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.
•