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PLoS Computational Biology, Volume 9

Volume 9, Number 1, January 2013

Message from ISCB

• 
  Jeroen de Ridder, Thomas Abeel, Magali Michaut, Venkata P. Satagopam, Nils Gehlenborg:
  Don't Wear Your New Shoes (Yet): Taking the Right Steps to Become a Successful Principal Investigator.

Education

• 
  Chiara Pastrello, David Otasek, Kristen Fortney, Giuseppe Agapito, Mario Cannataro, Elize Shirdel, Igor Jurisica:
  Visual Data Mining of Biological Networks: One Size Does Not Fit All.

Topic Page

• 
  Mikael Sunnåker, Alberto Giovanni Busetto, Elina Numminen, Jukka Corander, Matthieu Foll, Christophe Dessimoz:
  Approximate Bayesian Computation.

Research Articles

• 
  Luca Ciandrini, Ian Stansfield, M. Carmen Romano:
  Ribosome Traffic on mRNAs Maps to Gene Ontology: Genome-wide Quantification of Translation Initiation Rates and Polysome Size Regulation.
• 
  Gkikas Magiorkinis, Vana Sypsa, Emmanouil Magiorkinis, Dimitrios Paraskevis, Antigoni Katsoulidou, Robert Belshaw, Christophe Fraser, Oliver George Pybus, Angelos Hatzakis:
  Integrating Phylodynamics and Epidemiology to Estimate Transmission Diversity in Viral Epidemics.
• 
  Juliane Liepe, Sarah Filippi, Michal Komorowski, Michael P. H. Stumpf:
  Maximizing the Information Content of Experiments in Systems Biology.
• 
  Fabian H. Sinz, Matthias Bethge:
  Temporal Adaptation Enhances Efficient Contrast Gain Control on Natural Images.
• 
  Hang Yu, Klaus Schulten:
  Membrane Sculpting by F-BAR Domains Studied by Molecular Dynamics Simulations.
• 
  Ming Hu, Ke Deng, Zhaohui S. Qin, Jesse R. Dixon, Siddarth Selvaraj, Jennifer Fang, Bing Ren, Jun S. Liu:
  Bayesian Inference of Spatial Organizations of Chromosomes.
• 
  George Forrest Young, Luca Scardovi, Andrea Cavagna, Irene Giardina, Naomi Ehrich Leonard:
  Starling Flock Networks Manage Uncertainty in Consensus at Low Cost.
• 
  Mathieu d'Acremont, Eleonora Fornari, Peter Bossaerts:
  Activity in Inferior Parietal and Medial Prefrontal Cortex Signals the Accumulation of Evidence in a Probability Learning Task.
• 
  Linan Xu, Naushaba Hasin, Manli Shen, Jianwei He, Youlin Xue, Xiaohong Zhou, Sarah Perrett, Youtao Song, Gary W. Jones:
  Using Steered Molecular Dynamics to Predict and Assess Hsp70 Substrate-Binding Domain Mutants that Alter Prion Propagation.
• 
  Vladislav Volman, Maxim Bazhenov, Terrence J. Sejnowski:
  Divide and Conquer: Functional Segregation of Synaptic Inputs by Astrocytic Microdomains Could Alleviate Paroxysmal Activity Following Brain Trauma.
• 
  Michael A. Buice, Carson C. Chow:
  Dynamic Finite Size Effects in Spiking Neural Networks.
• 
  Holly E. Gerhard, Felix A. Wichmann, Matthias Bethge:
  How Sensitive Is the Human Visual System to the Local Statistics of Natural Images?
• 
  Andrew H. Beck, Nicholas W. Knoblauch, Marco M. Hefti, Jennifer Kaplan, Stuart J. Schnitt, Aedín C. Culhane, Markus S. Schröder, Thomas Risch, John Quackenbush, Benjamin Haibe-Kains:
  Significance Analysis of Prognostic Signatures.
• 
  Thomas Lemmin, Cinque S. Soto, Graham Clinthorne, William F. DeGrado, Matteo Dal Peraro:
  Assembly of the Transmembrane Domain of E. coli PhoQ Histidine Kinase: Implications for Signal Transduction from Molecular Simulations.
• 
  Stefan Wuchty, Dolores Arjona, Peter O. Bauer:
  Important miRs of Pathways in Different Tumor Types.
• 
  Yohan Kim, Jonathan W. Yewdell, Alessandro Sette, Björn Peters:
  Positional Bias of MHC Class I Restricted T-Cell Epitopes in Viral Antigens Is Likely due to a Bias in Conservation.
• 
  Karen E. Joyce, Satoru Hayasaka, Paul J. Laurienti:
  The Human Functional Brain Network Demonstrates Structural and Dynamical Resilience to Targeted Attack.
• 
  Corentin M. Barbu, Andrew Hong, Jennifer M. Manne, Dylan S. Small, Javier E. Quintanilla Calderón, Karthik Sethuraman, Víctor Quispe-Machaca, Jenny Ancca-Juárez, Juan G. Cornejo del Carpio, Fernando S. Málaga Chavez, César Náquira, Michael Z. Levy:
  The Effects of City Streets on an Urban Disease Vector.
• 
  Yann Le Cunff, Annette Baudisch, Khashayar Pakdaman:
  How Evolving Heterogeneity Distributions of Resource Allocation Strategies Shape Mortality Patterns.
• 
  Sebastian Funk, Hiroshi Nishiura, Hans Heesterbeek, W. John Edmunds, Francesco Checchi:
  Identifying Transmission Cycles at the Human-Animal Interface: The Role of Animal Reservoirs in Maintaining Gambiense Human African Trypanosomiasis.
• 
  A. Ercüment Çiçek, Ilya Bederman, Leigh Henderson, Mitchell L. Drumm, Gultekin Özsoyoglu:
  ADEMA: An Algorithm to Determine Expected Metabolite Level Alterations Using Mutual Information.
• 
  Cédric Debès, Minglei Wang, Gustavo Caetano-Anollés, Frauke Gräter:
  Evolutionary Optimization of Protein Folding.
• 
  Giovanni Settanni, David Serquera, Piotr E. Marszalek, Emanuele Paci, Laura S. Itzhaki:
  Effects of Ligand Binding on the Mechanical Properties of Ankyrin Repeat Protein Gankyrin.
• 
  Jeromos Vukov, Flávio L. Pinheiro, Francisco C. Santos, Jorge M. Pacheco:
  Reward from Punishment Does Not Emerge at All Costs.
• 
  Jing Dong, Jiazhang Qiu, Yu Zhang, Chongjian Lu, Xiaohan Dai, Jianfeng Wang, Hongen Li, Xin Wang, Wei Tan, Mingjing Luo, Xiaodi Niu, Xuming Deng:
  Oroxylin A Inhibits Hemolysis via Hindering the Self-Assembly of α-Hemolysin Heptameric Transmembrane Pore.
• 
  Giovanni Lo Iacono, Frank van den Bosch, Chris A. Gilligan:
  Durable Resistance to Crop Pathogens: An Epidemiological Framework to Predict Risk under Uncertainty.
• 
  Niklas Wilming, Simon Harst, Nico M. Schmidt, Peter König:
  Saccadic Momentum and Facilitation of Return Saccades Contribute to an Optimal Foraging Strategy.
• 
  Ruian Ke, Piers J. Ingram, Ken Haynes:
  An Integrative Model of Ion Regulation in Yeast.
• 
  Wyming Lee Pang, Amardeep Kaur, Alexander V. Ratushny, Aleksandar Cvetkovic, Sunil Kumar, Min Pan, Adam P. Arkin, John D. Aitchison, Michael W. W. Adams, Nitin S. Baliga:
  Metallochaperones Regulate Intracellular Copper Levels.
• 
  Kristy Nowak-Lovato, Ludmil B. Alexandrov, Afsheen Banisadr, Amy L. Bauer, Alan R. Bishop, Anny Usheva, Fangping Mu, Elizabeth Hong-Geller, Kim Ø. Rasmussen, William S. Hlavacek, Boian S. Alexandrov:
  Binding of Nucleoid-Associated Protein Fis to DNA Is Regulated by DNA Breathing Dynamics.
• 
  Graham Rockwell, Nicholas J. Guido, George M. Church:
  Redirector: Designing Cell Factories by Reconstructing the Metabolic Objective.
• 
  Sandra V. Bennun, Kevin J. Yarema, Michael J. Betenbaugh, Frederick J. Krambeck:
  Integration of the Transcriptome and Glycome for Identification of Glycan Cell Signatures.
• 
  Cibele Vieira Falkenberg, Leslie M. Loew:
  Computational Analysis of Rho GTPase Cycling.
• 
  Stefka Tyanova, Jürgen Cox, Jesper V. Olsen, Matthias Mann, Dmitrij Frishman:
  Phosphorylation Variation during the Cell Cycle Scales with Structural Propensities of Proteins.
• 
  Nol Chindapol, Jaap A. Kaandorp, Carolina Cronemberger, Tali Mass, Amatzia Genin:
  Modelling Growth and Form of the Scleractinian Coral Pocillopora verrucosa and the Influence of Hydrodynamics.
• 
  Anatoly Rinberg, Adam L. Taylor, Eve Marder:
  The Effects of Temperature on the Stability of a Neuronal Oscillator.
• 
  Satomi Matsuoka, Tatsuo Shibata, Masahiro Ueda:
  Asymmetric PTEN Distribution Regulated by Spatial Heterogeneity in Membrane-Binding State Transitions.
• 
  Omry Koren, Dan Knight, Antonio González, Levi Waldron, Nicola Segata, Rob Knight, Curtis Huttenhower, Ruth E. Ley:
  A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets.
• 
  Cornelis van de Kamp, Peter J. Gawthrop, Henrik Gollee, Ian D. Loram:
  Refractoriness in Sustained Visuo-Manual Control: Is the Refractory Duration Intrinsic or Does It Depend on External System Properties?
• 
  Pengsheng Zheng, Christos Dimitrakakis, Jochen Triesch:
  Network Self-Organization Explains the Statistics and Dynamics of Synaptic Connection Strengths in Cortex.
• 
  Nives Skunca, Matko Bosnjak, Anita Krisko, Pance Panov, Saso Dzeroski, Tomislav Smuc, Fran Supek:
  Phyletic Profiling with Cliques of Orthologs Is Enhanced by Signatures of Paralogy Relationships.
• 
  Anne L. Wheeler, Cátia M. Teixeira, Afra H. Wang, Xuejian Xiong, Natasa Kovacevic, Jason P. Lerch, Anthony Randal McIntosh, John Parkinson, Paul W. Frankland:
  Identification of a Functional Connectome for Long-Term Fear Memory in Mice.
• 
  Martin H. Schaefer, Tiago J. S. Lopes, Nancy Mah, Jason E. Shoemaker, Yukiko Matsuoka, Jean-Fred Fontaine, Caroline Louis-Jeune, Amie J. Eisfeld, Gabriele Neumann, Carol Perez-Iratxeta, Yoshihiro Kawaoka, Hiroaki Kitano, Miguel A. Andrade-Navarro:
  Adding Protein Context to the Human Protein-Protein Interaction Network to Reveal Meaningful Interactions.
• 
  Mario Pujato, Thomas MacCarthy, András Fiser, Aviv Bergman:
  The Underlying Molecular and Network Level Mechanisms in the Evolution of Robustness in Gene Regulatory Networks.

Volume 9, Number 2, February 2013

Editorial

• 
  Philip E. Bourne:
  Let's Make Those Book Chapters Open Too!

Research Articles

• 
  Romain Daniel Cazé, Mark D. Humphries, Boris S. Gutkin:
  Passive Dendrites Enable Single Neurons to Compute Linearly Non-separable Functions.
• 
  Andrea Censi, Andrew D. Straw, Rosalyn W. Sayaman, Richard M. Murray, Michael H. Dickinson:
  Discriminating External and Internal Causes for Heading Changes in Freely Flying Drosophila.
• 
  Carsten Magnus:
  Virus Neutralisation: New Insights from Kinetic Neutralisation Curves.
• 
  Paul Michael Loriaux, Glenn Tesler, Alexander Hoffmann:
  Characterizing the Relationship between Steady State and Response Using Analytical Expressions for the Steady States of Mass Action Models.
• 
  Lizhe Zhu, Peter G. Bolhuis, Jocelyne Vreede:
  The HAMP Signal Relay Domain Adopts Multiple Conformational States through Collective Piston and Tilt Motions.
• 
  Michael Thomas, Dylan Jayatilaka, Ben Corry:
  An Entropic Mechanism of Generating Selective Ion Binding in Macromolecules.
• 
  Kolbjørn Tunstrøm, Yael Katz, Christos C. Ioannou, Cristián Huepe, Matthew J. Lutz, Iain D. Couzin:
  Collective States, Multistability and Transitional Behavior in Schooling Fish.
• 
  Kieran Alden, Mark Read, Jonathan Timmis, Paul S. Andrews, Henrique Veiga-Fernandes, Mark C. Coles:
  Spartan: A Comprehensive Tool for Understanding Uncertainty in Simulations of Biological Systems.
• 
  David Managadze, Alexander E. Lobkovsky, Yuri I. Wolf, Svetlana A. Shabalina, Igor B. Rogozin, Eugene V. Koonin:
  The Vast, Conserved Mammalian lincRNome.
• 
  David C. Sterratt, Daniel Lyngholm, David J. Willshaw, Ian D. Thompson:
  Standard Anatomical and Visual Space for the Mouse Retina: Computational Reconstruction and Transformation of Flattened Retinae with the Retistruct Package.
• 
  Andraz Stozer, Marko Gosak, Jurij Dolensek, Matjaz Perc, Marko Marhl, Marjan Slak Rupnik, Dean Korosak:
  Functional Connectivity in Islets of Langerhans from Mouse Pancreas Tissue Slices.
• 
  Zhe Zhang, Yueli Zheng, Margo Petukh, Anthony Pegg, Yoshihiko Ikeguchi, Emil Alexov:
  Enhancing Human Spermine Synthase Activity by Engineered Mutations.
• 
  Min-Cheol Kim, Devin M. Neal, Roger D. Kamm, H. Harry Asada:
  Dynamic Modeling of Cell Migration and Spreading Behaviors on Fibronectin Coated Planar Substrates and Micropatterned Geometries.
• 
  Shaiyan Keshvari, Ronald Van den Berg, Wei Ji Ma:
  No Evidence for an Item Limit in Change Detection.
• 
  Cherrie H. T. Kong, Derek R. Laver, Mark B. Cannell:
  Extraction of Sub-microscopic Ca Fluxes from Blurred and Noisy Fluorescent Indicator Images with a Detailed Model Fitting Approach.
• 
  Paul Michael Loriaux, Alexander Hoffmann:
  A Protein Turnover Signaling Motif Controls the Stimulus-Sensitivity of Stress Response Pathways.
• 
  Ying Li, Guang Li, Haifang Wang, Jiulin Du, Jun Yan:
  Analysis of a Gene Regulatory Cascade Mediating Circadian Rhythm in Zebrafish.
• 
  Tanya Gurieva, Martin C. J. Bootsma, Marc J. M. Bonten:
  Cost and Effects of Different Admission Screening Strategies to Control the Spread of Methicillin-resistant Staphylococcus aureus.
• 
  Gerard J. P. van Westen, Alwin Hendriks, Jörg K. Wegner, Adriaan P. IJzerman, Herman W. T. van Vlijmen, Andreas Bender:
  Significantly Improved HIV Inhibitor Efficacy Prediction Employing Proteochemometric Models Generated From Antivirogram Data.
• 
  Baktash Babadi, L. F. Abbott:
  Pairwise Analysis Can Account for Network Structures Arising from Spike-Timing Dependent Plasticity.
• 
  Thomas Stockner, Therese R. Montgomery, Oliver Kudlacek, Rene Weissensteiner, Gerhard F. Ecker, Michael Freissmuth, Harald H. Sitte:
  Mutational Analysis of the High-Affinity Zinc Binding Site Validates a Refined Human Dopamine Transporter Homology Model.
• 
  Jimin Song, Mona Singh:
  From Hub Proteins to Hub Modules: The Relationship Between Essentiality and Centrality in the Yeast Interactome at Different Scales of Organization.
• 
  Falk Lieder, Jean Daunizeau, Marta I. Garrido, Karl J. Friston, Klaas E. Stephan:
  Modelling Trial-by-Trial Changes in the Mismatch Negativity.
• 
  Charlotte Prévost, Daniel C. McNamee, Ryan K. Jessup, Peter Bossaerts, John P. O'Doherty:
  Evidence for Model-based Computations in the Human Amygdala during Pavlovian Conditioning.
• 
  Claudia Clopath, Nicolas Brunel:
  Optimal Properties of Analog Perceptrons with Excitatory Weights.
• 
  Wei-Yi Cheng, Tai-Hsien Ou Yang, Dimitris Anastassiou:
  Biomolecular Events in Cancer Revealed by Attractor Metagenes.
• 
  Alexander T. Dilthey, Stephen Leslie, Loukas Moutsianas, Judong Shen, Charles Cox, Matthew R. Nelson, Gil McVean:
  Multi-Population Classical HLA Type Imputation.
• 
  Davide Reato, Fernando Gasca, Abhishek Datta, Marom Bikson, Lisa Marshall, Lucas C. Parra:
  Transcranial Electrical Stimulation Accelerates Human Sleep Homeostasis.
• 
  Ryo Kanada, Takeshi Kuwata, Hiroo Kenzaki, Shoji Takada:
  Structure-based Molecular Simulations Reveal the Enhancement of Biased Brownian Motions in Single-headed Kinesin.
• 
  Roberto Latorre, Rafael Levi, Pablo Varona:
  Transformation of Context-dependent Sensory Dynamics into Motor Behavior.
• 
  Hamish Cunningham, Valentin Tablan, Angus Roberts, Kalina Bontcheva:
  Getting More Out of Biomedical Documents with GATE's Full Lifecycle Open Source Text Analytics.
• 
  Shao-Shan Carol Huang, David C. Clarke, Sara J. C. Gosline, Adam Labadorf, Candace R. Chouinard, William Gordon, Douglas A. Lauffenburger, Ernest Fraenkel:
  Linking Proteomic and Transcriptional Data through the Interactome and Epigenome Reveals a Map of Oncogene-induced Signaling.
• 
  Eduardo J. Izquierdo, Randall D. Beer:
  Connecting a Connectome to Behavior: An Ensemble of Neuroanatomical Models of C. elegans Klinotaxis.
• 
  Robert R. Kerr, Anthony N. Burkitt, Doreen A. Thomas, Matthieu Gilson, David B. Grayden:
  Delay Selection by Spike-Timing-Dependent Plasticity in Recurrent Networks of Spiking Neurons Receiving Oscillatory Inputs.
• 
  Shanshan Cheng, Charles L. Brooks III:
  Viral Capsid Proteins Are Segregated in Structural Fold Space.
• 
  Benjamin M. Althouse, Oscar Patterson-Lomba, Georg M. Goerg, Laurent Hébert-Dufresne:
  The Timing and Targeting of Treatment in Influenza Pandemics Influences the Emergence of Resistance in Structured Populations.

Volume 9, Number 3, March 2013

Editorial

• 
  Thomas Lengauer, Ruth Nussinov:
  New Methods Section in PLOS Computational Biology.

Topic Pages

• 
  Erik M. Volz, Katia Koelle, Trevor Bedford:
  Viral Phylodynamics.
• 
  Miguel A. Fortuna, Luis Zaman, Aaron P. Wagner, Charles Ofria:
  Evolving Digital Ecological Networks.

Research Articles

• 
  Simon Garnier, Maud Combe, Christian Jost, Guy Theraulaz:
  Do Ants Need to Estimate the Geometrical Properties of Trail Bifurcations to Find an Efficient Route? A Swarm Robotics Test Bed.
• 
  Tina Toni, Bruce Tidor:
  Combined Model of Intrinsic and Extrinsic Variability for Computational Network Design with Application to Synthetic Biology.
• 
  Clive G. Bowsher, Margaritis Voliotis, Peter S. Swain:
  The Fidelity of Dynamic Signaling by Noisy Biomolecular Networks.
• 
  James B. Gilmore, Anthony D. Kelleher, David A. Cooper, John M. Murray:
  Explaining the Determinants of First Phase HIV Decay Dynamics through the Effects of Stage-dependent Drug Action.
• 
  Brad Busse, Stephen J. Smith:
  Automated Analysis of a Diverse Synapse Population.
• 
  Michael A. Carlin, Mounya Elhilali:
  Sustained Firing of Model Central Auditory Neurons Yields a Discriminative Spectro-temporal Representation for Natural Sounds.
• 
  Simon Garnier, Tucker Murphy, Matthew J. Lutz, Edward Hurme, Simon Leblanc, Iain D. Couzin:
  Stability and Responsiveness in a Self-Organized Living Architecture.
• 
  Christoph Schmal, Peter Reimann, Dorothee Staiger:
  A Circadian Clock-Regulated Toggle Switch Explains AtGRP7 and AtGRP8 Oscillations in Arabidopsis thaliana.
• 
  Christopher P. Said, David J. Heeger:
  A Model of Binocular Rivalry and Cross-orientation Suppression.
• 
  Kirill S. Korolev:
  The Fate of Cooperation during Range Expansions.
• 
  Marta I. Garrido, Maneesh Sahani, Raymond J. Dolan:
  Outlier Responses Reflect Sensitivity to Statistical Structure in the Human Brain.
• 
  Oscar Franzén, Jon Jerlström-Hultqvist, Elin Einarsson, Johan Ankarklev, Marcela Ferella, Björn Andersson, Staffan G. Svärd:
  Transcriptome Profiling of Giardia intestinalis Using Strand-specific RNA-Seq.
• 
  Himadri Mukhopadhyay, Shaun-Paul Cordoba, Philip K. Maini, P. Anton van der Merwe, Omer Dushek:
  Systems Model of T Cell Receptor Proximal Signaling Reveals Emergent Ultrasensitivity.
• 
  Hermann B. Frieboes, Bryan R. Smith, Yao-Li Chuang, Ken Ito, Allison M. Roettgers, Sanjiv Sam Gambhir, Vittorio Cristini:
  An Integrated Computational/Experimental Model of Lymphoma Growth.
• 
  Syed Abbas Bukhari, Gustavo Caetano-Anollés:
  Origin and Evolution of Protein Fold Designs Inferred from Phylogenomic Analysis of CATH Domain Structures in Proteomes.
• 
  Yuguo Yu, Thomas S. McTavish, Michael L. Hines, Gordon M. Shepherd, Cesare Valenti, Michele Migliore:
  Sparse Distributed Representation of Odors in a Large-scale Olfactory Bulb Circuit.
• 
  Marco Di Stefano, Angelo Rosa, Vincenzo Belcastro, Diego di Bernardo, Cristian Micheletti:
  Colocalization of Coregulated Genes: A Steered Molecular Dynamics Study of Human Chromosome 19.
• 
  Philip Stegmaier, Alexander E. Kel, Edgar Wingender, Jürgen Borlak:
  A Discriminative Approach for Unsupervised Clustering of DNA Sequence Motifs.
• 
  Richard P. Mann, Andrea Perna, Daniel Strömbom, Roman Garnett, James E. Herbert-Read, David J. T. Sumpter, Ashley J. W. Ward:
  Multi-scale Inference of Interaction Rules in Animal Groups Using Bayesian Model Selection.
• 
  Laura Matrajt, M. Elizabeth Halloran, Ira M. Longini Jr.:
  Optimal Vaccine Allocation for the Early Mitigation of Pandemic Influenza.
• 
  Alane Izu, Ted Cohen, Victor DeGruttola:
  Bayesian Estimation of Mixture Models with Prespecified Elements to Compare Drug Resistance in Treatment-Naïve and Experienced Tuberculosis Cases.
• 
  Luis E. C. Rocha, Vincent D. Blondel:
  Bursts of Vertex Activation and Epidemics in Evolving Networks.
• 
  Wei Zhang, Takayo Ota, Viji Shridhar, Jeremy Chien, Baolin Wu, Rui Kuang:
  Network-based Survival Analysis Reveals Subnetwork Signatures for Predicting Outcomes of Ovarian Cancer Treatment.
• 
  Katarzyna Bozek, Thomas Lengauer, Saleta Sierra, Rolf Kaiser, Francisco S. Domingues:
  Analysis of Physicochemical and Structural Properties Determining HIV-1 Coreceptor Usage.
• 
  Rasmus Agren, Liming Liu, Saeed Shoaie, Wanwipa Vongsangnak, Intawat Nookaew, Jens Nielsen:
  The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum.
• 
  Dazhi Jiao, Yuzhen Ye, Haixu Tang:
  Probabilistic Inference of Biochemical Reactions in Microbial Communities from Metagenomic Sequences.
• 
  Timothy W. Secomb, Jonathan P. Alberding, Richard Hsu, Mark W. Dewhirst, Axel R. Pries:
  Angiogenesis: An Adaptive Dynamic Biological Patterning Problem.
• 
  Viola Priesemann, Mario Valderrama, Michael Wibral, Michel Le Van Quyen:
  Neuronal Avalanches Differ from Wakefulness to Deep Sleep - Evidence from Intracranial Depth Recordings in Humans.
• 
  Sergio Rossell, Martijn A. Huynen, Richard A. Notebaart:
  Inferring Metabolic States in Uncharacterized Environments Using Gene-Expression Measurements.
• 
  Andreas Handel, Justin Brown, David E. Stallknecht, Pejman Rohani:
  A Multi-scale Analysis of Influenza A Virus Fitness Trade-offs due to Temperature-dependent Virus Persistence.
• 
  Frank H. Wallrapp, Alexander A. Voityuk, Victor Guallar:
  In-silico Assessment of Protein-Protein Electron Transfer. A Case Study: Cytochrome c Peroxidase - Cytochrome c.
• 
  Alexander J. Stewart, Robert M. Seymour, Andrew Pomiankowski, Max Reuter:
  Under-Dominance Constrains the Evolution of Negative Autoregulation in Diploids.
• 
  Hyun-Jun Nam, Seong Kyu Han, James U. Bowie, Sanguk Kim:
  Rampant Exchange of the Structure and Function of Extramembrane Domains between Membrane and Water Soluble Proteins.
• 
  Jialiang Huang, Chaoqun Niu, Christopher D. Green, Lun Yang, Hongkang Mei, Jing-Dong J. Han:
  Systematic Prediction of Pharmacodynamic Drug-Drug Interactions through Protein-Protein-Interaction Network.
• 
  Silvio a Beccara, Tatjana Skrbic, Roberto Covino, Cristian Micheletti, Pietro Faccioli:
  Folding Pathways of a Knotted Protein with a Realistic Atomistic Force Field.
• 
  Paul C. Whitford, Scott C. Blanchard, Jamie H. D. Cate, Karissa Y. Sanbonmatsu:
  Connecting the Kinetics and Energy Landscape of tRNA Translocation on the Ribosome.
• 
  Einat Granot-Atedgi, Gasper Tkacik, Ronen Segev, Elad Schneidman:
  Stimulus-dependent Maximum Entropy Models of Neural Population Codes.
• 
  Robert W. Mill, Tamás Bohm, Alexandra Bendixen, István Winkler, Susan L. Denham:
  Modelling the Emergence and Dynamics of Perceptual Organisation in Auditory Streaming.
• 
  Zhixing Feng, Gang Fang, Jonas Korlach, Tyson Clark, Khai Luong, Xuegong Zhang, Wing Wong, Eric E. Schadt:
  Detecting DNA Modifications from SMRT Sequencing Data by Modeling Sequence Context Dependence of Polymerase Kinetic.
• 
  Christian G. Fink, Geoffrey G. Murphy, Michal Zochowski, Victoria Booth:
  A Dynamical Role for Acetylcholine in Synaptic Renormalization.
• 
  Sunhwan Jo, Hui Sun Lee, Jeffrey Skolnick, Wonpil Im:
  Restricted N-glycan Conformational Space in the PDB and Its Implication in Glycan Structure Modeling.
• 
  Mehrdad Mehrbod, Mohammad R. K. Mofrad:
  Localized Lipid Packing of Transmembrane Domains Impedes Integrin Clustering.
• 
  Douglas E. White, Melissa A. Kinney, Todd C. McDevitt, Melissa L. Kemp:
  Spatial Pattern Dynamics of 3D Stem Cell Loss of Pluripotency via Rules-Based Computational Modeling.
• 
  BoHung Kim, Sarah L. Hawes, Fawad Gillani, Lane J. Wallace, Kim T. Blackwell:
  Signaling Pathways Involved in Striatal Synaptic Plasticity are Sensitive to Temporal Pattern and Exhibit Spatial Specificity.
• 
  Christopher Y. Park, Aaron K. Wong, Casey S. Greene, Jessica Rowland, Yuanfang Guan, Lars Ailo Bongo, Rebecca D. Burdine, Olga G. Troyanskaya:
  Functional Knowledge Transfer for High-accuracy Prediction of Under-studied Biological Processes.
• 
  Libin Rong, Jérémie Guedj, Harel Dahari, Daniel J. Coffield Jr., Micha Levi, Patrick Smith, Alan S. Perelson:
  Analysis of Hepatitis C Virus Decline during Treatment with the Protease Inhibitor Danoprevir Using a Multiscale Model.
• 
  Jan Grau, Annett Wolf, Maik Reschke, Ulla Bonas, Stefan Posch, Jens Boch:
  Computational Predictions Provide Insights into the Biology of TAL Effector Target Sites.
• 
  Stefanie Hertel, Christian Brettschneider, Ilka M. Axmann:
  Revealing a Two-Loop Transcriptional Feedback Mechanism in the Cyanobacterial Circadian Clock.
• 
  Winston A. Haynes, Roger Higdon, Larissa Stanberry, Dwayne Collins, Eugene Kolker:
  Differential Expression Analysis for Pathways.
• 
  Nisha Rajagopal, Wei Xie, Yan Li, Uli Wagner, Wei Wang, John A. Stamatoyannopoulos, Jason Ernst, Manolis Kellis, Bing Ren:
  RFECS: A Random-Forest Based Algorithm for Enhancer Identification from Chromatin State.
• 
  Syed Y. Abbas, Khaldoun C. Hamade, Ellen J. Yang, Scott Nawy, Robert G. Smith, Diana L. Pettit:
  Directional Summation in Non-direction Selective Retinal Ganglion Cells.
• 
  Gary R. Mirams, Christopher J. Arthurs, Miguel O. Bernabeu, Rafel Bordas, Jonathan Cooper, Alberto Corrias, Yohan Davit, Sara-Jane Dunn, Alexander G. Fletcher, Daniel G. Harvey, Megan E. Marsh, James M. Osborne, Pras Pathmanathan, Joe Pitt-Francis, James Southern, Nejib Zemzemi, David Gavaghan:
  Chaste: An Open Source C++ Library for Computational Physiology and Biology.
• 
  Anton Spanne, Henrik Jörntell:
  Processing of Multi-dimensional Sensorimotor Information in the Spinal and Cerebellar Neuronal Circuitry: A New Hypothesis.
• 
  Ekta Khurana, Yao Fu, Jieming Chen, Mark Gerstein:
  Interpretation of Genomic Variants Using a Unified Biological Network Approach.
• 
  Pouria Dasmeh, Adrian W. R. Serohijos, Kasper P. Kepp, Eugene I. Shakhnovich:
  Positively Selected Sites in Cetacean Myoglobins Contribute to Protein Stability.
• 
  Bóris Marin, William H. Barnett, Anca Doloc-Mihu, Ronald L. Calabrese, Gennady S. Cymbalyuk:
  High Prevalence of Multistability of Rest States and Bursting in a Database of a Model Neuron.
• 
  Jonathan Woodsmith, Atanas Kamburov, Ulrich Stelzl:
  Dual Coordination of Post Translational Modifications in Human Protein Networks.
• 
  Ophir Shalem, Lucas B. Carey, Danny Zeevi, Eilon Sharon, Leeat Keren, Adina Weinberger, Orna Dahan, Yitzhak Pilpel, Eran Segal:
  Measurements of the Impact of 3′ End Sequences on Gene Expression Reveal Wide Range and Sequence Dependent Effects.
• 
  Ron M. Stewart, Cynthia Alexander Rascón, Shulan Tian, Jeff Nie, Chris Barry, Li-Fang Chu, Hamisha Ardalani, Ryan J. Wagner, Mitchell D. Probasco, Jennifer M. Bolin, Ning Leng, Srikumar Sengupta, Michael Volkmer, Bianca Habermann, Elly M. Tanaka, James A. Thomson, Colin N. Dewey:
  Comparative RNA-seq Analysis in the Unsequenced Axolotl: The Oncogene Burst Highlights Early Gene Expression in the Blastema.
• 
  Yuhan Chen, Shengjun Wang, Claus C. Hilgetag, Changsong Zhou:
  Trade-off between Multiple Constraints Enables Simultaneous Formation of Modules and Hubs in Neural Systems.
• 
  Andrew M. Reynolds, Mathieu Lihoreau, Lars Chittka:
  A Simple Iterative Model Accurately Captures Complex Trapline Formation by Bumblebees Across Spatial Scales and Flower Arrangements.
• 
  R. Channing Moore, Tyler Lee, Frédéric E. Theunissen:
  Noise-invariant Neurons in the Avian Auditory Cortex: Hearing the Song in Noise.
• 
  Tomoki Kurikawa, Kunihiko Kaneko:
  Embedding Responses in Spontaneous Neural Activity Shaped through Sequential Learning.
• 
  Néstor Sepúlveda, Laurence Petitjean, Olivier Cochet, Erwan Grasland-Mongrain, Pascal Silberzan, Vincent Hakim:
  Collective Cell Motion in an Epithelial Sheet Can Be Quantitatively Described by a Stochastic Interacting Particle Model.
• 
  Chad R. Wells, Eili Y. Klein, Chris T. Bauch:
  Policy Resistance Undermines Superspreader Vaccination Strategies for Influenza.
• 
  Munia Amin, Steven L. Porter, Orkun S. Soyer:
  Split Histidine Kinases Enable Ultrasensitivity and Bistability in Two-Component Signaling Networks.
• 
  Per Larsson, Peter M. Kasson:
  Lipid Tail Protrusion in Simulations Predicts Fusogenic Activity of Influenza Fusion Peptide Mutants and Conformational Models.
• 
  David K. Johnson, John Karanicolas:
  Druggable Protein Interaction Sites Are More Predisposed to Surface Pocket Formation than the Rest of the Protein Surface.
• 
  David Amar, Hershel Safer, Ron Shamir:
  Dissection of Regulatory Networks that Are Altered in Disease via Differential Co-expression.
• 
  Zheng Chen, Weixiong Zhang:
  Integrative Analysis Using Module-Guided Random Forests Reveals Correlated Genetic Factors Related to Mouse Weight.

Volume 9, Number 4, April 2013

Education Articles

• 
  Yana Bromberg:
  Chapter 15: Disease Gene Prioritization.
• 
  K. Bretonnel Cohen, Lawrence E. Hunter:
  Chapter 16: Text Mining for Translational Bioinformatics.
• 
  Fuhai Li, Zheng Yin, Guangxu Jin, Hong Zhao, Stephen T. C. Wong:
  Chapter 17: Bioimage Informatics for Systems Pharmacology.

Perspective

• 
  Matthew R. Nassar, Joshua I. Gold:
  A Healthy Fear of the Unknown: Perspectives on the Interpretation of Parameter Fits from Computational Models in Neuroscience.

Research Articles

• 
  Javad Golji, Mohammad R. K. Mofrad:
  The Interaction of Vinculin with Actin.
• 
  Recep Colak, TaeHyung Kim, Magali Michaut, Mark G. F. Sun, Manuel Irimia, Jeremy Bellay, Chad L. Myers, Benjamin J. Blencowe, Philip M. Kim:
  Distinct Types of Disorder in the Human Proteome: Functional Implications for Alternative Splicing.
• 
  Bernhard Nessler, Michael Pfeiffer, Lars Buesing, Wolfgang Maass:
  Bayesian Computation Emerges in Generic Cortical Microcircuits through Spike-Timing-Dependent Plasticity.
• 
  Anne-Sophie Coquel, Jean-Pascal Jacob, Maël Primet, Alice Demarez, Mariella Dimiccoli, Thomas Julou, Lionel Moisan, Ariel B. Lindner, Hugues Berry:
  Localization of Protein Aggregation in Escherichia coli Is Governed by Diffusion and Nucleoid Macromolecular Crowding Effect.
• 
  Jordan R. Willis, Bryan S. Briney, Samuel L. DeLuca, James E. Crowe Jr., Jens Meiler:
  Human Germline Antibody Gene Segments Encode Polyspecific Antibodies.
• 
  Hans B. Sieburg, Giulio Cattarossi, Christa E. Müller-Sieburg:
  Lifespan Differences in Hematopoietic Stem Cells are Due to Imperfect Repair and Unstable Mean-Reversion.
• 
  Julian E. Fuchs, Susanne von Grafenstein, Roland G. Huber, Michael A. Margreiter, Gudrun M. Spitzer, Hannes G. Wallnoefer, Klaus R. Liedl:
  Cleavage Entropy as Quantitative Measure of Protease Specificity.
• 
  Yassmine Chebaro, Ismail Amal, Natacha Rochel, Cécile Rochette-Egly, Roland H. Stote, Annick Dejaegere:
  Phosphorylation of the Retinoic Acid Receptor Alpha Induces a Mechanical Allosteric Regulation and Changes in Internal Dynamics.
• 
  Juho Rousu, Daniel D. Agranoff, Olugbemiro Sodeinde, John Shawe-Taylor, Delmiro Fernandez-Reyes:
  Biomarker Discovery by Sparse Canonical Correlation Analysis of Complex Clinical Phenotypes of Tuberculosis and Malaria.
• 
  Geoffrey L. Johnston, David L. Smith, David A. Fidock:
  Malaria's Missing Number: Calculating the Human Component of R₀ by a Within-Host Mechanistic Model of Plasmodium falciparum Infection and Transmission.
• 
  Henrik Failmezger, Benjamin Jaegle, Andrea Schrader, Martin Hülskamp, Achim Tresch:
  Semi-automated 3D Leaf Reconstruction and Analysis of Trichome Patterning from Light Microscopic Images.
• 
  Joseph G. Makin, Matthew R. Fellows, Philip N. Sabes:
  Learning Multisensory Integration and Coordinate Transformation via Density Estimation.
• 
  Kyriakos Kentzoglanakis, Diana García López, Sam P. Brown, Richard A. Goldstein:
  The Evolution of Collective Restraint: Policing and Obedience among Non-conjugative Plasmids.
• 
  Adam Ponzi, Jeffery R. Wickens:
  Optimal Balance of the Striatal Medium Spiny Neuron Network.
• 
  Nicolas Frémaux, Henning Sprekeler, Wulfram Gerstner:
  Reinforcement Learning Using a Continuous Time Actor-Critic Framework with Spiking Neurons.
• 
  Lauren M. Bragg, Glenn Stone, Margaret K. Butler, Philip Hugenholtz, Gene W. Tyson:
  Shining a Light on Dark Sequencing: Characterising Errors in Ion Torrent PGM Data.
• 
  Joseph L. Baker, Nicolas Biais, Florence Tama:
  Steered Molecular Dynamics Simulations of a Type IV Pilus Probe Initial Stages of a Force-Induced Conformational Transition.
• 
  Joseph E. Goose, Mark S. P. Sansom:
  Reduced Lateral Mobility of Lipids and Proteins in Crowded Membranes.
• 
  Daniel L. Parton, Alex Tek, Marc Baaden, Mark S. P. Sansom:
  Formation of Raft-Like Assemblies within Clusters of Influenza Hemagglutinin Observed by MD Simulations.
• 
  Matthias Schultze-Kraft, Markus Diesmann, Sonja Grün, Moritz Helias:
  Noise Suppression and Surplus Synchrony by Coincidence Detection.
• 
  Gabriela V. Cohen Freue, Anna Meredith, Derek Smith, Axel Bergman, Mayu Sasaki, Karen K. Y. Lam, Zsuzsanna Hollander, Nina Opushneva, Mandeep Takhar, David Lin, Janet Wilson-McManus, Robert Balshaw, Paul A. Keown, Christoph H. Borchers, Bruce McManus, Raymond T. Ng, W. Robert McMaster:
  Computational Biomarker Pipeline from Discovery to Clinical Implementation: Plasma Proteomic Biomarkers for Cardiac Transplantation.
• 
  Domenico Campolo, Ferdinan Widjaja, Hong Xu, Wei Tech Ang, Etienne Burdet:
  Analysis of Accuracy in Pointing with Redundant Hand-held Tools: A Geometric Approach to the Uncontrolled Manifold Method.
• 
  Juergen Dukart, Ferath Kherif, Karsten Mueller, Stanislaw Adaszewski, Matthias L. Schroeter, Richard S. J. Frackowiak, Bogdan Draganski:
  Generative FDG-PET and MRI Model of Aging and Disease Progression in Alzheimer's Disease.
• 
  Nicole C. Kleinstreuer, David Dix, Michael Rountree, Nancy Baker, Nisha Sipes, David M. Reif, Richard Spencer, Thomas Knudsen:
  A Computational Model Predicting Disruption of Blood Vessel Development.
• 
  Masayo Inoue, Kunihiko Kaneko:
  Cooperative Adaptive Responses in Gene Regulatory Networks with Many Degrees of Freedom.
• 
  Stefano Lonardi, Denisa Duma, Matthew Alpert, Francesca Cordero, Marco Beccuti, Prasanna R. Bhat, Yonghui Wu, Gianfranco Ciardo, Burair Alsaihati, Yaqin Ma, Steve Wanamaker, Josh Resnik, Serdar Bozdag, Ming-Cheng Luo, Timothy J. Close:
  Combinatorial Pooling Enables Selective Sequencing of the Barley Gene Space.
• 
  Annabelle Ballesta, Jonathan Lopez, Nikolay Popgeorgiev, Philippe Gonzalo, Marie Doumic, Germain Gillet:
  Data-Driven Modeling of Src Control on the Mitochondrial Pathway of Apoptosis: Implication for Anticancer Therapy Optimization.
• 
  Marie Devaine, Florian Waszak, Pascal Mamassian:
  Dual Process for Intentional and Reactive Decisions.
• 
  Andrei Yu. Zinovyev, Inna Kuperstein, Emmanuel Barillot, Wolf-Dietrich Heyer:
  Synthetic Lethality between Gene Defects Affecting a Single Non-essential Molecular Pathway with Reversible Steps.
• 
  Emily V. Chambers, Wendy A. Bickmore, Colin A. M. Semple:
  Divergence of Mammalian Higher Order Chromatin Structure Is Associated with Developmental Loci.
• 
  Lin-Tai Da, Fátima Pardo Avila, Dong Wang, Xuhui Huang:
  A Two-State Model for the Dynamics of the Pyrophosphate Ion Release in Bacterial RNA Polymerase.
• 
  Dominic I. Standage, Hongzhi You, Da-Hui Wang, Michael C. Dorris:
  Trading Speed and Accuracy by Coding Time: A Coupled-circuit Cortical Model.
• 
  Xiaobo Wan, Yue Ma, Christopher L. McClendon, Lily Jun-shen Huang, Niu Huang:
  Ab Initio Modeling and Experimental Assessment of Janus Kinase 2 (JAK2) Kinase-Pseudokinase Complex Structure.
• 
  Purushottam D. Dixit, Sergei Maslov:
  Evolutionary Capacitance and Control of Protein Stability in Protein-Protein Interaction Networks.
• 
  Adria Carbo, Raquel Hontecillas, Barbara Kronsteiner, Monica Viladomiu, Mireia Pedragosa, Pinyi Lu, Casandra W. Philipson, Stefan Hoops, Madhav V. Marathe, Stephen G. Eubank, Keith R. Bisset, Katherine V. Wendelsdorf, Abdul Salam Jarrah, Yongguo Mei, Josep Bassaganya-Riera:
  Systems Modeling of Molecular Mechanisms Controlling Cytokine-driven CD4+ T Cell Differentiation and Phenotype Plasticity.
• 
  Yosef Y. Kuttner, Tal Nagar, Stanislav Engel:
  Surface Dynamics in Allosteric Regulation of Protein-Protein Interactions: Modulation of Calmodulin Functions by Ca²⁺.

Volume 9, Number 5, May 2013

Message from ISCB

• 
  Lawrence E. Hunter:
  Rocky Mountain Conference on Bioinformatics Celebrates 10 Years.

Perspective

• 
  Janusz M. Bujnicki, Jerzy Tiuryn:
  Bioinformatics and Computational Biology in Poland.

Research Articles

• 
  Alexandra M. Schnoes, David C. Ream, Alexander W. Thorman, Patricia C. Babbitt, Iddo Friedberg:
  Biases in the Experimental Annotations of Protein Function and Their Effect on Our Understanding of Protein Function Space.
• 
  Peng Jiang, Mona Singh, Hilary A. Coller:
  Computational Assessment of the Cooperativity between RNA Binding Proteins and MicroRNAs in Transcript Decay.
• 
  Po-Wei Chen, Luís L. Fonseca, Yusuf A. Hannun, Eberhard O. Voit:
  Coordination of Rapid Sphingolipid Responses to Heat Stress in Yeast.
• 
  Kendrick N. Kay, Jonathan Winawer, Ariel Rokem, Aviv A. Mezer, Brian A. Wandell:
  A Two-Stage Cascade Model of BOLD Responses in Human Visual Cortex.
• 
  Adam S. LaPrad, Kenneth R. Lutchen, Béla Suki:
  A Mechanical Design Principle for Tissue Structure and Function in the Airway Tree.
• 
  Ayako Watanabe, Daisuke Hoshino, Naohiko Koshikawa, Motoharu Seiki, Takashi Suzuki, Kazuhisa Ichikawa:
  Critical Role of Transient Activity of MT1-MMP for ECM Degradation in Invadopodia.
• 
  Alessio Franci, Guillaume Drion, Vincent Seutin, Rodolphe Sepulchre:
  A Balance Equation Determines a Switch in Neuronal Excitability.
• 
  Mark D. M. Leiserson, Dima Blokh, Roded Sharan, Benjamin J. Raphael:
  Simultaneous Identification of Multiple Driver Pathways in Cancer.
• 
  Xiaodong Cai, Juan Andrés Bazerque, Georgios B. Giannakis:
  Inference of Gene Regulatory Networks with Sparse Structural Equation Models Exploiting Genetic Perturbations.
• 
  Yunlang Li, Tamar Schlick:
  "Gate-keeper" Residues and Active-Site Rearrangements in DNA Polymerase μ Help Discriminate Non-cognate Nucleotides.
• 
  Hang Zhang, Nathaniel D. Daw, Laurence T. Maloney:
  Testing Whether Humans Have an Accurate Model of Their Own Motor Uncertainty in a Speeded Reaching Task.
• 
  Anurag Sethi, Jianhui Tian, Cynthia A. Derdeyn, Bette T. Korber, S. Gnanakaran:
  A Mechanistic Understanding of Allosteric Immune Escape Pathways in the HIV-1 Envelope Glycoprotein.
• 
  James G. Dyke, Iain S. Weaver:
  The Emergence of Environmental Homeostasis in Complex Ecosystems.
• 
  Christoph A. Haselwandter, Rob Phillips:
  Connection between Oligomeric State and Gating Characteristics of Mechanosensitive Ion Channels.
• 
  Julian Garrec, Ivano Tavernelli, Ursula Rothlisberger:
  Two Misfolding Routes for the Prion Protein around pH 4.5.
• 
  Haipeng Li, Thomas Wiehe:
  Coalescent Tree Imbalance and a Simple Test for Selective Sweeps Based on Microsatellite Variation.
• 
  Pete Riley, Michal Ben-Nun, Richard Armenta, Jon A. Linker, Angela A. Eick, Jose L. Sanchez, Dylan B. George, David P. Bacon, Steven Riley:
  Multiple Estimates of Transmissibility for the 2009 Influenza Pandemic Based on Influenza-like-Illness Data from Small US Military Populations.
• 
  Margaret E. Johnson, Gerhard Hummer:
  Interface-Resolved Network of Protein-Protein Interactions.
• 
  Gouri Shankar Pandey, Chen Yanover, Tom E. Howard, Zuben E. Sauna:
  Polymorphisms in the F8 Gene and MHC-II Variants as Risk Factors for the Development of Inhibitory Anti-Factor VIII Antibodies during the Treatment of Hemophilia A: A Computational Assessment.
• 
  Wei Huang, Joohyun Kim, Shantenu Jha, Fareed Aboul-Ela:
  The Impact of a Ligand Binding on Strand Migration in the SAM-I Riboswitch.
• 
  Alexey Solovyev, Qi Mi, Yi-Ting Tzen, David M. Brienza, Yoram Vodovotz:
  Hybrid Equation/Agent-Based Model of Ischemia-Induced Hyperemia and Pressure Ulcer Formation Predicts Greater Propensity to Ulcerate in Subjects with Spinal Cord Injury.
• 
  Vincent Vagenende, Alvin X. Han, Han B. Pek, Bernard L. W. Loo:
  Quantifying the Molecular Origins of Opposite Solvent Effects on Protein-Protein Interactions.
• 
  Wei-Hua Chen, Xing-Ming Zhao, Vera van Noort, Peer Bork:
  Human Monogenic Disease Genes Have Frequently Functionally Redundant Paralogs.
• 
  Jonathan J. Hunt, Peter Dayan, Geoffrey J. Goodhill:
  Sparse Coding Can Predict Primary Visual Cortex Receptive Field Changes Induced by Abnormal Visual Input.
• 
  Fanny Gascuel, Marc Choisy, Jean-Marc Duplantier, Florence Débarre, Carine Brouat:
  Host Resistance, Population Structure and the Long-Term Persistence of Bubonic Plague: Contributions of a Modelling Approach in the Malagasy Focus.
• 
  Richard A. White, Jørgen V. Bjørnholt, Donna D. Baird, Tore Midtvedt, Jennifer R. Harris, Marcello Pagano, Winston Hide, Knut Rudi, Birgitte Moen, Nina Iszatt, Shyamal D. Peddada, Merete Eggesbø:
  Novel Developmental Analyses Identify Longitudinal Patterns of Early Gut Microbiota that Affect Infant Growth.
• 
  Erhan Bilal, Janusz Dutkowski, Justin Guinney, In Sock Jang, Benjamin A. Logsdon, Gaurav Pandey, Benjamin A. Sauerwine, Yishai Shimoni, Hans Kristian Moen Vollan, Brigham H. Mecham, Oscar M. Rueda, Jorg Tost, Christina Curtis, Mariano J. Alvarez, Vessela N. Kristensen, Samuel Aparicio, Anne-Lise Børresen-Dale, Carlos Caldas, Andrea Califano, Stephen H. Friend, Trey Ideker, Eric E. Schadt, Gustavo A. Stolovitzky, Adam A. Margolin:
  Improving Breast Cancer Survival Analysis through Competition-Based Multidimensional Modeling.
• 
  Ginestra Bianconi, Kun Zhao, Irene A. Chen, Martin A. Nowak:
  Selection for Replicases in Protocells.
• 
  Yunpeng Wang, Jon Olav Vik, Stig W. Omholt, Arne B. Gjuvsland:
  Effect of Regulatory Architecture on Broad versus Narrow Sense Heritability.
• 
  Szymon Stoma, Alexandre Donzé, François Bertaux, Oded Maler, Grégory Batt:
  STL-based Analysis of TRAIL-induced Apoptosis Challenges the Notion of Type I/Type II Cell Line Classification.
• 
  Seth Blumberg, James O. Lloyd-Smith:
  Inference of R₀ and Transmission Heterogeneity from the Size Distribution of Stuttering Chains.
• 
  Rafael A. Barrio, José Roberto Romero-Arias, Marco A. Noguez, Eugenio Azpeitia, Elizabeth Ortiz-Gutiérrez, Valeria Hernández-Hernández, Yuriria Cortes-Poza, Elena R. Álvarez-Buylla:
  Cell Patterns Emerge from Coupled Chemical and Physical Fields with Cell Proliferation Dynamics: The Arabidopsis thaliana Root as a Study System.
• 
  Can Guven, Erin Rericha, Edward Ott, Wolfgang Losert:
  Modeling and Measuring Signal Relay in Noisy Directed Migration of Cell Groups.
• 
  Jonathan L. Robinson, Mark P. Brynildsen:
  A Kinetic Platform to Determine the Fate of Nitric Oxide in Escherichia coli.
• 
  Jeffrey E. Markowitz, Elizabeth Ivie, Laura Kligler, Timothy J. Gardner:
  Long-range Order in Canary Song.
• 
  Tobias Linder, Bert L. de Groot, Anna Stary-Weinzinger:
  Probing the Energy Landscape of Activation Gating of the Bacterial Potassium Channel KcsA.
• 
  David W. Eyre, Madeleine L. Cule, David Griffiths, Derrick W. Crook, Tim E. A. Peto, A. Sarah Walker, Daniel J. Wilson:
  Detection of Mixed Infection from Bacterial Whole Genome Sequence Data Allows Assessment of Its Role in Clostridium difficile Transmission.
• 
  Michiel van Boven, Wilhelmina L. M. Ruijs, Jacco Wallinga, Philip D. O'Neill, Susan Hahné:
  Estimation of Vaccine Efficacy and Critical Vaccination Coverage in Partially Observed Outbreaks.

Volume 9, Number 6, June 2013

Message from ISCB

• 
  Christiana N. Fogg, Diane E. Kovats:
  International Society for Computational Biology Honors David Eisenberg with 2013 Accomplishment by a Senior Scientist Award.

Education

• 
  Louisa Wood, Philipp Gebhardt:
  Bioinformatics Goes to School - New Avenues for Teaching Contemporary Biology.

Topic Page

• 
  Melanie I. Stefan, Nicolas Le Novère:
  Cooperative Binding.

Research Articles

• 
  Yan Zhang, Hye Kyong Kweon, Christian A. Shively, Anuj Kumar, Philip C. Andrews:
  Towards Systematic Discovery of Signaling Networks in Budding Yeast Filamentous Growth Stress Response Using Interventional Phosphorylation Data.
• 
  Henning Knoop, Marianne Gründel, Yvonne Zilliges, Robert Lehmann, Sabrina Hoffmann, Wolfgang Lockau, Ralf Steuer:
  Flux Balance Analysis of Cyanobacterial Metabolism: The Metabolic Network of Synechocystis sp. PCC 6803.
• 
  Ritwik K. Niyogi, KongFatt Wong-Lin:
  Dynamic Excitatory and Inhibitory Gain Modulation Can Produce Flexible, Robust and Optimal Decision-making.
• 
  Gabriel E. Hoffman, Benjamin A. Logsdon, Jason G. Mezey:
  PUMA: A Unified Framework for Penalized Multiple Regression Analysis of GWAS Data.
• 
  Koichi Fujimoto, Satoshi Sawai:
  A Design Principle of Group-level Decision Making in Cell Populations.
• 
  Diane M. Longo, Jangir Selimkhanov, Jeffrey D. Kearns, Jeff Hasty, Alexander Hoffmann, Lev S. Tsimring:
  Dual Delayed Feedback Provides Sensitivity and Robustness to the NF-κB Signaling Module.
• 
  Lyudmyla Dorosh, Olesya A. Kharenko, Nandhakishore Rajagopalan, Michele C. Loewen, Maria Stepanova:
  Molecular Mechanisms in the Activation of Abscisic Acid Receptor PYR1.
• 
  Annalisa Nuccitelli, C. Daniela Rinaudo, Barbara Brogioni, Roberta Cozzi, Mario Ferrer-Navarro, Daniel Yero, John L. Telford, Guido Grandi, Xavier Daura, Martin Zacharias, Domenico Maione:
  Understanding the Molecular Determinants Driving the Immunological Specificity of the Protective Pilus 2a Backbone Protein of Group B Streptococcus.
• 
  William R. Harcombe, Nigel F. Delaney, Nicholas Leiby, Niels Klitgord, Christopher J. Marx:
  The Ability of Flux Balance Analysis to Predict Evolution of Central Metabolism Scales with the Initial Distance to the Optimum.
• 
  Kristian Ovaska, Filomena Matarese, Korbinian Grote, Iryna Charapitsa, Alejandra Cervera, Chengyu Liu, George Reid, Martin Seifert, Hendrik G. Stunnenberg, Sampsa Hautaniemi:
  Integrative Analysis of Deep Sequencing Data Identifies Estrogen Receptor Early Response Genes and Links ATAD3B to Poor Survival in Breast Cancer.
• 
  Katy Robinson, Nick Fyson, Ted Cohen, Christophe Fraser, Caroline Colijn:
  How the Dynamics and Structure of Sexual Contact Networks Shape Pathogen Phylogenies.
• 
  David R. Riley, Karsten B. Sieber, Kelly M. Robinson, James Robert White, Ashwinkumar Ganesan, Syrus Nourbakhsh, Julie C. Dunning Hotopp:
  Bacteria-Human Somatic Cell Lateral Gene Transfer Is Enriched in Cancer Samples.
• 
  Rui Zhao, Franziska Michor:
  Patterns of Proliferative Activity in the Colonic Crypt Determine Crypt Stability and Rates of Somatic Evolution.
• 
  Louis-François Handfield, Yolanda T. Chong, Jibril Simmons, Brenda J. Andrews, Alan M. Moses:
  Unsupervised Clustering of Subcellular Protein Expression Patterns in High-Throughput Microscopy Images Reveals Protein Complexes and Functional Relationships between Proteins.
• 
  S. G. Raju, Annika F. Barber, David N. LeBard, Michael L. Klein, Vincenzo Carnevale:
  Exploring Volatile General Anesthetic Binding to a Closed Membrane-Bound Bacterial Voltage-Gated Sodium Channel via Computation.
• 
  Richard A. Morton, Jonathan R. Stone, Rama S. Singh:
  Mate Choice and the Origin of Menopause.
• 
  Mateus Joffily, Giorgio Coricelli:
  Emotional Valence and the Free-Energy Principle.
• 
  Oleg V. Kim, Zhiliang Xu, Elliot D. Rosen, Mark S. Alber:
  Fibrin Networks Regulate Protein Transport during Thrombus Development.
• 
  Hannah C. Slater, Manoj Gambhir, Paul E. Parham, Edwin Michael:
  Modelling Co-Infection with Malaria and Lymphatic Filariasis.
• 
  Amneet Pal Singh Bhalla, Boyce E. Griffith, Neelesh A. Patankar:
  A Forced Damped Oscillation Framework for Undulatory Swimming Provides New Insights into How Propulsion Arises in Active and Passive Swimming.
• 
  Antonio G. Zippo, Riccardo Storchi, Sara Nencini, Giancarlo Caramenti, Maurizio Valente, Gabriele Eliseo M. Biella:
  Neuronal Functional Connection Graphs among Multiple Areas of the Rat Somatosensory System during Spontaneous and Evoked Activities.
• 
  Meagan C. Small, Pedro E. M. Lopes, Rodrigo B. Andrade, Alexander D. MacKerell Jr.:
  Impact of Ribosomal Modification on the Binding of the Antibiotic Telithromycin Using a Combined Grand Canonical Monte Carlo/Molecular Dynamics Simulation Approach.
• 
  Jörg Bornschein, Marc Henniges, Jörg Lücke:
  Are V1 Simple Cells Optimized for Visual Occlusions? A Comparative Study.
• 
  Nicholas Ketz, Srinimisha G. Morkonda, Randall C. O'Reilly:
  Theta Coordinated Error-Driven Learning in the Hippocampus.
• 
  Joshua L. Payne, Andreas Wagner:
  Constraint and Contingency in Multifunctional Gene Regulatory Circuits.
• 
  Elzbieta Petelenz-Kurdziel, Clemens Kühn, Bodil Nordlander, Dagmara Klein, Kuk-Ki Hong, Therese Jacobson, Peter Dahl, Jörg Schaber, Jens Nielsen, Stefan Hohmann, Edda Klipp:
  Quantitative Analysis of Glycerol Accumulation, Glycolysis and Growth under Hyper Osmotic Stress.
• 
  Drew H. Bryant, Mark Moll, Paul W. Finn, Lydia E. Kavraki:
  Combinatorial Clustering of Residue Position Subsets Predicts Inhibitor Affinity across the Human Kinome.
• 
  Christian P. Koch, Anna Maria Perna, Max Pillong, Nickolay K. Todoroff, Paul Wrede, Gerd Folkers, Jan A. Hiss, Gisbert Schneider:
  Scrutinizing MHC-I Binding Peptides and Their Limits of Variation.
• 
  Nanye Long, Samuel P. Dickson, Jessica M. Maia, Hee Shin Kim, Qianqian Zhu, Andrew S. Allen:
  Leveraging Prior Information to Detect Causal Variants via Multi-Variant Regression.
• 
  Balázs Könnyü, S. Kashif Sadiq, Tamás Turányi, Rita Hírmondó, Barbara Müller, Hans-Georg Kräusslich, Peter V. Coveney, Viktor Müller:
  Gag-Pol Processing during HIV-1 Virion Maturation: A Systems Biology Approach.

Volume 9, Number 7, July 2013

Editorial

• 
  Marco Pautasso:
  Ten Simple Rules for Writing a Literature Review.

Review

• 
  Biswa Sengupta, Martin B. Stemmler, Karl J. Friston:
  Information and Efficiency in the Nervous System - A Synthesis.

Research Articles

• 
  Iren Bains, Hisse M. van Santen, Benedict Seddon, Andrew J. Yates:
  Models of Self-Peptide Sampling by Developing T Cells Identify Candidate Mechanisms of Thymic Selection.
• 
  Ashutosh Malhotra, Erfan Younesi, Harsha Gurulingappa, Martin Hofmann-Apitius:
  'HypothesisFinder: ' A Strategy for the Detection of Speculative Statements in Scientific Text.
• 
  Idan Menashe, Pascal Grange, Eric C. Larsen, Sharmila Banerjee-Basu, Partha P. Mitra:
  Co-expression Profiling of Autism Genes in the Mouse Brain.
• 
  Michael J. Lawson, Brian Drawert, Mustafa Khammash, Linda R. Petzold, Tau-Mu Yi:
  Spatial Stochastic Dynamics Enable Robust Cell Polarization.
• 
  Alex Roxin, Stefano Fusi:
  Efficient Partitioning of Memory Systems and Its Importance for Memory Consolidation.
• 
  Jaeyun Sung, Pan-Jun Kim, Shuyi Ma, Cory C. Funk, Andrew T. Magis, Yuliang Wang, Leroy E. Hood, Donald Geman, Nathan D. Price:
  Multi-study Integration of Brain Cancer Transcriptomes Reveals Organ-Level Molecular Signatures.
• 
  Robert C. Wilson, Matthew R. Nassar, Joshua I. Gold:
  A Mixture of Delta-Rules Approximation to Bayesian Inference in Change-Point Problems.
• 
  Justin Ritz, Joshua S. Martin, Alain Laederach:
  Evolutionary Evidence for Alternative Structure in RNA Sequence Co-variation.
• 
  Denis Bucher, Yuan-Hao Hsu, Varnavas D. Mouchlis, Edward A. Dennis, James Andrew McCammon:
  Insertion of the Ca²⁺-Independent Phospholipase A₂ into a Phospholipid Bilayer via Coarse-Grained and Atomistic Molecular Dynamics Simulations.
• 
  Nadine Veith, Anna Feldman-Salit, Vlad Cojocaru, Stefan Henrich, Ursula Kummer, Rebecca C. Wade:
  Organism-Adapted Specificity of the Allosteric Regulation of Pyruvate Kinase in Lactic Acid Bacteria.
• 
  C. J. Zopf, Katie Quinn, Joshua Zeidman, Narendra Maheshri:
  Cell-Cycle Dependence of Transcription Dominates Noise in Gene Expression.
• 
  Eleanor R. Brush, David C. Krakauer, Jessica C. Flack:
  A Family of Algorithms for Computing Consensus about Node State from Network Data.
• 
  Swagatam Mukhopadhyay, Anirvan M. Sengupta:
  The Role of Multiple Marks in Epigenetic Silencing and the Emergence of a Stable Bivalent Chromatin State.
• 
  Adrian Schneider, Michael F. Seidl, Berend Snel:
  Shared Protein Complex Subunits Contribute to Explaining Disrupted Co-occurrence.
• 
  Iaroslav Ispolatov, Anne Müsch:
  A Model for the Self-Organization of Vesicular Flux and Protein Distributions in the Golgi Apparatus.
• 
  Jonathan M. Dreyfuss, Jeremy D. Zucker, Heather M. Hood, Linda R. Ocasio, Matthew S. Sachs, James E. Galagan:
  Reconstruction and Validation of a Genome-Scale Metabolic Model for the Filamentous Fungus Neurospora crassa Using FARM.
• 
  Eduardo Serrano, Thomas Nowotny, Rafael Levi, Brian H. Smith, Ramón Huerta:
  Gain Control Network Conditions in Early Sensory Coding.
• 
  David P. Reichert, Peggy Seriès, Amos J. Storkey:
  Charles Bonnet Syndrome: Evidence for a Generative Model in the Cortex?
• 
  Szymon Leski, Henrik Lindén, Tom Tetzlaff, Klas H. Pettersen, Gaute T. Einevoll:
  Frequency Dependence of Signal Power and Spatial Reach of the Local Field Potential.
• 
  Burcu Aykaç Fas, Yusuf Tutar, Türkan Haliloglu:
  Dynamic Fluctuations Provide the Basis of a Conformational Switch Mechanism in Apo Cyclic AMP Receptor Protein.
• 
  Petter Holme:
  Epidemiologically Optimal Static Networks from Temporal Network Data.
• 
  James M. McFarland, Yuwei Cui, Daniel A. Butts:
  Inferring Nonlinear Neuronal Computation Based on Physiologically Plausible Inputs.
• 
  Natalia Pietrosemoli, Rita Pancsa, Peter Tompa:
  Structural Disorder Provides Increased Adaptability for Vesicle Trafficking Pathways.
• 
  Joshua I. Glaser, Bradley M. Zamft, Adam H. Marblestone, Jeffrey R. Moffitt, Keith E. J. Tyo, Edward S. Boyden III, George M. Church, Konrad P. Körding:
  Statistical Analysis of Molecular Signal Recording.
• 
  Katherine Kay, Ian M. Hastings:
  Improving Pharmacokinetic-Pharmacodynamic Modeling to Investigate Anti-Infective Chemotherapy with Application to the Current Generation of Antimalarial Drugs.
• 
  Umadevi Paila, Brad A. Chapman, Rory D. Kirchner, Aaron R. Quinlan:
  GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations.
• 
  Drazen Petrov, Christian Margreitter, Melanie Grandits, Chris Oostenbrink, Bojan Zagrovic:
  A Systematic Framework for Molecular Dynamics Simulations of Protein Post-Translational Modifications.
• 
  Deeptak Verma, Donald J. Jacobs, Dennis R. Livesay:
  Variations within Class-A β-Lactamase Physiochemical Properties Reflect Evolutionary and Environmental Patterns, but not Antibiotic Specificity.
• 
  James C. Robertson, Nate C. Hurley, Marcello Tortorici, Giuseppe Ciossani, Maria Teresa Borrello, Nadeem A. Vellore, A. Ganesan, Andrea Mattevi, Riccardo Baron:
  Expanding the Druggable Space of the LSD1/CoREST Epigenetic Target: New Potential Binding Regions for Drug-Like Molecules, Peptides, Protein Partners, and Chromatin.
• 
  Elad Noor, Hulda S. Haraldsdóttir, Ron Milo, Ronan M. T. Fleming:
  Consistent Estimation of Gibbs Energy Using Component Contributions.
• 
  Pinkesh K. Patel, Orian Shirihai, Kerwyn Casey Huang:
  Optimal Dynamics for Quality Control in Spatially Distributed Mitochondrial Networks.
• 
  Nikhil J. Joshi, Giulio Tononi, Christof Koch:
  The Minimal Complexity of Adapting Agents Increases with Fitness.
• 
  Xiujuan Wang, Bram Thijssen, Haiyuan Yu:
  Target Essentiality and Centrality Characterize Drug Side Effects.
• 
  Gibin G. Powathil, Douglas J. A. Adamson, Mark A. J. Chaplain:
  Towards Predicting the Response of a Solid Tumour to Chemotherapy and Radiotherapy Treatments: Clinical Insights from a Computational Model.
• 
  Andrew Cron, Cécile Gouttefangeas, Jacob Frelinger, Lin Lin, Satwinder K. Singh, Cedrik M. Britten, Marij J. P. Welters, Sjoerd H. van der Burg, Mike West, Cliburn Chan:
  Hierarchical Modeling for Rare Event Detection and Cell Subset Alignment across Flow Cytometry Samples.
• 
  Chao Cheng, Matthew Ung, Gavin D. Grant, Michael L. Whitfield:
  Transcription Factor Binding Profiles Reveal Cyclic Expression of Human Protein-coding Genes and Non-coding RNAs.
• 
  Kathryn Miller-Jensen, Ron Skupsky, Priya S. Shah, Adam P. Arkin, David V. Schaffer:
  Genetic Selection for Context-Dependent Stochastic Phenotypes: Sp1 and TATA Mutations Increase Phenotypic Noise in HIV-1 Gene Expression.
• 
  Hadas Zur, Tamir Tuller:
  New Universal Rules of Eukaryotic Translation Initiation Fidelity.
• 
  Felipe Gerhard, Tilman Kispersky, Gabrielle J. Gutierrez, Eve Marder, Mark A. Kramer, Uri T. Eden:
  Successful Reconstruction of a Physiological Circuit with Known Connectivity from Spiking Activity Alone.
• 
  Jincheng Wu, Emmanuel S. Tzanakakis:
  Distinct Allelic Patterns of Nanog Expression Impart Embryonic Stem Cell Population Heterogeneity.
• 
  Archana Bajpai, Anna Feoktistova, Jun-Song Chen, Dannel McCollum, Masamitsu Sato, Rafael Edgardo Carazo-Salas, Kathleen L. Gould, Attila Csikász-Nagy:
  Dynamics of SIN Asymmetry Establishment.
• 
  Changji Shi, Chuan-Hsiang Huang, Peter N. Devreotes, Pablo A. Iglesias:
  Interaction of Motility, Directional Sensing, and Polarity Modules Recreates the Behaviors of Chemotaxing Cells.
• 
  Shuzhao Li, Youngja Park, Sai Duraisingham, Frederick H. Strobel, Nooruddin Khan, Quinlyn A. Soltow, Dean P. Jones, Bali Pulendran:
  Predicting Network Activity from High Throughput Metabolomics.
• 
  Kai-Cheng Hsu, Wen-Chi Cheng, Yen-Fu Chen, Wen-Ching Wang, Jinn-Moon Yang:
  Pathway-based Screening Strategy for Multitarget Inhibitors of Diverse Proteins in Metabolic Pathways.
• 
  Xiangfei Song, Yefei Wang, Zhiyu Shu, Jingbo Hong, Tong Li, Lishan Yao:
  Engineering a More Thermostable Blue Light Photo Receptor Bacillus subtilis YtvA LOV Domain by a Computer Aided Rational Design Method.
• 
  Joshua T. Schiffer, Dave A. Swan, Daniel Stone, Keith R. Jerome:
  Predictors of Hepatitis B Cure Using Gene Therapy to Deliver DNA Cleavage Enzymes: A Mathematical Modeling Approach.

Volume 9, Number 8, August 2013

Message from ISCB

• 
  Christiana N. Fogg, Diane E. Kovats:
  International Society for Computational Biology Welcomes Its Newest Class of Fellows.

Research Articles

• 
  Ilaria Cataudella, Kim Sneppen, Kenn Gerdes, Namiko Mitarai:
  Conditional Cooperativity of Toxin - Antitoxin Regulation Can Mediate Bistability between Growth and Dormancy.
• 
  Joel Zylberberg, Michael Robert DeWeese:
  Sparse Coding Models Can Exhibit Decreasing Sparseness while Learning Sparse Codes for Natural Images.
• 
  Lendert Gelens, Lydia Hill, Alexandra Vandervelde, Jan Danckaert, Remy Loris:
  A General Model for Toxin-Antitoxin Module Dynamics Can Explain Persister Cell Formation in E. coli.
• 
  Mengchen Zhu, Christopher J. Rozell:
  Visual Nonclassical Receptive Field Effects Emerge from Sparse Coding in a Dynamical System.
• 
  Ed Reznik, Pankaj Mehta, Daniel Segrè:
  Flux Imbalance Analysis and the Sensitivity of Cellular Growth to Changes in Metabolite Pools.
• 
  Niko Beerenwinkel, Hesam Montazeri, Heike Schuhmacher, Patrick Knupfer, Viktor von Wyl, Hansjakob Furrer, Manuel Battegay, Bernard Hirschel, Matthias Cavassini, Pietro Vernazza, Enos Bernasconi, Sabine Yerly, Jürg Böni, Thomas Klimkait, Cristina Cellerai, Huldrych F. Günthard:
  The Individualized Genetic Barrier Predicts Treatment Response in a Large Cohort of HIV-1 Infected Patients.
• 
  Simona Mariani, Daniele Dell'Orco, Angelo Felline, Francesco Raimondi, Francesca Fanelli:
  Network and Atomistic Simulations Unveil the Structural Determinants of Mutations Linked to Retinal Diseases.
• 
  Yves Dehouck, Alexander S. Mikhailov:
  Effective Harmonic Potentials: Insights into the Internal Cooperativity and Sequence-Specificity of Protein Dynamics.
• 
  Kathrin Poos, Jan Smida, Michaela Nathrath, Doris Maugg, Daniel Baumhoer, Eberhard Korsching:
  How MicroRNA and Transcription Factor Co-regulatory Networks Affect Osteosarcoma Cell Proliferation.
• 
  Chun Wu, Joan-Emma Shea:
  Structural Similarities and Differences between Amyloidogenic and Non-Amyloidogenic Islet Amyloid Polypeptide (IAPP) Sequences and Implications for the Dual Physiological and Pathological Activities of These Peptides.
• 
  Simona Cocco, Rémi Monasson, Martin Weigt:
  From Principal Component to Direct Coupling Analysis of Coevolution in Proteins: Low-Eigenvalue Modes are Needed for Structure Prediction.
• 
  Matan Sorek, Nathalie Q. Balaban, Yonatan Loewenstein:
  Stochasticity, Bistability and the Wisdom of Crowds: A Model for Associative Learning in Genetic Regulatory Networks.
• 
  Evgeniy A. Ozonov, Erik van Nimwegen:
  Nucleosome Free Regions in Yeast Promoters Result from Competitive Binding of Transcription Factors That Interact with Chromatin Modifiers.
• 
  Neta S. Zuckerman, Yair Noam, Andrea J. Goldsmith, Peter P. Lee:
  A Self-Directed Method for Cell-Type Identification and Separation of Gene Expression Microarrays.
• 
  Eric T. C. Wong, Dokyun Na, Jörg Gsponer:
  On the Importance of Polar Interactions for Complexes Containing Intrinsically Disordered Proteins.
• 
  András Szilágyi, István Zachar, Eörs Szathmáry:
  Gause's Principle and the Effect of Resource Partitioning on the Dynamical Coexistence of Replicating Templates.
• 
  Casey O. Diekman, Mino D. C. Belle, Robert P. Irwin, Charles N. Allen, Hugh D. Piggins, Daniel B. Forger:
  Causes and Consequences of Hyperexcitation in Central Clock Neurons.
• 
  Jose Teles, Cristina Pina, Patrik Edén, Mattias Ohlsson, Tariq Enver, Carsten Peterson:
  Transcriptional Regulation of Lineage Commitment - A Stochastic Model of Cell Fate Decisions.
• 
  Ohad Manor, Eran Segal:
  Predicting Disease Risk Using Bootstrap Ranking and Classification Algorithms.
• 
  Harish Shankaran, Yi Zhang, Yunbing Tan, Haluk Resat:
  Model-Based Analysis of HER Activation in Cells Co-Expressing EGFR, HER2 and HER3.
• 
  Jordi Heijman, Antonio Zaza, Daniel M. Johnson, Yoram Rudy, Ralf L. M. Peeters, Paul G. A. Volders, Ronald L. Westra:
  Determinants of Beat-to-Beat Variability of Repolarization Duration in the Canine Ventricular Myocyte: A Computational Analysis.
• 
  Angelo Pavesi, Gkikas Magiorkinis, David G. Karlin:
  Viral Proteins Originated De Novo by Overprinting Can Be Identified by Codon Usage: Application to the "Gene Nursery" of Deltaretroviruses.
• 
  Chiara Poletto, Sandro Meloni, Vittoria Colizza, Yamir Moreno, Alessandro Vespignani:
  Host Mobility Drives Pathogen Competition in Spatially Structured Populations.
• 
  Christoph Bauermeister, Tilo Schwalger, David F. Russell, Alexander B. Neiman, Benjamin Lindner:
  Characteristic Effects of Stochastic Oscillatory Forcing on Neural Firing: Analytical Theory and Comparison to Paddlefish Electroreceptor Data.
• 
  Frederic Zubler, Andreas Hauri, Sabina S. Pfister, Roman Bauer, John C. Anderson, Adrian M. Whatley, Rodney J. Douglas:
  Simulating Cortical Development as a Self Constructing Process: A Novel Multi-Scale Approach Combining Molecular and Physical Aspects.
• 
  Frédéric Crevecoeur, Stephen H. Scott:
  Priors Engaged in Long-Latency Responses to Mechanical Perturbations Suggest a Rapid Update in State Estimation.
• 
  Andrew M. Hein, Scott A. McKinley:
  Sensory Information and Encounter Rates of Interacting Species.
• 
  Michael Graupner, Reinoud Maex, Boris S. Gutkin:
  Endogenous Cholinergic Inputs and Local Circuit Mechanisms Govern the Phasic Mesolimbic Dopamine Response to Nicotine.
• 
  Karen van Eunen, Sereh M. J. Simons, Albert Gerding, Aycha Bleeker, Gijs den Besten, Catharina M. L. Touw, Sander M. Houten, Bert K. Groen, Klaas Krab, Dirk-Jan Reijngoud, Barbara M. Bakker:
  Biochemical Competition Makes Fatty-Acid β-Oxidation Vulnerable to Substrate Overload.
• 
  Duncan J. MacGregor, Gareth Leng:
  Spike Triggered Hormone Secretion in Vasopressin Cells; a Model Investigation of Mechanism and Heterogeneous Population Function.
• 
  Michael F. Lawrence, Wolfgang Huber, Hervé Pagès, Patrick Aboyoun, Marc Carlson, Robert Gentleman, Martin T. Morgan, Vincent J. Carey:
  Software for Computing and Annotating Genomic Ranges.
• 
  Volodymyr Babin, Dongli Wang, Robert B. Rose, Celeste Sagui:
  Binding Polymorphism in the DNA Bound State of the Pdx1 Homeodomain.
• 
  Pablo Szekely, Hila Sheftel, Avi E. Mayo, Uri Alon:
  Evolutionary Tradeoffs between Economy and Effectiveness in Biological Homeostasis Systems.
• 
  Jung H. Lee, Miles A. Whittington, Nancy J. Kopell:
  Top-Down Beta Rhythms Support Selective Attention via Interlaminar Interaction: A Model.
• 
  Carlo Baldassi, Alireza Alemi-Neissi, Marino Pagan, James J. DiCarlo, Riccardo Zecchina, Davide Zoccolan:
  Shape Similarity, Better than Semantic Membership, Accounts for the Structure of Visual Object Representations in a Population of Monkey Inferotemporal Neurons.
• 
  Bruno M. C. Martins, Peter S. Swain:
  Ultrasensitivity in Phosphorylation-Dephosphorylation Cycles with Little Substrate.
• 
  Chunhe Li, Jin Wang:
  Quantifying Cell Fate Decisions for Differentiation and Reprogramming of a Human Stem Cell Network: Landscape and Biological Paths.
• 
  Christian A. Tiemann, Joep Vanlier, Maaike H. Oosterveer, Albert K. Groen, Peter A. J. Hilbers, Natal A. W. van Riel:
  Parameter Trajectory Analysis to Identify Treatment Effects of Pharmacological Interventions.
• 
  Guillermo Rodrigo, Thomas E. Landrain, Eszter Majer, José-Antonio Daròs, Alfonso Jaramillo:
  Full Design Automation of Multi-State RNA Devices to Program Gene Expression Using Energy-Based Optimization.

Volume 9, Number 9, September 2013

Editorial

• 
  Hassan Masum, Aarthi Rao, Benjamin M. Good, Matthew H. Todd, Aled M. Edwards, Leslie Chan, Barry A. Bunin, Andrew I. Su, Zakir Thomas, Philip E. Bourne:
  Ten Simple Rules for Cultivating Open Science and Collaborative R&D.

Messages from ISCB

• 
  Geoff MacIntyre, Magali Michaut, Thomas Abeel:
  The Regional Student Group Program of the ISCB Student Council: Stories from the Road.
• 
  Alex Bateman, Janet Kelso, Daniel Mietchen, Geoff MacIntyre, Tomás Di Domenico, Thomas Abeel, Darren W. Logan, Predrag Radivojac, Burkhard Rost:
  ISCB Computational Biology Wikipedia Competition.

Research Articles

• 
  Danielle S. Bassett, Nicholas F. Wymbs, M. Puck Rombach, Mason A. Porter, Peter J. Mucha, Scott T. Grafton:
  Task-Based Core-Periphery Organization of Human Brain Dynamics.
• 
  Dipak Barua, William S. Hlavacek:
  Modeling the Effect of APC Truncation on Destruction Complex Function in Colorectal Cancer Cells.
• 
  Stephen A. Smith, Joseph W. Brown, Cody E. Hinchliff:
  Analyzing and Synthesizing Phylogenies Using Tree Alignment Graphs.
• 
  Javier Garcia-Bernardo, Mary J. Dunlop:
  Tunable Stochastic Pulsing in the Escherichia coli Multiple Antibiotic Resistance Network from Interlinked Positive and Negative Feedback Loops.
• 
  Ben Mitchinson, Tony J. Prescott:
  Whisker Movements Reveal Spatial Attention: A Unified Computational Model of Active Sensing Control in the Rat.
• 
  Dilek Eren, Burak Alakent:
  Frequency Response of a Protein to Local Conformational Perturbations.
• 
  Jianhui Song, Sheung Chun Ng, Peter Tompa, Kevin A. W. Lee, Hue Sun Chan:
  Polycation-π Interactions Are a Driving Force for Molecular Recognition by an Intrinsically Disordered Oncoprotein Family.
• 
  Audrey Salles, Cyrille Billaudeau, Arnauld Sergé, Anne-Marie Bernard, Marie-Claire Phélipot, Nicolas Bertaux, Mathieu Fallet, Pierre Grenot, Didier Marguet, Hai-Tao He, Yannick Hamon:
  Barcoding T Cell Calcium Response Diversity with Methods for Automated and Accurate Analysis of Cell Signals (MAAACS).
• 
  Noa Liscovitch, Gal Chechik:
  Specialization of Gene Expression during Mouse Brain Development.
• 
  Emek Demir, Özgün Babur, Igor V. Rodchenkov, Bülent Arman Aksoy, Ken I. Fukuda, Benjamin E. Gross, Selçuk Onur Sümer, Gary D. Bader, Chris Sander:
  Using Biological Pathway Data with Paxtools.
• 
  William Pontius, Michael W. Sneddon, Thierry Emonet:
  Adaptation Dynamics in Densely Clustered Chemoreceptors.
• 
  James J. Lee, Justin Huang, Christopher G. England, Lacey R. McNally, Hermann B. Frieboes:
  Predictive Modeling of In Vivo Response to Gemcitabine in Pancreatic Cancer.
• 
  Martin D. Vesper, Bert L. de Groot:
  Collective Dynamics Underlying Allosteric Transitions in Hemoglobin.
• 
  Linhui Hao, Qiuling He, Zhishi Wang, Mark Craven, Michael A. Newton, Paul Ahlquist:
  Limited Agreement of Independent RNAi Screens for Virus-Required Host Genes Owes More to False-Negative than False-Positive Factors.
• 
  Vishal N. Patel, Giridharan Gokulrangan, Salim A. Chowdhury, Yanwen Chen, Andrew E. Sloan, Mehmet Koyutürk, Jill S. Barnholtz-Sloan, Mark R. Chance:
  Network Signatures of Survival in Glioblastoma Multiforme.
• 
  Jorge F. Mejías, Gary Marsat, Kieran Bol, Leonard Maler, André Longtin:
  Learning Contrast-Invariant Cancellation of Redundant Signals in Neural Systems.
• 
  Kobi Snitz, Adi Yablonka, Tali Weiss, Idan Frumin, Rehan M. Khan, Noam Sobel:
  Predicting Odor Perceptual Similarity from Odor Structure.
• 
  Izzet B. Yildiz, Katharina von Kriegstein, Stefan J. Kiebel:
  From Birdsong to Human Speech Recognition: Bayesian Inference on a Hierarchy of Nonlinear Dynamical Systems.
• 
  John C. Williams, Jianjin Xu, Zhongju Lu, Aleksandra Klimas, Xuxin Chen, Christina M. Ambrosi, Ira S. Cohen, Emilia Entcheva:
  Computational Optogenetics: Empirically-Derived Voltage- and Light-Sensitive Channelrhodopsin-2 Model.
• 
  Kartik Subramanian, Mark R. Paul, John J. Tyson:
  Potential Role of a Bistable Histidine Kinase Switch in the Asymmetric Division Cycle of Caulobacter crescentus.
• 
  Yun M. Zhao, Anthony R. French:
  Mechanistic Model of Natural Killer Cell Proliferative Response to IL-15 Receptor Stimulation.
• 
  Laurence T. Hunt, Mark William Woolrich, Matthew F. S. Rushworth, Timothy Edward John Behrens:
  Trial-Type Dependent Frames of Reference for Value Comparison.
• 
  Jing Tang, Leena Karhinen, Tao Xu, Agnieszka Szwajda, Bhagwan Yadav, Krister Wennerberg, Tero Aittokallio:
  Target Inhibition Networks: Predicting Selective Combinations of Druggable Targets to Block Cancer Survival Pathways.
• 
  Julia Lasserre, Ho-Ryun Chung, Martin Vingron:
  Finding Associations among Histone Modifications Using Sparse Partial Correlation Networks.
• 
  Sulyman Barkho, Levi C. T. Pierce, Maria L. McGlone, Sheng Li, Virgil L. Woods Jr., Ross C. Walker, Joseph A. Adams, Patricia A. Jennings:
  Distal Loop Flexibility of a Regulatory Domain Modulates Dynamics and Activity of C-Terminal Src Kinase (Csk).
• 
  Jing Chen, Zhen Hu, Mukta Phatak, John Reichard, Johannes M. Freudenberg, Siva Sivaganesan, Mario Medvedovic:
  Genome-Wide Signatures of Transcription Factor Activity: Connecting Transcription Factors, Disease, and Small Molecules.
• 
  Ioannis N. Melas, Regina Samaga, Leonidas G. Alexopoulos, Steffen Klamt:
  Detecting and Removing Inconsistencies between Experimental Data and Signaling Network Topologies Using Integer Linear Programming on Interaction Graphs.
• 
  Tristan Ursell, Rosanna Man Wah Chau, Susanne Wisen, Devaki Bhaya, Kerwyn Casey Huang:
  Motility Enhancement through Surface Modification Is Sufficient for Cyanobacterial Community Organization during Phototaxis.
• 
  Johnatan Aljadeff, Ronen Segev, Michael J. Berry II, Tatyana O. Sharpee:
  Spike Triggered Covariance in Strongly Correlated Gaussian Stimuli.
• 
  Eddy J. Bautista, Joseph Zinski, Steven M. Szczepanek, Erik L. Johnson, Edan R. Tulman, Wei-Mei Ching, Steven J. Geary, Ranjan Srivastava:
  Semi-automated Curation of Metabolic Models via Flux Balance Analysis: A Case Study with Mycoplasma gallisepticum.
• 
  Giuseppe Maccari, Mariagrazia Di Luca, Riccardo Nifosí, Francesco Cardarelli, Giovanni Signore, Claudia Boccardi, Angelo Bifone:
  Antimicrobial Peptides Design by Evolutionary Multiobjective Optimization.
• 
  Andrew J. K. Phillips, Ben D. Fulcher, Peter A. Robinson, Elizabeth B. Klerman:
  Mammalian Rest/Activity Patterns Explained by Physiologically Based Modeling.
• 
  Anthony Mathelier, Wyeth W. Wasserman:
  The Next Generation of Transcription Factor Binding Site Prediction.
• 
  Julián Candia, Ryan Maunu, Meghan K. Driscoll, Angélique Biancotto, Pradeep Dagur, J. Philip McCoy Jr., H. Nida Sen, Lai Wei, Amos Maritan, Kan Cao, Robert B. Nussenblatt, Jayanth R. Banavar, Wolfgang Losert:
  From Cellular Characteristics to Disease Diagnosis: Uncovering Phenotypes with Supercells.
• 
  Rudi Agius, Mieczyslaw Torchala, Iain H. Moal, Juan Fernández-Recio, Paul A. Bates:
  Characterizing Changes in the Rate of Protein-Protein Dissociation upon Interface Mutation Using Hotspot Energy and Organization.

Volume 9, Number 10, October 2013

Editorials

• 
  Geir Kjetil Sandve, Anton Nekrutenko, James Taylor, Eivind Hovig:
  Ten Simple Rules for Reproducible Computational Research.
• 
  Ruth Nussinov:
  How Can PLOS Computational Biology Help the Biological Sciences?

Messages from ISCB

• 
  Virginie Bernard, Magali Michaut:
  Explain Bioinformatics to Your Grandmother!
• 
  Asif M. Khan, Tin Wee Tan, Christian Schönbach, Shoba Ranganathan:
  APBioNet - Transforming Bioinformatics in the Asia-Pacific Region.

Research Articles

• 
  Stewart Heitmann, Tjeerd W. Boonstra, Michael Breakspear:
  A Dendritic Mechanism for Decoding Traveling Waves: Principles and Applications to Motor Cortex.
• 
  Kolja Becker, Eva Balsa-Canto, Damjan Cicin-Sain, Astrid Hoermann, Hilde Janssens, Julio R. Banga, Johannes Jaeger:
  Reverse-Engineering Post-Transcriptional Regulation of Gap Genes in Drosophila melanogaster.
• 
  Maryam Modir Shanechi, Jessica J. Chemali, Max Liberman, Ken Solt, Emery N. Brown:
  A Brain-Machine Interface for Control of Medically-Induced Coma.
• 
  Evan S. Schaffer, Srdjan Ostojic, L. F. Abbott:
  A Complex-Valued Firing-Rate Model That Approximates the Dynamics of Spiking Networks.
• 
  Christian Tetzlaff, Christoph Kolodziejski, Marc Timme, Misha Tsodyks, Florentin Wörgötter:
  Synaptic Scaling Enables Dynamically Distinct Short- and Long-Term Memory Formation.
• 
  Sebastian Gluth, Jörg Rieskamp, Christian Büchel:
  Deciding Not to Decide: Computational and Neural Evidence for Hidden Behavior in Sequential Choice.
• 
  Antreas C. Kalli, Iain D. Campbell, Mark S. P. Sansom:
  Conformational Changes in Talin on Binding to Anionic Phospholipid Membranes Facilitate Signaling by Integrin Transmembrane Helices.
• 
  Ramakrishnan Iyer, Vilas Menon, Michael A. Buice, Christof Koch, Stefan Mihalas:
  The Influence of Synaptic Weight Distribution on Neuronal Population Dynamics.
• 
  Qiang Luo, Tian Ge, Fabian Grabenhorst, Jianfeng Feng, Edmund T. Rolls:
  Attention-Dependent Modulation of Cortical Taste Circuits Revealed by Granger Causality with Signal-Dependent Noise.
• 
  Jorg J. A. Calis, Matt Maybeno, Jason A. Greenbaum, Daniela Weiskopf, Aruna D. De Silva, Alessandro Sette, Can Kesmir, Björn Peters:
  Properties of MHC Class I Presented Peptides That Enhance Immunogenicity.
• 
  Anna L. Tyler, Wei Lu, Justin J. Hendrick, Vivek M. Philip, Gregory W. Carter:
  CAPE: An R Package for Combined Analysis of Pleiotropy and Epistasis.
• 
  Pierre Yger, Kenneth D. Harris:
  The Convallis Rule for Unsupervised Learning in Cortical Networks.
• 
  Lennart Hilbert, Genevieve Bates, Horia N. Roman, Jenna L. Blumenthal, Nedjma B. Zitouni, Apolinary Sobieszek, Michael C. Mackey, Anne-Marie Lauzon:
  Molecular Mechanical Differences between Isoforms of Contractile Actin in the Presence of Isoforms of Smooth Muscle Tropomyosin.
• 
  Terry Lohrenz, Meghana Bhatt, Nathan Apple, P. Read Montague:
  Keeping up with the Joneses: Interpersonal Prediction Errors and the Correlation of Behavior in a Tandem Sequential Choice Task.
• 
  Gabriel Rosser, Alexander G. Fletcher, David A. Wilkinson, Jennifer A. de Beyer, Christian A. Yates, Judith P. Armitage, Philip K. Maini, Ruth E. Baker:
  Novel Methods for Analysing Bacterial Tracks Reveal Persistence in Rhodobacter sphaeroides.
• 
  Arnab Bhattacherjee, Stefan Wallin:
  Exploring Protein-Peptide Binding Specificity through Computational Peptide Screening.
• 
  Guilhem Faure, Isabelle Callebaut:
  Comprehensive Repertoire of Foldable Regions within Whole Genomes.
• 
  Luca Grieco, Laurence Calzone, Isabelle Bernard-Pierrot, François Radvanyi, Brigitte Kahn-Perlès, Denis Thieffry:
  Integrative Modelling of the Influence of MAPK Network on Cancer Cell Fate Decision.
• 
  Chunfeng Zhao, Sergei Yu Noskov:
  The Molecular Mechanism of Ion-Dependent Gating in Secondary Transporters.
• 
  Pralay Mitra, David Shultis, Jeffrey R. Brender, Jeff Czajka, David Marsh, Felicia Gray, Tomasz Cierpicki, Yang Zhang:
  An Evolution-Based Approach to De Novo Protein Design and Case Study on Mycobacterium tuberculosis.
• 
  Giovanna De Palo, Robert G. Endres:
  Unraveling Adaptation in Eukaryotic Pathways: Lessons from Protocells.
• 
  Mu Gao, Jeffrey Skolnick:
  A Comprehensive Survey of Small-Molecule Binding Pockets in Proteins.
• 
  Katrina M. Kutchko, Flavio Fröhlich:
  Emergence of Metastable State Dynamics in Interconnected Cortical Networks with Propagation Delays.
• 
  José Lourenço, Mario Recker:
  Natural, Persistent Oscillations in a Spatial Multi-Strain Disease System with Application to Dengue.
• 
  Dongjun Chung, Dan Park, Kevin Myers, Jeffrey Grass, Patricia J. Kiley, Robert Landick, Sündüz Keles:
  dPeak: High Resolution Identification of Transcription Factor Binding Sites from PET and SET ChIP-Seq Data.
• 
  Sushmita Roy, Stephen Lagree, Zhonggang Hou, James A. Thomson, Ron M. Stewart, Audrey P. Gasch:
  Integrated Module and Gene-Specific Regulatory Inference Implicates Upstream Signaling Networks.
• 
  Donald R. Olson, Kevin J. Konty, Marc Paladini, Cécile Viboud, Lone Simonsen:
  Reassessing Google Flu Trends Data for Detection of Seasonal and Pandemic Influenza: A Comparative Epidemiological Study at Three Geographic Scales.
• 
  Andreas Spitzmüller, Jordi Mestres:
  Prediction of the P. falciparum Target Space Relevant to Malaria Drug Discovery.
• 
  Tim Odenthal, Bart Smeets, Paul Van Liedekerke, Engelbert Tijskens, Hans Van Oosterwyck, Herman Ramon:
  Analysis of Initial Cell Spreading Using Mechanistic Contact Formulations for a Deformable Cell Model.
• 
  Martin M. Monti, Evan S. Lutkenhoff, Mikail Rubinov, Pierre Boveroux, Audrey Vanhaudenhuyse, Olivia Gosseries, Marie-Aurélie Bruno, Quentin Noirhomme, Mélanie Boly, Steven Laureys:
  Dynamic Change of Global and Local Information Processing in Propofol-Induced Loss and Recovery of Consciousness.
• 
  Tyler Drake, Dimitrios Vavylonis:
  Model of Fission Yeast Cell Shape Driven by Membrane-Bound Growth Factors and the Cytoskeleton.
• 
  Patrick M. Buck, Sandeep Kumar, Satish Kumar Singh:
  On the Role of Aggregation Prone Regions in Protein Evolution, Stability, and Enzymatic Catalysis: Insights from Diverse Analyses.
• 
  Rogan Carr, Shai S. Shen-Orr, Elhanan Borenstein:
  Reconstructing the Genomic Content of Microbiome Taxa through Shotgun Metagenomic Deconvolution.
• 
  Francesca Falcetta, Monica Lupi, Valentina Colombo, Paolo Ubezio:
  Dynamic Rendering of the Heterogeneous Cell Response to Anticancer Treatments.
• 
  Kriti Puniyani, Eric P. Xing:
  GINI: From ISH Images to Gene Interaction Networks.
• 
  Hanna Julienne, Azedine Zoufir, Benjamin Audit, Alain Arneodo:
  Human Genome Replication Proceeds through Four Chromatin States.
• 
  Julien Racle, Flora Picard, Laurence Girbal, Muriel Cocaign-Bousquet, Vassily Hatzimanikatis:
  A Genome-Scale Integration and Analysis of Lactococcus lactis Translation Data.
• 
  Yuri Pritykin, Mona Singh:
  Simple Topological Features Reflect Dynamics and Modularity in Protein Interaction Networks.
• 
  Omar Hadzipasic, James O. Wrabl, Vincent J. Hilser:
  A Horizontal Alignment Tool for Numerical Trend Discovery in Sequence Data: Application to Protein Hydropathy.
• 
  Ricardo Aguas, Neil M. Ferguson:
  Feature Selection Methods for Identifying Genetic Determinants of Host Species in RNA Viruses.
• 
  Joshua G. Schraiber, Yulia Mostovoy, Tiffany Y. Hsu, Rachel B. Brem:
  Inferring Evolutionary Histories of Pathway Regulation from Transcriptional Profiling Data.
• 
  Markus Butz, Arjen van Ooyen:
  A Simple Rule for Dendritic Spine and Axonal Bouton Formation Can Account for Cortical Reorganization after Focal Retinal Lesions.
• 
  Paola Carrillo-Bustamante, Can Kesmir, Rob J. De Boer:
  Virus Encoded MHC-Like Decoys Diversify the Inhibitory KIR Repertoire.
• 
  Daniel B. Larremore, Aaron Clauset, Caroline O. Buckee:
  A Network Approach to Analyzing Highly Recombinant Malaria Parasite Genes.
• 
  Ryan Suderman, Eric J. Deeds:
  Machines vs. Ensembles: Effective MAPK Signaling through Heterogeneous Sets of Protein Complexes.
• 
  Kate A. Stafford, Paul Robustelli, Arthur G. Palmer III:
  Thermal Adaptation of Conformational Dynamics in Ribonuclease H.
• 
  Rene Rex, Nelli Bill, Kerstin Schmidt-Hohagen, Dietmar Schomburg:
  Swimming in Light: A Large-Scale Computational Analysis of the Metabolism of Dinoroseobacter shibae.
• 
  Sven-Eric Schelhorn, Matthias Fischer, Laura Tolosi, Janine Altmüller, Peter Nürnberg, Herbert Pfister, Thomas Lengauer, Frank Berthold:
  Sensitive Detection of Viral Transcripts in Human Tumor Transcriptomes.
• 
  André Yoshiaki Kashiwabara, Ígor Bonadio, Vitor Onuchic, Felipe Amado, Rafael Mathias, Alan Mitchell Durham:
  ToPS: A Framework to Manipulate Probabilistic Models of Sequence Data.
• 
  Fan Jin, Chen Yu, Luhua Lai, Zhirong Liu:
  Ligand Clouds around Protein Clouds: A Scenario of Ligand Binding with Intrinsically Disordered Proteins.
• 
  Thomas Hannagan, Jonathan Grainger:
  The Lazy Visual Word Form Area: Computational Insights into Location-Sensitivity.
• 
  Farzad Farkhooi, Anja Froese, Eilif B. Müller, Randolf Menzel, Martin P. Nawrot:
  Cellular Adaptation Facilitates Sparse and Reliable Coding in Sensory Pathways.
• 
  Francisco Martínez-Jiménez, George Papadatos, Lun Yang, Iain M. Wallace, Vinod Kumar, Ursula Pieper, Andrej Sali, James R. Brown, John P. Overington, Marc A. Martí-Renom:
  Target Prediction for an Open Access Set of Compounds Active against Mycobacterium tuberculosis.
• 
  Shuguang Yuan, Rongliang Wu, Dorota Latek, Bartosz Trzaskowski, Slawomir Filipek:
  Lipid Receptor S1P₁ Activation Scheme Concluded from Microsecond All-Atom Molecular Dynamics Simulations.
• 
  Biswa Sengupta, Simon B. Laughlin, Jeremy E. Niven:
  Balanced Excitatory and Inhibitory Synaptic Currents Promote Efficient Coding and Metabolic Efficiency.

Volume 9, Number 11, November 2013

Editorials

• 
  Avinash Kumar Shanmugam, Geoff MacIntyre, Magali Michaut, Thomas Abeel:
  Ten Simple Rules for Starting a Regional Student Group.
• 
  Theodore Alexandrov, Philip E. Bourne:
  Learning How to Run a Lab: Interviews with Principal Investigators.

Message from ISCB

• 
  Miranda D. Stobbe, Tarun Mishra, Geoff MacIntyre:
  Breaking the Ice and Forging Links: The Importance of Socializing in Research.

Education Articles

• 
  Timothy Bailey, Pawel Krajewski, Istvan Ladunga, Céline Lefebvre, Qunhua Li, Tao Liu, Pedro Madrigal, Cenny Taslim, Jie Zhang:
  Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data.
• 
  Judith A. Blake:
  Ten Quick Tips for Using the Gene Ontology.

Perspectives

• 
  Lennart Martens:
  About Dice, Bouldering, and Team Empowerment: Running the CompOmics Group at VIB and Ghent University, Belgium.
• 
  Olga Vitek:
  Leading a Statistical Bioinformatics Lab: It's All About Finding Balance.
• 
  Jeroen de Ridder, Yana Bromberg, Magali Michaut, Venkata P. Satagopam, Manuel Corpas, Geoff MacIntyre, Theodore Alexandrov:
  The Young PI Buzz: Learning from the Organizers of the Junior Principal Investigator Meeting at ISMB-ECCB 2013.

Research Articles

• 
  Peter Man-Un Ung, Andrea D. Thompson, Lyra Chang, Jason E. Gestwicki, Heather A. Carlson:
  Identification of Key Hinge Residues Important for Nucleotide-Dependent Allostery in E. coli Hsp70/DnaK.
• 
  Shayoni Ray, Daniel Yuan, Nimit Dhulekar, Basak Oztan, Bülent Yener, Melinda Larsen:
  Cell-Based Multi-Parametric Model of Cleft Progression during Submandibular Salivary Gland Branching Morphogenesis.
• 
  Nickolay A. Khazanov, Heather A. Carlson:
  Exploring the Composition of Protein-Ligand Binding Sites on a Large Scale.
• 
  Xiaoxia Wang, Sarada Panchanathan, Gerardo Chowell:
  A Data-Driven Mathematical Model of CA-MRSA Transmission among Age Groups: Evaluating the Effect of Control Interventions.
• 
  Luca Albergante, Jon Timmis, Lynette Beattie, Paul M. Kaye:
  A Petri Net Model of Granulomatous Inflammation: Implications for IL-10 Mediated Control of Leishmania donovani Infection.
• 
  Giles W. Story, Ivaylo Vlaev, Ben Seymour, Joel S. Winston, Ara Darzi, Raymond J. Dolan:
  Dread and the Disvalue of Future Pain.
• 
  Antoine Frénoy, François Taddei, Dusan Misevic:
  Genetic Architecture Promotes the Evolution and Maintenance of Cooperation.
• 
  Weronika Sikora-Wohlfeld, Marit Ackermann, Eleni G. Christodoulou, Singaravelu Kalaimathy, Andreas Beyer:
  Assessing Computational Methods for Transcription Factor Target Gene Identification Based on ChIP-seq Data.
• 
  Erez Persi, David Horn:
  Systematic Analysis of Compositional Order of Proteins Reveals New Characteristics of Biological Functions and a Universal Correlate of Macroevolution.
• 
  Rotem Ben-Hamo, Sol Efroni:
  MicroRNA-Gene Association As a Prognostic Biomarker in Cancer Exposes Disease Mechanisms.
• 
  Guillem Portella, Federica Battistini, Modesto Orozco:
  Understanding the Connection between Epigenetic DNA Methylation and Nucleosome Positioning from Computer Simulations.
• 
  Lucas Theis, André Maia Chagas, Daniel Arnstein, Cornelius Schwarz, Matthias Bethge:
  Beyond GLMs: A Generative Mixture Modeling Approach to Neural System Identification.
• 
  Takeshi Hase, Samik Ghosh, Ryota Yamanaka, Hiroaki Kitano:
  Harnessing Diversity towards the Reconstructing of Large Scale Gene Regulatory Networks.
• 
  Debabani Ganguly, Weihong Zhang, Jianhan Chen:
  Electrostatically Accelerated Encounter and Folding for Facile Recognition of Intrinsically Disordered Proteins.
• 
  Frank S. Heldt, Timo Frensing, Antje Pflugmacher, Robin Gröpler, Britta Peschel, Udo Reichl:
  Multiscale Modeling of Influenza A Virus Infection Supports the Development of Direct-Acting Antivirals.
• 
  Tobias Warnecke, Erin A. Becker, Marc T. Facciotti, Corey Nislow, Ben Lehner:
  Conserved Substitution Patterns around Nucleosome Footprints in Eukaryotes and Archaea Derive from Frequent Nucleosome Repositioning through Evolution.
• 
  Martin Boerlin, Christian K. Machens, Sophie Denève:
  Predictive Coding of Dynamical Variables in Balanced Spiking Networks.
• 
  Teresa Ruiz-Herrero, Javier Estrada, Raúl Guantes, David G. Miguez:
  A Tunable Coarse-Grained Model for Ligand-Receptor Interaction.
• 
  Adam M. Sullivan, Xiaopeng Zhao, Yasuhiro Suzuki, Eri Ochiai, Stephen Crutcher, Michael A. Gilchrist:
  Evidence for Finely-Regulated Asynchronous Growth of Toxoplasma gondii Cysts Based on Data-Driven Model Selection.
• 
  Damon A. Clark, Raphael Benichou, Markus Meister, Rava Azeredo da Silveira:
  Dynamical Adaptation in Photoreceptors.
• 
  Harald Kempf, Haralampos Hatzikirou, Marcus Bleicher, Michael Meyer-Hermann:
  In Silico Analysis of Cell Cycle Synchronisation Effects in Radiotherapy of Tumour Spheroids.
• 
  Noa Chapal-Ilani, Yosef E. Maruvka, Adam Spiro, Yitzhak Reizel, Rivka Adar, Liran I. Shlush, Ehud Shapiro:
  Comparing Algorithms That Reconstruct Cell Lineage Trees Utilizing Information on Microsatellite Mutations.
• 
  Oliwia M. Szklarczyk, Nélido González-Segredo, Philipp Kukura, Ariella Oppenheim, Daniel Choquet, Vahid Sandoghdar, Ari Helenius, Ivo F. Sbalzarini, Helge Ewers:
  Receptor Concentration and Diffusivity Control Multivalent Binding of Sv40 to Membrane Bilayers.
• 
  Stefan Habenschuss, Zeno Jonke, Wolfgang Maass:
  Stochastic Computations in Cortical Microcircuit Models.
• 
  Noah Ollikainen, Tanja Kortemme:
  Computational Protein Design Quantifies Structural Constraints on Amino Acid Covariation.
• 
  Kazunari Mouri, Yasushi Sako:
  Optimality Conditions for Cell-Fate Heterogeneity That Maximize the Effects of Growth Factors in PC12 Cells.
• 
  Alex Dickson, Charles L. Brooks III:
  Quantifying Chaperone-Mediated Transitions in the Proteostasis Network of E. coli.
• 
  Hannah Edwards, Sanne Abeln, Charlotte M. Deane:
  Exploring Fold Space Preferences of New-born and Ancient Protein Superfamilies.
• 
  Friedemann Zenke, Guillaume Hennequin, Wulfram Gerstner:
  Synaptic Plasticity in Neural Networks Needs Homeostasis with a Fast Rate Detector.
• 
  Guido Polles, Giuliana Indelicato, Raffaello Potestio, Paolo Cermelli, Reidun Twarock, Cristian Micheletti:
  Mechanical and Assembly Units of Viral Capsids Identified via Quasi-Rigid Domain Decomposition.
• 
  Christophe Micheyl, Paul R. Schrater, Andrew J. Oxenham:
  Auditory Frequency and Intensity Discrimination Explained Using a Cortical Population Rate Code.
• 
  Davi R. Ortega, Guoya Mo, Kwangwoon Lee, Hongjun Zhou, Jérôme Baudry, Frederick W. Dahlquist, Igor B. Zhulin:
  Conformational Coupling between Receptor and Kinase Binding Sites through a Conserved Salt Bridge in a Signaling Complex Scaffold Protein.
• 
  Janez Konc, Milan Hodoscek, Mitja Ogrizek, Joanna Trykowska Konc, Dusanka Janezic:
  Structure-Based Function Prediction of Uncharacterized Protein Using Binding Sites Comparison.
• 
  Julian E. Fuchs, Susanne von Grafenstein, Roland G. Huber, Christian Kramer, Klaus R. Liedl:
  Substrate-Driven Mapping of the Degradome by Comparison of Sequence Logos.
• 
  Murat Çetinbas, Eugene I. Shakhnovich:
  Catalysis of Protein Folding by Chaperones Accelerates Evolutionary Dynamics in Adapting Cell Populations.
• 
  Peter Godfrey-Smith, Manolo Martínez:
  Communication and Common Interest.
• 
  Falk Lieder, Klaas E. Stephan, Jean Daunizeau, Marta I. Garrido, Karl J. Friston:
  A Neurocomputational Model of the Mismatch Negativity.
• 
  Simon Mitchell, Pedro Mendes:
  A Computational Model of Liver Iron Metabolism.
• 
  Jakob J. Metzger, Stephan Eule:
  Distribution of the Fittest Individuals and the Rate of Muller's Ratchet in a Model with Overlapping Generations.
• 
  Natalie Berestovsky, Wanding Zhou, Deepak Nagrath, Luay Nakhleh:
  Modeling Integrated Cellular Machinery Using Hybrid Petri-Boolean Networks.
• 
  Denis Valle, James S. Clark:
  Improving the Modeling of Disease Data from the Government Surveillance System: A Case Study on Malaria in the Brazilian Amazon.
• 
  Ridvan Eksi, Hongdong Li, Rajasree Menon, Yuchen Wen, Gilbert S. Omenn, Matthias Kretzler, Yuanfang Guan:
  Systematically Differentiating Functions for Alternatively Spliced Isoforms through Integrating RNA-seq Data.
• 
  Kejian Wang, Jiazhi Sun, Shufeng Zhou, Chunling Wan, Shengying Qin, Can Li, Lin He, Lun Yang:
  Prediction of Drug-Target Interactions for Drug Repositioning Only Based on Genomic Expression Similarity.
• 
  Varun B. Kothamachu, Elisenda Feliu, Carsten Wiuf, Luca Cardelli, Orkun S. Soyer:
  Phosphorelays Provide Tunable Signal Processing Capabilities for the Cell.
• 
  Ashwini Patil, Yutaro Kumagai, Kuo-ching Liang, Yutaka Suzuki, Kenta Nakai:
  Linking Transcriptional Changes over Time in Stimulated Dendritic Cells to Identify Gene Networks Activated during the Innate Immune Response.
• 
  Guido Scarabelli, Barry J. Grant:
  Mapping the Structural and Dynamical Features of Kinesin Motor Domains.
• 
  Biyu J. He, John M. Zempel:
  Average Is Optimal: An Inverted-U Relationship between Trial-to-Trial Brain Activity and Behavioral Performance.

Volume 9, Number 12, December 2013

Editorials

• 
  Fran Lewitter:
  Moving Education Forward, Again!
• 
  Joanne A. Fox, B. F. Francis Ouellette:
  Education in Computational Biology Today and Tomorrow.

Message from ISCB

• 
  Teresa Szczepinska, Wataru Iwasaki, Thomas Abeel:
  The Spirit of Competition: To Win or Not To Win.

Topic Page

• 
  Kieran O'Neill, Nima Aghaeepour, Josef Spidlen, Ryan Remy Brinkman:
  Flow Cytometry Bioinformatics.

Review

• 
  Sara El-Metwally, Taher Hamza, Magdi Zakaria, Mohamed Helmy:
  Next-Generation Sequence Assembly: Four Stages of Data Processing and Computational Challenges.

Research Articles

• 
  Sylvie Estrela, Sam P. Brown:
  Metabolic and Demographic Feedbacks Shape the Emergent Spatial Structure and Function of Microbial Communities.
• 
  Sébastien Béhuret, Charlotte Deleuze, Leonel Gómez, Yves Frégnac, Thierry Bal:
  Cortically-Controlled Population Stochastic Facilitation as a Plausible Substrate for Guiding Sensory Transfer across the Thalamic Gateway.
• 
  Antoine Neuraz, Laurent Chouchana, Georgia Malamut, Christine Le Beller, Denis Roche, Philippe Beaune, Patrice Degoulet, Anita Burgun, Marie-Anne Loriot, Paul Avillach:
  Phenome-Wide Association Studies on a Quantitative Trait: Application to TPMT Enzyme Activity and Thiopurine Therapy in Pharmacogenomics.
• 
  Evan J. Molinelli, Anil Korkut, Weiqing Wang, Martin L. Miller, Nicholas Paul Gauthier, Xiaohong Jing, Poorvi Kaushik, Qin He, Gordon B. Mills, David B. Solit, Christine A. Pratilas, Martin Weigt, Alfredo Braunstein, Andrea Pagnani, Riccardo Zecchina, Chris Sander:
  Perturbation Biology: Inferring Signaling Networks in Cellular Systems.
• 
  Max Sajitz-Hermstein, Zoran Nikoloski:
  Structural Control of Metabolic Flux.
• 
  Geir Halnes, Ivar Østby, Klas H. Pettersen, Stig W. Omholt, Gaute T. Einevoll:
  Electrodiffusive Model for Astrocytic and Neuronal Ion Concentration Dynamics.
• 
  Patrick G. Blachly, César Augusto F. de Oliveira, Sarah L. Williams, James Andrew McCammon:
  Utilizing a Dynamical Description of IspH to Aid in the Development of Novel Antimicrobial Drugs.
• 
  Erik M. Volz, Simon D. W. Frost:
  Inferring the Source of Transmission with Phylogenetic Data.
• 
  Artemis Koukounari, Christl A. Donnelly, Irini Moustaki, Edridah M. Tukahebwa, Narcis B. Kabatereine, Shona Wilson, Joanne P. Webster, André M. Deelder, Birgitte J. Vennervald, Govert J. van Dam:
  A Latent Markov Modelling Approach to the Evaluation of Circulating Cathodic Antigen Strips for Schistosomiasis Diagnosis Pre- and Post-Praziquantel Treatment in Uganda.
• 
  Srinivasan Sivanandan, Athi N. Naganathan:
  A Disorder-Induced Domino-Like Destabilization Mechanism Governs the Folding and Functional Dynamics of the Repeat Protein IκBα.
• 
  T. Alex Perkins, Thomas W. Scott, Arnaud Le Menach, David L. Smith:
  Heterogeneity, Mixing, and the Spatial Scales of Mosquito-Borne Pathogen Transmission.
• 
  Christel Kamp, Mathieu Moslonka-Lefebvre, Samuel Alizon:
  Epidemic Spread on Weighted Networks.
• 
  Adrien Nicolaï, Patrice Delarue, Patrick Senet:
  Decipher the Mechanisms of Protein Conformational Changes Induced by Nucleotide Binding through Free-Energy Landscape Analysis: ATP Binding to Hsp70.
• 
  Masaki Sasai, Yudai Kawabata, Koh Makishi, Kazuhito Itoh, Tomoki P. Terada:
  Time Scales in Epigenetic Dynamics and Phenotypic Heterogeneity of Embryonic Stem Cells.
• 
  Tjaart A. P. de Beer, Roman A. Laskowski, Sarah L. Parks, Botond Sipos, Nick Goldman, Janet M. Thornton:
  Amino Acid Changes in Disease-Associated Variants Differ Radically from Variants Observed in the 1000 Genomes Project Dataset.
• 
  Will D. Penny, Peter Zeidman, Neil Burgess:
  Forward and Backward Inference in Spatial Cognition.
• 
  Adam Mahdi, Jacob Sturdy, Johnny T. Ottesen, Mette S. Olufsen:
  Modeling the Afferent Dynamics of the Baroreflex Control System.
• 
  Richard R. Stein, Vanni Bucci, Nora C. Toussaint, Charlie G. Buffie, Gunnar Rätsch, Eric G. Pamer, Chris Sander, João B. Xavier:
  Ecological Modeling from Time-Series Inference: Insight into Dynamics and Stability of Intestinal Microbiota.
• 
  Regina Joice, Vagheesh Narasimhan, Jacqui Montgomery, Amar Bir Sidhu, Keunyoung Oh, Evan Meyer, Willythssa Pierre-Louis, Karl Seydel, Danny Milner, Kim Williamson, Roger Wiegand, Daouda Ndiaye, Johanna Daily, Dyann Wirth, Terrie Taylor, Curtis Huttenhower, Matthias Marti:
  Inferring Developmental Stage Composition from Gene Expression in Human Malaria.
• 
  Michela Candotti, Alberto Pérez, Carles Ferrer-Costa, Manuel Rueda, Tim Meyer, Josep Lluis Gelpí, Modesto Orozco:
  Exploring Early Stages of the Chemical Unfolding of Proteins at the Proteome Scale.
• 
  Ben Klünder, Tina Freisinger, Roland Wedlich-Söldner, Erwin Frey:
  GDI-Mediated Cell Polarization in Yeast Provides Precise Spatial and Temporal Control of Cdc42 Signaling.
• 
  Romain Brette:
  Sharpness of Spike Initiation in Neurons Explained by Compartmentalization.
• 
  Kristina D. Simmons, Jason S. Prentice, Gasper Tkacik, Jan Homann, Heather K. Yee, Stephanie E. Palmer, Philip C. Nelson, Vijay Balasubramanian:
  Transformation of Stimulus Correlations by the Retina.
• 
  Mike Bonny, Elisabeth Fischer-Friedrich, Martin Loose, Petra Schwille, Karsten Kruse:
  Membrane Binding of MinE Allows for a Comprehensive Description of Min-Protein Pattern Formation.
• 
  Matthias Jeschke, Stephan Baumgärtner, Stefan Legewie:
  Determinants of Cell-to-Cell Variability in Protein Kinase Signaling.
• 
  Xiaoqiang Sun, Jiguang Bao, Kyle C. Nelson, King Chuen Li, George Kulik, Xiaobo Zhou:
  Systems Modeling of Anti-apoptotic Pathways in Prostate Cancer: Psychological Stress Triggers a Synergism Pattern Switch in Drug Combination Therapy.
• 
  Nevena Todorova, Adam J. Makarucha, Nicholas D. M. Hine, Arash A. Mostofi, Irene Yarovsky:
  Dimensionality of Carbon Nanomaterials Determines the Binding and Dynamics of Amyloidogenic Peptides: Multiscale Theoretical Simulations.
• 
  Alexander M. Walter, Paulo S. Pinheiro, Matthijs Verhage, Jakob B. Sørensen:
  A Sequential Vesicle Pool Model with a Single Release Sensor and a Ca²⁺-Dependent Priming Catalyst Effectively Explains Ca²⁺-Dependent Properties of Neurosecretion.
• 
  Amir Dezfouli, Bernard W. Balleine:
  Actions, Action Sequences and Habits: Evidence That Goal-Directed and Habitual Action Control Are Hierarchically Organized.
• 
  Ayse Ozlem Aykut, Ali Rana Atilgan, Canan Atilgan:
  Designing Molecular Dynamics Simulations to Shift Populations of the Conformational States of Calmodulin.
• 
  Chieh-Chun Chen, Shu Xiao, Dan Xie, Xiaoyi Cao, Chun-Xiao Song, Ting Wang, Chuan He, Sheng Zhong:
  Understanding Variation in Transcription Factor Binding by Modeling Transcription Factor Genome-Epigenome Interactions.
• 
  Anne Lopes, Sophie Sacquin-Mora, Viktoriya Dimitrova, Elodie Laine, Yann Ponty, Alessandra Carbone:
  Protein-Protein Interactions in a Crowded Environment: An Analysis via Cross-Docking Simulations and Evolutionary Information.
• 
  Sriram Chandrasekaran, Nathan D. Price:
  Metabolic Constraint-Based Refinement of Transcriptional Regulatory Networks.
• 
  Eduard J. Kerkhoven, Fiona Achcar, Vincent P. Alibu, Richard J. Burchmore, Ian H. Gilbert, Maciej Trybilo, Nicole N. Driessen, David R. Gilbert, Rainer Breitling, Barbara M. Bakker, Michael P. Barrett:
  Handling Uncertainty in Dynamic Models: The Pentose Phosphate Pathway in Trypanosoma brucei.
• 
  Roger Guimerà, Marta Sales-Pardo:
  A Network Inference Method for Large-Scale Unsupervised Identification of Novel Drug-Drug Interactions.
• 
  Shouneng Peng, Jingze Tan, Sile Hu, Hang Zhou, Jing Guo, Li Jin, Kun Tang:
  Detecting Genetic Association of Common Human Facial Morphological Variation Using High Density 3D Image Registration.
• 
  Bin Wu, Julián García, Christoph Hauert, Arne Traulsen:
  Extrapolating Weak Selection in Evolutionary Games.
• 
  Aaron M. Bornstein, Nathaniel D. Daw:
  Cortical and Hippocampal Correlates of Deliberation during Model-Based Decisions for Rewards in Humans.