PLoS Computational Biology, Volume 8

Volume 8, Number 1, January 2012

Editorial

• 
  Rosemary Dickin, Chris James Hall, Laura K. Taylor, Andrew M. Collings, Ruth Nussinov, Philip E. Bourne:
  A Review of 2011 for PLoS Computational Biology.

Perspective

• 
  Ioannis Vlachos, Ad Aertsen, Arvind Kumar:
  Beyond Statistical Significance: Implications of Network Structure on Neuronal Activity.

Review

• 
  William Stafford Noble, Michael J. MacCoss:
  Computational and Statistical Analysis of Protein Mass Spectrometry Data.

Research Articles

• 
  Justin Hsia, William J. Holtz, Daniel C. Huang, Murat Arcak, Michel M. Maharbiz:
  A Feedback Quenched Oscillator Produces Turing Patterning with One Diffuser.
• 
  Yotam Luz, Maoz Shamir:
  Balancing Feed-Forward Excitation and Inhibition via Hebbian Inhibitory Synaptic Plasticity.
• 
  Patrick D. McMullen, Erin Z. Aprison, Peter B. Winter, Luis A. Nunes Amaral, Richard I. Morimoto, Ilya Ruvinsky:
  Macro-level Modeling of the Response of C. elegans Reproduction to Chronic Heat Stress.
• 
  Xinan Yang, Kelly Regan, Yong Huang, Qingbei Zhang, Jianrong Li, Tanguy Y. Seiwert, Ezra E. W. Cohen, H. Rosie Xing, Yves A. Lussier:
  Single Sample Expression-Anchored Mechanisms Predict Survival in Head and Neck Cancer.
• 
  Caterina A. M. La Porta, Stefano Zapperi, James P. Sethna:
  Senescent Cells in Growing Tumors: Population Dynamics and Cancer Stem Cells.
• 
  Justin R. Chumbley, Guillaume Flandin, Dominik R. Bach, Jean Daunizeau, Ernst Fehr, Raymond J. Dolan, Karl J. Friston:
  Learning and Generalization under Ambiguity: An fMRI Study.
• 
  J. Naudé, J. T. Paz, Hugues Berry, Bruno Delord:
  A Theory of Rate Coding Control by Intrinsic Plasticity Effects.
• 
  Fiona Achcar, Eduard J. Kerkhoven, Barbara M. Bakker, Michael P. Barrett, Rainer Breitling:
  Dynamic Modelling under Uncertainty: The Case of Trypanosoma brucei Energy Metabolism.
• 
  Michael N. Economo, John A. White:
  Membrane Properties and the Balance between Excitation and Inhibition Control Gamma-Frequency Oscillations Arising from Feedback Inhibition.
• 
  Max von Kleist, Philipp Metzner, Roland Marquet, Christof Schütte:
  HIV-1 Polymerase Inhibition by Nucleoside Analogs: Cellular- and Kinetic Parameters of Efficacy, Susceptibility and Resistance Selection.
• 
  Navneet Rai, Rajat Anand, Krishna Ramkumar, Varun Sreenivasan, Sugat Dabholkar, Kareenhalli V. Venkatesh, Mukund Thattai:
  Prediction by Promoter Logic in Bacterial Quorum Sensing.
• 
  Michael Seifert, André Gohr, Marc Strickert, Ivo Grosse:
  Parsimonious Higher-Order Hidden Markov Models for Improved Array-CGH Analysis with Applications to Arabidopsis thaliana.
• 
  Artturi Koivuniemi, Timo Vuorela, Petri T. Kovanen, Ilpo Vattulainen, Marja T. Hyvönen:
  Lipid Exchange Mechanism of the Cholesteryl Ester Transfer Protein Clarified by Atomistic and Coarse-grained Simulations.
• 
  Felix A. Krüger, John P. Overington:
  Global Analysis of Small Molecule Binding to Related Protein Targets.
• 
  Pablo Gainza, Kyle E. Roberts, Bruce Randall Donald:
  Protein Design Using Continuous Rotamers.
• 
  Eyal Akiva, Gilgi Friedlander, Zohar Itzhaki, Hanah Margalit:
  A Dynamic View of Domain-Motif Interactions.
• 
  Kyung Hyuk Kim, Herbert M. Sauro:
  Adjusting Phenotypes by Noise Control.
• 
  Juilee Thakar, Ashutosh K. Pathak, Lisa Murphy, Réka Albert, Isabella M. Cattadori:
  Network Model of Immune Responses Reveals Key Effectors to Single and Co-infection Dynamics by a Respiratory Bacterium and a Gastrointestinal Helminth.
• 
  Ken Takiyama, Masato Okada:
  Maximization of Learning Speed in the Motor Cortex Due to Neuronal Redundancy.
• 
  Iain H. Moal, Paul A. Bates:
  Kinetic Rate Constant Prediction Supports the Conformational Selection Mechanism of Protein Binding.
• 
  Weihong Zhang, Debabani Ganguly, Jianhan Chen:
  Residual Structures, Conformational Fluctuations, and Electrostatic Interactions in the Synergistic Folding of Two Intrinsically Disordered Proteins.
• 
  Shuoguo Wang, Lakshmi Chandrasekaran, Fernando R. Fernandez, John A. White, Carmen C. Canavier:
  Short Conduction Delays Cause Inhibition Rather than Excitation to Favor Synchrony in Hybrid Neuronal Networks of the Entorhinal Cortex.
• 
  (Withdrawn) Multi-scale Inference of Interaction Rules in Animal Groups Using Bayesian Model Selection.
• 
  Christian Meisel, Alexander Storch, Susanne Hallmeyer-Elgner, Ed Bullmore, Thilo Gross:
  Failure of Adaptive Self-Organized Criticality during Epileptic Seizure Attacks.
• 
  Karl J. Friston, Tamara Shiner, Thomas H. B. FitzGerald, Joseph M. Galea, Rick A. Adams, Harriet R. Brown, Raymond J. Dolan, Rosalyn J. Moran, Klaas Enno Stephan, Sven Bestmann:
  Dopamine, Affordance and Active Inference.
• 
  João A. N. Filipe, Richard C. Cobb, Ross K. Meentemeyer, Christopher A. Lee, Yana S. Valachovic, Alex R. Cook, David M. Rizzo, Christopher A. Gilligan:
  Landscape Epidemiology and Control of Pathogens with Cryptic and Long-Distance Dispersal: Sudden Oak Death in Northern Californian Forests.
• 
  Benjamin Pfeuty, Jean-François Bodart, Ralf Blossey, Marc Lefranc:
  A Dynamical Model of Oocyte Maturation Unveils Precisely Orchestrated Meiotic Decisions.
• 
  Nicoló Fusi, Oliver Stegle, Neil D. Lawrence:
  Joint Modelling of Confounding Factors and Prominent Genetic Regulators Provides Increased Accuracy in Genetical Genomics Studies.
• 
  Bart Baddeley, Paul Graham, Philip Husbands, Andrew Philippides:
  A Model of Ant Route Navigation Driven by Scene Familiarity.
• 
  Yu-Kang Cheng, Rameen Beroukhim, Ross L. Levine, Ingo K. Mellinghoff, Eric C. Holland, Franziska Michor:
  A Mathematical Methodology for Determining the Temporal Order of Pathway Alterations Arising during Gliomagenesis.
• 
  Bambang S. Adiwijaya, Tara L. Kieffer, Joshua Henshaw, Karen Eisenhauer, Holly Kimko, John J. Alam, Robert S. Kauffman, Varun Garg:
  A Viral Dynamic Model for Treatment Regimens with Direct-acting Antivirals for Chronic Hepatitis C Infection.

Volume 8, Number 2, February 2012

Reviews

• 
  Purvesh Khatri, Marina Sirota, Atul J. Butte:
  Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges.
• 
  Marjet Elemans, Nafisa-Katrin Seich al Basatena, Becca Asquith:
  The Efficiency of the Human CD8+ T Cell Response: How Should We Quantify It, What Determines It, and Does It Matter?

Research Articles

• 
  Jing-yu Yu, Nan Zheng, Gerta Mane, Kyoung Ah Min, Juan P. Hinestroza, Huaning Zhu, Kathleen A. Stringer, Gus R. Rosania:
  A Cell-based Computational Modeling Approach for Developing Site-Directed Molecular Probes.
• 
  Vered Kunik, Bjoern Peters, Yanay Ofran:
  Structural Consensus among Antibodies Defines the Antigen Binding Site.
• 
  Trine Krogh-Madsen, Geoffrey W. Abbott, David J. Christini:
  Effects of Electrical and Structural Remodeling on Atrial Fibrillation Maintenance: A Simulation Study.
• 
  Santiago Treviño III, Yudong Sun, Tim F. Cooper, Kevin E. Bassler:
  Robust Detection of Hierarchical Communities from Escherichia coli Gene Expression Data.
• 
  Cai Chen, David Frankhouser, Ralf Bundschuh:
  Comparison of Insertional RNA Editing in Myxomycetes.
• 
  Yukikazu Hidaka, Cheol E. Han, Steven L. Wolf, Carolee J. Winstein, Nicolas Schweighofer:
  Use It and Improve It or Lose It: Interactions between Arm Function and Use in Humans Post-stroke.
• 
  António Roldão, Maria Candida M. Mellado, J. C. Lima, Manuel J. T. Carrondo, Paula M. Alves, Rui Oliveira:
  On the Effect of Thermodynamic Equilibrium on the Assembly Efficiency of Complex Multi-Layered Virus-Like Particles (VLP): the Case of Rotavirus VLP.
• 
  Giulio Quarta, Ken Sin, Tamar Schlick:
  Dynamic Energy Landscapes of Riboswitches Help Interpret Conformational Rearrangements and Function.
• 
  Shingo Iwami, Hiroshi Haeno, Franziska Michor:
  A Race between Tumor Immunoescape and Genome Maintenance Selects for Optimum Levels of (epi)genetic Instability.
• 
  Yael Baran, Eran Halperin:
  Joint Analysis of Multiple Metagenomic Samples.
• 
  Denis Menshykau, Conradin Kraemer, Dagmar Iber:
  Branch Mode Selection during Early Lung Development.
• 
  K. Sriram, Maria Rodriguez-Fernandez, Francis J. Doyle III:
  Modeling Cortisol Dynamics in the Neuro-endocrine Axis Distinguishes Normal, Depression, and Post-traumatic Stress Disorder (PTSD) in Humans.
• 
  Markus Hartenfeller, Heiko Zettl, Miriam Walter, Matthias Rupp, Felix Reisen, Ewgenij Proschak, Sascha Weggen, Holger Stark, Gisbert Schneider:
  DOGS: Reaction-Driven de novo Design of Bioactive Compounds.
• 
  Johannes Rüter, Nicolas Marcille, Henning Sprekeler, Wulfram Gerstner, Michael H. Herzog:
  Paradoxical Evidence Integration in Rapid Decision Processes.
• 
  Paul D. Thomas, Valerie Wood, Christopher J. Mungall, Suzanna E. Lewis, Judith A. Blake:
  On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report.
• 
  Vincent Mirabet, Fabrice Besnard, Teva Vernoux, Arezki Boudaoud:
  Noise and Robustness in Phyllotaxis.
• 
  Priyanka Prakash, Abdallah Sayyed-Ahmad, Alemayehu A. Gorfe:
  The Role of Conserved Waters in Conformational Transitions of Q61H K-ras.
• 
  Daichi Shigemizu, Zhenjun Hu, Jui-Hung Hung, Chia-Ling Huang, Yajie Wang, Charles DeLisi:
  Using Functional Signatures to Identify Repositioned Drugs for Breast, Myelogenous Leukemia and Prostate Cancer.
• 
  Christoph Börgers, Giovanni Talei Franzesi, Fiona E. N. LeBeau, Edward S. Boyden, Nancy Kopell:
  Minimal Size of Cell Assemblies Coordinated by Gamma Oscillations.
• 
  Theo Arts, Joost Lumens, Wilco Kroon, Tammo Delhaas:
  Control of Whole Heart Geometry by Intramyocardial Mechano-Feedback: A Model Study.
• 
  Iraj Hosseini, Feilim Mac Gabhann:
  Multi-Scale Modeling of HIV Infection in vitro and APOBEC3G-Based Anti-Retroviral Therapy.
• 
  Rodrigo Freire Oliveira, Myungsook Kim, Kim T. Blackwell:
  Subcellular Location of PKA Controls Striatal Plasticity: Stochastic Simulations in Spiny Dendrites.
• 
  Camille Morvan, Laurence T. Maloney:
  Human Visual Search Does Not Maximize the Post-Saccadic Probability of Identifying Targets.
• 
  Yu Wu, Yao Lu, Weiqiang Chen, Jianping Fu, Rong Fan:
  In silico Experimentation of Glioma Microenvironment Development and Anti-tumor Therapy.
• 
  István Miklós, Zoltán Zádori:
  Positive Evolutionary Selection of an HD Motif on Alzheimer Precursor Protein Orthologues Suggests a Functional Role.
• 
  Pranidhi Sood, Robert J. Johnston Jr., Edo Kussell:
  Stochastic De-repression of Rhodopsins in Single Photoreceptors of the Fly Retina.
• 
  Steven John Lade, Thilo Gross:
  Early Warning Signals for Critical Transitions: A Generalized Modeling Approach.
• 
  Ali R. Zomorrodi, Costas D. Maranas:
  OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities.
• 
  Nadav Rappoport, Michal Linial:
  Viral Proteins Acquired from a Host Converge to Simplified Domain Architectures.
• 
  Ekaterina Kotelnikova, Maria A. Shkrob, Mikhail A. Pyatnitskiy, Alessandra Ferlini, Nikolai Daraselia:
  Novel Approach to Meta-Analysis of Microarray Datasets Reveals Muscle Remodeling-related Drug Targets and Biomarkers in Duchenne Muscular Dystrophy.
• 
  Kaustubh Supekar, Vinod Menon:
  Developmental Maturation of Dynamic Causal Control Signals in Higher-Order Cognition: A Neurocognitive Network Model.
• 
  Xueyang Feng, You Xu, Yixin Chen, Yinjie J. Tang:
  Integrating Flux Balance Analysis into Kinetic Models to Decipher the Dynamic Metabolism of Shewanella oneidensis MR-1.

Volume 8, Number 3, March 2012

Editorials

• 
  Anthony C. Fletcher, Philip E. Bourne:
  Ten Simple Rules for Starting a Company.
• 
  Shoshana J. Wodak, Daniel Mietchen, Andrew M. Collings, Robert B. Russell, Philip E. Bourne:
  Topic Pages: PLoS Computational Biology Meets Wikipedia.

Education

• 
  Marc S. Sherman, Barak A. Cohen:
  Thermodynamic State Ensemble Models of cis-Regulation.

Research Articles

• 
  Gustavo Deco, Etienne Hugues:
  Neural Network Mechanisms Underlying Stimulus Driven Variability Reduction.
• 
  Tyler J. Glembo, Daniel W. Farrell, Z. Nevin Gerek, M. F. Thorpe, S. Banu Ozkan:
  Collective Dynamics Differentiates Functional Divergence in Protein Evolution.
• 
  Yu-Yao Tseng, Suzanne M. Hunt, Christian Heintzen, Susan K. Crosthwaite, Jean-Marc Schwartz:
  Comprehensive Modelling of the Neurospora Circadian Clock and Its Temperature Compensation.
• 
  Spiro P. Pantazatos, Ardesheer Talati, Paul Pavlidis, Joy Hirsch:
  Decoding Unattended Fearful Faces with Whole-Brain Correlations: An Approach to Identify Condition-Dependent Large-Scale Functional Connectivity.
• 
  Jesse A. Gillis, Paul Pavlidis:
  "Guilt by Association" Is the Exception Rather Than the Rule in Gene Networks.
• 
  Rémi Lehe, Oskar Hallatschek, Luca Peliti:
  The Rate of Beneficial Mutations Surfing on the Wave of a Range Expansion.
• 
  Graciano Dieck Kattas, Xiaoke Xu, Michael Small:
  Dynamical Modeling of Collective Behavior from Pigeon Flight Data: Flock Cohesion and Dispersion.
• 
  James Trousdale, Yu Hu, Eric Shea-Brown, Kresimir Josic:
  Impact of Network Structure and Cellular Response on Spike Time Correlations.
• 
  Ana Duarte, E. Scholtens, Franz J. Weissing:
  Implications of Behavioral Architecture for the Evolution of Self-Organized Division of Labor.
• 
  Christian Keck, Cristina Savin, Jörg Lücke:
  Feedforward Inhibition and Synaptic Scaling - Two Sides of the Same Coin?
• 
  Giulia Morra, Raffaello Potestio, Cristian Micheletti, Giorgio Colombo:
  Corresponding Functional Dynamics across the Hsp90 Chaperone Family: Insights from a Multiscale Analysis of MD Simulations.
• 
  Kevin M. Aquino, Mark M. Schira, Peter A. Robinson, Peter M. Drysdale, Michael Breakspear:
  Hemodynamic Traveling Waves in Human Visual Cortex.
• 
  Frederik Graw, Roland R. Regoes:
  Influence of the Fibroblastic Reticular Network on Cell-Cell Interactions in Lymphoid Organs.
• 
  Demian Battaglia, Annette Witt, Fred Wolf, Theo Geisel:
  Dynamic Effective Connectivity of Inter-Areal Brain Circuits.
• 
  Mehdi Moussaïd, Elsa G. Guillot, Mathieu Moreau, Jérôme Fehrenbach, Olivier Chabiron, Samuel Lemercier, Julien Pettré, Cécile Appert-Rolland, Pierre Degond, Guy Theraulaz:
  Traffic Instabilities in Self-Organized Pedestrian Crowds.
• 
  Meghan K. Driscoll, Colin McCann, Rael Kopace, Tess Homan, John T. Fourkas, Carole Parent, Wolfgang Losert:
  Cell Shape Dynamics: From Waves to Migration.
• 
  Jacob D. Durrant, James Andrew McCammon:
  AutoClickChem: Click Chemistry in Silico.
• 
  Siu-Fai Chow, Stuart D. Wick, Hermann Riecke:
  Neurogenesis Drives Stimulus Decorrelation in a Model of the Olfactory Bulb.
• 
  Mark G. F. Sun, Martin Sikora, Michael Costanzo, Charles Boone, Philip M. Kim:
  Network Evolution: Rewiring and Signatures of Conservation in Signaling.
• 
  Alexander R. Macalalad, Michael C. Zody, Patrick Charlebois, Niall J. Lennon, Ruchi M. Newman, Christine M. Malboeuf, Elizabeth M. Ryan, Christian L. Boutwell, Karen A. Power, Doug E. Brackney, Kendra N. Pesko, Joshua Z. Levin, Gregory D. Ebel, Todd M. Allen, Bruce W. Birren, Matthew R. Henn:
  Highly Sensitive and Specific Detection of Rare Variants in Mixed Viral Populations from Massively Parallel Sequence Data.
• 
  Elif Nihal Korkmaz, Ruth Nussinov, Türkan Haliloglu:
  Conformational Control of the Binding of the Transactivation Domain of the MLL Protein and c-Myb to the KIX Domain of CREB.
• 
  Leonard Kaczmarek:
  Gradients and Modulation of K⁺ Channels Optimize Temporal Accuracy in Networks of Auditory Neurons.
• 
  Ying-Ying Jiang, De-Xin Kong, Tao Qin, Xiao Li, Gustavo Caetano-Anollés, Hong-yu Zhang:
  The Impact of Oxygen on Metabolic Evolution: A Chemoinformatic Investigation.
• 
  Martin Lindén, Pierre Sens, Rob Phillips:
  Entropic Tension in Crowded Membranes.
• 
  Hideaki Shimazaki, Shun-ichi Amari, Emery N. Brown, Sonja Grün:
  State-Space Analysis of Time-Varying Higher-Order Spike Correlation for Multiple Neural Spike Train Data.
• 
  Cyril F. Reboul, Grischa R. Meyer, Benjamin T. Porebski, Natalie A. Borg, Ashley M. Buckle:
  Epitope Flexibility and Dynamic Footprint Revealed by Molecular Dynamics of a pMHC-TCR Complex.
• 
  Quentin J. M. Huys, Neir Eshel, Elizabeth J. P. O'Nions, Luke Sheridan, Peter Dayan, Jonathan P. Roiser:
  Bonsai Trees in Your Head: How the Pavlovian System Sculpts Goal-Directed Choices by Pruning Decision Trees.
• 
  Gabriel E. Leventhal, Roger D. Kouyos, Tanja Stadler, Viktor von Wyl, Sabine Yerly, Jürg Böni, Cristina Cellerai, Thomas Klimkait, Huldrych F. Günthard, Sebastian Bonhoeffer:
  Inferring Epidemic Contact Structure from Phylogenetic Trees.
• 
  Carlos J. Melián, David Alonso, Stefano Allesina, Richard S. Condit, Rampal S. Etienne:
  Does Sex Speed Up Evolutionary Rate and Increase Biodiversity?
• 
  Iain G. Johnston, Bernadett Gaal, Ricardo Pires das Neves, Tariq Enver, Francisco J. Iborra, Nick S. Jones:
  Mitochondrial Variability as a Source of Extrinsic Cellular Noise.
• 
  Marc Hafner, Heinz Koeppl, Didier Gonze:
  Effect of Network Architecture on Synchronization and Entrainment Properties of the Circadian Oscillations in the Suprachiasmatic Nucleus.
• 
  Travis J. A. Craddock, Jack A. Tuszynski, Stuart R. Hameroff:
  Cytoskeletal Signaling: Is Memory Encoded in Microtubule Lattices by CaMKII Phosphorylation?
• 
  Sang O. K. Song, Justin Hogg, Zhi-Yong Peng, Robert S. Parker, John A. Kellum, Gilles Clermont:
  Ensemble Models of Neutrophil Trafficking in Severe Sepsis.
• 
  David M. Richards, Antje M. Hempel, Klas Flärdh, Mark J. Buttner, Martin Howard:
  Mechanistic Basis of Branch-Site Selection in Filamentous Bacteria.
• 
  Ken T. D. Eames, Natasha L. Tilston, Ellen Brooks-Pollock, W. John Edmunds:
  Measured Dynamic Social Contact Patterns Explain the Spread of H1N1v Influenza.
• 
  Xiaodong Pang, Huan-Xiang Zhou:
  A Common Model for Cytokine Receptor Activation: Combined Scissor-Like Rotation and Self-Rotation of Receptor Dimer Induced by Class I Cytokine.
• 
  Stefano Mostarda, David Gfeller, Francesco Rao:
  Beyond the Binding Site: The Role of the β2 - β3 Loop and Extra-Domain Structures in PDZ Domains.
• 
  András Lörincz, Zsolt Palotai, Gábor Szirtes:
  Efficient Sparse Coding in Early Sensory Processing: Lessons from Signal Recovery.
• 
  Kendra S. Burbank, Gabriel Kreiman:
  Depression-Biased Reverse Plasticity Rule Is Required for Stable Learning at Top-Down Connections.
• 
  Mathieu Lemay, Enno de Lange, Jan P. Kucera:
  Uncovering the Dynamics of Cardiac Systems Using Stochastic Pacing and Frequency Domain Analyses.
• 
  Dimitrios V. Vavoulis, Volko A. Straub, John A. D. Aston, Jianfeng Feng:
  A Self-Organizing State-Space-Model Approach for Parameter Estimation in Hodgkin-Huxley-Type Models of Single Neurons.
• 
  Athanasius F. M. Marée, Verônica A. Grieneisen, Leah Edelstein-Keshet:
  How Cells Integrate Complex Stimuli: The Effect of Feedback from Phosphoinositides and Cell Shape on Cell Polarization and Motility.
• 
  Nicholas Furnham, Ian Sillitoe, Gemma L. Holliday, Alison L. Cuff, Roman A. Laskowski, Christine A. Orengo, Janet M. Thornton:
  Exploring the Evolution of Novel Enzyme Functions within Structurally Defined Protein Superfamilies.
• 
  Ruben Coen Cagli, Peter Dayan, Odelia Schwartz:
  Cortical Surround Interactions and Perceptual Salience via Natural Scene Statistics.
• 
  Hongyan Song, John Parkinson:
  Modelling the Self-Assembly of Elastomeric Proteins Provides Insights into the Evolution of Their Domain Architectures.
• 
  Deeptak Verma, Donald J. Jacobs, Dennis R. Livesay:
  Changes in Lysozyme Flexibility upon Mutation Are Frequent, Large and Long-Ranged.
• 
  Jorg J. A. Calis, Rob J. De Boer, Can Kesmir:
  Degenerate T-cell Recognition of Peptides on MHC Molecules Creates Large Holes in the T-cell Repertoire.
• 
  Stefan J. Jol, Anne Kümmel, Marco Terzer, Jörg Stelling, Matthias Heinemann:
  System-Level Insights into Yeast Metabolism by Thermodynamic Analysis of Elementary Flux Modes.
• 
  Mathieu Andraud, Olivier Lejeune, Jammbe Z. Musoro, Benson Ogunjimi, Philippe Beutels, Niel Hens:
  Living on Three Time Scales: The Dynamics of Plasma Cell and Antibody Populations Illustrated for Hepatitis A Virus.

Volume 8, Number 4, April 2012

Perspective

• 
  Daniel Lobo, Wendy S. Beane, Michael Levin:
  Modeling Planarian Regeneration: A Primer for Reverse-Engineering the Worm.

Review

• 
  Christos A. Ouzounis:
  Rise and Demise of Bioinformatics? Promise and Progress.

Research Articles

• 
  Claudia Clopath, Jean-Pierre Nadal, Nicolas Brunel:
  Storage of Correlated Patterns in Standard and Bistable Purkinje Cell Models.
• 
  Christopher C. Poirier, Win Pin Ng, Douglas N. Robinson, Pablo A. Iglesias:
  Deconvolution of the Cellular Force-Generating Subsystems that Govern Cytokinesis Furrow Ingression.
• 
  Boris V. Schmid, Mirjam E. Kretzschmar:
  Determinants of Sexual Network Structure and Their Impact on Cumulative Network Measures.
• 
  Suzanne Gaudet, Sabrina L. Spencer, William W. Chen, Peter K. Sorger:
  Exploring the Contextual Sensitivity of Factors that Determine Cell-to-Cell Variability in Receptor-Mediated Apoptosis.
• 
  Karen van Eunen, José A. L. Kiewiet, Hans V. Westerhoff, Barbara M. Bakker:
  Testing Biochemistry Revisited: How In Vivo Metabolism Can Be Understood from In Vitro Enzyme Kinetics.
• 
  Dina Zhabinskaya, Craig J. Benham:
  Theoretical Analysis of Competing Conformational Transitions in Superhelical DNA.
• 
  Judith Reichmann, James H. Crichton, Monika J. Madej, Mary Taggart, Philippe Gautier, Jose Luis Garcia-Perez, Richard R. Meehan, Ian R. Adams:
  Microarray Analysis of LTR Retrotransposon Silencing Identifies Hdac1 as a Regulator of Retrotransposon Expression in Mouse Embryonic Stem Cells.
• 
  Kyriaki Sidiropoulou, Panayiota Poirazi:
  Predictive Features of Persistent Activity Emergence in Regular Spiking and Intrinsic Bursting Model Neurons.
• 
  Jeffrey V. Wong, Bochong Li, Lingchong You:
  Tension and Robustness in Multitasking Cellular Networks.
• 
  Vanni Bucci, Serena Bradde, Giulio Biroli, João B. Xavier:
  Social Interaction, Noise and Antibiotic-Mediated Switches in the Intestinal Microbiota.
• 
  Mahmoud Moradi, Volodymyr Babin, Christopher Roland, Celeste Sagui:
  Are Long-Range Structural Correlations Behind the Aggregration Phenomena of Polyglutamine Diseases?
• 
  Raoul-Martin Memmesheimer, Marc Timme:
  Non-Additive Coupling Enables Propagation of Synchronous Spiking Activity in Purely Random Networks.
• 
  Rogier Braakman, Eric Smith:
  The Emergence and Early Evolution of Biological Carbon-Fixation.
• 
  Yong Wang, Chun Tang, Erkang Wang, Jin Wang:
  Exploration of Multi-State Conformational Dynamics and Underlying Global Functional Landscape of Maltose Binding Protein.
• 
  Jufang Shan, George Khelashvili, Sayan Mondal, Ernest L. Mehler, Harel Weinstein:
  Ligand-Dependent Conformations and Dynamics of the Serotonin 5-HT_2A Receptor Determine Its Activation and Membrane-Driven Oligomerization Properties.
• 
  Ariel D. Weinberger, Christine L. Sun, Mateusz M. Plucinski, Vincent J. Denef, Brian C. Thomas, Philippe Horvath, Rodolphe Barrangou, Michael S. Gilmore, Wayne M. Getz, Jillian F. Banfield:
  Persisting Viral Sequences Shape Microbial CRISPR-based Immunity.
• 
  Kyle E. Roberts, Patrick R. Cushing, Prisca Boisguerin, Dean R. Madden, Bruce Randall Donald:
  Computational Design of a PDZ Domain Peptide Inhibitor that Rescues CFTR Activity.
• 
  Lars Steinbrück, Alice Carolyn McHardy:
  Inference of Genotype-Phenotype Relationships in the Antigenic Evolution of Human Influenza A (H3N2) Viruses.
• 
  Rebekah C. Evans, Teresa Morera-Herreras, Yihui Cui, Kai Du, Tom Sheehan, Jeanette Hellgren Kotaleski, Laurent Venance, Kim T. Blackwell:
  The Effects of NMDA Subunit Composition on Calcium Influx and Spike Timing-Dependent Plasticity in Striatal Medium Spiny Neurons.
• 
  Caroline O. Buckee, Mario Recker:
  Evolution of the Multi-Domain Structures of Virulence Genes in the Human Malaria Parasite, Plasmodium falciparum.
• 
  Tom Putzeys, Matthias Bethge, Felix A. Wichmann, Johan Wagemans, Robbe Goris:
  A New Perceptual Bias Reveals Suboptimal Population Decoding of Sensory Responses.
• 
  Ben S. Cooper, Theodore Kypraios, Rahul Batra, Duncan Wyncoll, Olga Tosas, Jonathan D. Edgeworth:
  Quantifying Type-Specific Reproduction Numbers for Nosocomial Pathogens: Evidence for Heightened Transmission of an Asian Sequence Type 239 MRSA Clone.
• 
  Yuguo Yu, Adam P. Hill, David A. McCormick:
  Warm Body Temperature Facilitates Energy Efficient Cortical Action Potentials.
• 
  Yasuhiro Tsubo, Yoshikazu Isomura, Tomoki Fukai:
  Power-Law Inter-Spike Interval Distributions Infer a Conditional Maximization of Entropy in Cortical Neurons.
• 
  J. Lucas McKay, Lena H. Ting:
  Optimization of Muscle Activity for Task-Level Goals Predicts Complex Changes in Limb Forces across Biomechanical Contexts.
• 
  João F. Matias Rodrigues, Daniel J. Rankin, Valentina Rossetti, Andreas Wagner, Homayoun C. Bagheri:
  Differences in Cell Division Rates Drive the Evolution of Terminal Differentiation in Microbes.
• 
  Martial L. Ndeffo Mbah, Jingzhou Liu, Chris T. Bauch, Yonas I. Tekel, Jan Medlock, Lauren Ancel Meyers, Alison P. Galvani:
  The Impact of Imitation on Vaccination Behavior in Social Contact Networks.
• 
  Samuel V. Scarpino, Nedialko B. Dimitrov, Lauren Ancel Meyers:
  Optimizing Provider Recruitment for Influenza Surveillance Networks.
• 
  Yihwa Kim, Robert Sinclair, Nol Chindapol, Jaap A. Kaandorp, Erik De Schutter:
  Geometric Theory Predicts Bifurcations in Minimal Wiring Cost Trees in Biology Are Flat.
• 
  Josef Ladenbauer, Moritz Augustin, LieJune Shiau, Klaus Obermayer:
  Impact of Adaptation Currents on Synchronization of Coupled Exponential Integrate-and-Fire Neurons.
• 
  Daisuke Hoshino, Naohiko Koshikawa, Takashi Suzuki, Vito Quaranta, Alissa M. Weaver, Motoharu Seiki, Kazuhisa Ichikawa:
  Establishment and Validation of Computational Model for MT1-MMP Dependent ECM Degradation and Intervention Strategies.
• 
  Dmitry Nevozhay, Rhys M. Adams, Elizabeth Van Itallie, Matthew R. Bennett, Gábor Balázsi:
  Mapping the Environmental Fitness Landscape of a Synthetic Gene Circuit.
• 
  Antoine Baker, Benjamin Audit, Chun-Long Chen, Benoit Moindrot, Antoine Leleu, Guillaume Guilbaud, Aurélien Rappailles, Cédric Vaillant, Arach Goldar, Fabien Mongelard, Yves D'Aubenton-Carafa, Olivier Hyrien, Claude Thermes, Alain Arneodo:
  Replication Fork Polarity Gradients Revealed by Megabase-Sized U-Shaped Replication Timing Domains in Human Cell Lines.
• 
  L. Niels Cornelisse, Evgeni Tsivtsivadze, Marieke Meijer, Tjeerd Dijkstra, Tom Heskes, Matthijs Verhage:
  Molecular Machines in the Synapse: Overlapping Protein Sets Control Distinct Steps in Neurosecretion.
• 
  Chris T. Bauch, Samit Bhattacharyya:
  Evolutionary Game Theory and Social Learning Can Determine How Vaccine Scares Unfold.
• 
  Anna Bauer-Mehren, Erik M. van Mulligen, Paul Avillach, María del Carmen Carrascosa, Ricard García-Serna, Janet Piñero González, Bharat Singh, Pedro Lopes, José Luís Oliveira, Gayo Diallo, Ernst Ahlberg Helgee, Scott Boyer, Jordi Mestres, Ferran Sanz, Jan A. Kors, Laura Inés Furlong:
  Automatic Filtering and Substantiation of Drug Safety Signals.
• 
  Rachael Hageman Blair, Daniel J. Kliebenstein, Gary A. Churchill:
  What Can Causal Networks Tell Us about Metabolic Pathways?
• 
  Yunpeng Wang, Arne B. Gjuvsland, Jon Olav Vik, Nicolas Smith, Peter J. Hunter, Stig W. Omholt:
  Parameters in Dynamic Models of Complex Traits are Containers of Missing Heritability.
• 
  Trang T. Vu, Sergey M. Stolyar, Grigoriy E. Pinchuk, Eric A. Hill, Leo A. Kucek, Roslyn N. Brown, Mary S. Lipton, Andrei Osterman, Jim K. Fredrickson, Allan E. Konopka, Alexander S. Beliaev, Jennifer L. Reed:
  Genome-Scale Modeling of Light-Driven Reductant Partitioning and Carbon Fluxes in Diazotrophic Unicellular Cyanobacterium Cyanothece sp. ATCC 51142.
• 
  J. Dongun Kim, Agustina Rodriguez-Granillo, David A. Case, Vikas Nanda, Paul G. Falkowski:
  Energetic Selection of Topology in Ferredoxins.
• 
  Onur Sakarya, Heinz Breu, Milan Radovich, Yongzhi Chen, Yulei N. Wang, Catalin C. Barbacioru, Sowmi Utiramerur, Penn P. Whitley, Joel P. Brockman, Paolo Vatta, Zheng Zhang, Liviu Popescu, Matthew W. Muller, Vidya Kudlingar, Nriti Garg, Chieh-Yuan Li, Benjamin S. Kong, John P. Bodeau, Robert C. Nutter, Jian Gu, Kelli S. Bramlett, Jeffrey K. Ichikawa, Fiona C. Hyland, Asim S. Siddiqui:
  RNA-Seq Mapping and Detection of Gene Fusions with a Suffix Array Algorithm.
• 
  Simone Furini, Carmen Domene:
  On Conduction in a Bacterial Sodium Channel.

Volume 8, Number 5, May 2012

Message from ISCB

• 
  Justin Mullins, B. J. Morrison McKay:
  International Society for Computational Biology Honours Gunnar von Heijne and Ziv Bar-Joseph with Top Bioinformatics/Computational Biology Awards for 2012.

Education Articles

• 
  Miguel Arenas:
  Simulation of Molecular Data under Diverse Evolutionary Scenarios.
• 
  Reed B. Jacob, Timothy L. Andersen, Owen M. McDougal:
  Accessible High-Throughput Virtual Screening Molecular Docking Software for Students and Educators.
• 
  Saad Mneimneh:
  Crossing Over...Markov Meets Mendel.

Research Articles

• 
  Sten Rüdiger, Peter Jung, Jian-Wei Shuai:
  Termination of Ca²⁺ Release for Clustered IP₃R Channels.
• 
  Claude Gérard, Albert Goldbeter:
  Entrainment of the Mammalian Cell Cycle by the Circadian Clock: Modeling Two Coupled Cellular Rhythms.
• 
  Alexander V. Favorov, Loris Mularoni, Leslie M. Cope, Yulia A. Medvedeva, Andrey A. Mironov, Vsevolod J. Makeev, Sarah J. Wheelan:
  Exploring Massive, Genome Scale Datasets with the GenometriCorr Package.
• 
  David N. LeBard, Jérôme Hénin, Roderic G. Eckenhoff, Michael L. Klein, Grace Brannigan:
  General Anesthetics Predicted to Block the GLIC Pore with Micromolar Affinity.
• 
  Nives Skunca, Adrian M. Altenhoff, Christophe Dessimoz:
  Quality of Computationally Inferred Gene Ontology Annotations.
• 
  Hyung-June Woo, Ravi Vijaya Satya, Jaques Reifman:
  Thermodynamic Basis for the Emergence of Genomes during Prebiotic Evolution.
• 
  Adam Alexander Thil Smith, Eugeni Belda, Alain Viari, Claudine Médigue, David Vallenet:
  The CanOE Strategy: Integrating Genomic and Metabolic Contexts across Multiple Prokaryote Genomes to Find Candidate Genes for Orphan Enzymes.
• 
  Macarena Toll-Riera, David L. Bostick, M. Mar Albà, Joshua B. Plotkin:
  Structure and Age Jointly Influence Rates of Protein Evolution.
• 
  Wei Tang, Steven L. Bressler, Chad M. Sylvester, Gordon L. Shulman, Maurizio Corbetta:
  Measuring Granger Causality between Cortical Regions from Voxelwise fMRI BOLD Signals with LASSO.
• 
  Sara-Jane Dunn, Paul L. Appleton, Scott A. Nelson, Inke S. Näthke, David Gavaghan, James M. Osborne:
  A Two-Dimensional Model of the Colonic Crypt Accounting for the Role of the Basement Membrane and Pericryptal Fibroblast Sheath.
• 
  Udo A. Ernst, Sunita Mandon, Nadja Schinkel-Bielefeld, Simon D. Neitzel, Andreas K. Kreiter, Klaus R. Pawelzik:
  Optimality of Human Contour Integration.
• 
  Qi Ma, Dan V. Nicolau Jr., Philip K. Maini, Richard M. Berry, Fan Bai:
  Conformational Spread in the Flagellar Motor Switch: A Model Study.
• 
  Young-Ah Rho, Steven A. Prescott:
  Identification of Molecular Pathologies Sufficient to Cause Neuropathic Excitability in Primary Somatosensory Afferents Using Dynamical Systems Theory.
• 
  Rafal Mostowy, Roger D. Kouyos, Ilka Hoof, Trevor Hinkley, Mojgan Haddad, Jeannette M. Whitcomb, Christos J. Petropoulos, Can Kesmir, Sebastian Bonhoeffer:
  Estimating the Fitness Cost of Escape from HLA Presentation in HIV-1 Protease and Reverse Transcriptase.
• 
  Brittany Burton, Michael T. Zimmermann, Robert L. Jernigan, Yongmei Wang:
  A Computational Investigation on the Connection between Dynamics Properties of Ribosomal Proteins and Ribosome Assembly.
• 
  Bree Cummins, Ricardo Cortez, Ivo M. Foppa, Justin Walbeck, James Mac Hyman:
  A Spatial Model of Mosquito Host-Seeking Behavior.
• 
  M. S. Vijayabaskar, Saraswathi Vishveshwara:
  Insights into the Fold Organization of TIM Barrel from Interaction Energy Based Structure Networks.
• 
  H. H. L. M. Goossens, A. John van Opstal:
  Optimal Control of Saccades by Spatial-Temporal Activity Patterns in the Monkey Superior Colliculus.
• 
  Christof Winter, Glen Kristiansen, Stephan Kersting, Janine Roy, Daniela Aust, Thomas Knösel, Petra Rümmele, Beatrix Jahnke, Vera Hentrich, Felix Rückert, Marco Niedergethmann, Wilko Weichert, Marcus Bahra, Hans J. Schlitt, Utz Settmacher, Helmut Friess, Markus W. Büchler, Hans-Detlev Saeger, Michael Schroeder, Christian Pilarsky, Robert Grützmann:
  Google Goes Cancer: Improving Outcome Prediction for Cancer Patients by Network-Based Ranking of Marker Genes.
• 
  Kevin K. Chiou, Lars Hufnagel, Boris I. Shraiman:
  Mechanical Stress Inference for Two Dimensional Cell Arrays.
• 
  Adrian M. Altenhoff, Romain A. Studer, Marc Robinson-Rechavi, Christophe Dessimoz:
  Resolving the Ortholog Conjecture: Orthologs Tend to Be Weakly, but Significantly, More Similar in Function than Paralogs.
• 
  Ilka Hoof, Debbie van Baarle, William H. Hildebrand, Can Kesmir:
  Proteome Sampling by the HLA Class I Antigen Processing Pathway.
• 
  Rasmus Agren, Sergio Bordel, Adil Mardinoglu, Natapol Pornputtapong, Intawat Nookaew, Jens Nielsen:
  Reconstruction of Genome-Scale Active Metabolic Networks for 69 Human Cell Types and 16 Cancer Types Using INIT.
• 
  Ivan Raikov, Erik De Schutter:
  The Layer-Oriented Approach to Declarative Languages for Biological Modeling.
• 
  Julia H. Downes, Mark W. Hammond, Dimitris Xydas, Matthew C. Spencer, Victor M. Becerra, Kevin Warwick, Benjamin J. Whalley, Slawomir J. Nasuto:
  Emergence of a Small-World Functional Network in Cultured Neurons.
• 
  Yan Fu, Trevor Glaros, Meng Zhu, Ping Wang, Zhanghan Wu, John J. Tyson, Liwu Li, Jianhua Xing:
  Network Topologies and Dynamics Leading to Endotoxin Tolerance and Priming in Innate Immune Cells.
• 
  Matthew C. Schmidt, Andrea M. Rocha, Kanchana Padmanabhan, Yekaterina Shpanskaya, Jillian F. Banfield, Kathleen Scott, James R. Mihelcic, Nagiza F. Samatova:
  NIBBS-Search for Fast and Accurate Prediction of Phenotype-Biased Metabolic Systems.
• 
  Sepideh Bazazi, Frederic Bartumeus, Joseph J. Hale, Iain D. Couzin:
  Intermittent Motion in Desert Locusts: Behavioural Complexity in Simple Environments.
• 
  Daniel S. D. Larsson, Lars Liljas, David van der Spoel:
  Virus Capsid Dissolution Studied by Microsecond Molecular Dynamics Simulations.
• 
  Feixiong Cheng, Chuang Liu, Jing Jiang, Weiqiang Lu, Weihua Li, Guixia Liu, Wei-Xing Zhou, Jin Huang, Yun Tang:
  Prediction of Drug-Target Interactions and Drug Repositioning via Network-Based Inference.
• 
  Bertrand C. W. Tanner, Thomas L. Daniel, Michael Regnier:
  Filament Compliance Influences Cooperative Activation of Thin Filaments and the Dynamics of Force Production in Skeletal Muscle.
• 
  Ben Murrell, Tulio de Oliveira, Chris Seebregts, Sergei L. Kosakovsky Pond, Konrad Scheffler:
  Modeling HIV-1 Drug Resistance as Episodic Directional Selection.
• 
  Scott A. Edwards, Johannes A. Wagner, Frauke Gräter:
  Dynamic Prestress in a Globular Protein.
• 
  Jason J. Kutch, Francisco J. Valero Cuevas:
  Challenges and New Approaches to Proving the Existence of Muscle Synergies of Neural Origin.
• 
  Abbas Shirinifard, James A. Glazier, Maciej Swat, J. Scott Gens, Fereydoon Family, Yi Jiang, Hans E. Grossniklaus:
  Adhesion Failures Determine the Pattern of Choroidal Neovascularization in the Eye: A Computer Simulation Study.
• 
  Michiel W. H. Remme, Wytse J. Wadman:
  Homeostatic Scaling of Excitability in Recurrent Neural Networks.
• 
  Christopher A. Penfold, Paul E. Brown, Neil D. Lawrence, Alastair S. H. Goldman:
  Modeling Meiotic Chromosomes Indicates a Size Dependent Contribution of Telomere Clustering and Chromosome Rigidity to Homologue Juxtaposition.

Volume 8, Number 6, June 2012

Message from ISCB

• 
  Lonnie R. Welch, Russell Schwartz, Fran Lewitter:
  A Report of the Curriculum Task Force of the ISCB Education Committee.

Education

• 
  Fuhui Long, Jianlong Zhou, Hanchuan Peng:
  Visualization and Analysis of 3D Microscopic Images.

Perspective

• 
  Indika Rajapakse, Mark Groudine, Mehran Mesbahi:
  What Can Systems Theory of Networks Offer to Biology?

Review

• 
  Claus O. Wilke:
  Bringing Molecules Back into Molecular Evolution.

Research Articles

• 
  Rebecca B. Hoyle, Daniele Avitabile, Andrzej M. Kierzek:
  Equation-Free Analysis of Two-Component System Signalling Model Reveals the Emergence of Co-Existing Phenotypes in the Absence of Multistationarity.
• 
  Natali Gulbahce, Han Yan, Amélie Dricot, Megha Padi, Danielle Byrdsong, Rachel Franchi, Deok-Sun Lee, Orit Rozenblatt-Rosen, Jessica Cara Mar, Michael A. Calderwood, Amy Baldwin, Bo Zhao, Balaji Santhanam, Pascal Braun, Nicolas Simonis, Kyung-Won Huh, Karin Hellner, Miranda Grace, Alyce Chen, Renee Rubio, Jarrod A. Marto, Nicholas A. Christakis, Elliott Kieff, Frederick P. Roth, Jennifer Roecklein-Canfield, James A. DeCaprio, Michael E. Cusick, John Quackenbush, David E. Hill, Karl Münger, Marc Vidal, Albert-László Barabási:
  Viral Perturbations of Host Networks Reflect Disease Etiology.
• 
  Ezequiel M. Arneodo, Yonatan Sanz Perl, Franz Goller, Gabriel B. Mindlin:
  Prosthetic Avian Vocal Organ Controlled by a Freely Behaving Bird Based on a Low Dimensional Model of the Biomechanical Periphery.
• 
  Erik M. Volz, James S. Koopman, Melissa J. Ward, Andrew J. Leigh Brown, Simon D. W. Frost:
  Simple Epidemiological Dynamics Explain Phylogenetic Clustering of HIV from Patients with Recent Infection.
• 
  Florian Raudies, Michael E. Hasselmo:
  Modeling Boundary Vector Cell Firing Given Optic Flow as a Cue.
• 
  Xin Wang, Mauro A. A. Castro, Klaas W. Mulder, Florian Markowetz:
  Posterior Association Networks and Functional Modules Inferred from Rich Phenotypes of Gene Perturbations.
• 
  John A. Capra, Alexander G. Williams, Katherine S. Pollard:
  ProteinHistorian: Tools for the Comparative Analysis of Eukaryote Protein Origin.
• 
  Eftychios A. Pnevmatikakis, Keith J. Kelleher, Rebecca Chen, Petter Saggau, Kresimir Josic, Liam Paninski:
  Fast Spatiotemporal Smoothing of Calcium Measurements in Dendritic Trees.
• 
  Robert Moss, Thibault Grosse, Ivanny Marchant, Nathalie Lassau, François Gueyffier, S. Randall Thomas:
  Virtual Patients and Sensitivity Analysis of the Guyton Model of Blood Pressure Regulation: Towards Individualized Models of Whole-Body Physiology.
• 
  R. Zachariah Aandahl, Josephine F. Reyes, Scott A. Sisson, Mark M. Tanaka:
  A Model-Based Bayesian Estimation of the Rate of Evolution of VNTR Loci in Mycobacterium tuberculosis.
• 
  Marc Thilo Figge, Andreas S. Reichert, Michael Meyer-Hermann, Heinz D. Osiewacz:
  Deceleration of Fusion-Fission Cycles Improves Mitochondrial Quality Control during Aging.
• 
  Hendrik B. Tiedemann, Elida Schneltzer, Stefan Zeiser, Bastian Hoesel, Johannes Beckers, Gerhard K. H. Przemeck, Martin Hrabé de Angelis:
  From Dynamic Expression Patterns to Boundary Formation in the Presomitic Mesoderm.
• 
  Kasia A. Pawelek, Giao T. Huynh, Michelle Quinlivan, Ann Cullinane, Libin Rong, Alan S. Perelson:
  Modeling Within-Host Dynamics of Influenza Virus Infection Including Immune Responses.
• 
  Masaya Hirashima, Daichi Nozaki:
  Learning with Slight Forgetting Optimizes Sensorimotor Transformation in Redundant Motor Systems.
• 
  William R. Holmes, Benjamin Lin, Andre Levchenko, Leah Edelstein-Keshet:
  Modelling Cell Polarization Driven by Synthetic Spatially Graded Rac Activation.
• 
  Matthias Kahm, Clara Navarrete, Vicent Llopis-Torregrosa, Rito Herrera, Lina Barreto, Lynne Yenush, Joaquín Ariño, Jose Ramos, Maik Kschischo:
  Potassium Starvation in Yeast: Mechanisms of Homeostasis Revealed by Mathematical Modeling.
• 
  Carlo Chan, Xinfeng Liu, Liming Wang, Lee Bardwell, Qing Nie, Germán A. Enciso:
  Protein Scaffolds Can Enhance the Bistability of Multisite Phosphorylation Systems.
• 
  Robert Rosenbaum, Jonathan E. Rubin, Brent Doiron:
  Short Term Synaptic Depression Imposes a Frequency Dependent Filter on Synaptic Information Transfer.
• 
  Magali Michaut, Gary D. Bader:
  Multiple Genetic Interaction Experiments Provide Complementary Information Useful for Gene Function Prediction.
• 
  Marcus T. Wilson, Peter A. Robinson, Ben O'Neill, D. A. Steyn-Ross:
  Complementarity of Spike- and Rate-Based Dynamics of Neural Systems.
• 
  Daniele De Martino, Matteo Figliuzzi, Andrea De Martino, Enzo Marinari:
  A Scalable Algorithm to Explore the Gibbs Energy Landscape of Genome-Scale Metabolic Networks.
• 
  Theresa Niederberger, Stefanie Etzold, Michael Lidschreiber, Kerstin C. Maier, Dietmar E. Martin, Holger Fröhlich, Patrick Cramer, Achim Tresch:
  MC EMiNEM Maps the Interaction Landscape of the Mediator.
• 
  Matthias König, Sascha Bulik, Hermann-Georg Holzhütter:
  Quantifying the Contribution of the Liver to Glucose Homeostasis: A Detailed Kinetic Model of Human Hepatic Glucose Metabolism.
• 
  Tatjana Skrbic, Cristian Micheletti, Pietro Faccioli:
  The Role of Non-Native Interactions in the Folding of Knotted Proteins.
• 
  Oren Shriki, Adam Kohn, Maoz Shamir:
  Fast Coding of Orientation in Primary Visual Cortex.
• 
  David C. Sterratt, Martine R. Groen, Rhiannon M. Meredith, Arjen van Ooyen:
  Spine Calcium Transients Induced by Synaptically-Evoked Action Potentials Can Predict Synapse Location and Establish Synaptic Democracy.
• 
  Dominik Wodarz, Andrew Hofacre, John W. Lau, Zhiying Sun, Hung Fan, Natalia L. Komarova:
  Complex Spatial Dynamics of Oncolytic Viruses In Vitro: Mathematical and Experimental Approaches.
• 
  Monika Jadi, Alon Polsky, Jackie Schiller, Bartlett W. Mel:
  Location-Dependent Effects of Inhibition on Local Spiking in Pyramidal Neuron Dendrites.
• 
  Philip Gerlee, Sven Nelander:
  The Impact of Phenotypic Switching on Glioblastoma Growth and Invasion.
• 
  Hector Garcia-Seisdedos, Beatriz Ibarra-Molero, Jose M. Sanchez-Ruiz:
  Probing the Mutational Interplay between Primary and Promiscuous Protein Functions: A Computational-Experimental Approach.
• 
  Romain Brette:
  Computing with Neural Synchrony.
• 
  Crina-Maria Ionescu, Radka Svobodová Vareková, Jochen H. M. Prehn, Heinrich J. Huber, Jaroslav Koca:
  Charge Profile Analysis Reveals That Activation of Pro-apoptotic Regulators Bax and Bak Relies on Charge Transfer Mediated Allosteric Regulation.
• 
  Sahar Abubucker, Nicola Segata, Johannes Goll, Alyxandria M. Schubert, Jacques Izard, Brandi L. Cantarel, Beltran Rodriguez-Mueller, Jeremy Zucker, Mathangi Thiagarajan, Bernard Henrissat, Owen White, Scott T. Kelley, Barbara A. Methé, Patrick D. Schloss, Dirk Gevers, Makedonka Dautova Mitreva, Curtis Huttenhower:
  Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome.
• 
  James P. Crutchfield, Sean Whalen:
  Structural Drift: The Population Dynamics of Sequential Learning.
• 
  Pleuni Simone Pennings:
  Standing Genetic Variation and the Evolution of Drug Resistance in HIV.
• 
  Javier Carrera, Asun Fernández del Carmen, Rafael Fernández-Muñoz, Jose Luis Rambla, Clara Pons, Alfonso Jaramillo, Santiago F. Elena, Antonio Granell:
  Fine-Tuning Tomato Agronomic Properties by Computational Genome Redesign.
• 
  Cyril F. Reboul, Benjamin T. Porebski, M. D. W. Griffin, R. C. J. Dobson, M. A. Perugini, J. A. Gerrard, Ashley M. Buckle:
  Structural and Dynamic Requirements for Optimal Activity of the Essential Bacterial Enzyme Dihydrodipicolinate Synthase.
• 
  David Ruau, Joel Dudley, Rong Chen, Nicholas G. Phillips, Gary E. Swan, Laura Lazzeroni, J. David Clark, Atul J. Butte, Martin S. Angst:
  Integrative Approach to Pain Genetics Identifies Pain Sensitivity Loci across Diseases.
• 
  Arno Onken, Valentin Dragoi, Klaus Obermayer:
  A Maximum Entropy Test for Evaluating Higher-Order Correlations in Spike Counts.
• 
  Kevin P. Keegan, William L. Trimble, Jared Wilkening, Andreas Wilke, Travis Harrison, Mark D'Souza, Folker Meyer:
  A Platform-Independent Method for Detecting Errors in Metagenomic Sequencing Data: DRISEE.
• 
  Benjamin M. Friedrich, Elisabeth Fischer-Friedrich, Nir S. Gov, Samuel A. Safran:
  Sarcomeric Pattern Formation by Actin Cluster Coalescence.
• 
  Yasuhiro Matsunaga, Hiroshi Fujisaki, Tohru Terada, Tadaomi Furuta, Kei Moritsugu, Akinori Kidera:
  Minimum Free Energy Path of Ligand-Induced Transition in Adenylate Kinase.

Volume 8, Number 7, July 2012

Education

• 
  Andrew Morin, Jennifer Urban, Piotr Sliz:
  A Quick Guide to Software Licensing for the Scientist-Programmer.

Perspectives

• 
  Rob J. De Boer:
  Which of Our Modeling Predictions Are Robust?
• 
  Yann Joly, Edward S. Dove, Bartha M. Knoppers, Martin Bobrow, Don Chalmers:
  Data Sharing in the Post-Genomic World: The Experience of the International Cancer Genome Consortium (ICGC) Data Access Compliance Office (DACO).
• 
  Katrina Pavelin, Jennifer A. Cham, Paula de Matos, Catherine Brooksbank, Graham Cameron, Christoph Steinbeck:
  Bioinformatics Meets User-Centred Design: A Perspective.

Review

• 
  Marcel Salathé, Linus Bengtsson, Todd J. Bodnar, Devon D. Brewer, John S. Brownstein, Caroline O. Buckee, Ellsworth M. Campbell, Ciro Cattuto, Shashank Khandelwal, Patricia L. Mabry, Alessandro Vespignani:
  Digital Epidemiology.

Research Articles

• 
  Idit Kosti, Predrag Radivojac, Yael Mandel-Gutfreund:
  An Integrated Regulatory Network Reveals Pervasive Cross-Regulation among Transcription and Splicing Factors.
• 
  Fang Zheng, Chang-Guo Zhan:
  Modeling of Pharmacokinetics of Cocaine in Human Reveals the Feasibility for Development of Enzyme Therapies for Drugs of Abuse.
• 
  Marieke Pluijmert, Wilco Kroon, Alessandro C. Rossi, Peter Bovendeerd, Tammo Delhaas:
  Why SIT Works: Normal Function Despite Typical Myofiber Pattern in Situs Inversus Totalis (SIT) Hearts Derived by Shear-induced Myofiber Reorientation.
• 
  Haipeng Xing, Yifan Mo, Will Liao, Michael Q. Zhang:
  Genome-Wide Localization of Protein-DNA Binding and Histone Modification by a Bayesian Change-Point Method with ChIP-seq Data.
• 
  Craig N. Lumb, Mark S. P. Sansom:
  Finding a Needle in a Haystack: The Role of Electrostatics in Target Lipid Recognition by PH Domains.
• 
  Jingchun Sun, Xue Gong, Benjamin Purow, Zhongming Zhao:
  Uncovering MicroRNA and Transcription Factor Mediated Regulatory Networks in Glioblastoma.
• 
  Alessandro Vato, Marianna Semprini, Emma Maggiolini, Francois D. Szymanski, Luciano Fadiga, Stefano Panzeri, Ferdinando A. Mussa-Ivaldi:
  Shaping the Dynamics of a Bidirectional Neural Interface.
• 
  Miles Miller, Marc Hafner, Eduardo D. Sontag, Noah Davidsohn, Sairam Subramanian, Priscilla E. M. Purnick, Douglas A. Lauffenburger, Ron Weiss:
  Modular Design of Artificial Tissue Homeostasis: Robust Control through Synthetic Cellular Heterogeneity.
• 
  Andrea Perna, Boris Granovskiy, Simon Garnier, Stamatios C. Nicolis, Marjorie Labédan, Guy Theraulaz, Vincent Fourcassié, David J. T. Sumpter:
  Individual Rules for Trail Pattern Formation in Argentine Ants (Linepithema humile).
• 
  Maxime Louet, Jean Martinez, Nicolas Floquet:
  GDP Release Preferentially Occurs on the Phosphate Side in Heterotrimeric G-proteins.
• 
  George K. Acquaah-Mensah, Deepti Malhotra, Madhulika Vulimiri, Jason E. McDermott, Shyam Biswal:
  Suppressed Expression of T-Box Transcription Factors Is Involved in Senescence in Chronic Obstructive Pulmonary Disease.
• 
  Bardia F. Behabadi, Alon Polsky, Monika Jadi, Jackie Schiller, Bartlett W. Mel:
  Location-Dependent Excitatory Synaptic Interactions in Pyramidal Neuron Dendrites.
• 
  Michael Knott, Robert B. Best:
  A Preformed Binding Interface in the Unbound Ensemble of an Intrinsically Disordered Protein: Evidence from Molecular Simulations.
• 
  Alireza Soltani, Benedetto De Martino, Colin F. Camerer:
  A Range-Normalization Model of Context-Dependent Choice: A New Model and Evidence.
• 
  Collins Assisi, Mark Stopfer, Maxim Bazhenov:
  Excitatory Local Interneurons Enhance Tuning of Sensory Information.
• 
  Na Yu, Ginette Hupé, Charles Garfinkle, John E. Lewis, André Longtin:
  Coding Conspecific Identity and Motion in the Electric Sense.
• 
  Paul François, Nicolas Despierre, Eric D. Siggia:
  Adaptive Temperature Compensation in Circadian Oscillations.
• 
  Anton Crombach, Karl R. Wotton, Damjan Cicin-Sain, Maksat Ashyraliyev, Johannes Jaeger:
  Efficient Reverse-Engineering of a Developmental Gene Regulatory Network.
• 
  Nicole L. Carlson, Vivienne L. Ming, Michael Robert DeWeese:
  Sparse Codes for Speech Predict Spectrotemporal Receptive Fields in the Inferior Colliculus.
• 
  Kun Hu, Men-Tzung Lo, Chung-Kang Peng, Yanhui Liu, Vera Novak:
  A Nonlinear Dynamic Approach Reveals a Long-Term Stroke Effect on Cerebral Blood Flow Regulation at Multiple Time Scales.
• 
  Jason Flannick, Joshua M. Korn, Pierre Fontanillas, George B. Grant, Eric Banks, Mark A. DePristo, David Altshuler:
  Efficiency and Power as a Function of Sequence Coverage, SNP Array Density, and Imputation.
• 
  Karoline Faust, Jarupon Fah Sathirapongsasuti, Jacques Izard, Nicola Segata, Dirk Gevers, Jeroen Raes, Curtis Huttenhower:
  Microbial Co-occurrence Relationships in the Human Microbiome.
• 
  Xiakun Chu, Yong Wang, Linfeng Gan, Yawen Bai, Wei Han, Erkang Wang, Jin Wang:
  Importance of Electrostatic Interactions in the Association of Intrinsically Disordered Histone Chaperone Chz1 and Histone H2A.Z-H2B.
• 
  Jae-Seong Yang, Sang Woo Seo, Sungho Jang, Gyoo Yeol Jung, Sanguk Kim:
  Rational Engineering of Enzyme Allosteric Regulation through Sequence Evolution Analysis.
• 
  Bin Chen, Ying Ding, David J. Wild:
  Assessing Drug Target Association Using Semantic Linked Data.
• 
  Roi Adadi, Benjamin Volkmer, Ron Milo, Matthias Heinemann, Tomer Shlomi:
  Prediction of Microbial Growth Rate versus Biomass Yield by a Metabolic Network with Kinetic Parameters.
• 
  Benjamin Torben-Nielsen, Idan Segev, Yosef Yarom:
  The Generation of Phase Differences and Frequency Changes in a Network Model of Inferior Olive Subthreshold Oscillations.
• 
  Ethan G. Thompson, Timothy Galitski:
  Quantifying and Analyzing the Network Basis of Genetic Complexity.
• 
  Matthieu Gilson, Tomoki Fukai, Anthony N. Burkitt:
  Spectral Analysis of Input Spike Trains by Spike-Timing-Dependent Plasticity.
• 
  Peilin Jia, Lily Wang, Ayman H. Fanous, Carlos N. Pato, Todd L. Edwards, Zhongming Zhao:
  Network-Assisted Investigation of Combined Causal Signals from Genome-Wide Association Studies in Schizophrenia.
• 
  Nathan G. Clack, Daniel H. O'Connor, Daniel Huber, Leopoldo T. Petreanu, Andrew Hires, Simon Peron, Karel Svoboda, Eugene W. Myers:
  Automated Tracking of Whiskers in Videos of Head Fixed Rodents.
• 
  Diana Chang, Alon Keinan:
  Predicting Signatures of "Synthetic Associations" and "Natural Associations" from Empirical Patterns of Human Genetic Variation.

Volume 8, Number 8, August 2012

Message from ISCB

• 
  Todd A. Gibson:
  The Roots of Bioinformatics in ISMB.

Education

• 
  Jennifer McQueen, Jody J. Wright, Joanne A. Fox:
  Design and Implementation of a Genomics Field Trip Program Aimed at Secondary School Students.

Review

• 
  Jennifer L. Reed:
  Shrinking the Metabolic Solution Space Using Experimental Datasets.

Research Articles

• 
  Marek Kwiatkowski, Jan Engelstädter, Christoph Vorburger:
  On Genetic Specificity in Symbiont-Mediated Host-Parasite Coevolution.
• 
  Raheleh Salari, Damian Wójtowicz, Jie Zheng, David Levens, Yitzhak Pilpel, Teresa M. Przytycka:
  Teasing Apart Translational and Transcriptional Components of Stochastic Variations in Eukaryotic Gene Expression.
• 
  Thomas R. Sokolowski, Thorsten Erdmann, Pieter Rein ten Wolde:
  Mutual Repression Enhances the Steepness and Precision of Gene Expression Boundaries.
• 
  Jie Zhang, Kewei Lu, Yang Xiang, Muhtadi Islam, Shweta Kotian, Zeina Kais, Cindy Lee, Mansi Arora, Hui-wen Liu, Jeffrey D. Parvin, Kun Huang:
  Weighted Frequent Gene Co-expression Network Mining to Identify Genes Involved in Genome Stability.
• 
  Daniel R. Ripoll, Ilja V. Khavrutskii, Sidhartha Chaudhury, Jin Liu, Robert A. Kuschner, Anders Wallqvist, Jaques Reifman:
  Quantitative Predictions of Binding Free Energy Changes in Drug-Resistant Influenza Neuraminidase.
• 
  Oscar J. Avella Gonzalez, Karlijn I. van Aerde, Ronald A. J. van Elburg, Simon-Shlomo Poil, Huibert D. Mansvelder, Klaus Linkenkaer-Hansen, Jaap van Pelt, Arjen van Ooyen:
  External Drive to Inhibitory Cells Induces Alternating Episodes of High- and Low-Amplitude Oscillations.
• 
  Gordon Wang, Stephen J. Smith:
  Sub-diffraction Limit Localization of Proteins in Volumetric Space Using Bayesian Restoration of Fluorescence Images from Ultrathin Specimens.
• 
  J. Christian J. Ray, Oleg A. Igoshin:
  Interplay of Gene Expression Noise and Ultrasensitive Dynamics Affects Bacterial Operon Organization.
• 
  Andrei V. Pisliakov, Tomoya Hino, Yoshitsugu Shiro, Yuji Sugita:
  Molecular Dynamics Simulations Reveal Proton Transfer Pathways in Cytochrome C-Dependent Nitric Oxide Reductase.
• 
  Jessica Andreani, Guilhem Faure, Raphaël Guérois:
  Versatility and Invariance in the Evolution of Homologous Heteromeric Interfaces.
• 
  Guillaume Salbreux, Linda K. Barthel, Pamela A. Raymond, David K. Lubensky:
  Coupling Mechanical Deformations and Planar Cell Polarity to Create Regular Patterns in the Zebrafish Retina.
• 
  Aaditya V. Rangan:
  Functional Roles for Synaptic-Depression within a Model of the Fly Antennal Lobe.
• 
  Konstantin Kozlov, Svetlana Surkova, Ekaterina M. Myasnikova, John Reinitz, Maria Samsonova:
  Modeling of Gap Gene Expression in Drosophila Kruppel Mutants.
• 
  Elisabeth Humphris-Narayanan, Eyal Akiva, Rocco Varela, Shane Ó Conchúir, Tanja Kortemme:
  Prediction of Mutational Tolerance in HIV-1 Protease and Reverse Transcriptase Using Flexible Backbone Protein Design.
• 
  Rebeca García-Fandiño, Pau Bernadó, Sara Ayuso-Tejedor, Javier Sancho, Modesto Orozco:
  Defining the Nature of Thermal Intermediate in 3 State Folding Proteins: Apoflavodoxin, a Study Case.
• 
  Marco Patriarca, Svetlana Postnova, Hans A. Braun, Emilio Hernández-García, Raúl Toral:
  Diversity and Noise Effects in a Model of Homeostatic Regulation of the Sleep-Wake Cycle.
• 
  Maria Abou Chakra, Arne Traulsen:
  Evolutionary Dynamics of Strategic Behavior in a Collective-Risk Dilemma.
• 
  Olav Stetter, Demian Battaglia, Jordi Soriano, Theo Geisel:
  Model-Free Reconstruction of Excitatory Neuronal Connectivity from Calcium Imaging Signals.
• 
  Victor Seguritan, Nelson Alves Jr., Michael Arnoult, Amy Raymond, Don Lorimer, Alex B. Burgin Jr., Peter Salamon, Anca M. Segall:
  Artificial Neural Networks Trained to Detect Viral and Phage Structural Proteins.
• 
  Elodie Laine, Christian Auclair, Luba Tchertanov:
  Allosteric Communication across the Native and Mutated KIT Receptor Tyrosine Kinase.
• 
  Balaji Prabhakar, Katherine N. Dektar, Deborah M. Gordon:
  The Regulation of Ant Colony Foraging Activity without Spatial Information.
• 
  Willem de Haan, Katherine K. Mott, Elisabeth C. W. van Straaten, Philip Scheltens, Cornelis J. Stam:
  Activity Dependent Degeneration Explains Hub Vulnerability in Alzheimer's Disease.
• 
  Reuben H. Kraft, Phillip Justin Mckee, Amy M. Dagro, Scott T. Grafton:
  Combining the Finite Element Method with Structural Connectome-based Analysis for Modeling Neurotrauma: Connectome Neurotrauma Mechanics.
• 
  Laurent F. Thomas, Pål Sætrom:
  Single Nucleotide Polymorphisms Can Create Alternative Polyadenylation Signals and Affect Gene Expression through Loss of MicroRNA-Regulation.
• 
  Matthias S. Keil, Joan López-Moliner:
  Unifying Time to Contact Estimation and Collision Avoidance across Species.
• 
  Markus Arnoldini, Rafal Mostowy, Sebastian Bonhoeffer, Martin Ackermann:
  Evolution of Stress Response in the Face of Unreliable Environmental Signals.
• 
  David N. Quan, William E. Bentley:
  Gene Network Homology in Prokaryotes Using a Similarity Search Approach: Queries of Quorum Sensing Signal Transduction.
• 
  Saket Navlakha, Anthony Gitter, Ziv Bar-Joseph:
  A Network-based Approach for Predicting Missing Pathway Interactions.
• 
  Chad M. Topaz, Maria R. D'Orsogna, Leah Edelstein-Keshet, Andrew J. Bernoff:
  Locust Dynamics: Behavioral Phase Change and Swarming.
• 
  Kim Sneppen, Ian B. Dodd:
  A Simple Histone Code Opens Many Paths to Epigenetics.
• 
  Jennifer M. Johnston, Hao Wang, Davide Provasi, Marta Filizola:
  Assessing the Relative Stability of Dimer Interfaces in G Protein-Coupled Receptors.
• 
  Allen Cheung, David Ball, Michael Milford, Gordon F. Wyeth, Janet Wiles:
  Maintaining a Cognitive Map in Darkness: The Need to Fuse Boundary Knowledge with Path Integration.
• 
  Yu. Dabaghian, Facundo Mémoli, Loren M. Frank, Gunnar E. Carlsson:
  A Topological Paradigm for Hippocampal Spatial Map Formation Using Persistent Homology.
• 
  Jon D. Duke, Xu Han, Zhiping Wang, Abhinita Subhadarshini, Shreyas D. Karnik, Xiaochun Li, Stephen D. Hall, Yan Jin, J. Thomas Callaghan, J. Marc Overhage, David A. Flockhart, R. Matthew Strother, Sara K. Quinney, Lang Li:
  Literature Based Drug Interaction Prediction with Clinical Assessment Using Electronic Medical Records: Novel Myopathy Associated Drug Interactions.
• 
  Rahul Agarwal, Sridevi V. Sarma:
  Performance Limitations of Relay Neurons.
• 
  Robert Clewley:
  Hybrid Models and Biological Model Reduction with PyDSTool.
• 
  Frank Freyer, James A. Roberts, Petra Ritter, Michael Breakspear:
  A Canonical Model of Multistability and Scale-Invariance in Biological Systems.
• 
  Yuchun Guo, Shaun Mahony, David K. Gifford:
  High Resolution Genome Wide Binding Event Finding and Motif Discovery Reveals Transcription Factor Spatial Binding Constraints.
• 
  Iga Korneta, Janusz M. Bujnicki:
  Intrinsic Disorder in the Human Spliceosomal Proteome.
• 
  Deena M. A. Gendoo, Paul M. Harrison:
  The Landscape of the Prion Protein's Structural Response to Mutation Revealed by Principal Component Analysis of Multiple NMR Ensembles.
• 
  Tom Tetzlaff, Moritz Helias, Gaute T. Einevoll, Markus Diesmann:
  Decorrelation of Neural-Network Activity by Inhibitory Feedback.
• 
  Carolina Tropini, Kerwyn Casey Huang:
  Interplay between the Localization and Kinetics of Phosphorylation in Flagellar Pole Development of the Bacterium Caulobacter crescentus.
• 
  C. Scott Wylie, Eugene I. Shakhnovich:
  Mutation Induced Extinction in Finite Populations: Lethal Mutagenesis and Lethal Isolation.
• 
  Paul Smolen, Douglas A. Baxter, John H. Byrne:
  Molecular Constraints on Synaptic Tagging and Maintenance of Long-Term Potentiation: A Predictive Model.
• 
  Tobias Hamp, Burkhard Rost:
  Alternative Protein-Protein Interfaces Are Frequent Exceptions.
• 
  Georg K. Gerber, Andrew B. Onderdonk, Lynn Bry:
  Inferring Dynamic Signatures of Microbes in Complex Host Ecosystems.
• 
  Daniel A. Keedy, Ivelin Georgiev, Edward B. Triplett, Bruce Randall Donald, David C. Richardson, Jane S. Richardson:
  The Role of Local Backrub Motions in Evolved and Designed Mutations.

Volume 8, Number 9, September 2012

Editorials

• 
  Anthony C. Fletcher, Philip E. Bourne:
  Ten Simple Rules To Commercialize Scientific Research.
• 
  David B. Searls:
  Ten Simple Rules for Online Learning.

Perspectives

• 
  Antony J. Williams, John Wilbanks, Sean Ekins:
  Why Open Drug Discovery Needs Four Simple Rules for Licensing Data and Models.
• 
  David B. Searls:
  An Online Bioinformatics Curriculum.

Research Articles

• 
  Tristan Ursell, Eliane H. Trepagnier, Kerwyn Casey Huang, Julie A. Theriot:
  Analysis of Surface Protein Expression Reveals the Growth Pattern of the Gram-Negative Outer Membrane.
• 
  Oded Magger, Yedael Y. Waldman, Eytan Ruppin, Roded Sharan:
  Enhancing the Prioritization of Disease-Causing Genes through Tissue Specific Protein Interaction Networks.
• 
  Johannes Friedrich, Walter Senn:
  Spike-based Decision Learning of Nash Equilibria in Two-Player Games.
• 
  Thomas T. Joseph, Roman Osman:
  Convergent Transmission of RNAi Guide-Target Mismatch Information across Argonaute Internal Allosteric Network.
• 
  Yuanfang Guan, Dmitriy Gorenshteyn, Margit Burmeister, Aaron K. Wong, John C. Schimenti, Mary Ann Handel, Carol J. Bult, Matthew A. Hibbs, Olga G. Troyanskaya:
  Tissue-Specific Functional Networks for Prioritizing Phenotype and Disease Genes.
• 
  Jordi Grau-Moya, Pedro A. Ortega, Daniel A. Braun:
  Risk-Sensitivity in Bayesian Sensorimotor Integration.
• 
  Zeynep Kurkcuoglu, Ahmet Bakan, Duygu Kocaman, Ivet Bahar, Pemra Doruker:
  Coupling between Catalytic Loop Motions and Enzyme Global Dynamics.
• 
  Martin Löwer, Bernhard Y. Renard, Jos de Graaf, Meike Wagner, Claudia Paret, Christoph Kneip, Özlem Türeci, Mustafa Diken, Cedrik M. Britten, Sebastian Kreiter, Michael Koslowski, John C. Castle, Ugur Sahin:
  Confidence-based Somatic Mutation Evaluation and Prioritization.
• 
  Haiyang Zhang, Zalman Vaksman, Douglas B. Litwin, Peng Shi, Heidi B. Kaplan, Oleg A. Igoshin:
  The Mechanistic Basis of Myxococcus xanthus Rippling Behavior and Its Physiological Role during Predation.
• 
  Anna C. F. Lewis, Nick S. Jones, Mason A. Porter, Charlotte M. Deane:
  What Evidence Is There for the Homology of Protein-Protein Interactions?
• 
  Todd E. Hudson, Uta Wolfe, Laurence T. Maloney:
  Speeded Reaching Movements around Invisible Obstacles.
• 
  Evelyne Deplazes, Martti Louhivuori, Dylan Jayatilaka, Siewert J. Marrink, Ben Corry:
  Structural Investigation of MscL Gating Using Experimental Data and Coarse Grained MD Simulations.
• 
  Benjamin A. Hall, Judith P. Armitage, Mark S. P. Sansom:
  Mechanism of Bacterial Signal Transduction Revealed by Molecular Dynamics of Tsr Dimers and Trimers of Dimers in Lipid Vesicles.
• 
  Jonathan Friedman, Eric J. Alm:
  Inferring Correlation Networks from Genomic Survey Data.
• 
  Moritz Deger, Moritz Helias, Stefan Rotter, Markus Diesmann:
  Spike-Timing Dependence of Structural Plasticity Explains Cooperative Synapse Formation in the Neocortex.
• 
  Michael A. Jamros, Leandro C. Oliveira, Paul C. Whitford, José N. Onuchic, Joseph A. Adams, Patricia A. Jennings:
  Substrate-Specific Reorganization of the Conformational Ensemble of CSK Implicates Novel Modes of Kinase Function.
• 
  Christian Bodenstein, Marko Gosak, Stefan Schuster, Marko Marhl, Matjaz Perc:
  Modeling the Seasonal Adaptation of Circadian Clocks by Changes in the Network Structure of the Suprachiasmatic Nucleus.
• 
  Vitaly A. Selivanov, Marta Cascante, Mark Friedman, Mark F. Schumaker, Massimo Trucco, Tatyana V. Votyakova:
  Multistationary and Oscillatory Modes of Free Radicals Generation by the Mitochondrial Respiratory Chain Revealed by a Bifurcation Analysis.
• 
  Danielle E. Chandler, François Penin, Klaus Schulten, Christophe Chipot:
  The p7 Protein of Hepatitis C Virus Forms Structurally Plastic, Minimalist Ion Channels.
• 
  Catia Pesquita, Francisco M. Couto:
  Predicting the Extension of Biomedical Ontologies.
• 
  Ping-Chang Lee, Chao-Chun Chuang, Ann-Shyn Chiang, Yu-Tai Ching:
  High-throughput Computer Method for 3D Neuronal Structure Reconstruction from the Image Stack of the Drosophila Brain and Its Applications.
• 
  Tobias Sikosek, Erich Bornberg-Bauer, Hue Sun Chan:
  Evolutionary Dynamics on Protein Bi-stability Landscapes can Potentially Resolve Adaptive Conflicts.
• 
  Na Yu, Catherine E. Morris, Béla Joós, André Longtin:
  Spontaneous Excitation Patterns Computed for Axons with Injury-like Impairments of Sodium Channels and Na/K Pumps.
• 
  Ashok Litwin-Kumar, Maurice J. Chacron, Brent Doiron:
  The Spatial Structure of Stimuli Shapes the Timescale of Correlations in Population Spiking Activity.
• 
  Laura Fumanelli, Marco Ajelli, Piero Manfredi, Alessandro Vespignani, Stefano Merler:
  Inferring the Structure of Social Contacts from Demographic Data in the Analysis of Infectious Diseases Spread.
• 
  Jacques Gautrais, Francesco Ginelli, Richard Fournier, Stéphane Blanco, Marc Soria, Hugues Chaté, Guy Theraulaz:
  Deciphering Interactions in Moving Animal Groups.
• 
  David M. Devilbiss, Rick L. Jenison, Craig W. Berridge:
  Stress-Induced Impairment of a Working Memory Task: Role of Spiking Rate and Spiking History Predicted Discharge.
• 
  Iskra Staneva, Yongqi Huang, Zhirong Liu, Stefan Wallin:
  Binding of Two Intrinsically Disordered Peptides to a Multi-Specific Protein: A Combined Monte Carlo and Molecular Dynamics Study.
• 
  Kushal Tripathi, Rajesh Balagam, Nisheeth K. Vishnoi, Narendra M. Dixit:
  Stochastic Simulations Suggest that HIV-1 Survives Close to Its Error Threshold.
• 
  Aitana Neves, Robert Costalat, Luc Pellerin:
  Determinants of Brain Cell Metabolic Phenotypes and Energy Substrate Utilization Unraveled with a Modeling Approach.
• 
  Xin Fang, Anders Wallqvist, Jaques Reifman:
  Modeling Phenotypic Metabolic Adaptations of Mycobacterium tuberculosis H37Rv under Hypoxia.
• 
  Kai J. Miller, Dora Hermes, Christopher J. Honey, Adam O. Hebb, Nick F. Ramsey, Robert T. Knight, Jeffrey G. Ojemann, Eberhard E. Fetz:
  Human Motor Cortical Activity Is Selectively Phase-Entrained on Underlying Rhythms.
• 
  Liran Carmel, Eugene V. Koonin, Stella Dracheva:
  Dependencies among Editing Sites in Serotonin 2C Receptor mRNA.
• 
  Lisa Sanguinetti, Simona Toti, Valerio Reguzzi, Fabio Bagnoli, Claudio Donati:
  A Novel Computational Method Identifies Intra- and Inter-Species Recombination Events in Staphylococcus aureus and Streptococcus pneumoniae.
• 
  Christian Torres-Sosa, Sui Huang, Maximino Aldana:
  Criticality Is an Emergent Property of Genetic Networks that Exhibit Evolvability.
• 
  Omar Haq, Michael Andrec, Alexandre V. Morozov, Ronald M. Levy:
  Correlated Electrostatic Mutations Provide a Reservoir of Stability in HIV Protease.

Volume 8, Number 10, October 2012

Editorials

• 
  Ruth Nussinov:
  A Future Vision for PLOS Computational Biology.
• 
  Philip E. Bourne:
  Seven Years; It's Time for a Change.

Research Articles

• 
  Guillermo A. Cecchi, Lejian Huang, Javeria Ali Hashmi, Marwan N. Baliki, María V. Centeno, Irina Rish, Apkar Vania Apkarian:
  Predictive Dynamics of Human Pain Perception.
• 
  Ofri Raviv, Merav Ahissar, Yonatan Loewenstein:
  How Recent History Affects Perception: The Normative Approach and Its Heuristic Approximation.
• 
  Danesh Moradigaravand, Jan Engelstädter:
  The Effect of Bacterial Recombination on Adaptation on Fitness Landscapes with Limited Peak Accessibility.
• 
  Maria Ximena Sosa, I. K. Ashok Sivakumar, Samantha Maragh, Vamsi Veeramachaneni, Ramesh Hariharan, Minothi Parulekar, Karin M. Fredrikson, Timothy T. Harkins, Jeffrey Lin, Andrew B. Feldman, Pramila Tata, Georg B. Ehret, Aravinda Chakravarti:
  Next-Generation Sequencing of Human Mitochondrial Reference Genomes Uncovers High Heteroplasmy Frequency.
• 
  Adam J. Kucharski, Julia R. Gog:
  The Role of Social Contacts and Original Antigenic Sin in Shaping the Age Pattern of Immunity to Seasonal Influenza.
• 
  Peter S. Kim, Peter P. Lee:
  Modeling Protective Anti-Tumor Immunity via Preventative Cancer Vaccines Using a Hybrid Agent-based and Delay Differential Equation Approach.
• 
  Steven W. Kembel, Martin Wu, Jonathan A. Eisen, Jessica L. Green:
  Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance.
• 
  Ruian Ke, James O. Lloyd-Smith:
  Evolutionary Analysis of Human Immunodeficiency Virus Type 1 Therapies Based on Conditionally Replicating Vectors.
• 
  Valerii M. Sukhorukov, Daniel Dikov, Andreas S. Reichert, Michael Meyer-Hermann:
  Emergence of the Mitochondrial Reticulum from Fission and Fusion Dynamics.
• 
  Markus Krauss, Stephan Schaller, Steffen Borchers, Rolf Findeisen, Jörg Lippert, Lars Kuepfer:
  Integrating Cellular Metabolism into a Multiscale Whole-Body Model.
• 
  J. Vincent Toups, Jean-Marc Fellous, Peter J. Thomas, Terrence J. Sejnowski, Paul H. E. Tiesinga:
  Multiple Spike Time Patterns Occur at Bifurcation Points of Membrane Potential Dynamics.
• 
  James Truscott, Neil M. Ferguson:
  Evaluating the Adequacy of Gravity Models as a Description of Human Mobility for Epidemic Modelling.
• 
  Marc D. Ryser, Yiding Qu, Svetlana V. Komarova:
  Osteoprotegerin in Bone Metastases: Mathematical Solution to the Puzzle.
• 
  Eva Chovancová, Antonín Pavelka, Petr Benes, Ondrej Strnad, Jan Brezovsky, Barbora Kozlíková, Artur Góra, Vilém Sustr, Martin Klvana, Petr Medek, Lada Biedermannová, Jiri Sochor, Jirí Damborský:
  CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures.
• 
  Klaus Benndorf, Jana Kusch, Eckhard Schulz:
  Probability Fluxes and Transition Paths in a Markovian Model Describing Complex Subunit Cooperativity in HCN2 Channels.
• 
  Iris I. A. Groen, Sennay Ghebreab, Victor A. F. Lamme, H. Steven Scholte:
  Spatially Pooled Contrast Responses Predict Neural and Perceptual Similarity of Naturalistic Image Categories.
• 
  Mykola Pinkevych, Janka Petravic, Kiprotich Chelimo, James W. Kazura, Ann M. Moormann, Miles P. Davenport:
  The Dynamics of Naturally Acquired Immunity to Plasmodium falciparum Infection.
• 
  Andrew J. K. Conlan, Trevelyan J. McKinley, Katerina Karolemeas, Ellen Brooks-Pollock, Anthony V. Goodchild, Andrew P. Mitchell, Colin P. D. Birch, Richard S. Clifton-Hadley, James L. N. Wood:
  Estimating the Hidden Burden of Bovine Tuberculosis in Great Britain.
• 
  Federico Vaggi, James Dodgson, Archana Bajpai, Anatole Chessel, Ferenc Jordán, Masamitsu Sato, Rafael Edgardo Carazo-Salas, Attila Csikász-Nagy:
  Linkers of Cell Polarity and Cell Cycle Regulation in the Fission Yeast Protein Interaction Network.
• 
  Jiaxin Du, Viktor Vegh, David C. Reutens:
  The Laminar Cortex Model: A New Continuum Cortex Model Incorporating Laminar Architecture.
• 
  Jasmin Coulombe-Huntington, Yu Xia:
  Regulatory Network Structure as a Dominant Determinant of Transcription Factor Evolutionary Rate.
• 
  Bartosz Rózycki, Evzen Boura, James H. Hurley, Gerhard Hummer:
  Membrane-Elasticity Model of Coatless Vesicle Budding Induced by ESCRT Complexes.
• 
  Tammy M. K. Cheng, Lucas Goehring, Linda Jeffery, Yu-En Lu, Jacqueline Hayles, Béla Novák, Paul A. Bates:
  A Structural Systems Biology Approach for Quantifying the Systemic Consequences of Missense Mutations in Proteins.
• 
  Duncan J. MacGregor, Gareth Leng:
  Phasic Firing in Vasopressin Cells: Understanding Its Functional Significance through Computational Models.
• 
  Elsa W. Birch, Nicholas A. Ruggero, Markus W. Covert:
  Determining Host Metabolic Limitations on Viral Replication via Integrated Modeling and Experimental Perturbation.
• 
  Noah S. Bieler, Tuomas P. J. Knowles, Daan Frenkel, Robert Vácha:
  Connecting Macroscopic Observables and Microscopic Assembly Events in Amyloid Formation Using Coarse Grained Simulations.
• 
  Russell A. Poldrack, Jeanette A. Mumford, Tom Schonberg, Donald J. Kalar, Bishal Barman, Tal Yarkoni:
  Discovering Relations Between Mind, Brain, and Mental Disorders Using Topic Mapping.
• 
  Christoph Kayser, Robin A. A. Ince, Stefano Panzeri:
  Analysis of Slow (Theta) Oscillations as a Potential Temporal Reference Frame for Information Coding in Sensory Cortices.
• 
  Hang Zhang, Camille Morvan, Louis-Alexandre Etezad-Heydari, Laurence T. Maloney:
  Very Slow Search and Reach: Failure to Maximize Expected Gain in an Eye-Hand Coordination Task.
• 
  Osbaldo Resendis-Antonio, Magdalena Hernández, Yolanda Mora, Sergio Encarnación:
  Functional Modules, Structural Topology, and Optimal Activity in Metabolic Networks.
• 
  Jason E. McDermott, Kenneth D. Jarman, Ronald C. Taylor, Mary J. Lancaster, Harish Shankaran, Keri B. Vartanian, Susan L. Stevens, Mary P. Stenzel-Poore, Antonio Sanfilippo:
  Modeling Dynamic Regulatory Processes in Stroke.
• 
  Aurélie Carlier, Liesbet Geris, Katie Bentley, Geert Carmeliet, Peter Carmeliet, Hans Van Oosterwyck:
  MOSAIC: A Multiscale Model of Osteogenesis and Sprouting Angiogenesis with Lateral Inhibition of Endothelial Cells.
• 
  Stephen Grossberg, Praveen K. Pilly:
  How Entorhinal Grid Cells May Learn Multiple Spatial Scales from a Dorsoventral Gradient of Cell Response Rates in a Self-organizing Map.
• 
  Xiaodong Pang, Kenneth H. Zhou, Sanbo Qin, Huan-Xiang Zhou:
  Prediction and Dissection of Widely-Varying Association Rate Constants of Actin-Binding Proteins.
• 
  Jan H. Peters, Bert L. de Groot:
  Ubiquitin Dynamics in Complexes Reveal Molecular Recognition Mechanisms Beyond Induced Fit and Conformational Selection.
• 
  Vladimir Vacic, Phineus R. L. Markwick, Christopher J. Oldfield, Xiaoyue Zhao, Chad Haynes, Vladimir N. Uversky, Lilia M. Iakoucheva:
  Disease-Associated Mutations Disrupt Functionally Important Regions of Intrinsic Protein Disorder.
• 
  Samuel Murail, Rebecca J. Howard, Torben Broemstrup, Edward J. Bertaccini, R. Adron Harris, James R. Trudell, Erik Lindahl:
  Molecular Mechanism for the Dual Alcohol Modulation of Cys-loop Receptors.
• 
  Richard Naud, Wulfram Gerstner:
  Coding and Decoding with Adapting Neurons: A Population Approach to the Peri-Stimulus Time Histogram.
• 
  Philip A. Romero, Frances H. Arnold:
  Random Field Model Reveals Structure of the Protein Recombinational Landscape.
• 
  Lionel Rigoux, Emmanuel Guigon:
  A Model of Reward- and Effort-Based Optimal Decision Making and Motor Control.

Volume 8, Number 11, November 2012

Editorials

• 
  Andreas Prlic, Hilmar Lapp:
  The PLOS Computational Biology Software Section.
• 
  Mark Jolly, Anthony C. Fletcher, Philip E. Bourne:
  Ten Simple Rules to Protect Your Intellectual Property.

Perspective

• 
  Dirk Gevers, Mihai Pop, Patrick D. Schloss, Curtis Huttenhower:
  Bioinformatics for the Human Microbiome Project.

Research Articles

• 
  Luigi Acerbi, Daniel M. Wolpert, Sethu Vijayakumar:
  Internal Representations of Temporal Statistics and Feedback Calibrate Motor-Sensory Interval Timing.
• 
  Peter Michael Kekenes-Huskey, Steffen Lindert, James Andrew McCammon:
  Molecular Basis of Calcium-Sensitizing and Desensitizing Mutations of the Human Cardiac Troponin C Regulatory Domain: A Multi-Scale Simulation Study.
• 
  Yihan Lin, Ying Li, Sean Crosson, Aaron R. Dinner, Norbert F. Scherer:
  Phase Resetting Reveals Network Dynamics Underlying a Bacterial Cell Cycle.
• 
  Sara B. Collins, Ed Reznik, Daniel Segrè:
  Temporal Expression-based Analysis of Metabolism.
• 
  Jessica Nasica-Labouze, Normand Mousseau:
  Kinetics of Amyloid Aggregation: A Study of the GNNQQNY Prion Sequence.
• 
  Xiaoshu Chen, Jianzhi Zhang:
  The Ortholog Conjecture Is Untestable by the Current Gene Ontology but Is Supported by RNA Sequencing Data.
• 
  Sagi Snir, Yuri I. Wolf, Eugene V. Koonin:
  Universal Pacemaker of Genome Evolution.
• 
  Nicolas Perony, Claudio J. Tessone, Barbara König, Frank Schweitzer:
  How Random Is Social Behaviour? Disentangling Social Complexity through the Study of a Wild House Mouse Population.
• 
  Alexis B. Webb, Stephanie R. Taylor, Kurt A. Thoroughman, Francis J. Doyle III, Erik D. Herzog:
  Weakly Circadian Cells Improve Resynchrony.
• 
  Madineh Sedigh-Sarvestani, Steven J. Schiff, Bruce J. Gluckman:
  Reconstructing Mammalian Sleep Dynamics with Data Assimilation.
• 
  Andreas Kubicek, Christopher Muhando, Hauke Reuter:
  Simulations of Long-Term Community Dynamics in Coral Reefs - How Perturbations Shape Trajectories.
• 
  Zhonghua Xu, Scott C. Lenaghan, Benjamin E. Reese, Xinghua Jia, Mingjun Zhang:
  Experimental Studies and Dynamics Modeling Analysis of the Swimming and Diving of Whirligig Beetles (Coleoptera: Gyrinidae).
• 
  Elisa Cilia, Geerten W. Vuister, Tom Lenaerts:
  Accurate Prediction of the Dynamical Changes within the Second PDZ Domain of PTP1e.
• 
  Gergely Boza, Ádám Kun, István Scheuring, Ulf Dieckmann:
  Strategy Diversity Stabilizes Mutualism through Investment Cycles, Phase Polymorphism, and Spatial Bubbles.
• 
  Christian M. Zmasek, Adam Godzik:
  This Déjà Vu Feeling - Analysis of Multidomain Protein Evolution in Eukaryotic Genomes.
• 
  Renske M. A. Vroomans, Athanasius F. M. Marée, Rob J. De Boer, Joost B. Beltman:
  Chemotactic Migration of T Cells towards Dendritic Cells Promotes the Detection of Rare Antigens.
• 
  Marco J. Morelli, Gaël Thébaud, Joël Chadoeuf, Donald P. King, Daniel T. Haydon, Samuel Soubeyrand:
  A Bayesian Inference Framework to Reconstruct Transmission Trees Using Epidemiological and Genetic Data.
• 
  C. David Williams, Michael Regnier, Thomas L. Daniel:
  Elastic Energy Storage and Radial Forces in the Myofilament Lattice Depend on Sarcomere Length.
• 
  Christian Klaes, Sebastian Schneegans, Gregor Schöner, Alexander Gail:
  Sensorimotor Learning Biases Choice Behavior: A Learning Neural Field Model for Decision Making.
• 
  Ian H. Stevenson, Brian M. London, Emily R. Oby, Nicholas A. Sachs, Jacob Reimer, Bernhard Englitz, Stephen V. David, Shihab A. Shamma, Timothy J. Blanche, Kenji Mizuseki, Amin Zandvakili, Nicholas G. Hatsopoulos, Lee E. Miller, Konrad P. Körding:
  Functional Connectivity and Tuning Curves in Populations of Simultaneously Recorded Neurons.
• 
  Heiko Lammert, Jeffrey K. Noel, José N. Onuchic:
  The Dominant Folding Route Minimizes Backbone Distortion in SH3.
• 
  Biman Jana, Changbong Hyeon, José N. Onuchic:
  The Origin of Minus-end Directionality and Mechanochemistry of Ncd Motors.
• 
  Lars Reichl, Dominik Heide, Siegrid Löwel, Justin C. Crowley, Matthias Kaschube, Fred Wolf:
  Coordinated Optimization of Visual Cortical Maps (I) Symmetry-based Analysis.
• 
  Robert Stojnic, Audrey Qiuyan Fu, Boris Adryan:
  A Graphical Modelling Approach to the Dissection of Highly Correlated Transcription Factor Binding Site Profiles.
• 
  Anupam Saxena, Hod Lipson, Francisco J. Valero Cuevas:
  Functional Inference of Complex Anatomical Tendinous Networks at a Macroscopic Scale via Sparse Experimentation.
• 
  Lars Reichl, Dominik Heide, Siegrid Löwel, Justin C. Crowley, Matthias Kaschube, Fred Wolf:
  Coordinated Optimization of Visual Cortical Maps (II) Numerical Studies.
• 
  Thomas E. Akam, Dimitri M. Kullmann:
  Efficient "Communication through Coherence" Requires Oscillations Structured to Minimize Interference between Signals.
• 
  Roland R. Regoes:
  The Role of Exposure History on HIV Acquisition: Insights from Repeated Low-dose Challenge Studies.
• 
  Yun Lee, Luis Escamilla-Treviño, Richard A. Dixon, Eberhard O. Voit:
  Functional Analysis of Metabolic Channeling and Regulation in Lignin Biosynthesis: A Computational Approach.
• 
  Filippo Cacace, Paola Paci, Valerio Cusimano, Alfredo Germani, Lorenzo Farina:
  Stochastic Modeling of Expression Kinetics Identifies Messenger Half-Lives and Reveals Sequential Waves of Co-ordinated Transcription and Decay.
• 
  Austin T. Hilliard, Julie E. Miller, Steve Horvath, Stephanie A. White:
  Distinct Neurogenomic States in Basal Ganglia Subregions Relate Differently to Singing Behavior in Songbirds.
• 
  Michael J. Tildesley, Sadie J. Ryan:
  Disease Prevention versus Data Privacy: Using Landcover Maps to Inform Spatial Epidemic Models.
• 
  Simon McGregor, Vera Vasas, Phil Husbands, Chrisantha Fernando:
  Evolution of Associative Learning in Chemical Networks.
• 
  Rajamanickam Murugan, Gabriel Kreiman:
  Theory on the Coupled Stochastic Dynamics of Transcription and Splice-Site Recognition.
• 
  Maja Skataric, Eduardo D. Sontag:
  A Characterization of Scale Invariant Responses in Enzymatic Networks.
• 
  Márton Münz, Jotun Hein, Philip C. Biggin:
  The Role of Flexibility and Conformational Selection in the Binding Promiscuity of PDZ Domains.
• 
  Marc P. Hoeppner, Paul P. Gardner, Anthony M. Poole:
  Comparative Analysis of RNA Families Reveals Distinct Repertoires for Each Domain of Life.
• 
  Art F. Y. Poon, Luke C. Swenson, Evelien M. Bunnik, Diana Edo-Matas, Hanneke Schuitemaker, Angélique B. van 't Wout, P. Richard Harrigan:
  Reconstructing the Dynamics of HIV Evolution within Hosts from Serial Deep Sequence Data.
• 
  Sjoerd J. L. van Wijk, Adrien S. J. Melquiond, Sjoerd Jacob de Vries, H. Th. Marc Timmers, Alexandre M. J. J. Bonvin:
  Dynamic Control of Selectivity in the Ubiquitination Pathway Revealed by an ASP to GLU Substitution in an Intra-Molecular Salt-Bridge Network.
• 
  Alexandra Dana, Tamir Tuller:
  Determinants of Translation Elongation Speed and Ribosomal Profiling Biases in Mouse Embryonic Stem Cells.
• 
  Rachel Leander, Shipan Dai, Larry S. Schlesinger, Avner Friedman:
  A Mathematical Model of CR3/TLR2 Crosstalk in the Context of Francisella tularensis Infection.
• 
  Ana Rita Brochado, Sergej Andrejev, Costas D. Maranas, Kiran Raosaheb Patil:
  Impact of Stoichiometry Representation on Simulation of Genotype-Phenotype Relationships in Metabolic Networks.
• 
  Kailash Patil, Daniel Pressnitzer, Shihab A. Shamma, Mounya Elhilali:
  Music in Our Ears: The Biological Bases of Musical Timbre Perception.
• 
  Natali V. Di Russo, Dario A. Estrin, Marcelo A. Marti, Adrian E. Roitberg:
  pH-Dependent Conformational Changes in Proteins and Their Effect on Experimental pK_as: The Case of Nitrophorin 4.
• 
  Samuel M. D. Seaver, Marta Sales-Pardo, Roger Guimerà, Luís A. Nunes Amaral:
  Phenomenological Model for Predicting the Catabolic Potential of an Arbitrary Nutrient.
• 
  Jie Zhu, Alex Mogilner:
  Mesoscopic Model of Actin-Based Propulsion.
• 
  Roman Pleskot, Premysl Pejchar, Viktor Zárský, Christopher J. Staiger, Martin Potocký:
  Structural Insights into the Inhibition of Actin-Capping Protein by Interactions with Phosphatidic Acid and Phosphatidylinositol (4, 5)-Bisphosphate.

Volume 8, Number 12, December 2012

Editorial

• 
  Andreas Prlic, James B. Procter:
  Ten Simple Rules for the Open Development of Scientific Software.

Education Articles

• 
  Russ B. Altman:
  Introduction to Translational Bioinformatics Collection.
• 
  Philip R. O. Payne:
  Chapter 1: Biomedical Knowledge Integration.
• 
  Casey S. Greene, Olga G. Troyanskaya:
  Chapter 2: Data-Driven View of Disease Biology.
• 
  David S. Wishart:
  Chapter 3: Small Molecules and Disease.
• 
  Mileidy W. Gonzalez, Maricel G. Kann:
  Chapter 4: Protein Interactions and Disease.
• 
  Dong-Yeon Cho, Yoo-Ah Kim, Teresa M. Przytycka:
  Chapter 5: Network Biology Approach to Complex Diseases.
• 
  Benjamin J. Raphael:
  Chapter 6: Structural Variation and Medical Genomics.
• 
  Konrad J. Karczewski, Roxana Daneshjou, Russ B. Altman:
  Chapter 7: Pharmacogenomics.
• 
  Ju Han Kim:
  Chapter 8: Biological Knowledge Assembly and Interpretation.
• 
  Nigam H. Shah, Tyler Cole, Mark A. Musen:
  Chapter 9: Analyses Using Disease Ontologies.
• 
  Xiang Zhang, Shunping Huang, Zhaojun Zhang, Wei Wang:
  Chapter 10: Mining Genome-Wide Genetic Markers.
• 
  William S. Bush, Jason H. Moore:
  Chapter 11: Genome-Wide Association Studies.
• 
  Xochitl C. Morgan, Curtis Huttenhower:
  Chapter 12: Human Microbiome Analysis.
• 
  Joshua C. Denny:
  Chapter 13: Mining Electronic Health Records in the Genomics Era.
• 
  Miguel Vazquez, Victor de la Torre, Alfonso Valencia:
  Chapter 14: Cancer Genome Analysis.
• 
  Maria Victoria Schneider, Rafael C. Jiménez:
  Teaching the Fundamentals of Biological Data Integration Using Classroom Games.

Review

• 
  William R. Holmes, Leah Edelstein-Keshet:
  A Comparison of Computational Models for Eukaryotic Cell Shape and Motility.

Research Articles

• 
  Kishore R. Mosaliganti, Ramil R. Noche, Fengzhu Xiong, Ian A. Swinburne, Sean G. Megason:
  ACME: Automated Cell Morphology Extractor for Comprehensive Reconstruction of Cell Membranes.
• 
  Lior Kirsch, Noa Liscovitch, Gal Chechik:
  Localizing Genes to Cerebellar Layers by Classifying ISH Images.
• 
  David W. Schryer, Pearu Peterson, Ardo Illaste, Marko Vendelin:
  Sensitivity Analysis of Flux Determination in Heart by H₂¹⁸O -provided Labeling Using a Dynamic Isotopologue Model of Energy Transfer Pathways.
• 
  Mikhail Shugay, Iñigo Ortiz de Mendíbil, José L. Vizmanos, Francisco J. Novo:
  Genomic Hallmarks of Genes Involved in Chromosomal Translocations in Hematological Cancer.
• 
  Bartek Wilczynski, Ya-Hsin Liu, Zhen Xuan Yeo, Eileen E. M. Furlong:
  Predicting Spatial and Temporal Gene Expression Using an Integrative Model of Transcription Factor Occupancy and Chromatin State.
• 
  Niels Röckendorf, Markus Borschbach, Andreas Frey:
  Molecular Evolution of Peptide Ligands with Custom-Tailored Characteristics for Targeting of Glycostructures.
• 
  Philip J. Murray, Philip K. Maini, Maksim V. Plikus, Cheng-Ming Chuong, Ruth E. Baker:
  Modelling Hair Follicle Growth Dynamics as an Excitable Medium.
• 
  Kirsten E. Eilertson, James G. Booth, Carlos D. Bustamante:
  SnIPRE: Selection Inference Using a Poisson Random Effects Model.
• 
  Alexander N. Volkov, Nico A. J. van Nuland:
  Electron Transfer Interactome of Cytochrome c.
• 
  Ryan T. Canolty, Karunesh Ganguly, Jose M. Carmena:
  Task-Dependent Changes in Cross-Level Coupling between Single Neurons and Oscillatory Activity in Multiscale Networks.
• 
  Yang Ding, Sarah S. Sharpe, Andrew Masse, Daniel I. Goldman:
  Mechanics of Undulatory Swimming in a Frictional Fluid.
• 
  Robert C. Brewster, Daniel L. Jones, Rob Phillips:
  Tuning Promoter Strength through RNA Polymerase Binding Site Design in Escherichia coli.
• 
  David M. Richards, Emma Greer, Azahara C. Martin, Graham Moore, Peter J. Shaw, Martin Howard:
  Quantitative Dynamics of Telomere Bouquet Formation.
• 
  Jornt R. De Gruijl, Paolo Bazzigaluppi, Marcel T. G. de Jeu, Chris I. De Zeeuw:
  Climbing Fiber Burst Size and Olivary Sub-threshold Oscillations in a Network Setting.
• 
  Katja Rateitschak, Felix Winter, Falko Lange, Robert Jaster, Olaf Wolkenhauer:
  Parameter Identifiability and Sensitivity Analysis Predict Targets for Enhancement of STAT1 Activity in Pancreatic Cancer and Stellate Cells.
• 
  Jordi van Gestel, Martin A. Nowak, Corina E. Tarnita:
  The Evolution of Cell-to-Cell Communication in a Sporulating Bacterium.
• 
  Jens Vindahl Kringelum, Claus Lundegaard, Ole Lund, Morten Nielsen:
  Reliable B Cell Epitope Predictions: Impacts of Method Development and Improved Benchmarking.
• 
  Claudia Coronnello, Ryan J. Hartmaier, Arshi Arora, Luai Huleihel, Kusum V. Pandit, Abha S. Bais, Michael Butterworth, Naftali Kaminski, Gary D. Stormo, Steffi Oesterreich, Panayiotis V. Benos:
  Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density.
• 
  James P. O'Dwyer, Steven W. Kembel, Jessica L. Green:
  Phylogenetic Diversity Theory Sheds Light on the Structure of Microbial Communities.
• 
  Oliver Ratmann, Gé Donker, Adam Meijer, Christophe Fraser, Katia Koelle:
  Phylodynamic Inference and Model Assessment with Approximate Bayesian Computation: Influenza as a Case Study.
• 
  Mark C. W. van Rossum, Maria Shippi, Adam B. Barrett:
  Soft-bound Synaptic Plasticity Increases Storage Capacity.
• 
  Robert Egger, Rajeevan T. Narayanan, Moritz Helmstaedter, Christiaan P. J. de Kock, Marcel Oberländer:
  3D Reconstruction and Standardization of the Rat Vibrissal Cortex for Precise Registration of Single Neuron Morphology.
• 
  Wenlian Qiao, Gerald T. Quon, Elizabeth Csaszar, Mei Yu, Quaid Morris, Peter W. Zandstra:
  PERT: A Method for Expression Deconvolution of Human Blood Samples from Varied Microenvironmental and Developmental Conditions.
• 
  Ranjan V. Mannige, Charles L. Brooks III, Eugene I. Shakhnovich:
  A Universal Trend among Proteomes Indicates an Oily Last Common Ancestor.
• 
  Chris A. Kieslich, Dimitrios Morikis:
  The Two Sides of Complement C3d: Evolution of Electrostatics in a Link between Innate and Adaptive Immunity.
• 
  Ting Xiang, Debajyoti Ray, Terry Lohrenz, Peter Dayan, P. Read Montague:
  Computational Phenotyping of Two-Person Interactions Reveals Differential Neural Response to Depth-of-Thought.
• 
  Federica Chiappori, Ivan Merelli, Giorgio Colombo, Luciano Milanesi, Giulia Morra:
  Molecular Mechanism of Allosteric Communication in Hsp70 Revealed by Molecular Dynamics Simulations.
• 
  Mark J. Bradshaw, Man C. Cheung, Daniel J. Ehrlich, Michael L. Smith:
  Using Molecular Mechanics to Predict Bulk Material Properties of Fibronectin Fibers.
• 
  Tobias Warnecke, Fran Supek, Ben Lehner:
  Nucleoid-Associated Proteins Affect Mutation Dynamics in E. coli in a Growth Phase-Specific Manner.
• 
  Juexuan Long, Michael Junkin, Pak Kin Wong, James B. Hoying, Pierre Deymier:
  Calcium Wave Propagation in Networks of Endothelial Cells: Model-based Theoretical and Experimental Study.
• 
  Cameron W. Harvey, Huijing Du, Zhiliang Xu, Dale Kaiser, Igor S. Aranson, Mark S. Alber:
  Interconnected Cavernous Structure of Bacterial Fruiting Bodies.
• 
  Hujun Shen, Hui Sun, Guohui Li:
  What Is the Role of Motif D in the Nucleotide Incorporation Catalyzed by the RNA-dependent RNA Polymerase from Poliovirus?