Ivo F. Sbalzarini, Helge Ewers

Computational Protein Design Quantifies Structural Constraints on Amino Acid Covariation

Noah Ollikainen, Tanja Kortemme

Quantifying Chaperone-Mediated Transitions in the Proteostasis Network of E. coli

Alex Dickson, Charles L. Brooks III

Exploring Fold Space Preferences of New-born and Ancient Protein Superfamilies

Hannah Edwards, Sanne Abeln, Charlotte M. Deane

Synaptic Plasticity in Neural Networks Needs Homeostasis with a Fast Rate Detector

Friedemann Zenke, Guillaume Hennequin, Wulfram Gerstner

Mechanical and Assembly Units of Viral Capsids Identified via Quasi-Rigid Domain Decomposition

Guido Polles, Giuliana Indelicato, Raffaello Potestio, Paolo Cermelli, Reidun Twarock, Cristian Micheletti

Auditory Frequency and Intensity Discrimination Explained Using a Cortical Population Rate Code

Christophe Micheyl, Paul R. Schrater, Andrew J. Oxenham

Conformational Coupling between Receptor and Kinase Binding Sites through a Conserved Salt Bridge in a Signaling Complex Scaffold Protein

Davi R. Ortega, Guoya Mo, Kwangwoon Lee, Hongjun Zhou, Jerome Baudry, Frederick W. Dahlquist, Igor B. Zhulin

Structure-Based Function Prediction of Uncharacterized Protein Using Binding Sites Comparison

Janez Konc, Milan Hodošček, Mitja Ogrizek, Joanna Trykowska Konc, Dušanka Janežič

Substrate-Driven Mapping of the Degradome by Comparison of Sequence Logos

Julian E. Fuchs, Susanne von Grafenstein, Roland G. Huber, Christian Kramer, Klaus R. Liedl

Communication and Common Interest

Peter Godfrey-Smith, Manolo Martínez

A Neurocomputational Model of the Mismatch Negativity

Falk Lieder, Klaas E. Stephan, Jean Daunizeau, Marta I. Garrido, Karl J. Friston

Related Articles

  1. Correction: A Neurocomputational Model of the Mismatch Negativity

A Computational Model of Liver Iron Metabolism

Simon Mitchell, Pedro Mendes

Modeling Integrated Cellular Machinery Using Hybrid Petri-Boolean Networks

Natalie Berestovsky, Wanding Zhou, Deepak Nagrath, Luay Nakhleh

Systematically Differentiating Functions for Alternatively Spliced Isoforms through Integrating RNA-seq Data

Ridvan Eksi, Hong-Dong Li, Rajasree Menon, Yuchen Wen, Gilbert S. Omenn, Matthias Kretzler, Yuanfang Guan

Phosphorelays Provide Tunable Signal Processing Capabilities for the Cell

Varun B. Kothamachu, Elisenda Feliu, Carsten Wiuf, Luca Cardelli, Orkun S. Soyer

Linking Transcriptional Changes over Time in Stimulated Dendritic Cells to Identify Gene Networks Activated during the Innate Immune Response

Ashwini Patil, Yutaro Kumagai, Kuo-ching Liang, Yutaka Suzuki, Kenta Nakai

Mapping the Structural and Dynamical Features of Kinesin Motor Domains

Guido Scarabelli, Barry J. Grant