PLoS Computational Biology, Volume 7

Volume 7, Number 1, January 2011

Editorials

• 
  Rosemary Dickin, Cecy Marden, Andrew M. Collings, Ruth Nussinov, Philip E. Bourne:
  A Review of 2010 for PLoS Computational Biology.
• 
  Philip E. Bourne:
  Ten Simple Rules for Getting Ahead as a Computational Biologist in Academia.

Research Articles

• 
  Iain Melvin, Jason Weston, William Stafford Noble, Christina S. Leslie:
  Detecting Remote Evolutionary Relationships among Proteins by Large-Scale Semantic Embedding.
• 
  Hao Chen, Haipeng Xing, Nancy Ruonan Zhang:
  Estimation of Parent Specific DNA Copy Number in Tumors using High-Density Genotyping Arrays.
• 
  Daniel M. Cornforth, Timothy C. Reluga, Eunha Shim, Chris T. Bauch, Alison P. Galvani, Lauren Ancel Meyers:
  Erratic Flu Vaccination Emerges from Short-Sighted Behavior in Contact Networks.
• 
  Peter A. Appleby, Gerd Kempermann, Laurenz Wiskott:
  The Role of Additive Neurogenesis and Synaptic Plasticity in a Hippocampal Memory Model with Grid-Cell Like Input.
• 
  Nozomu Yachie, Rintaro Saito, Naoyuki Sugiyama, Masaru Tomita, Yasushi Ishihama:
  Integrative Features of the Yeast Phosphoproteome and Protein-Protein Interaction Map.
• 
  Jussi T. Koivumäki, Topi Korhonen, Pasi Tavi:
  Impact of Sarcoplasmic Reticulum Calcium Release on Calcium Dynamics and Action Potential Morphology in Human Atrial Myocytes: A Computational Study.
• 
  Marc Herant, Cheng-Yuk Lee, Micah Dembo, Volkmar Heinrich:
  Protrusive Push versus Enveloping Embrace: Computational Model of Phagocytosis Predicts Key Regulatory Role of Cytoskeletal Membrane Anchors.
• 
  Elise Payzan-LeNestour, Peter Bossaerts:
  Risk, Unexpected Uncertainty, and Estimation Uncertainty: Bayesian Learning in Unstable Settings.
• 
  Dina Zhabinskaya, Craig J. Benham:
  Theoretical Analysis of the Stress Induced B-Z Transition in Superhelical DNA.
• 
  Adam B. Barrett, Anil K. Seth:
  Practical Measures of Integrated Information for Time-Series Data.
• 
  Charlotte N. Henrichsen, Gábor Csárdi, Marie-Thérèse Zabot, Carmela Fusco, Sven Bergmann, Giuseppe Merla, Alexandre Reymond:
  Using Transcription Modules to Identify Expression Clusters Perturbed in Williams-Beuren Syndrome.
• 
  Srdjan Ostojic, Nicolas Brunel:
  From Spiking Neuron Models to Linear-Nonlinear Models.
• 
  Peter Langfelder, Rui Luo, Michael C. Oldham, Steve Horvath:
  Is My Network Module Preserved and Reproducible?
• 
  Bing Liu, Jing Zhang, Pei Yi Tan, David Hsu, Anna M. Blom, Benjamin Leong, Sunil Sethi, Bow Ho, Jeak Ling Ding, P. S. Thiagarajan:
  A Computational and Experimental Study of the Regulatory Mechanisms of the Complement System.
• 
  Thomas J. Sharpton, Samantha J. Riesenfeld, Steven W. Kembel, Joshua Ladau, James P. O'Dwyer, Jessica L. Green, Jonathan A. Eisen, Katherine S. Pollard:
  PhylOTU: A High-Throughput Procedure Quantifies Microbial Community Diversity and Resolves Novel Taxa from Metagenomic Data.
• 
  Lixia Yao, Anna Divoli, Ilya Mayzus, James A. Evans, Andrey Rzhetsky:
  Benchmarking Ontologies: Bigger or Better?
• 
  Srinivas Ramachandran, Lisa Vogel, Brian D. Strahl, Nikolay V. Dokholyan:
  Thermodynamic Stability of Histone H3 Is a Necessary but not Sufficient Driving Force for its Evolutionary Conservation.
• 
  Vincent H. Tam, Michael Nikolaou:
  A Novel Approach to Pharmacodynamic Assessment of Antimicrobial Agents: New Insights to Dosing Regimen Design.
• 
  Sreedevi Varier, Marcus Kaiser:
  Neural Development Features: Spatio-Temporal Development of the Caenorhabditis elegans Neuronal Network.
• 
  Peter Buske, Jörg Galle, Nick Barker, Gabriela Aust, Hans Clevers, Markus Loeffler:
  A Comprehensive Model of the Spatio-Temporal Stem Cell and Tissue Organisation in the Intestinal Crypt.
• 
  Wenjun Zheng, Anthony Auerbach:
  Decrypting the Sequence of Structural Events during the Gating Transition of Pentameric Ligand-Gated Ion Channels Based on an Interpolated Elastic Network Model.
• 
  Leon French, Paul Pavlidis:
  Relationships between Gene Expression and Brain Wiring in the Adult Rodent Brain.
• 
  Chong Shou, Nitin Bhardwaj, Hugo Y. K. Lam, Koon-Kiu Yan, Philip M. Kim, Michael Snyder, Mark B. Gerstein:
  Measuring the Evolutionary Rewiring of Biological Networks.
• 
  Stefano Vanni, Marilisa Neri, Ivano Tavernelli, Ursula Rothlisberger:
  Predicting Novel Binding Modes of Agonists to β Adrenergic Receptors Using All-Atom Molecular Dynamics Simulations.

Volume 7, Number 2, February 2011

Message from ISCB

• 
  Richard H. Lathrop, Burkhard Rost:
  ISCB Public Policy Statement on Open Access to Scientific and Technical Research Literature.

Perspectives

• 
  Xiaohong Li, Patricia L. Blount, Thomas L. Vaughan, Brian J. Reid:
  Application of Biomarkers in Cancer Risk Management: Evaluation from Stochastic Clonal Evolutionary and Dynamic System Optimization Points of View.
• 
  Michael Hawrylycz, Richard A. Baldock, Albert Burger, Tsutomu Hashikawa, G. Allan Johnson, Maryann E. Martone, Lydia Ng, Christopher Lau, Stephen D. Larson, Jonathan Nissanov, Luis Puelles, Seth Ruffins, Fons J. Verbeek, Ilya Zaslavsky, Jyl Boline:
  Digital Atlasing and Standardization in the Mouse Brain.

Research Articles

• 
  Erez Persi, David Hansel, Lionel Nowak, Pascal Barone, Carl van Vreeswijk:
  Power-Law Input-Output Transfer Functions Explain the Contrast-Response and Tuning Properties of Neurons in Visual Cortex.
• 
  Jiahai Shi, Nanyu Han, Liangzhong Lim, Shixiong Lua, J. Sivaraman, Lushan Wang, Yuguang Mu, Jianxing Song:
  Dynamically-Driven Inactivation of the Catalytic Machinery of the SARS 3C-Like Protease by the N214A Mutation on the Extra Domain.
• 
  Anna Grosberg, Po-Ling Kuo, Chin-Lin Guo, Nicholas A. Geisse, Mark-Anthony Bray, William J. Adams, Sean P. Sheehy, Kevin Kit Parker:
  Self-Organization of Muscle Cell Structure and Function.
• 
  Didier Delignières, Kjerstin Torre, Pierre-Louis Bernard:
  Transition from Persistent to Anti-Persistent Correlations in Postural Sway Indicates Velocity-Based Control.
• 
  Chikako Ragan, Michael Zuker, Mark A. Ragan:
  Quantitative Prediction of miRNA-mRNA Interaction Based on Equilibrium Concentrations.
• 
  Mark A. Bourjaily, Paul Miller:
  Synaptic Plasticity and Connectivity Requirements to Produce Stimulus-Pair Specific Responses in Recurrent Networks of Spiking Neurons.
• 
  Magali Michaut, Anastasia Baryshnikova, Michael Costanzo, Chad L. Myers, Brenda J. Andrews, Charles Boone, Gary D. Bader:
  Protein Complexes are Central in the Yeast Genetic Landscape.
• 
  José M. Ponciano, Marcos A. Capistran:
  First Principles Modeling of Nonlinear Incidence Rates in Seasonal Epidemics.
• 
  Martin Boerlin, Sophie Denève:
  Spike-Based Population Coding and Working Memory.
• 
  Amber M. Smith, Frederick R. Adler, Julie L. McAuley, Ryan N. Gutenkunst, Ruy M. Ribeiro, Jonathan A. McCullers, Alan S. Perelson:
  Effect of 1918 PB1-F2 Expression on Influenza A Virus Infection Kinetics.
• 
  André G. Mendonça, Renato J. Alves, José B. Pereira-Leal:
  Loss of Genetic Redundancy in Reductive Genome Evolution.
• 
  Mario A. Marchisio, Jörg Stelling:
  Automatic Design of Digital Synthetic Gene Circuits.
• 
  Neda Bagheri, Marisa Shiina, Douglas A. Lauffenburger, W. Michael Korn:
  A Dynamical Systems Model for Combinatorial Cancer Therapy Enhances Oncolytic Adenovirus Efficacy by MEK-Inhibition.
• 
  Wei Chen, Jizhong Lou, Jen Hsin, Klaus Schulten, Stephen C. Harvey, Cheng Zhu:
  Molecular Dynamics Simulations of Forced Unbending of Integrin α_Vβ₃.
• 
  Jens Keilwagen, Jan Grau, Ivan A. Paponov, Stefan Posch, Marc Strickert, Ivo Grosse:
  De-Novo Discovery of Differentially Abundant Transcription Factor Binding Sites Including Their Positional Preference.
• 
  Luciano Marcon, Carlos G. Arqués, Miguel S. Torres, James Sharpe:
  A Computational Clonal Analysis of the Developing Mouse Limb Bud.
• 
  T. Déirdre Hollingsworth, Don Klinkenberg, Hans Heesterbeek, Roy M. Anderson:
  Mitigation Strategies for Pandemic Influenza A: Balancing Conflicting Policy Objectives.
• 
  Rajat Singhania, R. Michael Sramkoski, James W. Jacobberger, John J. Tyson:
  A Hybrid Model of Mammalian Cell Cycle Regulation.
• 
  John E. Pearson, Paul Krapivsky, Alan S. Perelson:
  Stochastic Theory of Early Viral Infection: Continuous versus Burst Production of Virions.
• 
  Lav R. Varshney, Beth L. Chen, Eric Paniagua, David H. Hall, Dmitri B. Chklovskii:
  Structural Properties of the Caenorhabditis elegans Neuronal Network.
• 
  David M. Holloway, Francisco J. P. Lopes, Luciano da Fontoura Costa, Bruno Augusto Nassif Travençolo, Nina Golyandina, Konstantin Usevich, Alexander V. Spirov:
  Gene Expression Noise in Spatial Patterning: hunchback Promoter Structure Affects Noise Amplitude and Distribution in Drosophila Segmentation.
• 
  Sheeja M. Krishnan, Narendra M. Dixit:
  Ribavirin-Induced Anemia in Hepatitis C Virus Patients Undergoing Combination Therapy.
• 
  Hung-Yun Lin, Cornelia B. Landersdorfer, David London, Ran Meng, Chang-Uk Lim, Cassie Lin, Sharon Lin, Heng-Yuan Tang, David Brown, Brian Van Scoy, Robert Kulawy, Lurdes Queimado, George L. Drusano, Arnold Louie, Faith B. Davis, Shaker A. Mousa, Paul J. Davis:
  Pharmacodynamic Modeling of Anti-Cancer Activity of Tetraiodothyroacetic Acid in a Perfused Cell Culture System.
• 
  Maria D. Chikina, Olga G. Troyanskaya:
  Accurate Quantification of Functional Analogy among Close Homologs.
• 
  Wei Liu, Anuj Srivastava, Jinfeng Zhang:
  A Mathematical Framework for Protein Structure Comparison.
• 
  Danzhi Huang, Amedeo Caflisch:
  The Free Energy Landscape of Small Molecule Unbinding.

Volume 7, Number 3, March 2011

Perspectives

• 
  A. Murat Eren:
  PLoS Computational Biology Conference Postcard from PSB 2011.
• 
  Paulien Hogeweg:
  The Roots of Bioinformatics in Theoretical Biology.

Research Articles

• 
  Edward J. A. Turnham, Daniel A. Braun, Daniel M. Wolpert:
  Inferring Visuomotor Priors for Sensorimotor Learning.
• 
  Rachel Cavill, Atanas Kamburov, James K. Ellis, Toby J. Athersuch, Marcus S. C. Blagrove, Ralf Herwig, Timothy M. D. Ebbels, Hector C. Keun:
  Consensus-Phenotype Integration of Transcriptomic and Metabolomic Data Implies a Role for Metabolism in the Chemosensitivity of Tumour Cells.
• 
  Kelvin Xi Zhang, B. F. Francis Ouellette:
  CAERUS: Predicting CAncER oUtcomeS Using Relationship between Protein Structural Information, Protein Networks, Gene Expression Data, and Mutation Data.
• 
  Vitaly A. Selivanov, Tatyana V. Votyakova, Violetta N. Pivtoraiko, Jennifer Zeak, Tatiana Sukhomlin, Massimo Trucco, Josep Roca, Marta Cascante:
  Reactive Oxygen Species Production by Forward and Reverse Electron Fluxes in the Mitochondrial Respiratory Chain.
• 
  Matthew A. Oberhardt, Jacek Puchalka, Vítor A. P. Martins dos Santos, Jason A. Papin:
  Reconciliation of Genome-Scale Metabolic Reconstructions for Comparative Systems Analysis.
• 
  Lun Yang, Kejian Wang, Jian Chen, Anil G. Jegga, Heng Luo, Leming Shi, Chunling Wan, Xizhi Guo, Shengying Qin, Guang He, Guoyin Feng, Lin He:
  Exploring Off-Targets and Off-Systems for Adverse Drug Reactions via Chemical-Protein Interactome - Clozapine-Induced Agranulocytosis as a Case Study.
• 
  Trevelyan J. McKinley, Pablo R. Murcia, Julia R. Gog, Mariana Varela, James L. N. Wood:
  A Bayesian Approach to Analyse Genetic Variation within RNA Viral Populations.
• 
  Sanggyun Kim, David Putrino, Soumya Ghosh, Emery N. Brown:
  A Granger Causality Measure for Point Process Models of Ensemble Neural Spiking Activity.
• 
  Jeffrey D. Fitzgerald, Lawrence C. Sincich, Tatyana O. Sharpee:
  Minimal Models of Multidimensional Computations.
• 
  Cesar A. López, Alex H. de Vries, Siewert J. Marrink:
  Molecular Mechanism of Cyclodextrin Mediated Cholesterol Extraction.
• 
  Tamar Pashut, Shuki Wolfus, Alex Friedman, Michal Lavidor, Izhar Bar-Gad, Yosef Yeshurun, Alon Korngreen:
  Mechanisms of Magnetic Stimulation of Central Nervous System Neurons.
• 
  Jordi Silvestre-Ryan, Yuchun Lin, Jhih-Wei Chu:
  "Fluctuograms" Reveal the Intermittent Intra-Protein Communication in Subtilisin Carlsberg and Correlate Mechanical Coupling with Co-Evolution.
• 
  Nobuto Takeuchi, Paulien Hogeweg, Eugene V. Koonin:
  On the Origin of DNA Genomes: Evolution of the Division of Labor between Template and Catalyst in Model Replicator Systems.
• 
  Ioannis Vlachos, Cyril Herry, Andreas Lüthi, Ad Aertsen, Arvind Kumar:
  Context-Dependent Encoding of Fear and Extinction Memories in a Large-Scale Network Model of the Basal Amygdala.
• 
  Pavitra Krishnaswamy, Emery N. Brown, Hugh M. Herr:
  Human Leg Model Predicts Ankle Muscle-Tendon Morphology, State, Roles and Energetics in Walking.
• 
  Dezhe Z. Jin, Alexay A. Kozhevnikov:
  A Compact Statistical Model of the Song Syntax in Bengalese Finch.
• 
  Luis E. C. Rocha, Fredrik Liljeros, Petter Holme:
  Simulated Epidemics in an Empirical Spatiotemporal Network of 50, 185 Sexual Contacts.
• 
  Holk Cruse, Rüdiger Wehner:
  No Need for a Cognitive Map: Decentralized Memory for Insect Navigation.
• 
  Hannes Lüling, Ida Siveke, Benedikt Grothe, Christian Leibold:
  Frequency-Invariant Representation of Interaural Time Differences in Mammals.
• 
  Vincent T. Metzger, James O. Lloyd-Smith, Leor S. Weinberger:
  Autonomous Targeting of Infectious Superspreaders Using Engineered Transmissible Therapies.
• 
  Morten Ernebjerg, Roy Kishony:
  Dynamic Phenotypic Clustering in Noisy Ecosystems.
• 
  Matteo Osella, Carla Bosia, Davide Corà, Michele Caselle:
  The Role of Incoherent MicroRNA-Mediated Feedforward Loops in Noise Buffering.
• 
  Daniele Linaro, Marco Storace, Michele Giugliano:
  Accurate and Fast Simulation of Channel Noise in Conductance-Based Model Neurons by Diffusion Approximation.
• 
  Heming Xing, Paul D. McDonagh, Jadwiga R. Bienkowska, Tanya Cashorali, Karl Runge, Robert E. Miller, Dave DeCaprio, Bruce Church, Ronenn Roubenoff, Iya G. Khalil, John Carulli:
  Causal Modeling Using Network Ensemble Simulations of Genetic and Gene Expression Data Predicts Genes Involved in Rheumatoid Arthritis.
• 
  Lars Skjaerven, Barry J. Grant, Arturo Muga, Knut Teigen, James Andrew McCammon, Nathalie Reuter, Aurora Martinez:
  Conformational Sampling and Nucleotide-Dependent Transitions of the GroEL Subunit Probed by Unbiased Molecular Dynamics Simulations.
• 
  Oskar Hallatschek:
  Noise Driven Evolutionary Waves.
• 
  Richard I. Joh, Joshua S. Weitz:
  To Lyse or Not to Lyse: Transient-Mediated Stochastic Fate Determination in Cells Infected by Bacteriophages.
• 
  Pilhwa Lee, Charles W. Wolgemuth:
  Crawling Cells Can Close Wounds without Purse Strings or Signaling.
• 
  Luca Giuggioli, Jonathan R. Potts, Stephen Harris:
  Animal Interactions and the Emergence of Territoriality.
• 
  Elijah Roberts, Andrew T. Magis, Julio O. Ortiz, Wolfgang Baumeister, Zaida Luthey-Schulten:
  Noise Contributions in an Inducible Genetic Switch: A Whole-Cell Simulation Study.
• 
  Jun Izawa, Reza Shadmehr:
  Learning from Sensory and Reward Prediction Errors during Motor Adaptation.
• 
  Tomer Shlomi, Tomer Benyamini, Eyal Gottlieb, Roded Sharan, Eytan Ruppin:
  Genome-Scale Metabolic Modeling Elucidates the Role of Proliferative Adaptation in Causing the Warburg Effect.
• 
  François Serra, Leonardo Arbiza, Joaquín Dopazo, Hernán Dopazo:
  Natural Selection on Functional Modules, a Genome-Wide Analysis.
• 
  Roger D. Kouyos, Pia Abel zur Wiesch, Sebastian Bonhoeffer:
  Informed Switching Strongly Decreases the Prevalence of Antibiotic Resistance in Hospital Wards.
• 
  Yoo-Ah Kim, Stefan Wuchty, Teresa M. Przytycka:
  Identifying Causal Genes and Dysregulated Pathways in Complex Diseases.
• 
  Jordan A. Taylor, Richard B. Ivry:
  Flexible Cognitive Strategies during Motor Learning.
• 
  Dana Bar-On, Esther Nachliel, Menachem Gutman, Uri Ashery:
  Dynamic Conformational Changes in MUNC18 Prevent Syntaxin Binding.
• 
  Francesco Raimondi, Guillem Portella, Modesto Orozco, Francesca Fanelli:
  Nucleotide Binding Switches the Information Flow in Ras GTPases.
• 
  Melody K. Morris, Julio Saez-Rodriguez, David C. Clarke, Peter K. Sorger, Douglas A. Lauffenburger:
  Training Signaling Pathway Maps to Biochemical Data with Constrained Fuzzy Logic: Quantitative Analysis of Liver Cell Responses to Inflammatory Stimuli.
• 
  Alvaro Sanchez, Hernan G. Garcia, Daniel L. Jones, Rob Phillips, Jané Kondev:
  Effect of Promoter Architecture on the Cell-to-Cell Variability in Gene Expression.
• 
  Marjet Elemans, Rodolphe Thiébaut, Amitinder Kaur, Becca Asquith:
  Quantification of the Relative Importance of CTL, B Cell, NK Cell, and Target Cell Limitation in the Control of Primary SIV-Infection.
• 
  Rilei Yu, David J. Craik, Quentin Kaas:
  Blockade of Neuronal α7-nAChR by α-Conotoxin ImI Explained by Computational Scanning and Energy Calculations.

Volume 7, Number 4, April 2011

Perspective

• 
  Dagmar Waltemath, Richard R. Adams, Daniel A. Beard, Frank T. Bergmann, Upinder S. Bhalla, Randall Britten, Vijayalakshmi Chelliah, Mike T. Cooling, Jonathan Cooper, Edmund J. Crampin, Alan Garny, Stefan Hoops, Michael Hucka, Peter J. Hunter, Edda Klipp, Camille Laibe, Andrew K. Miller, Ion I. Moraru, David P. Nickerson, Poul M. F. Nielsen, Macha Nikolski, Sven Sahle, Herbert M. Sauro, Henning Schmidt, Jacky L. Snoep, Dominic P. Tolle, Olaf Wolkenhauer, Nicolas Le Novère:
  Minimum Information About a Simulation Experiment (MIASE).

Review

• 
  Alexandra Jilkine, Leah Edelstein-Keshet:
  A Comparison of Mathematical Models for Polarization of Single Eukaryotic Cells in Response to Guided Cues.

Research Articles

• 
  James M. McCaw, Nimalan Arinaminpathy, Aeron C. Hurt, Jodie McVernon, Angela R. McLean:
  A Mathematical Framework for Estimating Pathogen Transmission Fitness and Inoculum Size Using Data from a Competitive Mixtures Animal Model.
• 
  Jessica M. Conway, Daniel Coombs:
  A Stochastic Model of Latently Infected Cell Reactivation and Viral Blip Generation in Treated HIV Patients.
• 
  Li Xie, Thomas Evangelidis, Lei Xie, Philip E. Bourne:
  Drug Discovery Using Chemical Systems Biology: Weak Inhibition of Multiple Kinases May Contribute to the Anti-Cancer Effect of Nelfinavir.
• 
  Joël Tabak, John Rinzel, Richard Bertram:
  Quantifying the Relative Contributions of Divisive and Subtractive Feedback to Rhythm Generation.
• 
  Harikrishnan Parameswaran, Arnab Majumdar, Béla Suki:
  Linking Microscopic Spatial Patterns of Tissue Destruction in Emphysema to Macroscopic Decline in Stiffness Using a 3D Computational Model.
• 
  Quentin J. M. Huys, Roshan Cools, Martin Gölzer, Eva Friedel, Andreas Heinz, Raymond J. Dolan, Peter Dayan:
  Disentangling the Roles of Approach, Activation and Valence in Instrumental and Pavlovian Responding.
• 
  Denis Bucher, Barry J. Grant, Phineus R. Markwick, James Andrew McCammon:
  Accessing a Hidden Conformation of the Maltose Binding Protein Using Accelerated Molecular Dynamics.
• 
  Dong Long, Rafael Brüschweiler:
  In Silico Elucidation of the Recognition Dynamics of Ubiquitin.
• 
  Saket Navlakha, Carl Kingsford:
  Network Archaeology: Uncovering Ancient Networks from Present-Day Interactions.
• 
  Peng Qiu, Andrew J. Gentles, Sylvia K. Plevritis:
  Discovering Biological Progression Underlying Microarray Samples.
• 
  Karen A. Selz:
  A Third Measure-Metastable State in the Dynamics of Spontaneous Shape Change in Healthy Human's White Cells.
• 
  Jin Wang, Yong Wang, Xiakun Chu, Stephen J. Hagen, Wei Han, Erkang Wang:
  Multi-Scaled Explorations of Binding-Induced Folding of Intrinsically Disordered Protein Inhibitor IA3 to its Target Enzyme.
• 
  Regan Blythe Towal, Brian W. Quist, Venkatesh Gopal, Joseph H. Solomon, Mitra J. Z. Hartmann:
  The Morphology of the Rat Vibrissal Array: A Model for Quantifying Spatiotemporal Patterns of Whisker-Object Contact.
• 
  Sabine Schilling, Maria Willecke, Tinri Aegerter-Wilmsen, Olaf A. Cirpka, Konrad Basler, Christian von Mering:
  Cell-Sorting at the A/P Boundary in the Drosophila Wing Primordium: A Computational Model to Consolidate Observed Non-Local Effects of Hh Signaling.
• 
  Matteo D'Antonio, Francesca D. Ciccarelli:
  Modification of Gene Duplicability during the Evolution of Protein Interaction Network.
• 
  Jesse Engelberg, Anirban Datta, Keith E. Mostov, C. Anthony Hunt:
  MDCK Cystogenesis Driven by Cell Stabilization within Computational Analogues.

Volume 7, Number 5, May 2011

Editorial

• 
  Sebastian J. Schultheiß:
  Ten Simple Rules for Providing a Scientific Web Resource.

Education

• 
  Frank Emmert-Streib, Galina V. Glazko:
  Pathway Analysis of Expression Data: Deciphering Functional Building Blocks of Complex Diseases.

Research Articles

• 
  Guillaume Drion, Laurent Massotte, Rodolphe Sepulchre, Vincent Seutin:
  How Modeling Can Reconcile Apparently Discrepant Experimental Results: The Case of Pacemaking in Dopaminergic Neurons.
• 
  Daniel-Adriano Silva, Gregory R. Bowman, Alejandro Sosa-Peinado, Xuhui Huang:
  A Role for Both Conformational Selection and Induced Fit in Ligand Binding by the LAO Protein.
• 
  Mohammad Mehdi Keramati, Amir Dezfouli, Payam Piray:
  Speed/Accuracy Trade-Off between the Habitual and the Goal-Directed Processes.
• 
  Elena Papaleo, Valeria Ranzani, Farida Tripodi, Alessandro Vitriolo, Claudia Cirulli, Piercarlo Fantucci, Lilia Alberghina, Marco Vanoni, Luca De Gioia, Paola Coccetti:
  An Acidic Loop and Cognate Phosphorylation Sites Define a Molecular Switch That Modulates Ubiquitin Charging Activity in Cdc34-Like Enzymes.
• 
  Thomas O'Hara, László Virág, András Varró, Yoram Rudy:
  Simulation of the Undiseased Human Cardiac Ventricular Action Potential: Model Formulation and Experimental Validation.
• 
  Tin Yau Pang, Sergei Maslov:
  A Toolbox Model of Evolution of Metabolic Pathways on Networks of Arbitrary Topology.
• 
  Andrew W. McPherson, Fereydoun Hormozdiari, Abdalnasser Zayed, Ryan Giuliany, Gavin Ha, Mark G. F. Sun, Malachi Griffith, Alireza Heravi Moussavi, Janine Senz, Nataliya Melnyk, Marina Pacheco, Marco A. Marra, Martin Hirst, Torsten O. Nielsen, Süleyman Cenk Sahinalp, David G. Huntsman, Sohrab P. Shah:
  deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data.
• 
  Yunkyu Sohn, Myung-Kyu Choi, Yong-Yeol Ahn, Junho Lee, Jaeseung Jeong:
  Topological Cluster Analysis Reveals the Systemic Organization of the Caenorhabditis elegans Connectome.
• 
  Louis-Emmanuel Martinet, Denis Sheynikhovich, Karim Benchenane, Angelo Arleo:
  Spatial Learning and Action Planning in a Prefrontal Cortical Network Model.
• 
  Yun Lee, Fang Chen, Lina Gallego-Giraldo, Richard A. Dixon, Eberhard O. Voit:
  Integrative Analysis of Transgenic Alfalfa (Medicago sativa L.) Suggests New Metabolic Control Mechanisms for Monolignol Biosynthesis.
• 
  Jessica Nasica-Labouze, Massimiliano Meli, Philippe Derreumaux, Giorgio Colombo, Normand Mousseau:
  A Multiscale Approach to Characterize the Early Aggregation Steps of the Amyloid-Forming Peptide GNNQQNY from the Yeast Prion Sup-35.
• 
  Emili Balaguer-Ballester, Christopher C. Lapish, Jeremy K. Seamans, Daniel Durstewitz:
  Attracting Dynamics of Frontal Cortex Ensembles during Memory-Guided Decision-Making.
• 
  Volker Pernice, Benjamin Staude, Stefano Cardanobile, Stefan Rotter:
  How Structure Determines Correlations in Neuronal Networks.
• 
  Christian G. Fink, Victoria Booth, Michal Zochowski:
  Cellularly-Driven Differences in Network Synchronization Propensity Are Differentially Modulated by Firing Frequency.
• 
  Wiebke Potjans, Markus Diesmann, Abigail Morrison:
  An Imperfect Dopaminergic Error Signal Can Drive Temporal-Difference Learning.
• 
  Alain Pumir, Boris Shraiman:
  Epistasis in a Model of Molecular Signal Transduction.
• 
  Alistair N. Boettiger, Peter L. Ralph, Steven N. Evans:
  Transcriptional Regulation: Effects of Promoter Proximal Pausing on Speed, Synchrony and Reliability.
• 
  Freya Klepsch, Peter Chiba, Gerhard F. Ecker:
  Exhaustive Sampling of Docking Poses Reveals Binding Hypotheses for Propafenone Type Inhibitors of P-Glycoprotein.
• 
  Dan Siegal-Gaskins, Maria Katherine Mejia-Guerra, Gregory D. Smith, Erich Grotewold:
  Emergence of Switch-Like Behavior in a Large Family of Simple Biochemical Networks.
• 
  Hilary Phenix, Katy Morin, Cory Batenchuk, Jacob Parker, Vida Abedi, Liu Yang, Lioudmila Tepliakova, Theodore J. Perkins, Mads Kærn:
  Quantitative Epistasis Analysis and Pathway Inference from Genetic Interaction Data.
• 
  Doron Kabaso, Roie Shlomovitz, Kathrin Schloen, Theresia Stradal, Nir S. Gov:
  Theoretical Model for Cellular Shapes Driven by Protrusive and Adhesive Forces.
• 
  Pawel Krupinski, Vijay Chickarmane, Carsten Peterson:
  Simulating the Mammalian Blastocyst - Molecular and Mechanical Interactions Pattern the Embryo.
• 
  Jonathan Platkiewicz, Romain Brette:
  Impact of Fast Sodium Channel Inactivation on Spike Threshold Dynamics and Synaptic Integration.
• 
  Abdullah Hamadeh, Mark A. J. Roberts, Elias August, Patrick E. McSharry, Philip K. Maini, Judith P. Armitage, Antonis Papachristodoulou:
  Feedback Control Architecture and the Bacterial Chemotaxis Network.
• 
  Roberto F. S. Andrade, Ivan C. Rocha-Neto, Leonardo B. L. Santos, Charles N. de Santana, Marcelo V. C. Diniz, Thierry Petit Lobão, Aristóteles Góes-Neto, Suani T. R. Pinho, Charbel Niño El-Hani:
  Detecting Network Communities: An Application to Phylogenetic Analysis.
• 
  Andrea Sottoriva, Louis Vermeulen, Simon Tavaré:
  Modeling Evolutionary Dynamics of Epigenetic Mutations in Hierarchically Organized Tumors.
• 
  Jonathan Perreault, Zasha Weinberg, Adam Roth, Olivia Popescu, Pascal Chartrand, Gerardo Ferbeyre, Ronald R. Breaker:
  Identification of Hammerhead Ribozymes in All Domains of Life Reveals Novel Structural Variations.
• 
  Robert P. Erickson, Zhiyuan Jia, Steven P. Gross, Clare C. Yu:
  How Molecular Motors Are Arranged on a Cargo Is Important for Vesicular Transport.
• 
  Lior Wolf, Chen Goldberg, Nathan Manor, Roded Sharan, Eytan Ruppin:
  Gene Expression in the Rodent Brain is Associated with Its Regional Connectivity.
• 
  Zane N. Aldworth, Alexander G. Dimitrov, Graham I. Cummins, Tomás Gedeon, John P. Miller:
  Temporal Encoding in a Nervous System.
• 
  Olga V. Kalinina, Oliver Wichmann, Gordana Apic, Robert B. Russell:
  Combinations of Protein-Chemical Complex Structures Reveal New Targets for Established Drugs.
• 
  Ying Zhang, Mark T. Romanish, Dixie L. Mager:
  Distributions of Transposable Elements Reveal Hazardous Zones in Mammalian Introns.

Volume 7, Number 6, June 2011

Editorial

• 
  Philip E. Bourne, Virginia Barbour:
  Ten Simple Rules for Building and Maintaining a Scientific Reputation.

Message from ISCB

• 
  Justin Mullins, B. J. Morrison McKay:
  International Society for Computational Biology Honors Michael Ashburner and Olga Troyanskaya with Top Bioinformatics/Computational Biology Awards for 2011.

Perspectives

• 
  Muhammad Ilyas, Samrene Sadique, Kahlid Masood, Raheel Qamar, Shahid Nadeem Chohan:
  The Development of Computational Biology in Pakistan: Still a Long Way to Go.
• 
  Samuel Arbesman, Nicholas A. Christakis:
  Eurekometrics: Analyzing the Nature of Discovery.

Research Articles

• 
  Inbal Hecht, Monica L. Skoge, Pascale G. Charest, Eshel Ben-Jacob, Richard A. Firtel, William F. Loomis, Herbert Levine, Wouter-Jan Rappel:
  Activated Membrane Patches Guide Chemotactic Cell Motility.
• 
  Bhushan K. Bonde, Dany J. V. Beste, Emma Laing, Andrzej M. Kierzek, Johnjoe McFadden:
  Differential Producibility Analysis (DPA) of Transcriptomic Data with Metabolic Networks: Deconstructing the Metabolic Response of M. tuberculosis.
• 
  Ann M. Hermundstad, Kevin S. Brown, Danielle S. Bassett, Jean M. Carlson:
  Learning, Memory, and the Role of Neural Network Architecture.
• 
  Velia Siciliano, Filippo Menolascina, Lucia Marucci, Chiara Fracassi, Immacolata Garzilli, Maria Nicoletta Moretti, Diego di Bernardo:
  Construction and Modelling of an Inducible Positive Feedback Loop Stably Integrated in a Mammalian Cell-Line.
• 
  Peter W. Battaglia, Daniel J. Kersten, Paul R. Schrater:
  How Haptic Size Sensations Improve Distance Perception.
• 
  Myungsook Kim, Alan Jung Park, Robbert Havekes, Andrew Chay, Leonardo Antonio Guercio, Rodrigo Freire Oliveira, Ted Abel, Kim T. Blackwell:
  Colocalization of Protein Kinase A with Adenylyl Cyclase Enhances Protein Kinase A Activity during Induction of Long-Lasting Long-Term-Potentiation.
• 
  Alexander V. Ratushny, Ilya Shmulevich, John D. Aitchison:
  Trade-off between Responsiveness and Noise Suppression in Biomolecular System Responses to Environmental Cues.
• 
  Johannes Friedrich, Robert Urbanczik, Walter Senn:
  Spatio-Temporal Credit Assignment in Neuronal Population Learning.
• 
  Jouhyun Jeon, Jae Hoon Jeong, Je-Hyun Baek, Hyun-Jung Koo, Wook-Ha Park, Jae-Seong Yang, Myeong-Hee Yu, Sanguk Kim, Youngmi Kim Pak:
  Network Clustering Revealed the Systemic Alterations of Mitochondrial Protein Expression.
• 
  Teresa S. Barata, Ian Teo, Steve Brocchini, Mire Zloh, Sunil Shaunak:
  Partially Glycosylated Dendrimers Block MD-2 and Prevent TLR4-MD-2-LPS Complex Mediated Cytokine Responses.
• 
  Wopke van der Werf, Lia Hemerik, Just M. Vlak, Mark P. Zwart:
  Heterogeneous Host Susceptibility Enhances Prevalence of Mixed-Genotype Micro-Parasite Infections.
• 
  Pallab Singh, Adam J. Hockenberry, Vineet R. Tiruvadi, David F. Meaney:
  Computational Investigation of the Changing Patterns of Subtype Specific NMDA Receptor Activation during Physiological Glutamatergic Neurotransmission.
• 
  Luis Nicolas Gonzalez Castro, Craig Bryant Monsen, Maurice A. Smith:
  The Binding of Learning to Action in Motor Adaptation.
• 
  Diana Morozova, Gernot Guigas, Matthias Weiss:
  Dynamic Structure Formation of Peripheral Membrane Proteins.
• 
  Amanda Sorribes, Beatriz G. Armendariz, Diego Lopez-Pigozzi, Cristina Murga, Gonzalo G. de Polavieja:
  The Origin of Behavioral Bursts in Decision-Making Circuitry.
• 
  Kay Henning Brodersen, Thomas M. Schofield, Alexander P. Leff, Cheng Soon Ong, Ekaterina I. Lomakina, Joachim M. Buhmann, Klaas E. Stephan:
  Generative Embedding for Model-Based Classification of fMRI Data.
• 
  Elena Dolghih, Clifford Bryant, Adam R. Renslo, Matthew P. Jacobson:
  Predicting Binding to P-Glycoprotein by Flexible Receptor Docking.
• 
  Najaf A. Shah, Casim A. Sarkar:
  Robust Network Topologies for Generating Switch-Like Cellular Responses.
• 
  Larissa Albantakis, Gustavo Deco:
  Changes of Mind in an Attractor Network of Decision-Making.
• 
  Greet De Baets, Joke Reumers, Javier Delgado Blanco, Joaquín Dopazo, Joost Schymkowitz, Frederic Rousseau:
  An Evolutionary Trade-Off between Protein Turnover Rate and Protein Aggregation Favors a Higher Aggregation Propensity in Fast Degrading Proteins.
• 
  Wenyuan Li, Chun-Chi Liu, Tong Zhang, Haifeng Li, Michael S. Waterman, Xianghong Jasmine Zhou:
  Integrative Analysis of Many Weighted Co-Expression Networks Using Tensor Computation.
• 
  Sravanti Uppaluri, Jan Nagler, Eric Stellamanns, Niko Heddergott, Stephan Herminghaus, Markus Engstler, Thomas Pfohl:
  Impact of Microscopic Motility on the Swimming Behavior of Parasites: Straighter Trypanosomes are More Directional.
• 
  Elodie Laine, Isaure Chauvot de Beauchêne, David Perahia, Christian Auclair, Luba Tchertanov:
  Mutation D816V Alters the Internal Structure and Dynamics of c-KIT Receptor Cytoplasmic Region: Implications for Dimerization and Activation Mechanisms.
• 
  Maria J. Rosa, James Kilner, Will D. Penny:
  Bayesian Comparison of Neurovascular Coupling Models Using EEG-fMRI.
• 
  Richard Kennaway, Enrico Coen, Amelia Green, Andrew Bangham:
  Generation of Diverse Biological Forms through Combinatorial Interactions between Tissue Polarity and Growth.
• 
  Yongping Pan, Ruth Nussinov:
  The Role of Response Elements Organization in Transcription Factor Selectivity: The IFN-β Enhanceosome Example.
• 
  Dan Xie, Chieh-Chun Chen, Xin He, Xiaoyi Cao, Sheng Zhong:
  Towards an Evolutionary Model of Transcription Networks.
• 
  Benjamin P. Cossins, Matthew P. Jacobson, Victor Guallar:
  A New View of the Bacterial Cytosol Environment.
• 
  David Sprinzak, Amit Lakhanpal, Lauren LeBon, Jordi García-Ojalvo, Michael B. Elowitz:
  Mutual Inactivation of Notch Receptors and Ligands Facilitates Developmental Patterning.
• 
  Nathan L. Nehrt, Wyatt T. Clark, Predrag Radivojac, Matthew W. Hahn:
  Testing the Ortholog Conjecture with Comparative Functional Genomic Data from Mammals.
• 
  Mikail Rubinov, Olaf Sporns, Jean-Philippe Thivierge, Michael Breakspear:
  Neurobiologically Realistic Determinants of Self-Organized Criticality in Networks of Spiking Neurons.
• 
  Erik M. Volz, Joel C. Miller, Alison P. Galvani, Lauren Ancel Meyers:
  Effects of Heterogeneous and Clustered Contact Patterns on Infectious Disease Dynamics.
• 
  Ruhollah Moussavi-Baygi, Yousef Jamali, Reza Karimi, Mohammad R. Kaazempur Mofrad:
  Brownian Dynamics Simulation of Nucleocytoplasmic Transport: A Coarse-Grained Model for the Functional State of the Nuclear Pore Complex.
• 
  Bratislav Misic, Vasily A. Vakorin, Natasa Kovacevic, Tomás Paus, Anthony Randal McIntosh:
  Extracting Message Inter-Departure Time Distributions from the Human Electroencephalogram.

Volume 7, Number 7, July 2011

Review

• 
  Marc A. Martí-Renom, Leonid A. Mirny:
  Bridging the Resolution Gap in Structural Modeling of 3D Genome Organization.

Research Articles

• 
  Krisztian Magori, Waheed I. Bajwa, Sarah Bowden, John M. Drake:
  Decelerating Spread of West Nile Virus by Percolation in a Heterogeneous Urban Landscape.
• 
  Etay Hay, Sean L. Hill, Felix Schürmann, Henry Markram, Idan Segev:
  Models of Neocortical Layer 5b Pyramidal Cells Capturing a Wide Range of Dendritic and Perisomatic Active Properties.
• 
  Chuanhua Xing, David B. Dunson:
  Bayesian Inference for Genomic Data Integration Reduces Misclassification Rate in Predicting Protein-Protein Interactions.
• 
  Mitsuhiro Nakamura, Naoki Masuda:
  Indirect Reciprocity under Incomplete Observation.
• 
  Qian Wang, Kao-Chen Liang, Arkadiusz Czader, M. Neal Waxham, Margaret S. Cheung:
  The Effect of Macromolecular Crowding, Ionic Strength and Calcium Binding on Calmodulin Dynamics.
• 
  Tian Hong, Jianhua Xing, Liwu Li, John J. Tyson:
  A Mathematical Model for the Reciprocal Differentiation of T Helper 17 Cells and Induced Regulatory T Cells.
• 
  Cheng Peng, Teresa Head-Gordon:
  The Dynamical Mechanism of Auto-Inhibition of AMP-Activated Protein Kinase.
• 
  Federico Vaggi, Andrea Disanza, Francesca Milanesi, Pier Paolo Di Fiore, Elisabetta Menna, Michela Matteoli, Nir S. Gov, Giorgio Scita, Andrea Ciliberto:
  The Eps8/IRSp53/VASP Network Differentially Controls Actin Capping and Bundling in Filopodia Formation.
• 
  Iulian Pruteanu-Malinici, Daniel L. Mace, Uwe Ohler:
  Automatic Annotation of Spatial Expression Patterns via Sparse Bayesian Factor Models.
• 
  Julia Romanowska, James Andrew McCammon, Joanna Trylska:
  Understanding the Origins of Bacterial Resistance to Aminoglycosides through Molecular Dynamics Mutational Study of the Ribosomal A-Site.
• 
  Romain Silhol, Pierre-Yves Boëlle:
  Modelling the Effects of Population Structure on Childhood Disease: The Case of Varicella.
• 
  Ian M. Gemp, Richard W. Carthew, Sascha Hilgenfeldt:
  Cadherin-Dependent Cell Morphology in an Epithelium: Constructing a Quantitative Dynamical Model.
• 
  Christoph Kaleta, Luis F. de Figueiredo, Sarah Werner, Reinhard Guthke, Michael Ristow, Stefan Schuster:
  In Silico Evidence for Gluconeogenesis from Fatty Acids in Humans.
• 
  Bálint Mészáros, Judit Tóth, Beáta G. Vértessy, Zsuzsanna Dosztányi, István Simon:
  Proteins with Complex Architecture as Potential Targets for Drug Design: A Case Study of Mycobacterium tuberculosis.
• 
  Kristen M. Naegle, Roy E. Welsch, Michael B. Yaffe, Forest M. White, Douglas A. Lauffenburger:
  MCAM: Multiple Clustering Analysis Methodology for Deriving Hypotheses and Insights from High-Throughput Proteomic Datasets.
• 
  Adam D. Schneider, Kathleen Cullen, Maurice J. Chacron:
  In vivo Conditions Induce Faithful Encoding of Stimuli by Reducing Nonlinear Synchronization in Vestibular Sensory Neurons.
• 
  Takeru Honda, Tadashi Yamazaki, Shigeru Tanaka, Soichi Nagao, Tetsuro Nishino:
  Stimulus-Dependent State Transition between Synchronized Oscillation and Randomly Repetitive Burst in a Model Cerebellar Granular Layer.
• 
  Daniel J. Cole, Eeson Rajendra, Meredith Roberts-Thomson, Bryn Hardwick, Grahame J. McKenzie, Mike C. Payne, Ashok R. Venkitaraman, Chris-Kriton Skylaris:
  Interrogation of the Protein-Protein Interactions between Human BRCA2 BRC Repeats and RAD51 Reveals Atomistic Determinants of Affinity.
• 
  William S. Sanders, C. Ian Johnston, Susan M. Bridges, Shane C. Burgess, Kenneth O. Willeford:
  Prediction of Cell Penetrating Peptides by Support Vector Machines.
• 
  Michael D. Daily, George N. Phillips Jr., Qiang Cui:
  Interconversion of Functional Motions between Mesophilic and Thermophilic Adenylate Kinases.
• 
  R. Scott McIsaac, Kerwyn Casey Huang, Anirvan M. Sengupta, Ned S. Wingreen:
  Does the Potential for Chaos Constrain the Embryonic Cell-Cycle Oscillator?
• 
  Dongjun Chung, Pei Fen Kuan, Bo Li, Rajendran Sanalkumar, Kun Liang, Emery H. Bresnick, Colin N. Dewey, Sündüz Keles:
  Discovering Transcription Factor Binding Sites in Highly Repetitive Regions of Genomes with Multi-Read Analysis of ChIP-Seq Data.
• 
  Daniel B. Forger, David Paydarfar, John R. Clay:
  Optimal Stimulus Shapes for Neuronal Excitation.
• 
  Jing Kang, Bing Xu, Ye Yao, Wei Lin, Conor Hennessy, Peter Fraser, Jianfeng Feng:
  A Dynamical Model Reveals Gene Co-Localizations in Nucleus.

Volume 7, Number 8, August 2011

Education

• 
  Vincent A. Fusaro, Prasad Patil, Erik Gafni, Dennis P. Wall, Peter J. Tonellato:
  Biomedical Cloud Computing With Amazon Web Services.

Reviews

• 
  Eugene V. Koonin:
  Are There Laws of Genome Evolution?
• 
  Jan Gorodkin, Ivo L. Hofacker:
  From Structure Prediction to Genomic Screens for Novel Non-Coding RNAs.

Research Articles

• 
  Tim D. Williams, Nil Turan, Amer M. Diab, Huifeng Wu, Carolynn Mackenzie, Katie L. Bartie, Olga Hrydziuszko, Brett P. Lyons, Grant D. Stentiford, John M. Herbert, Joseph K. Abraham, Ioanna Katsiadaki, Michael J. Leaver, John B. Taggart, Stephen G. George, Mark R. Viant, Kevin J. Chipman, Francesco Falciani:
  Towards a System Level Understanding of Non-Model Organisms Sampled from the Environment: A Network Biology Approach.
• 
  David A. Rasmussen, Oliver Ratmann, Katia Koelle:
  Inference for Nonlinear Epidemiological Models Using Genealogies and Time Series.
• 
  Che-Chi Shu, Anushree Chatterjee, Gary Dunny, Wei-Shou Hu, Doraiswami Ramkrishna:
  Bistability versus Bimodal Distributions in Gene Regulatory Processes from Population Balance.
• 
  Francisco S. Roque, Peter Bjødstrup Jensen, Henriette Schmock, Marlene Dalgaard, Massimo Andreatta, Thomas Folkmann Hansen, Karen Søeby, Søren Bredkjær, Anders Juul, Thomas Werge, Lars Juhl Jensen, Søren Brunak:
  Using Electronic Patient Records to Discover Disease Correlations and Stratify Patient Cohorts.
• 
  Laia Sadeghi, Carolina Bonilla, Annelie Strålfors, Karl Ekwall, J. Peter Svensson:
  Podbat: A Novel Genomic Tool Reveals Swr1-Independent H2A.Z Incorporation at Gene Coding Sequences through Epigenetic Meta-Analysis.
• 
  Robert Mill, Martin Coath, Thomas Wennekers, Susan L. Denham:
  A Neurocomputational Model of Stimulus-Specific Adaptation to Oddball and Markov Sequences.
• 
  Lingyun Zhao, Zhaoping Li:
  Understanding Auditory Spectro-Temporal Receptive Fields and Their Changes with Input Statistics by Efficient Coding Principles.
• 
  Iskra Staneva, Stefan Wallin:
  Binding Free Energy Landscape of Domain-Peptide Interactions.
• 
  Shaul Druckmann, Thomas K. Berger, Felix Schürmann, Sean L. Hill, Henry Markram, Idan Segev:
  Effective Stimuli for Constructing Reliable Neuron Models.
• 
  Jasper Franke, Alexander Klözer, J. Arjan G. M. de Visser, Joachim Krug:
  Evolutionary Accessibility of Mutational Pathways.
• 
  Sourya Shrestha, Aaron A. King, Pejman Rohani:
  Statistical Inference for Multi-Pathogen Systems.
• 
  David N. Adamson, Han N. Lim:
  Essential Requirements for Robust Signaling in Hfq Dependent Small RNA Networks.
• 
  Fredrik Allenmark, Jenny C. A. Read:
  Spatial Stereoresolution for Depth Corrugations May Be Set in Primary Visual Cortex.
• 
  Rosalyn J. Moran, Nicolas Mallet, Vladimir Litvak, Raymond J. Dolan, Peter J. Magill, Karl J. Friston, Peter Brown:
  Alterations in Brain Connectivity Underlying Beta Oscillations in Parkinsonism.
• 
  Hannes Hettling, Johannes H. G. M. van Beek:
  Analyzing the Functional Properties of the Creatine Kinase System with Multiscale 'Sloppy' Modeling.
• 
  Vlad Cojocaru, Kia Balali-Mood, Mark S. P. Sansom, Rebecca C. Wade:
  Structure and Dynamics of the Membrane-Bound Cytochrome P450 2C9.
• 
  Nigel J. Burroughs, Karsten Köhler, Vladimir Miloserdov, Michael L. Dustin, P. Anton van der Merwe, Daniel M. Davis:
  Boltzmann Energy-based Image Analysis Demonstrates that Extracellular Domain Size Differences Explain Protein Segregation at Immune Synapses.
• 
  Vishal V. Gandhi, David C. Samuels:
  Enzyme Kinetics of the Mitochondrial Deoxyribonucleoside Salvage Pathway Are Not Sufficient to Support Rapid mtDNA Replication.
• 
  Steven Phillips, William H. Wilson:
  Categorial Compositionality II: Universal Constructions and a General Theory of (Quasi-)Systematicity in Human Cognition.
• 
  Andrea Malandrino, Jérôme Noailly, Damien Lacroix:
  The Effect of Sustained Compression on Oxygen Metabolic Transport in the Intervertebral Disc Decreases with Degenerative Changes.
• 
  Tilo Beyer, Mandy Busse, Kroum Hristov, Slavyana Gurbiel, Michal Smida, Utz-Uwe Haus, Kathrin Ballerstein, Frank Pfeuffer, Robert Weismantel, Burkhart Schraven, Jonathan A. Lindquist:
  Integrating Signals from the T-Cell Receptor and the Interleukin-2 Receptor.
• 
  A. Sofia F. Oliveira, António M. Baptista, Cláudio M. Soares:
  Inter-domain Communication Mechanisms in an ABC Importer: A Molecular Dynamics Study of the MalFGK₂E Complex.

Volume 7, Number 9, September 2011

Editorial

• 
  Giovanni Marco Dall'Olio, Jacopo Marino, Michael Schubert, Kevin L. Keys, Melanie I. Stefan, Colin S. Gillespie, Pierre Poulain, Khader Shameer, Robert Sugar, Brandon M. Invergo, Lars Juhl Jensen, Jaume Bertranpetit, Hafid Laayouni:
  Ten Simple Rules for Getting Help from Online Scientific Communities.

Review

• 
  Andrey Rzhetsky, James A. Evans:
  War of Ontology Worlds: Mathematics, Computer Code, or Esperanto?

Research Articles

• 
  Oriol Canela-Xandri, Francesc Sagués, Jaume Casademunt, Javier Buceta:
  Dynamics and Mechanical Stability of the Developing Dorsoventral Organizer of the Wing Imaginal Disc.
• 
  Stuart G. Campbell, P. Chris Hatfield, Kenneth S. Campbell:
  A Mathematical Model of Muscle Containing Heterogeneous Half-Sarcomeres Exhibits Residual Force Enhancement.
• 
  Michael Rule, Matthew Stoffregen, Bard Ermentrout:
  A Model for the Origin and Properties of Flicker-Induced Geometric Phosphenes.
• 
  Geir Halnes, Sigita Augustinaite, Paul Heggelund, Gaute T. Einevoll, Michele Migliore:
  A Multi-Compartment Model for Interneurons in the Dorsal Lateral Geniculate Nucleus.
• 
  Chandramouli Chandrasekaran, Luis Lemus, Andrea Trubanova, Matthias Gondan, Asif A. Ghazanfar:
  Monkeys and Humans Share a Common Computation for Face/Voice Integration.
• 
  Kateri H. DuBay, Jacques P. Bothma, Phillip L. Geissler:
  Long-Range Intra-Protein Communication Can Be Transmitted by Correlated Side-Chain Fluctuations Alone.
• 
  Sara Hooshangi, William E. Bentley:
  LsrR Quorum Sensing "Switch" Is Revealed by a Bottom-Up Approach.
• 
  Franco M. Neri, Anne Bates, Winnie S. Füchtbauer, Francisco J. Pérez-Reche, Sergei N. Taraskin, Wilfred Otten, Douglas J. Bailey, Christopher A. Gilligan:
  The Effect of Heterogeneity on Invasion in Spatial Epidemics: From Theory to Experimental Evidence in a Model System.
• 
  Adi Shklarsh, Gil Ariel, Elad Schneidman, Eshel Ben-Jacob:
  Smart Swarms of Bacteria-Inspired Agents with Performance Adaptable Interactions.
• 
  Janusz Dutkowski, Trey Ideker:
  Protein Networks as Logic Functions in Development and Cancer.
• 
  James N. Ingram, Ian S. Howard, J. Randall Flanagan, Daniel M. Wolpert:
  A Single-Rate Context-Dependent Learning Process Underlies Rapid Adaptation to Familiar Object Dynamics.
• 
  Dionysios Perdikis, Raoul Huys, Viktor K. Jirsa:
  Time Scale Hierarchies in the Functional Organization of Complex Behaviors.
• 
  Marjet Elemans, Nafisa-Katrin Seich al Basatena, Nichole R. Klatt, Christos Gkekas, Guido Silvestri, Becca Asquith:
  Why Don't CD8+ T Cells Reduce the Lifespan of SIV-Infected Cells In Vivo?
• 
  Enrique Marcos, Ramon Crehuet, Ivet Bahar:
  Changes in Dynamics upon Oligomerization Regulate Substrate Binding and Allostery in Amino Acid Kinase Family Members.
• 
  Stefano Merler, Marco Ajelli, Andrea Pugliese, Neil M. Ferguson:
  Determinants of the Spatiotemporal Dynamics of the 2009 H1N1 Pandemic in Europe: Implications for Real-Time Modelling.
• 
  Moran Elishmereni, Yuri Kheifetz, Henrik Søndergaard, Rune Viig Overgaard, Zvia Agur:
  An Integrated Disease/Pharmacokinetic/Pharmacodynamic Model Suggests Improved Interleukin-21 Regimens Validated Prospectively for Mouse Solid Cancers.
• 
  Edward J. Banigan, Michael A. Gelbart, Zemer Gitai, Ned S. Wingreen, Andrea J. Liu:
  Filament Depolymerization Can Explain Chromosome Pulling during Bacterial Mitosis.
• 
  Dagmar Sternad, Masaki O. Abe, Xiaogang Hu, Hermann Müller:
  Neuromotor Noise, Error Tolerance and Velocity-Dependent Costs in Skilled Performance.
• 
  T. M. Murali, Matthew D. Dyer, David Badger, Brett M. Tyler, Michael G. Katze:
  Network-Based Prediction and Analysis of HIV Dependency Factors.
• 
  Violeta Beleva Guthrie, Jennifer Allen, Manel Camps, Rachel Karchin:
  Network Models of TEM β-Lactamase Mutations Coevolving under Antibiotic Selection Show Modular Structure and Anticipate Evolutionary Trajectories.
• 
  Colin J. Torney, Andrew Berdahl, Iain D. Couzin:
  Signalling and the Evolution of Cooperative Foraging in Dynamic Environments.
• 
  Michael Z. Levy, Dylan S. Small, Daril A. Vilhena, Natalie M. Bowman, Vivian Kawai, Juan G. Cornejo del Carpio, Eleazar Cordova-Benzaquen, Robert H. Gilman, Caryn Bern, Joshua B. Plotkin:
  Retracing Micro-Epidemics of Chagas Disease Using Epicenter Regression.
• 
  Simon Mitternacht, Igor N. Berezovsky:
  Binding Leverage as a Molecular Basis for Allosteric Regulation.
• 
  Miklós Csürös, Igor B. Rogozin, Eugene V. Koonin:
  A Detailed History of Intron-rich Eukaryotic Ancestors Inferred from a Global Survey of 100 Complete Genomes.
• 
  Nnenna A. Finn, Harry W. Findley, Melissa L. Kemp:
  A Switching Mechanism in Doxorubicin Bioactivation Can Be Exploited to Control Doxorubicin Toxicity.
• 
  Jérémie Bourdon, Damien Eveillard, Anne Siegel:
  Integrating Quantitative Knowledge into a Qualitative Gene Regulatory Network.
• 
  Lipi Thukral, Isabella Daidone, Jeremy C. Smith:
  Structured Pathway across the Transition State for Peptide Folding Revealed by Molecular Dynamics Simulations.
• 
  Annabelle Ballesta, Sandrine Dulong, Chadi Abbara, Boris Cohen, Alper Okyar, Jean Clairambault, Francis Lévi:
  A Combined Experimental and Mathematical Approach for Molecular-based Optimization of Irinotecan Circadian Delivery.
• 
  Nicolas Doyon, Steven A. Prescott, Annie Castonguay, Antoine G. Godin, Helmut Kröger, Yves De Koninck:
  Efficacy of Synaptic Inhibition Depends on Multiple, Dynamically Interacting Mechanisms Implicated in Chloride Homeostasis.
• 
  Shlomi Reuveni, Isaac Meilijson, Martin Kupiec, Eytan Ruppin, Tamir Tuller:
  Genome-Scale Analysis of Translation Elongation with a Ribosome Flow Model.
• 
  Nil Turan, Susana G. Kalko, Anna Stincone, Kim Clarke, Ayesha Sabah, Katherine Howlett, S. John Curnow, Diego A. Rodriguez, Marta Cascante, Laura O'Neill, Stuart Egginton, Josep Roca, Francesco Falciani:
  A Systems Biology Approach Identifies Molecular Networks Defining Skeletal Muscle Abnormalities in Chronic Obstructive Pulmonary Disease.
• 
  Yvonne Y. Li, Jianghong An, Steven J. M. Jones:
  A Computational Approach to Finding Novel Targets for Existing Drugs.

Volume 7, Number 10, October 2011

Editorials

• 
  Magali Michaut:
  Ten Simple Rules for Getting Involved in Your Scientific Community.
• 
  Fran Lewitter, Philip E. Bourne:
  Teaching Bioinformatics at the Secondary School Level.
• 
  David Form, Fran Lewitter:
  Ten Simple Rules for Teaching Bioinformatics at the High School Level.
• 
  Allegra Via, Javier De Las Rivas, Teresa K. Attwood, David Landsman, Michelle D. Brazas, Jack A. M. Leunissen, Anna Tramontano, Maria Victoria Schneider:
  Ten Simple Rules for Developing a Short Bioinformatics Training Course.

Education

• 
  Suzanne Renick Gallagher, William Coon, Kristin Donley, Abby Scott, Debra Goldberg:
  A First Attempt to Bring Computational Biology into Advanced High School Biology Classrooms.

Perspective

• 
  Laurence D. Parnell, Pierre Lindenbaum, Khader Shameer, Giovanni Marco Dall'Olio, Daniel C. Swan, Lars Juhl Jensen, Simon J. Cockell, Brent S. Pedersen, Mary E. Mangan, Christopher A. Miller, István Albert:
  BioStar: An Online Question & Answer Resource for the Bioinformatics Community.

Research Articles

• 
  Mijung Park, Jonathan W. Pillow:
  Receptive Field Inference with Localized Priors.
• 
  Antonio Scialdone, Ilaria Cataudella, Mariano Barbieri, Antonella Prisco, Mario Nicodemi:
  Conformation Regulation of the X Chromosome Inactivation Center: A Model.
• 
  Matthieu Gilson, Timothée Masquelier, Etienne Hugues:
  STDP Allows Fast Rate-Modulated Coding with Poisson-Like Spike Trains.
• 
  Nicholas J. Gustafson, Nathaniel D. Daw:
  Grid Cells, Place Cells, and Geodesic Generalization for Spatial Reinforcement Learning.
• 
  Heidi Koldsø, Pernille Noer, Julie Grouleff, Henriette Elisabeth Autzen, Steffen Sinning, Birgit Schiøtt:
  Unbiased Simulations Reveal the Inward-Facing Conformation of the Human Serotonin Transporter and Na⁺ Ion Release.
• 
  Itai Hayut, Erika E. Fanselow, Barry W. Connors, David Golomb:
  LTS and FS Inhibitory Interneurons, Short-Term Synaptic Plasticity, and Cortical Circuit Dynamics.
• 
  Jeffrey D. Fitzgerald, Ryan J. Rowekamp, Lawrence C. Sincich, Tatyana O. Sharpee:
  Second Order Dimensionality Reduction Using Minimum and Maximum Mutual Information Models.
• 
  Joel Zylberberg, Jason Timothy Murphy, Michael Robert DeWeese:
  A Sparse Coding Model with Synaptically Local Plasticity and Spiking Neurons Can Account for the Diverse Shapes of V1 Simple Cell Receptive Fields.
• 
  Marko Sysi-Aho, Andrey Ermolov, Peddinti V. Gopalacharyulu, Abhishek Tripathi, Tuulikki Seppänen-Laakso, Johanna Maukonen, Ismo Mattila, Suvi T. Ruohonen, Laura Vähätalo, Laxman Yetukuri, Taina Härkönen, Erno Lindfors, Janne Nikkilä, Jorma Ilonen, Olli Simell, Maria Saarela, Mikael Knip, Samuel Kaski, Eriika Savontaus, Matej Oresic:
  Metabolic Regulation in Progression to Autoimmune Diabetes.
• 
  Sean R. Eddy:
  Accelerated Profile HMM Searches.
• 
  Benjamin A. Hall, Judith P. Armitage, Mark S. P. Sansom:
  Transmembrane Helix Dynamics of Bacterial Chemoreceptors Supports a Piston Model of Signalling.
• 
  Jun Namikawa, Ryunosuke Nishimoto, Jun Tani:
  A Neurodynamic Account of Spontaneous Behaviour.
• 
  Julia Tsitron, Addison D. Ault, James R. Broach, Alexandre V. Morozov:
  Decoding Complex Chemical Mixtures with a Physical Model of a Sensor Array.
• 
  Tyrone Ryba, Ichiro Hiratani, Takayo Sasaki, Dana Battaglia, Michael Kulik, Jinfeng Zhang, Stephen Dalton, David M. Gilbert:
  Replication Timing: A Fingerprint for Cell Identity and Pluripotency.
• 
  Yinyin Yuan, Richard S. Savage, Florian Markowetz:
  Patient-Specific Data Fusion Defines Prognostic Cancer Subtypes.
• 
  Alexis P. Yelton, Brian C. Thomas, Sheri L. Simmons, Paul Wilmes, Adam T. Zemla, Michael P. Thelen, Nicholas Justice, Jillian F. Banfield:
  A Semi-Quantitative, Synteny-Based Method to Improve Functional Predictions for Hypothetical and Poorly Annotated Bacterial and Archaeal Genes.
• 
  Hyun Joo, Archana G. Chavan, Ryan Day, Kristin P. Lennox, Paul Sukhanov, David B. Dahl, Marina Vannucci, Jerry W. Tsai:
  Near-Native Protein Loop Sampling Using Nonparametric Density Estimation Accommodating Sparcity.
• 
  Jeffrey A. Edlund, Nicolas Chaumont, Arend Hintze, Christof Koch, Giulio Tononi, Christoph Adami:
  Integrated Information Increases with Fitness in the Evolution of Animats.
• 
  Kate M. Mitchell, Francisca Mutapi, Nicholas J. Savill, Mark E. J. Woolhouse:
  Explaining Observed Infection and Antibody Age-Profiles in Populations with Urogenital Schistosomiasis.
• 
  Özlem Demir, Roberta Baronio, Faezeh Salehi, Christopher D. Wassman, Linda Hall, G. Wesley Hatfield, Richard Chamberlin, Peter Kaiser, Richard H. Lathrop, Rommie E. Amaro:
  Ensemble-Based Computational Approach Discriminates Functional Activity of p53 Cancer and Rescue Mutants.
• 
  Tatjana Tchumatchenko, Fred Wolf:
  Representation of Dynamical Stimuli in Populations of Threshold Neurons.
• 
  David Venet, Jacques E. Dumont, Vincent Detours:
  Most Random Gene Expression Signatures Are Significantly Associated with Breast Cancer Outcome.
• 
  Byron N. Roberts, David J. Christini:
  NHE Inhibition Does Not Improve Na⁺ or Ca²⁺ Overload During Reperfusion: Using Modeling to Illuminate the Mechanisms Underlying a Therapeutic Failure.
• 
  Sean A. Rands:
  The Effects of Dominance on Leadership and Energetic Gain: A Dynamic Game between Pairs of Social Foragers.
• 
  Neil Dalchau, James Andrew Phillips, Leonard D. Goldstein, Mark Howarth, Luca Cardelli, Stephen Emmott, Tim Elliott, Joern M. Werner:
  A Peptide Filtering Relation Quantifies MHC Class I Peptide Optimization.
• 
  Anthony W. Fitzpatrick, Tuomas P. J. Knowles, Christopher A. Waudby, Michele Vendruscolo, Christopher M. Dobson:
  Inversion of the Balance between Hydrophobic and Hydrogen Bonding Interactions in Protein Folding and Aggregation.
• 
  César Augusto F. de Oliveira, Barry J. Grant, Michelle Zhou, James Andrew McCammon:
  Large-Scale Conformational Changes of Trypanosoma cruzi Proline Racemase Predicted by Accelerated Molecular Dynamics Simulation.
• 
  Armin Biess, Eduard Korkotian, David Holcman:
  Barriers to Diffusion in Dendrites and Estimation of Calcium Spread Following Synaptic Inputs.
• 
  Bastien Berret, Enrico Chiovetto, Francesco Nori, Thierry Pozzo:
  Evidence for Composite Cost Functions in Arm Movement Planning: An Inverse Optimal Control Approach.
• 
  George Shirreff, Lorenzo Pellis, Oliver Laeyendecker, Christophe Fraser:
  Transmission Selects for HIV-1 Strains of Intermediate Virulence: A Modelling Approach.
• 
  Ágoston Mihalik, Peter Csermely:
  Heat Shock Partially Dissociates the Overlapping Modules of the Yeast Protein-Protein Interaction Network: A Systems Level Model of Adaptation.
• 
  Stuart P. Wilson, James A. Bednar, Tony J. Prescott, Benjamin Mitchinson:
  Neural Computation via Neural Geometry: A Place Code for Inter-whisker Timing in the Barrel Cortex?
• 
  Shun-Chieh Yang, Su-Sen Chang, Hsin-Yi Chen, Calvin Yu-Chian Chen:
  Identification of Potent EGFR Inhibitors from TCM Database@Taiwan.
• 
  Anurag Sethi, Byron Goldstein, S. Gnanakaran:
  Quantifying Intramolecular Binding in Multivalent Interactions: A Structure-Based Synergistic Study on Grb2-Sos1 Complex.
• 
  Davide Provasi, Marta Camacho-Artacho, Ana Negri, Juan Carlos Mobarec, Marta Filizola:
  Ligand-Induced Modulation of the Free-Energy Landscape of G Protein-Coupled Receptors Explored by Adaptive Biasing Techniques.
• 
  Marcel Salathé, Shashank Khandelwal:
  Assessing Vaccination Sentiments with Online Social Media: Implications for Infectious Disease Dynamics and Control.
• 
  Chris A. Brackley, M. Carmen Romano, Marco Thiel:
  The Dynamics of Supply and Demand in mRNA Translation.
• 
  G. Karl Steinke, Roberto F. Galán:
  Brain Rhythms Reveal a Hierarchical Network Organization.
• 
  Mark Hallen, Bochong Li, Yu Tanouchi, Cheemeng Tan, Mike West, Lingchong You:
  Computation of Steady-State Probability Distributions in Stochastic Models of Cellular Networks.
• 
  Anup Dewanji, Jihyoun Jeon, Rafael Meza, E. Georg Luebeck:
  Number and Size Distribution of Colorectal Adenomas under the Multistage Clonal Expansion Model of Cancer.
• 
  Qiang Zhu, Tao Qin, Ying-Ying Jiang, Cong Ji, De-Xin Kong, Bin-Guang Ma, Hong-yu Zhang:
  Chemical Basis of Metabolic Network Organization.
• 
  Stuart Aitken, Ross D. Alexander, Jean D. Beggs:
  Modelling Reveals Kinetic Advantages of Co-Transcriptional Splicing.
• 
  Yoan Diekmann, Elsa Seixas, Marc Gouw, Filipe Tavares-Cadete, Miguel C. Seabra, José B. Pereira-Leal:
  Thousands of Rab GTPases for the Cell Biologist.
• 
  Yaakov Maman, Ran Nir-Paz, Yoram Louzoun:
  Bacteria Modulate the CD8+ T Cell Epitope Repertoire of Host Cytosol-Exposed Proteins to Manipulate the Host Immune Response.
• 
  François Rebaudo, Olivier Dangles:
  Coupled Information Diffusion-Pest Dynamics Models Predict Delayed Benefits of Farmer Cooperation in Pest Management Programs.
• 
  Anna Divoli, Eneida A. Mendonça, James A. Evans, Andrey Rzhetsky:
  Conflicting Biomedical Assumptions for Mathematical Modeling: The Case of Cancer Metastasis.
• 
  Z. Nevin Gerek, S. Banu Ozkan:
  Change in Allosteric Network Affects Binding Affinities of PDZ Domains: Analysis through Perturbation Response Scanning.
• 
  Susan D. Hester, Julio M. Belmonte, J. Scott Gens, Sherry G. Clendenon, James A. Glazier:
  A Multi-cell, Multi-scale Model of Vertebrate Segmentation and Somite Formation.
• 
  Robert B. Levy, Alex D. Reyes:
  Coexistence of Lateral and Co-Tuned Inhibitory Configurations in Cortical Networks.
• 
  Vadas Gintautas, Michael I. Ham, Benjamin Kunsberg, Shawn Barr, Steven P. Brumby, Craig Rasmussen, John S. George, Ilya Nemenman, Luís M. A. Bettencourt, Garrett T. Kenyon:
  Model Cortical Association Fields Account for the Time Course and Dependence on Target Complexity of Human Contour Perception.
• 
  Arren Bar-Even, Elad Noor, Avi I. Flamholz, Joerg M. Buescher, Ron Milo:
  Hydrophobicity and Charge Shape Cellular Metabolite Concentrations.
• 
  Armita Nourmohammad, Michael Lässig:
  Formation of Regulatory Modules by Local Sequence Duplication.
• 
  Nir London, Corissa L. Lamphear, James L. Hougland, Carol A. Fierke, Ora Schueler-Furman:
  Identification of a Novel Class of Farnesylation Targets by Structure-Based Modeling of Binding Specificity.
• 
  Francesco Ricci, Alexis Vallée-Bélisle, Kevin W. Plaxco:
  High-Precision, In Vitro Validation of the Sequestration Mechanism for Generating Ultrasensitive Dose-Response Curves in Regulatory Networks.
• 
  Andrew Kuziemko, Barry Honig, Donald Petrey:
  Using Structure to Explore the Sequence Alignment Space of Remote Homologs.
• 
  Demian Battaglia, David Hansel:
  Synchronous Chaos and Broad Band Gamma Rhythm in a Minimal Multi-Layer Model of Primary Visual Cortex.
• 
  Anshuman Dixit, Gennady Verkhivker:
  Computational Modeling of Allosteric Communication Reveals Organizing Principles of Mutation-Induced Signaling in ABL and EGFR Kinases.
• 
  Keiko Yokoyama, Yuji Yamamoto:
  Three People Can Synchronize as Coupled Oscillators during Sports Activities.
• 
  Daniel J. van der Post, Dirk Semmann:
  Local Orientation and the Evolution of Foraging: Changes in Decision Making Can Eliminate Evolutionary Trade-offs.
• 
  Beata Hat, Bogdan Kazmierczak, Tomasz Lipniacki:
  B Cell Activation Triggered by the Formation of the Small Receptor Cluster: A Computational Study.
• 
  Kirsten H. ten Tusscher, Paulien Hogeweg:
  Evolution of Networks for Body Plan Patterning; Interplay of Modularity, Robustness and Evolvability.
• 
  Max Berniker, Konrad P. Körding:
  Estimating the Relevance of World Disturbances to Explain Savings, Interference and Long-Term Motor Adaptation Effects.
• 
  Jyh-Ying Peng, Chung-Chih Lin, Yen-Jen Chen, Lung-Sen Kao, Young-Chau Liu, Chung-Chien Chou, Yi-Hung Huang, Fang-Rong Chang, Yang-Chang Wu, Yuh-Show Tsai, Chun-Nan Hsu:
  Automatic Morphological Subtyping Reveals New Roles of Caspases in Mitochondrial Dynamics.

Volume 7, Number 11, November 2011

Perspective

• 
  Pedro Madrigal, Noa Sela, Simon M. Lin:
  PLoS Computational Biology Conference Postcards from ISMB/ECCB 2011.

Review

• 
  Joshua H. Goldwyn, Eric Shea-Brown:
  The What and Where of Adding Channel Noise to the Hodgkin-Huxley Equations.

Research Articles

• 
  Chao Cheng, Koon-Kiu Yan, Woochang Hwang, Jiang Qian, Nitin Bhardwaj, Joel S. Rozowsky, Zhi John Lu, Wei Niu, Pedro Alves, Masaomi Kato, Michael Snyder, Mark Gerstein:
  Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data.
• 
  Ralf Steuer, Steffen Waldherr, Victor Sourjik, Markus Kollmann:
  Robust Signal Processing in Living Cells.
• 
  Man Yi Yim, Ad Aertsen, Arvind Kumar:
  Significance of Input Correlations in Striatal Function.
• 
  Rutger Hermsen, David W. Erickson, Terence Hwa:
  Speed, Sensitivity, and Bistability in Auto-activating Signaling Circuits.
• 
  Andrew J. Yates, Minus Van Baalen, Rustom Antia:
  Virus Replication Strategies and the Critical CTL Numbers Required for the Control of Infection.
• 
  Zhiming Dai, Xianhua Dai:
  Gene Expression Divergence is Coupled to Evolution of DNA Structure in Coding Regions.
• 
  Jean Daunizeau, Kerstin Preuschoff, Karl J. Friston, Klaas E. Stephan:
  Optimizing Experimental Design for Comparing Models of Brain Function.
• 
  Zachary P. Kilpatrick, Bard Ermentrout:
  Sparse Gamma Rhythms Arising through Clustering in Adapting Neuronal Networks.
• 
  Alfonso Pérez-Escudero, Gonzalo G. de Polavieja:
  Collective Animal Behavior from Bayesian Estimation and Probability Matching.
• 
  Michael E. Wall, Sindhu Raghavan, Judith D. Cohn, John Dunbar:
  Genome Majority Vote Improves Gene Predictions.
• 
  Zhuo Song, Yang Cao, David C. Samuels:
  Replication Pauses of the Wild-Type and Mutant Mitochondrial DNA Polymerase Gamma: A Simulation Study.
• 
  Avraham Ben-Shimon, Masha Y. Niv:
  Deciphering the Arginine-Binding Preferences at the Substrate-Binding Groove of Ser/Thr Kinases by Computational Surface Mapping.
• 
  Arjun Narayanan, Lawrence L. LeClaire III, Diane L. Barber, Matthew P. Jacobson:
  Phosphorylation of the Arp2 Subunit Relieves Auto-inhibitory Interactions for Arp2/3 Complex Activation.
• 
  Gautham Vivek Sridharan, Soha Hassoun, Kyongbum Lee:
  Identification of Biochemical Network Modules Based on Shortest Retroactive Distances.
• 
  Joshua Lequieu, Anirikh Chakrabarti, Satyaprakash Nayak, Jeffrey D. Varner:
  Computational Modeling and Analysis of Insulin Induced Eukaryotic Translation Initiation.
• 
  Kresimir Josic, José Manuel López, William Ott, LieJune Shiau, Matthew R. Bennett:
  Stochastic Delay Accelerates Signaling in Gene Networks.
• 
  Yuichi Katori, Kazuhiro Sakamoto, Naohiro Saito, Jun Tanji, Hajime Mushiake, Kazuyuki Aihara:
  Representational Switching by Dynamical Reorganization of Attractor Structure in a Network Model of the Prefrontal Cortex.
• 
  Assieh Saadatpour, Rui-Sheng Wang, Aijun Liao, Xin Liu, Thomas P. Loughran, István Albert, Réka Albert:
  Dynamical and Structural Analysis of a T Cell Survival Network Identifies Novel Candidate Therapeutic Targets for Large Granular Lymphocyte Leukemia.
• 
  Alexandra Jilkine, Sigurd B. Angenent, Lani F. Wu, Steven J. Altschuler:
  A Density-Dependent Switch Drives Stochastic Clustering and Polarization of Signaling Molecules.
• 
  Anna Kuchina, Lorena Espinar, Jordi García-Ojalvo, Gürol M. Süel:
  Reversible and Noisy Progression towards a Commitment Point Enables Adaptable and Reliable Cellular Decision-Making.
• 
  Lars Buesing, Johannes Bill, Bernhard Nessler, Wolfgang Maass:
  Neural Dynamics as Sampling: A Model for Stochastic Computation in Recurrent Networks of Spiking Neurons.
• 
  Melissa J. Morine, Audrey C. Tierney, Ben van Ommen, Hannelore Daniel, Sinead Toomey, Ingrid M. F. Gjelstad, Isobel Claire Gormley, Pablo Pérez-Martinez, Christian A. Drevon, Jose López-Miranda, Helen M. Roche:
  Transcriptomic Coordination in the Human Metabolic Network Reveals Links between n-3 Fat Intake, Adipose Tissue Gene Expression and Metabolic Health.
• 
  Ernesto P. Raposo, Frederic Bartumeus, Marcos G. E. da Luz, P. J. Ribeiro-Neto, T. A. Souza, Gandhi M. Viswanathan:
  How Landscape Heterogeneity Frames Optimal Diffusivity in Searching Processes.
• 
  Natalia L. Komarova, Craig J. Thalhauser:
  High Degree of Heterogeneity in Alzheimer's Disease Progression Patterns.
• 
  Sohrab Saeb, Cornelius Weber, Jochen Triesch:
  Learning the Optimal Control of Coordinated Eye and Head Movements.
• 
  Paul M. Magwene, John H. Willis, John K. Kelly:
  The Statistics of Bulk Segregant Analysis Using Next Generation Sequencing.
• 
  Seyed Yahya Anvar, Allan Tucker, Veronica Vinciotti, Andrea Venema, Gert-Jan B. van Ommen, Silvere M. van der Maarel, Vered Raz, Peter A. C. 't Hoen:
  Interspecies Translation of Disease Networks Increases Robustness and Predictive Accuracy.
• 
  Philipp M. Altrock, Arne Traulsen, Floyd A. Reed:
  Stability Properties of Underdominance in Finite Subdivided Populations.
• 
  Bruno M. C. Martins, Peter S. Swain:
  Trade-Offs and Constraints in Allosteric Sensing.

Volume 7, Number 12, December 2011

Education Articles

• 
  Yuliet Mazola, Glay Chinea, Alexis Musacchio:
  Integrating Bioinformatics Tools to Handle Glycosylation.
• 
  Matthew E. Ritchie, Mark J. Dunning, Mike L. Smith, Wei Shi, Andy G. Lynch:
  BeadArray Expression Analysis Using Bioconductor.
• 
  Lukas Käll, Olga Vitek:
  Computational Mass Spectrometry-Based Proteomics.

Reviews

• 
  Konrad P. Körding:
  Of Toasters and Molecular Ticker Tapes.
• 
  Dov Greenbaum, Andrea Sboner, Xinmeng Jasmine Mu, Mark Gerstein:
  Genomics and Privacy: Implications of the New Reality of Closed Data for the Field.

Research Articles

• 
  Amin R. Mazloom, Ruth Dannenfelser, Neil R. Clark, Arsen V. Grigoryan, Kathryn M. Linder, Timothy Cardozo, Julia C. Bond, Aislyn D. W. Boran, Ravi Iyengar, Anna Malovannaya, Rainer B. Lanz, Avi Ma'ayan:
  Recovering Protein-Protein and Domain-Domain Interactions from Aggregation of IP-MS Proteomics of Coregulator Complexes.
• 
  Edward B. Baskerville, Andy P. Dobson, Trevor Bedford, Stefano Allesina, T. Michael Anderson, Mercedes Pascual:
  Spatial Guilds in the Serengeti Food Web Revealed by a Bayesian Group Model.
• 
  Guillaume Guilbaud, Aurélien Rappailles, Antoine Baker, Chun-Long Chen, Alain Arneodo, Arach Goldar, Yves D'Aubenton-Carafa, Claude Thermes, Benjamin Audit, Olivier Hyrien:
  Evidence for Sequential and Increasing Activation of Replication Origins along Replication Timing Gradients in the Human Genome.
• 
  Xing-Ming Zhao, Murat Iskar, Georg Zeller, Michael Kuhn, Vera van Noort, Peer Bork:
  Prediction of Drug Combinations by Integrating Molecular and Pharmacological Data.
• 
  Faisal Naqib, Carole A. Farah, Christopher C. Pack, Wayne S. Sossin:
  The Rates of Protein Synthesis and Degradation Account for the Differential Response of Neurons to Spaced and Massed Training Protocols.
• 
  Tianyun Liu, Russ B. Altman:
  Using Multiple Microenvironments to Find Similar Ligand-Binding Sites: Application to Kinase Inhibitor Binding.
• 
  Chuan Xue, Elena O. Budrene, Hans G. Othmer:
  Radial and Spiral Stream Formation in Proteus mirabilis Colonies.
• 
  Pan-Jun Kim, Nathan D. Price:
  Genetic Co-Occurrence Network across Sequenced Microbes.
• 
  Andreas Spiegler, Thomas R. Knösche, Karin Schwab, Jens Haueisen, Fatihcan M. Atay:
  Modeling Brain Resonance Phenomena Using a Neural Mass Model.
• 
  Rui Chang, Robert Shoemaker, Wei Wang:
  Systematic Search for Recipes to Generate Induced Pluripotent Stem Cells.
• 
  Jonathan Göke, Marc Jung, Sarah Behrens, Lukas Chavez, Sean O'Keeffe, Bernd Timmermann, Hans Lehrach, James Adjaye, Martin Vingron:
  Combinatorial Binding in Human and Mouse Embryonic Stem Cells Identifies Conserved Enhancers Active in Early Embryonic Development.
• 
  Ashok Litwin-Kumar, Anne-Marie M. Oswald, Nathaniel N. Urban, Brent Doiron:
  Balanced Synaptic Input Shapes the Correlation between Neural Spike Trains.
• 
  Yang Jiao, Salvatore Torquato:
  Emergent Behaviors from a Cellular Automaton Model for Invasive Tumor Growth in Heterogeneous Microenvironments.
• 
  Su-Sen Chang, Hung-Jin Huang, Calvin Yu-Chian Chen:
  Two Birds with One Stone? Possible Dual-Targeting H1N1 Inhibitors from Traditional Chinese Medicine.
• 
  Ying Zhang, Olga Zagnitko, Irina Rodionova, Andrei Osterman, Adam Godzik:
  The FGGY Carbohydrate Kinase Family: Insights into the Evolution of Functional Specificities.
• 
  Christian Frech, Nansheng Chen:
  Genome Comparison of Human and Non-Human Malaria Parasites Reveals Species Subset-Specific Genes Potentially Linked to Human Disease.
• 
  Daniel Shriner, Adebowale Adeyemo, Charles Rotimi:
  Joint Ancestry and Association Testing in Admixed Individuals.
• 
  Mithun Biswas, Karine Voltz, Jeremy C. Smith, Jörg Langowski:
  Role of Histone Tails in Structural Stability of the Nucleosome.
• 
  Dejan Pecevski, Lars Buesing, Wolfgang Maass:
  Probabilistic Inference in General Graphical Models through Sampling in Stochastic Networks of Spiking Neurons.
• 
  Alexander E. Lobkovsky, Yuri I. Wolf, Eugene V. Koonin:
  Predictability of Evolutionary Trajectories in Fitness Landscapes.
• 
  Izzet B. Yildiz, Stefan J. Kiebel:
  A Hierarchical Neuronal Model for Generation and Online Recognition of Birdsongs.
• 
  Angela Relógio, Pål O. Westermark, Thomas Wallach, Katja Schellenberg, Achim Kramer, Hanspeter Herzel:
  Tuning the Mammalian Circadian Clock: Robust Synergy of Two Loops.
• 
  Zhichao Liu, Qiang Shi, Don Ding, Reagan Kelly, Hong Fang, Weida Tong:
  Translating Clinical Findings into Knowledge in Drug Safety Evaluation - Drug Induced Liver Injury Prediction System (DILIps).
• 
  Ismail Adeniran, Mark J. McPate, Harry J. Witchel, Jules C. Hancox, Henggui Zhang:
  Increased Vulnerability of Human Ventricle to Re-entrant Excitation in hERG-linked Variant 1 Short QT Syndrome.
• 
  Lan K. Nguyen, Javier Muñoz-García, Helene Maccario, Aaron Ciechanover, Walter Kolch, Boris N. Kholodenko:
  Switches, Excitable Responses and Oscillations in the Ring1B/Bmi1 Ubiquitination System.
• 
  Franck Gallier, Perrine Lallemand, Maïa Meurillon, Lars P. Jordheim, Charles Dumontet, Christian Périgaud, Corinne Lionne, Suzanne Peyrottes, Laurent Chaloin:
  Structural Insights into the Inhibition of Cytosolic 5′-Nucleotidase II (cN-II) by Ribonucleoside 5′-Monophosphate Analogues.
• 
  Núria Domedel-Puig, Pau Rué, Antonio J. Pons Rivero, Jordi García-Ojalvo:
  Information Routing Driven by Background Chatter in a Signaling Network.
• 
  Simon Mitternacht, Igor N. Berezovsky:
  Coherent Conformational Degrees of Freedom as a Structural Basis for Allosteric Communication.
• 
  Pranesh Padmanabhan, Narendra M. Dixit:
  Mathematical Model of Viral Kinetics In Vitro Estimates the Number of E2-CD81 Complexes Necessary for Hepatitis C Virus Entry.
• 
  Thadeous Kacmarczyk, Peter Waltman, Ashley Bate, Patrick Eichenberger, Richard Bonneau:
  Comparative Microbial Modules Resource: Generation and Visualization of Multi-species Biclusters.
• 
  Andrew T. Kwon, Alice Yi Chou, David J. Arenillas, Wyeth W. Wasserman:
  Validation of Skeletal Muscle cis-Regulatory Module Predictions Reveals Nucleotide Composition Bias in Functional Enhancers.
• 
  Dieter Vanderelst, Jonas Reijniers, Uwe Firzlaff, Herbert Peremans:
  Dominant Glint Based Prey Localization in Horseshoe Bats: A Possible Strategy for Noise Rejection.
• 
  Christopher J. Creevey, Jean Muller, Tobias Doerks, Julie Dawn Thompson, Detlev Arendt, Peer Bork:
  Identifying Single Copy Orthologs in Metazoa.
• 
  Dmitry A. Fedosov, Huan Lei, Bruce Caswell, Subra Suresh, George E. Karniadakis:
  Multiscale Modeling of Red Blood Cell Mechanics and Blood Flow in Malaria.
• 
  Ke Xu, Kevin T. Morgan, Abby Todd Gehris, Timothy C. Elston, Shawn M. Gomez:
  A Whole-Body Model for Glycogen Regulation Reveals a Critical Role for Substrate Cycling in Maintaining Blood Glucose Homeostasis.
• 
  Sakuntala Chatterjee, Rava Azeredo da Silveira, Yariv Kafri:
  Chemotaxis when Bacteria Remember: Drift versus Diffusion.
• 
  Helen R. Fryer, Angela R. McLean:
  Modelling the Spread of HIV Immune Escape Mutants in a Vaccinated Population.
• 
  Benjamin Werner, David Dingli, Tom Lenaerts, Jorge M. Pacheco, Arne Traulsen:
  Dynamics of Mutant Cells in Hierarchical Organized Tissues.
• 
  Alessandro Ambrosi, Ingrid Kristine Glad, Danilo Pellin, Claudia Cattoglio, Fulvio Mavilio, Clelia Di Serio, Arnoldo Frigessi:
  Estimated Comparative Integration Hotspots Identify Different Behaviors of Retroviral Gene Transfer Vectors.
• 
  Maurizio De Pittà, Vladislav Volman, Hugues Berry, Eshel Ben-Jacob:
  A Tale of Two Stories: Astrocyte Regulation of Synaptic Depression and Facilitation.