PLoS Computational Biology, Volume 11

Volume 11, Number 1, January 2015

Editorials

• 
  Aidan Budd, Holger Dinkel, Manuel Corpas, Jonathan C. Fuller, Laura Rubinat, Damien P. Devos, Pierre H. Khoueiry, Konrad U. Förstner, Fotis Georgatos, Francis Rowland, Malvika Sharan, Janos X. Binder, Tom Grace, Karyn Traphagen, Adam Gristwood, Natasha T. Wood:
  Ten Simple Rules for Organizing an Unconference.
• 
  Ruth Nussinov:
  Advancements and Challenges in Computational Biology.

Message from ISCB

• 
  Peter D. Karp, Bonnie Berger, Diane E. Kovats, Thomas Lengauer, Michal Linial, Pardis Sabeti, Winston Hide, Burkhard Rost:
  ISCB Ebola Award for Important Future Research on the Computational Biology of Ebola Virus.

Perspective

• 
  Eberhard O. Voit, Harald A. Martens, Stig W. Omholt:
  150 Years of the Mass Action Law.

Research Articles

• 
  Alboukadel Kassambara, Thierry Rème, Michel Jourdan, Thierry Fest, Dirk Hose, Karin Tarte, Bernard Klein:
  GenomicScape: An Easy-to-Use Web Tool for Gene Expression Data Analysis. Application to Investigate the Molecular Events in the Differentiation of B Cells into Plasma Cells.
• 
  Ueli Rutishauser, Jean-Jacques E. Slotine, Rodney J. Douglas:
  Computation in Dynamically Bounded Asymmetric Systems.
• 
  Helen L. Ramsden, Gülsen Sürmeli, Steven G. McDonagh, Matthew F. Nolan:
  Laminar and Dorsoventral Molecular Organization of the Medial Entorhinal Cortex Revealed by Large-scale Anatomical Analysis of Gene Expression.
• 
  Loic Matthey, Paul M. Bays, Peter Dayan:
  A Probabilistic Palimpsest Model of Visual Short-term Memory.
• 
  Erick Andres Perez-Alday, Michael A. Colman, Philip Langley, Timothy D. Butters, Jonathan Higham, Antony J. Workman, Jules C. Hancox, Henggui Zhang:
  A New Algorithm to Diagnose Atrial Ectopic Origin from Multi Lead ECG Systems - Insights from 3D Virtual Human Atria and Torso.
• 
  Daeyong Jin, Hyunju Lee:
  A Computational Approach to Identifying Gene-microRNA Modules in Cancer.
• 
  Massimo Lai, Denis Brun, Stuart J. Edelstein, Nicolas Le Novère:
  Modulation of Calmodulin Lobes by Different Targets: An Allosteric Model with Hemiconcerted Conformational Transitions.
• 
  Diana Stefan, Corinne Pinel, Stéphane Pinhal, Eugenio Cinquemani, Johannes Geiselmann, Hidde de Jong:
  Inference of Quantitative Models of Bacterial Promoters from Time-Series Reporter Gene Data.
• 
  Michael Fauth, Florentin Wörgötter, Christian Tetzlaff:
  The Formation of Multi-synaptic Connections by the Interaction of Synaptic and Structural Plasticity and Their Functional Consequences.
• 
  Nigel Stepp, Dietmar Plenz, Narayan Srinivasa:
  Synaptic Plasticity Enables Adaptive Self-Tuning Critical Networks.
• 
  Emilie Montastier, Nathalie Villa-Vialaneix, Sylvie Caspar-Bauguil, Petr Hlavaty, Eva Tvrzicka, Ignacio Gonzalez, Wim H. M. Saris, Dominique Langin, Marie Kunesova, Nathalie Viguerie:
  System Model Network for Adipose Tissue Signatures Related to Weight Changes in Response to Calorie Restriction and Subsequent Weight Maintenance.
• 
  Jamie T. Griffin:
  The Interaction between Seasonality and Pulsed Interventions against Malaria in Their Effects on the Reproduction Number.
• 
  Frédéric Boudon, Jérôme Chopard, Olivier Ali, Benjamin Gilles, Olivier Hamant, Arezki Boudaoud, Jan Traas, Christophe Godin:
  A Computational Framework for 3D Mechanical Modeling of Plant Morphogenesis with Cellular Resolution.
• 
  Martin Rückl, Ian Parker, Jonathan S. Marchant, Chamakuri Nagaiah, Friedrich W. Johenning, Sten Rüdiger:
  Modulation of Elementary Calcium Release Mediates a Transition from Puffs to Waves in an IP₃R Cluster Model.
• 
  Davod Alizadehrad, Timothy Krüger, Markus Engstler, Holger Stark:
  Simulating the Complex Cell Design of Trypanosoma brucei and Its Motility.
• 
  Ioannis Andrianakis, Ian R. Vernon, Nicky McCreesh, Trevelyan J. McKinley, Jeremy E. Oakley, Rebecca N. Nsubuga, Michael Goldstein, Richard G. White:
  Bayesian History Matching of Complex Infectious Disease Models Using Emulation: A Tutorial and a Case Study on HIV in Uganda.
• 
  Regina S. Salvat, Andrew S. Parker, Yoonjoo Choi, Chris Bailey-Kellogg, Karl E. Griswold:
  Mapping the Pareto Optimal Design Space for a Functionally Deimmunized Biotherapeutic Candidate.
• 
  J. Matthew Mahoney, Jaclyn N. Taroni, Viktor Martyanov, Tammara A. Wood, Casey S. Greene, Patricia A. Pioli, Monique E. Hinchcliff, Michael L. Whitfield:
  Systems Level Analysis of Systemic Sclerosis Shows a Network of Immune and Profibrotic Pathways Connected with Genetic Polymorphisms.
• 
  Andreas Wilke, Jared Bischof, Travis Harrison, Tom Brettin, Mark D'Souza, Wolfgang Gerlach, Hunter Matthews, Tobias Paczian, Jared Wilkening, Elizabeth M. Glass, Narayan Desai, Folker Meyer:
  A RESTful API for Accessing Microbial Community Data for MG-RAST.
• 
  Raimon Sabate, Frederic Rousseau, Joost Schymkowitz, Salvador Ventura:
  What Makes a Protein Sequence a Prion?
• 
  Lu Chen, Lei Du-Cuny, Sylvestor Moses, Sabrina Dumas, Zuohe Song, Abdol Hossein Rezaeian, Hui-Kuan Lin, Emmanuelle J. Meuillet, Shuxing Zhang:
  Novel Inhibitors Induce Large Conformational Changes of GAB1 Pleckstrin Homology Domain and Kill Breast Cancer Cells.
• 
  Markus Niklasson, Alexandra Ahlner, Cecilia Andresen, Joseph A. Marsh, Patrik Lundström:
  Fast and Accurate Resonance Assignment of Small-to-Large Proteins by Combining Automated and Manual Approaches.
• 
  Andrei N. Lupas, Hongbo Zhu, Mateusz Korycinski:
  The Thalidomide-Binding Domain of Cereblon Defines the CULT Domain Family and Is a New Member of the β-Tent Fold.
• 
  Eduard Porta-Pardo, Adam Godzik:
  Analysis of Individual Protein Regions Provides Novel Insights on Cancer Pharmacogenomics.
• 
  Thomas Sakoparnig, Patrick Fried, Niko Beerenwinkel:
  Identification of Constrained Cancer Driver Genes Based on Mutation Timing.
• 
  Elizabeth N. Davison, Kimberly J. Schlesinger, Danielle S. Bassett, Mary-Ellen Lynall, Michael B. Miller, Scott T. Grafton, Jean M. Carlson:
  Brain Network Adaptability across Task States.
• 
  Benjamin Simmonds, Maurice J. Chacron:
  Activation of Parallel Fiber Feedback by Spatially Diffuse Stimuli Reduces Signal and Noise Correlations via Independent Mechanisms in a Cerebellum-Like Structure.
• 
  Sadra Sadeh, Stefan Rotter:
  Orientation Selectivity in Inhibition-Dominated Networks of Spiking Neurons: Effect of Single Neuron Properties and Network Dynamics.

Volume 11, Number 2, February 2015

Editorials

• 
  Thomas C. Erren, Tracy E. Slanger, J. Valérie Groß, Philip E. Bourne, Paul Cullen:
  Ten Simple Rules for Lifelong Learning, According to Hamming.
• 
  Thomas Lengauer, Ruth Nussinov:
  How to Write a Presubmission Inquiry.
• 
  Effy Vayena, Marcel Salathé, Lawrence C. Madoff, John S. Brownstein:
  Ethical Challenges of Big Data in Public Health.
• 
  Philip E. Bourne:
  Confronting the Ethical Challenges of Big Data in Public Health.

Education

• 
  Aidan Budd, Manuel Corpas, Michelle D. Brazas, Jonathan C. Fuller, Jeremy Goecks, Nicola J. Mulder, Magali Michaut, B. F. Francis Ouellette, Aleksandra Pawlik, Niklas Blomberg:
  A Quick Guide for Building a Successful Bioinformatics Community.

Research Articles

• 
  David G. García Münzer, Margaritis Kostoglou, Michael C. Georgiadis, Efstratios N. Pistikopoulos, Athanasios Mantalaris:
  Cyclin and DNA Distributed Cell Cycle Model for GS-NS0 Cells.
• 
  Tiberiu Tesileanu, Lucy J. Colwell, Stanislas Leibler:
  Protein Sectors: Statistical Coupling Analysis versus Conservation.
• 
  Saheed Imam, Daniel R. Noguera, Timothy J. Donohue:
  An Integrated Approach to Reconstructing Genome-Scale Transcriptional Regulatory Networks.
• 
  J. Harry Caufield, Marco Abreu, Christopher Wimble, Peter Uetz:
  Protein Complexes in Bacteria.
• 
  Mei Yan Lee, Scott L. Diamond:
  A Human Platelet Calcium Calculator Trained by Pairwise Agonist Scanning.
• 
  Daniel M. Keenan, Amy W. Quinkert, Donald W. Pfaff:
  Stochastic Modeling of Mouse Motor Activity under Deep Brain Stimulation: The Extraction of Arousal Information.
• 
  Renaud Jolivet, Jay S. Coggan, Igor Allaman, Pierre J. Magistretti:
  Multi-timescale Modeling of Activity-Dependent Metabolic Coupling in the Neuron-Glia-Vasculature Ensemble.
• 
  Benjamin J. Binder, Joanna F. Sundstrom, Jennifer M. Gardner, Vladimir Jiranek, Stephen G. Oliver:
  Quantifying Two-Dimensional Filamentous and Invasive Growth Spatial Patterns in Yeast Colonies.
• 
  Benjamin Allen, Christine Sample, Yulia Dementieva, Ruben C. Medeiros, Christopher Paoletti, Martin A. Nowak:
  The Molecular Clock of Neutral Evolution Can Be Accelerated or Slowed by Asymmetric Spatial Structure.
• 
  Benjamin A. Dunn, Maria Mørreaunet, Yasser Roudi:
  Correlations and Functional Connections in a Population of Grid Cells.
• 
  Jagannath Swaminathan, Alexander A. Boulgakov, Edward M. Marcotte:
  A Theoretical Justification for Single Molecule Peptide Sequencing.
• 
  Ying Li, Guang Li, Benjamin Görling, Burkhard Luy, Jiulin Du, Jun Yan:
  Integrative Analysis of Circadian Transcriptome and Metabolic Network Reveals the Role of De Novo Purine Synthesis in Circadian Control of Cell Cycle.
• 
  Yonatan Schweitzer, Michael M. Kozlov:
  Membrane-Mediated Interaction between Strongly Anisotropic Protein Scaffolds.
• 
  David K. Johnson, John Karanicolas:
  Selectivity by Small-Molecule Inhibitors of Protein Interactions Can Be Driven by Protein Surface Fluctuations.
• 
  Martina Kutmon, Martijn P. van Iersel, Anwesha Bohler, Thomas Kelder, Nuno Nunes, Alexander R. Pico, Chris T. A. Evelo:
  PathVisio 3: An Extendable Pathway Analysis Toolbox.
• 
  Renske M. A. Vroomans, Paulien Hogeweg, Kirsten H. W. J. ten Tusscher:
  Segment-Specific Adhesion as a Driver of Convergent Extension.
• 
  Christian Meisel, Andreas Klaus, Christian Kuehn, Dietmar Plenz:
  Critical Slowing Down Governs the Transition to Neuron Spiking.
• 
  Jorge M. Pacheco, Vítor V. Vasconcelos, Francisco C. Santos, Brian Skyrms:
  Co-evolutionary Dynamics of Collective Action with Signaling for a Quorum.
• 
  Andrew J. K. Conlan, Ellen Brooks-Pollock, Trevelyan J. McKinley, Andrew P. Mitchell, Gareth J. Jones, Martin Vordermeier, James L. N. Wood:
  Potential Benefits of Cattle Vaccination as a Supplementary Control for Bovine Tuberculosis.
• 
  Vladimir Potapov, Jenifer B. Kaplan, Amy E. Keating:
  Data-Driven Prediction and Design of bZIP Coiled-Coil Interactions.
• 
  Elisa M. Tartaglia, Nicolas Brunel, Gianluigi Mongillo:
  Modulation of Network Excitability by Persistent Activity: How Working Memory Affects the Response to Incoming Stimuli.
• 
  Johannes Eckstein, Nikolaus Berndt, Hermann-Georg Holzhütter:
  Computer Simulations Suggest a Key Role of Membranous Nanodomains in Biliary Lipid Secretion.
• 
  Renaud Bastien, Stéphane Douady, Bruno Moulia:
  A Unified Model of Shoot Tropism in Plants: Photo-, Gravi- and Propio-ception.
• 
  Guangyou Duan, Dirk Walther:
  The Roles of Post-translational Modifications in the Context of Protein Interaction Networks.
• 
  Edward J. Banigan, Tajie H. Harris, David A. Christian, Christopher A. Hunter, Andrea J. Liu:
  Heterogeneous CD8⁺ T Cell Migration in the Lymph Node in the Absence of Inflammation Revealed by Quantitative Migration Analysis.
• 
  Ishutesh Jain, Mandar M. Inamdar, Ranjith Padinhateeri:
  Statistical Mechanics Provides Novel Insights into Microtubule Stability and Mechanism of Shrinkage.
• 
  Adrián Ponce-Alvarez, Gustavo Deco, Patric Hagmann, Gian Luca Romani, Dante Mantini, Maurizio Corbetta:
  Resting-State Temporal Synchronization Networks Emerge from Connectivity Topology and Heterogeneity.
• 
  Laura R. González-Ramírez, Omar J. Ahmed, Sydney S. Cash, C. Eugene Wayne, Mark A. Kramer:
  A Biologically Constrained, Mathematical Model of Cortical Wave Propagation Preceding Seizure Termination.
• 
  Eric Bonnet, Laurence Calzone, Tom Michoel:
  Integrative Multi-omics Module Network Inference with Lemon-Tree.
• 
  Eric Lowet, Mark J. Roberts, Avgis Hadjipapas, Alina Peter, Jan van der Eerden, Peter De Weerd:
  Input-Dependent Frequency Modulation of Cortical Gamma Oscillations Shapes Spatial Synchronization and Enables Phase Coding.
• 
  Ignacia Echeverria, Garegin A. Papoian:
  DNA Exit Ramps Are Revealed in the Binding Landscapes Obtained from Simulations in Helical Coordinates.
• 
  Xavier Didelot, Daniel J. Wilson:
  ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes.
• 
  Daniel Malagarriga, Alessandro E. P. Villa, Jordi García-Ojalvo, Antonio J. Pons Rivero:
  Mesoscopic Segregation of Excitation and Inhibition in a Brain Network Model.
• 
  Kasper Jensen, Yueqiong Ni, Gianni Panagiotou, Irene Kouskoumvekaki:
  Developing a Molecular Roadmap of Drug-Food Interactions.
• 
  Yoonji Lee, Sun Choi, Changbong Hyeon:
  Communication over the Network of Binary Switches Regulates the Activation of A_2A Adenosine Receptor.
• 
  Hanna Julienne, Benjamin Audit, Alain Arneodo:
  Embryonic Stem Cell Specific "Master" Replication Origins at the Heart of the Loss of Pluripotency.
• 
  Claude Gérard, John J. Tyson, Damien Coudreuse, Béla Novák:
  Cell Cycle Control by a Minimal Cdk Network.
• 
  Bence Ferdinandy, Enys Mones, Tamás Vicsek, Viktor Müller:
  HIV Competition Dynamics over Sexual Networks: First Comer Advantage Conserves Founder Effects.
• 
  Paul Thatcher Edlefsen, Morgane Rolland, Tomer Hertz, Sodsai Tovanabutra, Andrew J. Gartland, Allan C. deCamp, Craig A. Magaret, Hasan Ahmed, Raphael Gottardo, Michal Juraska, Connor McCoy, Brendan B. Larsen, Eric Sanders-Buell, Chris Carrico, Sergey Menis, Meera Bose, Miguel A. Arroyo, Robert J. O'Connell, Sorachai Nitayaphan, Punnee Pitisuttithum, Jaranit Kaewkungwal, Supachai Rerks-Ngarm, Merlin L. Robb, Tatsiana Kirys, Ivelin Georgiev, Peter D. Kwong, Konrad Scheffler, Sergei L. Kosakovsky Pond, Jonathan M. Carlson, Nelson Michael, William R. Schief, James I. Mullins, Jerome H. Kim, Peter B. Gilbert:
  : Comprehensive Sieve Analysis of Breakthrough HIV-1 Sequences in the RV144 Vaccine Efficacy Trial.
• 
  Hinrich Arnoldt, Shuwen Chang, Sven Jahnke, Birk Urmersbach, Holger Taschenberger, Marc Timme:
  When Less Is More: Non-monotonic Spike Sequence Processing in Neurons.
• 
  Julien Jorda, Yu Liu, Thomas A. Bobik, Todd O. Yeates:
  Exploring Bacterial Organelle Interactomes: A Model of the Protein-Protein Interaction Network in the Pdu Microcompartment.

Volume 11, Number 3, March 2015

Education Articles

• 
  Marco D. Visser, Sean M. McMahon, Cory Merow, Philip M. Dixon, Sydne Record, Eelke Jongejans:
  Speeding Up Ecological and Evolutionary Computations in R; Essentials of High Performance Computing for Biologists.
• 
  Tomás Helikar, Christine E. Cutucache, Lauren M. Dahlquist, Tyler A. Herek, Joshua J. Larson, Jim A. Rogers:
  Integrating Interactive Computational Modeling in Biology Curricula.

Research Articles

• 
  Dimitri Yatsenko, Kresimir Josic, Alexander S. Ecker, Emmanouil Froudarakis, R. James Cotton, Andreas S. Tolias:
  Improved Estimation and Interpretation of Correlations in Neural Circuits.
• 
  Jérémie Sibille, Khanh Dao Duc, David Holcman, Nathalie Rouach:
  The Neuroglial Potassium Cycle during Neurotransmission: Role of Kir4.1 Channels.
• 
  Yu-Chen Lo, Silvia Senese, Chien-Ming Li, Qiyang Hu, Yong Huang, Robert Damoiseaux, Jorge Z. Torres:
  Large-Scale Chemical Similarity Networks for Target Profiling of Compounds Identified in Cell-Based Chemical Screens.
• 
  Davide Provasi, Mustafa Burak Boz, Jennifer M. Johnston, Marta Filizola:
  Preferred Supramolecular Organization and Dimer Interfaces of Opioid Receptors from Simulated Self-Association.
• 
  Maxim Volgushev, Vladimir Ilin, Ian H. Stevenson:
  Identifying and Tracking Simulated Synaptic Inputs from Neuronal Firing: Insights from In Vitro Experiments.
• 
  Adrian M. Haith, David M. Huberdeau, John W. Krakauer:
  Hedging Your Bets: Intermediate Movements as Optimal Behavior in the Context of an Incomplete Decision.
• 
  Deborah A. Weighill, Daniel A. Jacobson:
  3-way Networks: Application of Hypergraphs for Modelling Increased Complexity in Comparative Genomics.
• 
  Alistair M. Senior, Michael A. Charleston, Mathieu Lihoreau, Jérôme Buhl, David Raubenheimer, Stephen J. Simpson:
  Evolving Nutritional Strategies in the Presence of Competition: A Geometric Agent-Based Model.
• 
  Miriam C. Klein-Flügge, Steven W. Kennerley, Ana C. Saraiva, Will D. Penny, Sven Bestmann:
  Behavioral Modeling of Human Choices Reveals Dissociable Effects of Physical Effort and Temporal Delay on Reward Devaluation.
• 
  Carson C. Chow, Kelsey K. Finn, Geoffery B. Storchan, Xinping Lu, Xiaoyan Sheng, S. Stoney Simons Jr.:
  Kinetically-Defined Component Actions in Gene Repression.
• 
  Alejandro Torres-Sánchez, Jesús Gómez-Gardeñes, Fernando Falo:
  An Integrative Approach for Modeling and Simulation of Heterocyst Pattern Formation in Cyanobacteria Filaments.
• 
  Francisco Martínez-Jiménez, Marc A. Martí-Renom:
  Ligand-Target Prediction by Structural Network Biology Using nAnnoLyze.
• 
  Bruno B. Averbeck:
  Theory of Choice in Bandit, Information Sampling and Foraging Tasks.
• 
  Loes C. J. van Dam, Marc O. Ernst:
  Mapping Shape to Visuomotor Mapping: Learning and Generalisation of Sensorimotor Behaviour Based on Contextual Information.
• 
  Davide Albanese, Carlotta De Filippo, Duccio Cavalieri, Claudio Donati:
  Explaining Diversity in Metagenomic Datasets by Phylogenetic-Based Feature Weighting.
• 
  Luca Giuggioli, Thomas J. McKetterick, Marc Holderied:
  Delayed Response and Biosonar Perception Explain Movement Coordination in Trawling Bats.
• 
  Amanda Miguel, Jen Hsin, Tianyun Liu, Grace W. Tang, Russ B. Altman, Kerwyn Casey Huang:
  Variations in the Binding Pocket of an Inhibitor of the Bacterial Division Protein FtsZ across Genotypes and Species.
• 
  Vassilios N. Christopoulos, James Bonaiuto, Richard A. Andersen:
  A Biologically Plausible Computational Theory for Value Integration and Action Selection in Decisions with Competing Alternatives.
• 
  Tamar Friedlander, Avraham E. Mayo, Tsvi Tlusty, Uri Alon:
  Evolution of Bow-Tie Architectures in Biology.
• 
  Giles W. Story, Ivo Vlaev, Peter Dayan, Ben Seymour, Ara Darzi, Raymond J. Dolan:
  Anticipation and Choice Heuristics in the Dynamic Consumption of Pain Relief.
• 
  Adrien Wohrer, Christian K. Machens:
  On the Number of Neurons and Time Scale of Integration Underlying the Formation of Percepts in the Brain.
• 
  Alan L. Hutchison, Mark Maienschein-Cline, Andrew H. Chiang, S. M. Ali Tabei, Herman Gudjonson, Neil Bahroos, Ravi Allada, Aaron R. Dinner:
  Improved Statistical Methods Enable Greater Sensitivity in Rhythm Detection for Genome-Wide Data.
• 
  Fiete Haack, Heiko Lemcke, Roland Ewald, Tareck Rharass, Adelinde M. Uhrmacher:
  Spatio-temporal Model of Endogenous ROS and Raft-Dependent WNT/Beta-Catenin Signaling Driving Cell Fate Commitment in Human Neural Progenitor Cells.
• 
  Christopher R. S. Banerji, Simone Severini, Carlos Caldas, Andrew E. Teschendorff:
  Intra-Tumour Signalling Entropy Determines Clinical Outcome in Breast and Lung Cancer.
• 
  Omar Al Hammal, David Alonso, Rampal S. Etienne, Stephen J. Cornell:
  When Can Species Abundance Data Reveal Non-neutrality?
• 
  James A. Geraets, Eric C. Dykeman, Peter G. Stockley, Neil A. Ranson, Reidun Twarock:
  Asymmetric Genome Organization in an RNA Virus Revealed via Graph-Theoretical Analysis of Tomographic Data.
• 
  Fan Yang, Evangelia Petsalaki, Thomas Rolland, David E. Hill, Marc Vidal, Frederick P. Roth:
  Protein Domain-Level Landscape of Cancer-Type-Specific Somatic Mutations.
• 
  Cheng Lv, Xiaoguang Li, Fangting Li, Tiejun Li:
  Energy Landscape Reveals That the Budding Yeast Cell Cycle Is a Robust and Adaptive Multi-stage Process.
• 
  Feng Fu, Martin A. Nowak, Sebastian Bonhoeffer:
  Spatial Heterogeneity in Drug Concentrations Can Facilitate the Emergence of Resistance to Cancer Therapy.
• 
  Thomas Obadia, Romain Silhol, Lulla Opatowski, Laura Temime, Judith Legrand, Anne C. M. Thiébaut, Jean-Louis Herrmann, Eric Fleury, Didier Guillemot, Pierre-Yves Boëlle:
  Detailed Contact Data and the Dissemination of Staphylococcus aureus in Hospitals.
• 
  Kristen Fortney, Joshua Griesman, Max Kotlyar, Chiara Pastrello, Marc Angeli, Ming-Sound Tsao, Igor Jurisica:
  Prioritizing Therapeutics for Lung Cancer: An Integrative Meta-analysis of Cancer Gene Signatures and Chemogenomic Data.
• 
  Matthew Hartfield, Samuel Alizon:
  Within-Host Stochastic Emergence Dynamics of Immune-Escape Mutants.
• 
  David Lovell, Vera Pawlowsky-Glahn, Juan José Egozcue, Samuel Marguerat, Jürg Bähler:
  Proportionality: A Valid Alternative to Correlation for Relative Data.
• 
  João Couto, Daniele Linaro, Erik De Schutter, Michele Giugliano:
  On the Firing Rate Dependency of the Phase Response Curve of Rat Purkinje Neurons In Vitro.
• 
  Minseung Kim, Violeta Zorraquino, Ilias Tagkopoulos:
  Microbial Forensics: Predicting Phenotypic Characteristics and Environmental Conditions from Large-Scale Gene Expression Profiles.
• 
  Nicolas Guex, Isaac Crespo, Sylvian Bron, Assia Ifticene-Treboux, Eveline Faes-van't Hull, Solange Kharoubi, Robin Liechti, Patricia Werffeli, Mark Ibberson, Francois Majo, Michäel Nicolas, Julien Laurent, Abhishek Garg, Khalil Zaman, Hans-Anton Lehr, Brian J. Stevenson, Curzio Rüegg, George Coukos, Jean-François Delaloye, Ioannis Xenarios, Marie-Agnes Doucey:
  Angiogenic Activity of Breast Cancer Patients' Monocytes Reverted by Combined Use of Systems Modeling and Experimental Approaches.
• 
  Adam Sol Shai, Costas A. Anastassiou, Matthew E. Larkum, Christof Koch:
  Physiology of Layer 5 Pyramidal Neurons in Mouse Primary Visual Cortex: Coincidence Detection through Bursting.
• 
  Christopher M. DeBoever, Emanuela M. Ghia, Peter J. Shepard, Laura Rassenti, Christian L. Barrett, Kristen Jepsen, Catriona H. M. Jamieson, Dennis Carson, Thomas J. Kipps, Kelly A. Frazer:
  Transcriptome Sequencing Reveals Potential Mechanism of Cryptic 3' Splice Site Selection in SF3B1-mutated Cancers.
• 
  Marc D. Ryser, Evan R. Myers, Rick Durrett:
  HPV Clearance and the Neglected Role of Stochasticity.
• 
  Matteo Mainetti, Giorgio A. Ascoli:
  A Neural Mechanism for Background Information-Gated Learning Based on Axonal-Dendritic Overlaps.
• 
  Eugenio Valdano, Chiara Poletto, Armando Giovannini, Diana Palma, Lara Savini, Vittoria Colizza:
  Predicting Epidemic Risk from Past Temporal Contact Data.
• 
  Jérôme R. D. Soiné, Christoph A. Brand, Jonathan Stricker, Patrick W. Oakes, Margaret L. Gardel, Ulrich S. Schwarz:
  Model-based Traction Force Microscopy Reveals Differential Tension in Cellular Actin Bundles.
• 
  Jan Poleszczuk, Philip Hahnfeldt, Heiko Enderling:
  Evolution and Phenotypic Selection of Cancer Stem Cells.
• 
  Lucas A. Defelipe, Esteban Lanzarotti, Diego F. Gauto, Marcelo A. Marti, Adrian Gustavo Turjanski:
  Protein Topology Determines Cysteine Oxidation Fate: The Case of Sulfenyl Amide Formation among Protein Families.
• 
  Jaldert O. Rombouts, Sander M. Bohté, Pieter R. Roelfsema:
  How Attention Can Create Synaptic Tags for the Learning of Working Memories in Sequential Tasks.
• 
  Vesna Memisevic, Nela Zavaljevski, Seesandra V. Rajagopala, Keehwan Kwon, Rembert Pieper, David DeShazer, Jaques Reifman, Anders Wallqvist:
  Mining Host-Pathogen Protein Interactions to Characterize Burkholderia mallei Infectivity Mechanisms.
• 
  Woochul Nam, Bogdan I. Epureanu:
  Highly Loaded Behavior of Kinesins Increases the Robustness of Transport Under High Resisting Loads.
• 
  Oren E. Livne, Lide Han, Gorka Alkorta-Aranburu, William Wentworth-Sheilds, Mark Abney, Carole Ober, Dan L. Nicolae:
  PRIMAL: Fast and Accurate Pedigree-based Imputation from Sequence Data in a Founder Population.
• 
  Antreas C. Kalli, Mark S. P. Sansom, Reinhart A. F. Reithmeier:
  Molecular Dynamics Simulations of the Bacterial UraA H⁺-Uracil Symporter in Lipid Bilayers Reveal a Closed State and a Selective Interaction with Cardiolipin.

Volume 11, Number 4, April 2015

Editorials

• 
  Cody J. Weinberger, James A. Evans, Stefano Allesina:
  Ten Simple (Empirical) Rules for Writing Science.
• 
  Bernhard Knapp, Rémi Bardenet, Miguel O. Bernabeu, Rafel Bordas, Maria Bruna, Ben Calderhead, Jonathan Cooper, Alexander G. Fletcher, Derek Groen, Bram Kuijper, Joanna Lewis, Greg J. McInerny, Timo Minssen, James M. Osborne, Verena Paulitschke, Joe Pitt-Francis, Jelena Todoric, Christian A. Yates, David Gavaghan, Charlotte M. Deane:
  Ten Simple Rules for a Successful Cross-Disciplinary Collaboration.
• 
  Iddo Friedberg, Mark N. Wass, Sean D. Mooney, Predrag Radivojac:
  Ten Simple Rules for a Community Computational Challenge.
• 
  Anne-Laure Boulesteix:
  Ten Simple Rules for Reducing Overoptimistic Reporting in Methodological Computational Research.
• 
  Holly M. Bik, Alistair D. M. Dove, Miriam C. Goldstein, Rebecca R. Helm, Rick MacPherson, Kim Martini, Alexandria Warneke, Craig McClain:
  Ten Simple Rules for Effective Online Outreach.
• 
  Richard J. Roberts:
  Ten Simple Rules to Win a Nobel Prize.

Education

• 
  Melanie I. Stefan, Johanna L. Gutlerner, Richard T. Born, Michael Springer:
  The Quantitative Methods Boot Camp: Teaching Quantitative Thinking and Computing Skills to Graduate Students in the Life Sciences.

Perspective

• 
  Teresa K. Attwood, Erik Bongcam-Rudloff, Michelle D. Brazas, Manuel Corpas, Pascale Gaudet, Fran Lewitter, Nicola J. Mulder, Patricia M. Palagi, Maria Victoria Schneider, Celia W. G. van Gelder:
  GOBLET: The Global Organisation for Bioinformatics Learning, Education and Training.

Review

• 
  Romain Brette:
  What Is the Most Realistic Single-Compartment Model of Spike Initiation?

Research Articles

• 
  Tom Lindström, Michael J. Tildesley, Colleen Webb:
  A Bayesian Ensemble Approach for Epidemiological Projections.
• 
  Albertas Janulevicius, Mark C. M. van Loosdrecht, Cristian Picioreanu:
  Short-Range Guiding Can Result in the Formation of Circular Aggregates in Myxobacteria Populations.
• 
  Willemijn Groenendaal, Francis A. Ortega, Armen R. Kherlopian, Andrew C. Zygmunt, Trine Krogh-Madsen, David J. Christini:
  Cell-Specific Cardiac Electrophysiology Models.
• 
  Kevin Thurley, Daniel Gerecht, Elfriede Friedmann, Thomas Höfer:
  Three-Dimensional Gradients of Cytokine Signaling between T Cells.
• 
  Simon Sponberg, Thomas L. Daniel, Adrienne L. Fairhall:
  Dual Dimensionality Reduction Reveals Independent Encoding of Motor Features in a Muscle Synergy for Insect Flight Control.
• 
  Fernando R. Fernandez, Paola Malerba, John A. White:
  Non-linear Membrane Properties in Entorhinal Cortical Stellate Cells Reduce Modulation of Input-Output Responses by Voltage Fluctuations.
• 
  Mei Zhan, Matthew M. Crane, Eugeni V. Entchev, Antonio Caballero, Diana Andrea Fernandes de Abreu, QueeLim Ch'ng, Hang Lu:
  Automated Processing of Imaging Data through Multi-tiered Classification of Biological Structures Illustrated Using Caenorhabditis elegans.
• 
  Thomas W. Spiesser, Clemens Kühn, Marcus Krantz, Edda Klipp:
  Bud-Localization of CLB2 mRNA Can Constitute a Growth Rate Dependent Daughter Sizer.
• 
  Naoki Hiratani, Tomoki Fukai:
  Mixed Signal Learning by Spike Correlation Propagation in Feedback Inhibitory Circuits.
• 
  Jyotika Bahuguna, Ad Aertsen, Arvind Kumar:
  Existence and Control of Go/No-Go Decision Transition Threshold in the Striatum.
• 
  Katja N. Rybakova, Frank J. Bruggeman, Aleksandra Tomaszewska, Martijn J. Moné, Carsten Carlberg, Hans V. Westerhoff:
  Multiplex Eukaryotic Transcription (In)activation: Timing, Bursting and Cycling of a Ratchet Clock Mechanism.
• 
  Ayala Matzner, Izhar Bar-Gad:
  Quantifying Spike Train Oscillations: Biases, Distortions and Solutions.
• 
  Manoj Gambhir, Thomas A. Clark, Simon Cauchemez, Sara Y. Tartof, David L. Swerdlow, Neil M. Ferguson:
  A Change in Vaccine Efficacy and Duration of Protection Explains Recent Rises in Pertussis Incidence in the United States.
• 
  Daniel K. Wells, Yishan Chuang, Louis M. Knapp, Dirk Brockmann, William L. Kath, Joshua N. Leonard:
  Spatial and Functional Heterogeneities Shape Collective Behavior of Tumor-Immune Networks.
• 
  Lorenza Alice D'Alessandro, Regina Samaga, Tim Maiwald, Seong-Hwan Rho, Sandra Bonefas, Andreas Raue, Nao Iwamoto, Alexandra Kienast, Katharina Waldow, Rene Meyer, Marcel Schilling, Jens Timmer, Steffen Klamt, Ursula Klingmüller:
  Disentangling the Complexity of HGF Signaling by Combining Qualitative and Quantitative Modeling.
• 
  Hannah R. Meredith, Allison J. Lopatkin, Deverick J. Anderson, Lingchong You:
  Bacterial Temporal Dynamics Enable Optimal Design of Antibiotic Treatment.
• 
  Jian Tian, Jaie C. Woodard, Anna Whitney, Eugene I. Shakhnovich:
  Thermal Stabilization of Dihydrofolate Reductase Using Monte Carlo Unfolding Simulations and Its Functional Consequences.
• 
  Noa Slater, Yoram Louzoun, Loren Gragert, Martin Maiers, Ansu Chatterjee, Mark Albrecht:
  Power Laws for Heavy-Tailed Distributions: Modeling Allele and Haplotype Diversity for the National Marrow Donor Program.
• 
  Debabani Ganguly, Jianhan Chen:
  Modulation of the Disordered Conformational Ensembles of the p53 Transactivation Domain by Cancer-Associated Mutations.
• 
  Ethan S. Sokol, Sandhya Sanduja, Dexter X. Jin, Daniel H. Miller, Robert A. Mathis, Piyush B. Gupta:
  Perturbation-Expression Analysis Identifies RUNX1 as a Regulator of Human Mammary Stem Cell Differentiation.
• 
  William F. Flynn, Max W. Chang, Zhiqiang Tan, Glenn Oliveira, Jinyun Yuan, Jason F. Okulicz, Bruce E. Torbett, Ronald M. Levy:
  Deep Sequencing of Protease Inhibitor Resistant HIV Patient Isolates Reveals Patterns of Correlated Mutations in Gag and Protease.
• 
  Rodrigo Cilla, Vinodh Mechery, Beatriz Hernandez de Madrid, Steven Del Signore, Iván Dotú, Victor Hatini:
  Segmentation and Tracking of Adherens Junctions in 3D for the Analysis of Epithelial Tissue Morphogenesis.
• 
  Juan Palacios-Moreno, Lauren Foltz, Ailan Guo, Matthew P. Stokes, Emily D. Kuehn, Lynn George, Michael Comb, Mark L. Grimes:
  Neuroblastoma Tyrosine Kinase Signaling Networks Involve FYN and LYN in Endosomes and Lipid Rafts.
• 
  Daifeng Wang, Koon-Kiu Yan, Cristina Sisu, Chao Cheng, Joel S. Rozowsky, William Meyerson, Mark B. Gerstein:
  Loregic: A Method to Characterize the Cooperative Logic of Regulatory Factors.
• 
  Ka Wai Lin, Angela Liao, Amina A. Qutub:
  Simulation Predicts IGFBP2-HIF1α Interaction Drives Glioblastoma Growth.
• 
  Paul Egan, Jeffrey Moore, Christian D. Schunn, Jonathan Cagan, Philip R. Leduc:
  Emergent Systems Energy Laws for Predicting Myosin Ensemble Processivity.
• 
  Nils A. Berglund, Thomas J. Piggot, Damien Jefferies, Richard B. Sessions, Peter J. Bond, Syma Khalid:
  Interaction of the Antimicrobial Peptide Polymyxin B1 with Both Membranes of E. coli: A Molecular Dynamics Study.
• 
  Xiliang Zheng, Jin Wang:
  The Universal Statistical Distributions of the Affinity, Equilibrium Constants, Kinetics and Specificity in Biomolecular Recognition.
• 
  Stuart Aitken, Shigeyuki Magi, Ahmad M. N. Alhendi, Masayoshi Itoh, Hideya Kawaji, Timo Lassmann, Carsten O. Daub, Erik Arner, Piero Carninci, Alistair R. R. Forrest, Yoshihide Hayashizaki, Levon M. Khachigian, Mariko Okada-Hatakeyama, Colin A. M. Semple:
  Transcriptional Dynamics Reveal Critical Roles for Non-coding RNAs in the Immediate-Early Response.
• 
  Christiaan A. de Leeuw, Joris M. Mooij, Tom Heskes, Danielle Posthuma:
  MAGMA: Generalized Gene-Set Analysis of GWAS Data.
• 
  Juliane Siebourg-Polster, Daria Mudrak, Mario Emmenlauer, Pauli Rämö, Christoph Dehio, Urs F. Greber, Holger Fröhlich, Niko Beerenwinkel:
  NEMix: Single-cell Nested Effects Models for Probabilistic Pathway Stimulation.
• 
  Michael D. O'Connell, Gregory T. Reeves:
  The Presence of Nuclear Cactus in the Early Drosophila Embryo May Extend the Dynamic Range of the Dorsal Gradient.
• 
  Stefan Flasche, Olivier Le Polain de Waroux, Katherine L. O'Brien, W. John Edmunds:
  The Serotype Distribution among Healthy Carriers before Vaccination Is Essential for Predicting the Impact of Pneumococcal Conjugate Vaccine on Invasive Disease.
• 
  Daniel Bendor:
  The Role of Inhibition in a Computational Model of an Auditory Cortical Neuron during the Encoding of Temporal Information.
• 
  Tae J. Lee, Jeffrey V. Wong, Sena Bae, Anna Jisu Lee, Allison J. Lopatkin, Fan Yuan, Lingchong You:
  A Power-Law Dependence of Bacterial Invasion on Mammalian Host Receptors.
• 
  Gabriel Rodrigues Alves Margarido, David Heckerman:
  ConPADE: Genome Assembly Ploidy Estimation from Next-Generation Sequencing Data.
• 
  Federica Lombardi, Kalyan Golla, Darren J. Fitzpatrick, Fergal P. Casey, Niamh Moran, Denis C. Shields:
  Discovering Anti-platelet Drug Combinations with an Integrated Model of Activator-Inhibitor Relationships, Activator-Activator Synergies and Inhibitor-Inhibitor Synergies.
• 
  Pedro A. Saa, Lars Keld Nielsen:
  A General Framework for Thermodynamically Consistent Parameterization and Efficient Sampling of Enzymatic Reactions.
• 
  Joon-Young Moon, UnCheol Lee, Stefanie Blain-Moraes, George A. Mashour:
  General Relationship of Global Topology, Local Dynamics, and Directionality in Large-Scale Brain Networks.
• 
  Noorain Khan, Narendar Kolimi, Thenmalarchelvi Rathinavelan:
  Twisting Right to Left: A...A Mismatch in a CAG Trinucleotide Repeat Overexpansion Provokes Left-Handed Z-DNA Conformation.
• 
  Ickwon Choi, Amy W. Chung, Todd J. Suscovich, Supachai Rerks-Ngarm, Punnee Pitisuttithum, Sorachai Nitayaphan, Jaranit Kaewkungwal, Robert J. O'Connell, Donald Francis, Merlin L. Robb, Nelson Michael, Jerome H. Kim, Galit Alter, Margaret E. Ackerman, Chris Bailey-Kellogg:
  Machine Learning Methods Enable Predictive Modeling of Antibody Feature: Function Relationships in RV144 Vaccinees.
• 
  Nik J. Cunniffe, Richard O. J. H. Stutt, R. Erik DeSimone, Tim R. Gottwald, Christopher A. Gilligan:
  Optimising and Communicating Options for the Control of Invasive Plant Disease When There Is Epidemiological Uncertainty.
• 
  Giulia Menconi, Andrea Bedini, Roberto Barale, Isabella Sbrana:
  Global Mapping of DNA Conformational Flexibility on Saccharomyces cerevisiae.
• 
  Adam J. Kucharski, W. John Edmunds:
  Characterizing the Transmission Potential of Zoonotic Infections from Minor Outbreaks.
• 
  Peter Klimek, Alexandra Kautzky-Willer, Anna Chmiel, Irmgard Schiller-Frühwirth, Stefan Thurner:
  Quantification of Diabetes Comorbidity Risks across Life Using Nation-Wide Big Claims Data.
• 
  Tor D. Wager, Jian Kang, Timothy D. Johnson, Thomas E. Nichols, Ajay B. Satpute, Lisa Feldman Barrett:
  A Bayesian Model of Category-Specific Emotional Brain Responses.
• 
  Susan Dina Ghiassian, Jörg Menche, Albert-László Barabási:
  A DIseAse MOdule Detection (DIAMOnD) Algorithm Derived from a Systematic Analysis of Connectivity Patterns of Disease Proteins in the Human Interactome.
• 
  Tomás Trnka, Stanislav Kozmon, Igor Tvaroska, Jaroslav Koca:
  Stepwise Catalytic Mechanism via Short-Lived Intermediate Inferred from Combined QM/MM MERP and PES Calculations on Retaining Glycosyltransferase ppGalNAcT2.
• 
  Sébastien Giguère, François Laviolette, Mario Marchand, Denise M. Tremblay, Sylvain Moineau, Xinxia Liang, Éric Biron, Jacques Corbeil:
  Machine Learning Assisted Design of Highly Active Peptides for Drug Discovery.
• 
  Nathan F. Lepora, Giovanni Pezzulo:
  Embodied Choice: How Action Influences Perceptual Decision Making.
• 
  Fabio Pardi, Céline Scornavacca:
  Reconstructible Phylogenetic Networks: Do Not Distinguish the Indistinguishable.
• 
  Timo R. Maarleveld, Meike T. Wortel, Brett G. Olivier, Bas Teusink, Frank J. Bruggeman:
  Interplay between Constraints, Objectives, and Optimality for Genome-Scale Stoichiometric Models.
• 
  Nancy K. Drew, Mackenzie A. Eagleson, Danny B. Baldo Jr., Kevin Kit Parker, Anna Grosberg:
  Metrics for Assessing Cytoskeletal Orientational Correlations and Consistency.
• 
  Jorge G. T. Zañudo, Réka Albert:
  Cell Fate Reprogramming by Control of Intracellular Network Dynamics.
• 
  Kai Olav Ellefsen, Jean-Baptiste Mouret, Jeff Clune:
  Neural Modularity Helps Organisms Evolve to Learn New Skills without Forgetting Old Skills.
• 
  Changwang Zhang, Shi Zhou, Elisabetta Groppelli, Pierre Pellegrino, Ian Williams, Persephone Borrow, Benjamin M. Chain, Clare Jolly:
  Hybrid Spreading Mechanisms and T Cell Activation Shape the Dynamics of HIV-1 Infection.
• 
  Andy Phaiboun, Yiming Zhang, Boryung Park, Minsu Kim:
  Survival Kinetics of Starving Bacteria Is Biphasic and Density-Dependent.
• 
  Ross S. Williamson, Maneesh Sahani, Jonathan W. Pillow:
  The Equivalence of Information-Theoretic and Likelihood-Based Methods for Neural Dimensionality Reduction.

Volume 11, Number 5, May 2015

Perspective

• 
  Jonathan R. Karr, Alex H. Williams, Jeremy D. Zucker, Andreas Raue, Bernhard Steiert, Jens Timmer, Clemens Kreutz, Simon Wilkinson, Brandon A. Allgood, Brian M. Bot, Bruce R. Hoff, Michael R. Kellen, Markus W. Covert, Gustavo A. Stolovitzky, Pablo Meyer:
  Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models.

Topic Page

• 
  Matt Ravenhall, Nives Skunca, Florent Lassalle, Christophe Dessimoz:
  Inferring Horizontal Gene Transfer.

Research Articles

• 
  Christoph W. Korn, Dominik R. Bach:
  Maintaining Homeostasis by Decision-Making.
• 
  Augustin Luna, Geoffrey B. McFadden, Mirit I. Aladjem, Kurt W. Kohn:
  Predicted Role of NAD Utilization in the Control of Circadian Rhythms during DNA Damage Response.
• 
  Wilfredo Blanco, Catia M. Pereira, Vinicius R. Cota, Annie C. Souza, César Rennó-Costa, Sharlene Santos, Gabriella Dias, Ana M. G. Guerreiro, Adriano B. L. Tort, Adrião D. D. Neto, Sidarta Ribeiro:
  Synaptic Homeostasis and Restructuring across the Sleep-Wake Cycle.
• 
  David W. P. Dolan, Anze Zupanic, Glyn Nelson, Philip Hall, Satomi Miwa, Thomas B. L. Kirkwood, Daryl P. Shanley:
  Integrated Stochastic Model of DNA Damage Repair by Non-homologous End Joining and p53/p21- Mediated Early Senescence Signalling.
• 
  Bader Al-Anzi, Patrick Arpp, Sherif Gerges, Christopher Ormerod, Noah Olsman, Kai Zinn:
  Experimental and Computational Analysis of a Large Protein Network That Controls Fat Storage Reveals the Design Principles of a Signaling Network.
• 
  Emily A. Cooper, Anthony M. Norcia:
  Predicting Cortical Dark/Bright Asymmetries from Natural Image Statistics and Early Visual Transforms.
• 
  Julia C. Engelmann, Thomas Amann, Birgitta Ott-Rötzer, Margit Nützel, Yvonne Reinders, Jörg Reinders, Wolfgang E. Thasler, Theresa Kristl, Andreas Teufel, Christian G. Huber, Peter J. Oefner, Rainer Spang, Claus Hellerbrand:
  Causal Modeling of Cancer-Stromal Communication Identifies PAPPA as a Novel Stroma-Secreted Factor Activating NFκB Signaling in Hepatocellular Carcinoma.
• 
  Gaëlle Letort, Antonio Z. Politi, Hajer Ennomani, Manuel Théry, François Nédélec, Laurent Blanchoin:
  Geometrical and Mechanical Properties Control Actin Filament Organization.
• 
  Tao Chen, Hue Sun Chan:
  Native Contact Density and Nonnative Hydrophobic Effects in the Folding of Bacterial Immunity Proteins.
• 
  Manu Setty, Christina S. Leslie:
  SeqGL Identifies Context-Dependent Binding Signals in Genome-Wide Regulatory Element Maps.
• 
  Stepan Tymoshenko, Rebecca D. Oppenheim, Rasmus Agren, Jens Nielsen, Dominique Soldati-Favre, Vassily Hatzimanikatis:
  Metabolic Needs and Capabilities of Toxoplasma gondii through Combined Computational and Experimental Analysis.
• 
  Kit Curtius, William D. Hazelton, Jihyoun Jeon, E. Georg Luebeck:
  A Multiscale Model Evaluates Screening for Neoplasia in Barrett's Esophagus.
• 
  Erik van Dijk, Arlo Hoogeveen, Sanne Abeln:
  The Hydrophobic Temperature Dependence of Amino Acids Directly Calculated from Protein Structures.
• 
  Alon Diament, Tamir Tuller:
  Improving 3D Genome Reconstructions Using Orthologous and Functional Constraints.
• 
  Zhi Yang Tam, Jan Gruber, Barry Halliwell, Rudiyanto Gunawan:
  Context-Dependent Role of Mitochondrial Fusion-Fission in Clonal Expansion of mtDNA Mutations.
• 
  Matthew H. Ung, Frederick S. Varn, Shaoke Lou, Chao Cheng:
  Regulators Associated with Clinical Outcomes Revealed by DNA Methylation Data in Breast Cancer.
• 
  Wiktor Mlynarski:
  The Opponent Channel Population Code of Sound Location Is an Efficient Representation of Natural Binaural Sounds.
• 
  Christopher A. Lavender, Ronny Lorenz, Ge Zhang, Rita Tamayo, Ivo L. Hofacker, Kevin M. Weeks:
  Model-Free RNA Sequence and Structure Alignment Informed by SHAPE Probing Reveals a Conserved Alternate Secondary Structure for 16S rRNA.
• 
  Christopher A. Lavender, Robert J. Gorelick, Kevin M. Weeks:
  Structure-Based Alignment and Consensus Secondary Structures for Three HIV-Related RNA Genomes.
• 
  Jacopo Grilli, György Barabás, Stefano Allesina:
  Metapopulation Persistence in Random Fragmented Landscapes.
• 
  Cengiz Günay, Fred H. Sieling, Logesh Dharmar, Wei-Hsiang Lin, Verena Wolfram, Richard Marley, Richard A. Baines, Astrid A. Prinz:
  Distal Spike Initiation Zone Location Estimation by Morphological Simulation of Ionic Current Filtering Demonstrated in a Novel Model of an Identified Drosophila Motoneuron.
• 
  Gianluca Ascolani, Annalisa Occhipinti, Pietro Liò:
  Modelling Circulating Tumour Cells for Personalised Survival Prediction in Metastatic Breast Cancer.
• 
  Isamu Okada, Hitoshi Yamamoto, Fujio Toriumi, Tatsuya Sasaki:
  The Effect of Incentives and Meta-incentives on the Evolution of Cooperation.
• 
  Kyle S. Hickmann, Geoffrey Fairchild, Reid Priedhorsky, Nicholas Generous, James Mac Hyman, Alina Deshpande, Sara Y. Del Valle:
  Forecasting the 2013-2014 Influenza Season Using Wikipedia.
• 
  Sébastien Naze, Christophe Bernard, Viktor K. Jirsa:
  Computational Modeling of Seizure Dynamics Using Coupled Neuronal Networks: Factors Shaping Epileptiform Activity.
• 
  Emma Pierson, Daphne Koller, Alexis J. Battle, Sara Mostafavi:
  Sharing and Specificity of Co-expression Networks across 35 Human Tissues.
• 
  Yaroslav I. Molkov, Bartholomew J. Bacak, Adolfo E. Talpalar, Ilya A. Rybak:
  Mechanisms of Left-Right Coordination in Mammalian Locomotor Pattern Generation Circuits: A Mathematical Modeling View.
• 
  Sepideh Babaei, Ahmed Mahfouz, Marc Hulsman, Boudewijn P. F. Lelieveldt, Jeroen de Ridder, Marcel J. T. Reinders:
  Hi-C Chromatin Interaction Networks Predict Co-expression in the Mouse Cortex.
• 
  Gary K. Chen, Eric C. Chi, John M. O. Ranola, Kenneth Lange:
  Convex Clustering: An Attractive Alternative to Hierarchical Clustering.
• 
  Thibaud O. Taillefumier, Ned S. Wingreen:
  Optimal Census by Quorum Sensing.
• 
  Ed Reznik, Chris Sander:
  Extensive Decoupling of Metabolic Genes in Cancer.
• 
  Michael J. Hull, Stephen R. Soffe, David J. Willshaw, Alan Roberts:
  Modelling the Effects of Electrical Coupling between Unmyelinated Axons of Brainstem Neurons Controlling Rhythmic Activity.
• 
  Torsten Neher, Sen Cheng, Laurenz Wiskott:
  Memory Storage Fidelity in the Hippocampal Circuit: The Role of Subregions and Input Statistics.
• 
  Wanling Song, Harsha Bajaj, Chady Nasrallah, Hualiang Jiang, Mathias Winterhalter, Jacques-Philippe Colletier, Yechun Xu:
  Understanding Voltage Gating of Providencia stuartii Porins at Atomic Level.
• 
  Mookyung Cheon, Carol K. Hall, Iksoo Chang:
  Structural Conversion of Aβ_17-42 Peptides from Disordered Oligomers to U-Shape Protofilaments via Multiple Kinetic Pathways.
• 
  Fabio Vandin, Alexandra Papoutsaki, Benjamin J. Raphael, Eli Upfal:
  Accurate Computation of Survival Statistics in Genome-Wide Studies.
• 
  Miho S. Kitazawa, Koichi Fujimoto:
  A Dynamical Phyllotaxis Model to Determine Floral Organ Number.
• 
  Zachary D. Kurtz, Christian L. Müller, Emily R. Miraldi, Dan R. Littman, Martin J. Blaser, Richard A. Bonneau:
  Sparse and Compositionally Robust Inference of Microbial Ecological Networks.
• 
  Daniel Keller, Norbert Babai, Olexiy Kochubey, Yunyun Han, Henry Markram, Felix Schürmann, Ralf Schneggenburger:
  An Exclusion Zone for Ca²⁺ Channels around Docked Vesicles Explains Release Control by Multiple Channels at a CNS Synapse.
• 
  Kiana Toufighi, Jae-Seong Yang, Nuno Miguel Luis, Salvador Aznar Benitah, Ben Lehner, Luis Serrano, Christina Kiel:
  Dissecting the Calcium-Induced Differentiation of Human Primary Keratinocytes Stem Cells by Integrative and Structural Network Analyses.
• 
  T. Scott Chen, Donald Petrey, José Ignacio Garzón, Barry Honig:
  Predicting Peptide-Mediated Interactions on a Genome-Wide Scale.
• 
  Victor Garcia, Kirsten Richter, Frederik Graw, Annette Oxenius, Roland R. Regoes:
  Estimating the In Vivo Killing Efficacy of Cytotoxic T Lymphocytes across Different Peptide-MHC Complex Densities.
• 
  Thomas P. Prescott, Moritz Lang, Antonis Papachristodoulou:
  Quantification of Interactions between Dynamic Cellular Network Functionalities by Cascaded Layering.

Formal Comments

• 
  Manfred G. Kitzbichler, Edward T. Bullmore:
  Power Law Scaling in Human and Empty Room MEG Recordings.
• 
  Simon F. Farmer:
  Comment on "Broadband Criticality of Human Brain Network Synchronization" by Kitzbichler MG, Smith ML, Christensen SR, Bullmore E (2009) PLoS Comput Biol 5: e1000314.

Volume 11, Number 6, June 2015

Editorial

• 
  Philip E. Bourne, Steven E. Brenner, Michael B. Eisen:
  Ten Years of PLoS^‡ Computational Biology: A Decade of Appreciation and Innovation.

Messages from ISCB

• 
  Christiana N. Fogg, Diane E. Kovats:
  Computational Biology: Moving into the Future One Click at a Time.
• 
  Christiana N. Fogg, Diane E. Kovats:
  2015 ISCB Overton Prize Awarded to Curtis Huttenhower.
• 
  Christiana N. Fogg, Diane E. Kovats:
  ISMB/ECCB Rebooted: 2015 Brings Major Update to the Meeting Program.

Research Articles

• 
  Ruian Ke, Claude Loverdo, Hangfei Qi, Ren Sun, James O. Lloyd-Smith:
  Rational Design and Adaptive Management of Combination Therapies for Hepatitis C Virus Infection.
• 
  Daisuke Ohshima, Kyoko Arimoto-Matsuzaki, Taichiro Tomida, Mutsuhiro Takekawa, Kazuhisa Ichikawa:
  Spatio-temporal Dynamics and Mechanisms of Stress Granule Assembly.
• 
  Giulia Palermo, Inga Bauer, Pablo Campomanes, Andrea Cavalli, Andrea Armirotti, Stefania Girotto, Ursula Rothlisberger, Marco de Vivo:
  Keys to Lipid Selection in Fatty Acid Amide Hydrolase Catalysis: Structural Flexibility, Gating Residues and Multiple Binding Pockets.
• 
  Andrew E. Brennan, Maurice A. Smith:
  The Decay of Motor Memories Is Independent of Context Change Detection.
• 
  Cordelia Ziraldo, Alexey Solovyev, Ana Allegretti, Shilpa Krishnan, M. Kristi Henzel, Gwendolyn A. Sowa, David M. Brienza, Gary An, Qi Mi, Yoram Vodovotz:
  A Computational, Tissue-Realistic Model of Pressure Ulcer Formation in Individuals with Spinal Cord Injury.
• 
  Boris P. Hejblum, Jason Skinner, Rodolphe Thiébaut:
  Time-Course Gene Set Analysis for Longitudinal Gene Expression Data.
• 
  Uri Obolski, Gideon Y. Stein, Lilach Hadany:
  Antibiotic Restriction Might Facilitate the Emergence of Multi-drug Resistance.
• 
  Lishibanya Mohapatra, Bruce L. Goode, Jané Kondev:
  Antenna Mechanism of Length Control of Actin Cables.
• 
  J. Brendan Ritchie, David A. Tovar, Thomas A. Carlson:
  Emerging Object Representations in the Visual System Predict Reaction Times for Categorization.
• 
  Catalina A. Vallejos, John C. Marioni, Sylvia Richardson:
  BASiCS: Bayesian Analysis of Single-Cell Sequencing Data.
• 
  Kerry E. Boyle, Hilary Monaco, Dave van Ditmarsch, Maxime Deforet, João B. Xavier:
  Integration of Metabolic and Quorum Sensing Signals Governing the Decision to Cooperate in a Bacterial Social Trait.
• 
  Steven N. Steinway, Matthew B. Biggs, Thomas P. Loughran Jr., Jason A. Papin, Réka Albert:
  Inference of Network Dynamics and Metabolic Interactions in the Gut Microbiome.
• 
  Vicente Reyes-Puerta, Suam Kim, Jyh-Jang Sun, Barbara Imbrosci, Werner Kilb, Heiko J. Luhmann:
  High Stimulus-Related Information in Barrel Cortex Inhibitory Interneurons.
• 
  Sadra Sadeh, Claudia Clopath, Stefan Rotter:
  Emergence of Functional Specificity in Balanced Networks with Synaptic Plasticity.
• 
  Mariana Esther Martinez-Sanchez, Luis Mendoza, Carlos Villarreal, Elena R. Álvarez-Buylla:
  A Minimal Regulatory Network of Extrinsic and Intrinsic Factors Recovers Observed Patterns of CD4+ T Cell Differentiation and Plasticity.
• 
  Assaf Zvuloni, Yael Artzy-Randrup, Guy Katriel, Yossi Loya, Lewi Stone:
  Modeling the Impact of White-Plague Coral Disease in Climate Change Scenarios.
• 
  Robert C. Wilson, Yael Niv:
  Is Model Fitting Necessary for Model-Based fMRI?
• 
  Jingchun Sun, Min Zhao, Peilin Jia, Lily Wang, Yonghui Wu, Carissa Iverson, Yubo Zhou, Erica A. Bowton, Dan M. Roden, Joshua C. Denny, Melinda C. Aldrich, Hua Xu, Zhongming Zhao:
  Deciphering Signaling Pathway Networks to Understand the Molecular Mechanisms of Metformin Action.
• 
  Christian Pozzorini, Skander Mensi, Olivier Hagens, Richard Naud, Christof Koch, Wulfram Gerstner:
  Automated High-Throughput Characterization of Single Neurons by Means of Simplified Spiking Models.
• 
  Xiaoke Ma, Long Gao, Georgios Karamanlidis, Peng Gao, Chi Fung Lee, Lorena Garcia-Menendez, Rong Tian, Kai Tan:
  Revealing Pathway Dynamics in Heart Diseases by Analyzing Multiple Differential Networks.
• 
  Richard F. Murray, Khushbu Patel, Alan Yee:
  Posterior Probability Matching and Human Perceptual Decision Making.
• 
  Florent Meyniel, Daniel Schlunegger, Stanislas Dehaene:
  The Sense of Confidence during Probabilistic Learning: A Normative Account.
• 
  Lindsay Wendel Clegg, Feilim Mac Gabhann:
  Site-Specific Phosphorylation of VEGFR2 Is Mediated by Receptor Trafficking: Insights from a Computational Model.
• 
  Kai Ueltzhöffer, Diana J. N. Armbruster-Genç, Christian J. Fiebach:
  Stochastic Dynamics Underlying Cognitive Stability and Flexibility.
• 
  Felipe Merino, Benjamin Bouvier, Vlad Cojocaru:
  Cooperative DNA Recognition Modulated by an Interplay between Protein-Protein Interactions and DNA-Mediated Allostery.
• 
  Pierre Broly, Jean-Louis Deneubourg:
  Behavioural Contagion Explains Group Cohesion in a Social Crustacean.
• 
  Jeffrey W. Brown, Esther Bullitt, Sira Sriswasdi, Sandra Harper, David W. Speicher, C. James McKnight:
  The Physiological Molecular Shape of Spectrin: A Compact Supercoil Resembling a Chinese Finger Trap.
• 
  Federico Abascal, Iakes Ezkurdia, Juan Rodriguez-Rivas, Jose Manuel Rodriguez, Angela del Pozo, Jesús Vázquez, Alfonso Valencia, Michael L. Tress:
  Alternatively Spliced Homologous Exons Have Ancient Origins and Are Highly Expressed at the Protein Level.
• 
  Andreas Hula, P. Read Montague, Peter Dayan:
  Monte Carlo Planning Method Estimates Planning Horizons during Interactive Social Exchange.
• 
  Hanae Shimo, Satya Nanda Vel Arjunan, Hiroaki Machiyama, Taiko Nishino, Makoto Suematsu, Hideaki Fujita, Masaru Tomita, Koichi Takahashi:
  Particle Simulation of Oxidation Induced Band 3 Clustering in Human Erythrocytes.
• 
  Duccio Malinverni, Simone Marsili, Alessandro Barducci, Paolo De Los Rios:
  Large-Scale Conformational Transitions and Dimerization Are Encoded in the Amino-Acid Sequences of Hsp70 Chaperones.
• 
  João Sacramento, Andreas Wichert, Mark C. W. van Rossum:
  Energy Efficient Sparse Connectivity from Imbalanced Synaptic Plasticity Rules.
• 
  Juan A. Bueren-Calabuig, Julien Michel:
  Elucidation of Ligand-Dependent Modulation of Disorder-Order Transitions in the Oncoprotein MDM2.
• 
  Michael A. Andrews, Chris T. Bauch:
  Disease Interventions Can Interfere with One Another through Disease-Behaviour Interactions.
• 
  Daniel Lobo, Michael Levin:
  Inferring Regulatory Networks from Experimental Morphological Phenotypes: A Computational Method Reverse-Engineers Planarian Regeneration.
• 
  Ingmar Kanitscheider, Ruben Coen Cagli, Adam Kohn, Alexandre Pouget:
  Measuring Fisher Information Accurately in Correlated Neural Populations.
• 
  Gabriele Micali, Gerardo Aquino, David M. Richards, Robert G. Endres:
  Accurate Encoding and Decoding by Single Cells: Amplitude Versus Frequency Modulation.
• 
  Josh Merel, Donald M. Pianto, John P. Cunningham, Liam Paninski:
  Encoder-Decoder Optimization for Brain-Computer Interfaces.
• 
  Imen Lassadi, Alain Kamgoué, Isabelle Goiffon, Nicolas Tanguy-le-Gac, Kerstin Bystricky:
  Differential Chromosome Conformations as Hallmarks of Cellular Identity Revealed by Mathematical Polymer Modeling.
• 
  Ahmed T. Ayoub, Mariusz Klobukowski, Jack A. Tuszynski:
  Detailed Per-residue Energetic Analysis Explains the Driving Force for Microtubule Disassembly.

Volume 11, Number 7, July 2015

Editorial

• 
  Ruth Nussinov, Sebastian Bonhoeffer, Jason A. Papin, Olaf Sporns:
  From "What Is?" to "What Isn't?" Computational Biology.

Review

• 
  Richard R. Stein, Debora S. Marks, Chris Sander:
  Inferring Pairwise Interactions from Biological Data Using Maximum-Entropy Probability Models.

Research Articles

• 
  Omri Harish, David Hansel:
  Asynchronous Rate Chaos in Spiking Neuronal Circuits.
• 
  César A. Ramírez-Sarmiento, Jeffrey K. Noel, Sandro L. Valenzuela, Irina Artsimovitch:
  Interdomain Contacts Control Native State Switching of RfaH on a Dual-Funneled Landscape.
• 
  Jian K. Liu, Tim Gollisch:
  Spike-Triggered Covariance Analysis Reveals Phenomenological Diversity of Contrast Adaptation in the Retina.
• 
  Weston Cox, Brian J. Fischer:
  Optimal Prediction of Moving Sound Source Direction in the Owl.
• 
  Wan Yang, Benjamin J. Cowling, Eric H. Y. Lau, Jeffrey Shaman:
  Forecasting Influenza Epidemics in Hong Kong.
• 
  Bethany Percha, Russ B. Altman:
  Learning the Structure of Biomedical Relationships from Unstructured Text.
• 
  Saket Navlakha, Alison L. Barth, Ziv Bar-Joseph:
  Decreasing-Rate Pruning Optimizes the Construction of Efficient and Robust Distributed Networks.
• 
  Dimitar V. Pachov, Henry van den Bedem:
  Nullspace Sampling with Holonomic Constraints Reveals Molecular Mechanisms of Protein Gαs.
• 
  John Walmsley, Theo Arts, Nicolas Derval, Pierre Bordachar, Hubert Cochet, Sylvain Ploux, Frits W. Prinzen, Tammo Delhaas, Joost Lumens:
  Fast Simulation of Mechanical Heterogeneity in the Electrically Asynchronous Heart Using the MultiPatch Module.
• 
  Qinglong Zeng, Jeet Sukumaran, Steven H. Wu, Allen G. Rodrigo:
  Neutral Models of Microbiome Evolution.
• 
  Truong D. Nguyen-Huu, Chinmaya Gupta, Bo Ma, William Ott, Kresimir Josic, Matthew R. Bennett:
  Timing and Variability of Galactose Metabolic Gene Activation Depend on the Rate of Environmental Change.
• 
  Elizabeth L. Sander, J. Timothy Wootton, Stefano Allesina:
  What Can Interaction Webs Tell Us About Species Roles?
• 
  Thomas Hoffmann, Angela M. Krackhardt, Iris Antes:
  Quantitative Analysis of the Association Angle between T-cell Receptor Vα/Vβ Domains Reveals Important Features for Epitope Recognition.
• 
  Kartik Subramanian, Mark R. Paul, John J. Tyson:
  Dynamical Localization of DivL and PleC in the Asymmetric Division Cycle of Caulobacter crescentus: A Theoretical Investigation of Alternative Models.
• 
  Chris Neale, Nilmadhab Chakrabarti, Pawel Pomorski, Emil F. Pai, Régis Pomès:
  Hydrophobic Gating of Ion Permeation in Magnesium Channel CorA.
• 
  Param Priya Singh, Jatin Arora, Hervé Isambert:
  Identification of Ohnolog Genes Originating from Whole Genome Duplication in Early Vertebrates, Based on Synteny Comparison across Multiple Genomes.
• 
  Hanlun Jiang, Fu Kit Sheong, Lizhe Zhu, Xin Gao, Julie Bernauer, Xuhui Huang:
  Markov State Models Reveal a Two-Step Mechanism of miRNA Loading into the Human Argonaute Protein: Selective Binding followed by Structural Re-arrangement.
• 
  Michael T. Schaub, Yazan N. Billeh, Costas A. Anastassiou, Christof Koch, Mauricio Barahona:
  Emergence of Slow-Switching Assemblies in Structured Neuronal Networks.
• 
  Blake T. Thomas, Davis W. Blalock, William B. Levy:
  Adaptive Synaptogenesis Constructs Neural Codes That Benefit Discrimination.
• 
  Mengchen Zhu, Christopher J. Rozell:
  Modeling Inhibitory Interneurons in Efficient Sensory Coding Models.
• 
  Marijn B. Martens, Tansu Celikel, Paul H. E. Tiesinga:
  A Developmental Switch for Hebbian Plasticity.
• 
  Yael Korem, Pablo Szekely, Yuval Hart, Hila Sheftel, Jean Hausser, Avi E. Mayo, Michael E. Rothenberg, Tomer Kalisky, Uri Alon:
  Geometry of the Gene Expression Space of Individual Cells.
• 
  Daniel S. Himmelstein, Sergio E. Baranzini:
  Heterogeneous Network Edge Prediction: A Data Integration Approach to Prioritize Disease-Associated Genes.
• 
  Jan M. Ache, Volker Dürr:
  A Computational Model of a Descending Mechanosensory Pathway Involved in Active Tactile Sensing.
• 
  Amy Wesolowski, Wendy Prudhomme O'Meara, Nathan Eagle, Andrew J. Tatem, Caroline O. Buckee:
  Evaluating Spatial Interaction Models for Regional Mobility in Sub-Saharan Africa.
• 
  Malachi Griffith, Obi L. Griffith, Scott M. Smith, Avinash Ramu, Matthew B. Callaway, Anthony M. Brummett, Michael J. Kiwala, Adam C. Coffman, Allison A. Regier, Benjamin J. Oberkfell, Gabriel E. Sanderson, Thomas P. Mooney, Nathaniel G. Nutter, Edward A. Belter, Feiyu Du, Robert L. Long, Travis E. Abbott, Ian T. Ferguson, David L. Morton, Mark M. Burnett, James V. Weible, Joshua B. Peck, Adam Dukes, Joshua F. McMichael, Justin T. Lolofie, Brian R. Derickson, Jasreet Hundal, Zachary L. Skidmore, Benjamin J. Ainscough, Nathan D. Dees, William S. Schierding, Cyriac Kandoth, Kyung H. Kim, Charles Lu, Christopher C. Harris, Nicole Maher, Christopher A. Maher, Vincent J. Magrini, Benjamin S. Abbott, Ken Chen, Eric Clark, Indraniel Das, Xian Fan, Amy E. Hawkins, Todd G. Hepler, Todd N. Wylie, Shawn M. Leonard, William E. Schroeder, Xiaoqi Shi, Lynn K. Carmichael, Matthew R. Weil, Richard W. Wohlstadter, Gary Stiehr, Michael D. McLellan, Craig S. Pohl, Christopher A. Miller, Daniel C. Koboldt, Jason R. Walker, James M. Eldred, David E. Larson, David J. Dooling, Li Ding, Elaine R. Mardis, Richard K. Wilson:
  Genome Modeling System: A Knowledge Management Platform for Genomics.
• 
  Tomohiro Tanaka, Naoto Hori, Shoji Takada:
  How Co-translational Folding of Multi-domain Protein Is Affected by Elongation Schedule: Molecular Simulations.
• 
  Yann Sweeney, Jeanette Hellgren Kotaleski, Matthias H. Hennig:
  A Diffusive Homeostatic Signal Maintains Neural Heterogeneity and Responsiveness in Cortical Networks.
• 
  Daniel Harnack, Miha Pelko, Antoine Chaillet, Yacine Chitour, Mark C. W. van Rossum:
  Stability of Neuronal Networks with Homeostatic Regulation.
• 
  Marharyta Petukh, Minghui Li, Emil Alexov:
  Predicting Binding Free Energy Change Caused by Point Mutations with Knowledge-Modified MM/PBSA Method.
• 
  Alexander M. Sevy, Tim M. Jacobs, James E. Crowe Jr., Jens Meiler:
  Design of Protein Multi-specificity Using an Independent Sequence Search Reduces the Barrier to Low Energy Sequences.
• 
  Bethany L. Dearlove, Simon D. W. Frost:
  Measuring Asymmetry in Time-Stamped Phylogenies.
• 
  Joshua J. Hamilton, Montserrat Calixto Contreras, Jennifer L. Reed:
  Thermodynamics and H₂ Transfer in a Methanogenic, Syntrophic Community.
• 
  Lu Zhang, Daniel-Adriano Silva, Fátima Pardo Avila, Dong Wang, Xuhui Huang:
  Structural Model of RNA Polymerase II Elongation Complex with Complete Transcription Bubble Reveals NTP Entry Routes.
• 
  Olivier Marre, Vicente Botella-Soler, Kristina D. Simmons, Thierry Mora, Gasper Tkacik, Michael J. Berry II:
  High Accuracy Decoding of Dynamical Motion from a Large Retinal Population.
• 
  Tong Li, Malgorzata B. Tracka, Shahid Uddin, Jose Casas-Finet, Donald J. Jacobs, Dennis R. Livesay:
  Rigidity Emerges during Antibody Evolution in Three Distinct Antibody Systems: Evidence from QSFR Analysis of Fab Fragments.

Volume 11, Number 8, August 2015

Education

• 
  Malachi Griffith, Jason R. Walker, Nicholas C. Spies, Benjamin J. Ainscough, Obi L. Griffith:
  Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud.

Research Articles

• 
  Songjian Lu, Kevin N. Lu, Shi-Yuan Cheng, Bo Hu, Xiaojun Ma, Nicholas Nystrom, Xinghua Lu:
  Identifying Driver Genomic Alterations in Cancers by Searching Minimum-Weight, Mutually Exclusive Sets.
• 
  Liping Xiong, Ganhui Lan:
  An Optimal Free Energy Dissipation Strategy of the MinCDE Oscillator in Regulating Symmetric Bacterial Cell Division.
• 
  Chris G. Antonopoulos, Shambhavi Srivastava, Sandro E. de S. Pinto, Murilo S. Baptista:
  Do Brain Networks Evolve by Maximizing Their Information Flow Capacity?
• 
  Logan C. Brooks, David C. Farrow, Sangwon Hyun, Ryan J. Tibshirani, Roni Rosenfeld:
  Flexible Modeling of Epidemics with an Empirical Bayes Framework.
• 
  Kirill Lykov, Xuejin Li, Huan Lei, Igor V. Pivkin, George E. Karniadakis:
  Inflow/Outflow Boundary Conditions for Particle-Based Blood Flow Simulations: Application to Arterial Bifurcations and Trees.
• 
  Åsmund Flobak, Anaïs Baudot, Elisabeth Remy, Liv Thommesen, Denis Thieffry, Martin Kuiper, Astrid Lægreid:
  Discovery of Drug Synergies in Gastric Cancer Cells Predicted by Logical Modeling.
• 
  Assaf Amitai, Mathias Toulouze, Karine Dubrana, David Holcman:
  Analysis of Single Locus Trajectories for Extracting In Vivo Chromatin Tethering Interactions.
• 
  Adrián Ponce-Alvarez, Biyu J. He, Patric Hagmann, Gustavo Deco:
  Task-Driven Activity Reduces the Cortical Activity Space of the Brain: Experiment and Whole-Brain Modeling.
• 
  Marc Breit, Michael Netzer, Klaus Weinberger, Christian Baumgartner:
  Modeling and Classification of Kinetic Patterns of Dynamic Metabolic Biomarkers in Physical Activity.
• 
  Mitchell G. Newberry, Daniel B. Ennis, Van M. Savage:
  Testing Foundations of Biological Scaling Theory Using Automated Measurements of Vascular Networks.
• 
  Claudia Schillings, Mikael Sunnåker, Jörg Stelling, Christoph Schwab:
  Efficient Characterization of Parametric Uncertainty of Complex (Bio)chemical Networks.
• 
  Chengsheng Zhu, Tom O. Delmont, Timothy M. Vogel, Yana Bromberg:
  Functional Basis of Microorganism Classification.
• 
  Zachary A. King, Andreas Dräger, Ali Ebrahim, Nikolaus Sonnenschein, Nathan E. Lewis, Bernhard O. Palsson:
  Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways.
• 
  Jeffrey R. Johnson, Silvia D. Santos, Tasha Johnson, Ursula Pieper, Marta Strumillo, Omar Wagih, Andrej Sali, Nevan J. Krogan, Pedro Beltrão:
  Prediction of Functionally Important Phospho-Regulatory Events in Xenopus laevis Oocytes.
• 
  Alex McAvoy, Christoph Hauert:
  Asymmetric Evolutionary Games.
• 
  James E. M. Bennett, Wyeth Bair:
  Refinement and Pattern Formation in Neural Circuits by the Interaction of Traveling Waves with Spike-Timing Dependent Plasticity.
• 
  Rajesh Balagam, Oleg A. Igoshin:
  Mechanism for Collective Cell Alignment in Myxococcus xanthus Bacteria.
• 
  Tadashi Miyamoto, Chikara Furusawa, Kunihiko Kaneko:
  Pluripotency, Differentiation, and Reprogramming: A Gene Expression Dynamics Model with Epigenetic Feedback Regulation.
• 
  Tim Genewein, Eduard Hez, Zeynab Razzaghpanah, Daniel A. Braun:
  Structure Learning in Bayesian Sensorimotor Integration.
• 
  Roland F. Schwarz, Robyn Branicky, Laura J. Grundy, William R. Schafer, André E. X. Brown:
  Changes in Postural Syntax Characterize Sensory Modulation and Natural Variation of C. elegans Locomotion.
• 
  Cahit Dalgicdir, Christoph Globisch, Christine Peter, Mehmet Sayar:
  Tipping the Scale from Disorder to Alpha-helix: Folding of Amphiphilic Peptides in the Presence of Macroscopic and Molecular Interfaces.
• 
  James P. Roach, Eshel Ben-Jacob, Leonard M. Sander, Michal R. Zochowski:
  Formation and Dynamics of Waves in a Cortical Model of Cholinergic Modulation.
• 
  Paul M. Harrison, Laurent Badel, Mark J. Wall, Magnus J. E. Richardson:
  Experimentally Verified Parameter Sets for Modelling Heterogeneous Neocortical Pyramidal-Cell Populations.
• 
  James Tamerius, Cécile Viboud, Jeffrey Shaman, Gerardo Chowell:
  Impact of School Cycles and Environmental Forcing on the Timing of Pandemic Influenza Activity in Mexican States, May-December 2009.
• 
  Zing Tsung-Yeh Tsai, Shin-Han Shiu, Huai-Kuang Tsai:
  Contribution of Sequence Motif, Chromatin State, and DNA Structure Features to Predictive Models of Transcription Factor Binding in Yeast.
• 
  Alireza Alemi, Carlo Baldassi, Nicolas Brunel, Riccardo Zecchina:
  A Three-Threshold Learning Rule Approaches the Maximal Capacity of Recurrent Neural Networks.
• 
  Gabriel Koch Ocker, Ashok Litwin-Kumar, Brent Doiron:
  Self-Organization of Microcircuits in Networks of Spiking Neurons with Plastic Synapses.
• 
  Huijing Du, Qing Nie, William R. Holmes:
  The Interplay between Wnt Mediated Expansion and Negative Regulation of Growth Promotes Robust Intestinal Crypt Structure and Homeostasis.
• 
  Pengxing Cao, Ada W. C. Yan, Jane Marie Heffernan, Stephen M. Petrie, Robert G. Moss, Louise A. Carolan, Teagan A. Guarnaccia, Anne Kelso, Ian G. Barr, Jodie McVernon, Karen L. Laurie, James M. McCaw:
  Innate Immunity and the Inter-exposure Interval Determine the Dynamics of Secondary Influenza Virus Infection and Explain Observed Viral Hierarchies.
• 
  Chuan Xue, Blerta Shtylla, Anthony Brown:
  A Stochastic Multiscale Model That Explains the Segregation of Axonal Microtubules and Neurofilaments in Neurological Diseases.
• 
  Ariel Afek, Hila Cohen, Shiran Barber-Zucker, Raluca Gordân, David B. Lukatsky:
  Nonconsensus Protein Binding to Repetitive DNA Sequence Elements Significantly Affects Eukaryotic Genomes.
• 
  Alexey A. Gritsenko, Marc Hulsman, Marcel J. T. Reinders, Dick de Ridder:
  Unbiased Quantitative Models of Protein Translation Derived from Ribosome Profiling Data.
• 
  John R. Houser, Craig Barnhart, Daniel R. Boutz, Sean M. Carroll, Aurko Dasgupta, Joshua K. Michener, Brittany D. Needham, Ophelia Papoulas, Viswanadham Sridhara, Dariya K. Sydykova, Christopher J. Marx, M. Stephen Trent, Jeffrey E. Barrick, Edward M. Marcotte, Claus O. Wilke:
  Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation.
• 
  Shaun S. Sanders, Dale D. O. Martin, Stefanie L. Butland, Mathieu Lavallée-Adam, Diego Calzolari, Chris Kay, John R. Yates III, Michael R. Hayden:
  Curation of the Mammalian Palmitoylome Indicates a Pivotal Role for Palmitoylation in Diseases and Disorders of the Nervous System and Cancers.
• 
  Ghanim Ullah, Yina Wei, Markus A. Dahlem, Martin Wechselberger, Steven J. Schiff:
  The Role of Cell Volume in the Dynamics of Seizure, Spreading Depression, and Anoxic Depolarization.
• 
  Liat Rockah-Shmuel, Ágnes Tóth-Petróczy, Dan S. Tawfik:
  Systematic Mapping of Protein Mutational Space by Prolonged Drift Reveals the Deleterious Effects of Seemingly Neutral Mutations.
• 
  Deborah A. Striegel, Manami Hara, Vipul Periwal:
  The Beta Cell in Its Cluster: Stochastic Graphs of Beta Cell Connectivity in the Islets of Langerhans.
• 
  Sebastian Bitzer, Jelle P. Bruineberg, Stefan J. Kiebel:
  A Bayesian Attractor Model for Perceptual Decision Making.
• 
  Shuai Yuan, H. Richard Johnston, Guosheng Zhang, Yun Li, Yi-Juan Hu, Zhaohui S. Qin:
  One Size Doesn't Fit All - RefEditor: Building Personalized Diploid Reference Genome to Improve Read Mapping and Genotype Calling in Next Generation Sequencing Studies.
• 
  Sander Land, Steven A. Niederer:
  A Spatially Detailed Model of Isometric Contraction Based on Competitive Binding of Troponin I Explains Cooperative Interactions between Tropomyosin and Crossbridges.
• 
  Jonas Paulsen, Odin Gramstad, Philippe Collas:
  Manifold Based Optimization for Single-Cell 3D Genome Reconstruction.
• 
  Hiroo Kenzaki, Shoji Takada:
  Partial Unwrapping and Histone Tail Dynamics in Nucleosome Revealed by Coarse-Grained Molecular Simulations.
• 
  Sayed-Rzgar Hosseini, Aditya Barve, Andreas Wagner:
  Exhaustive Analysis of a Genotype Space Comprising 10¹⁵ Central Carbon Metabolisms Reveals an Organization Conducive to Metabolic Innovation.
• 
  Pengyi Yang, Xiaofeng Zheng, Vivek Jayaswal, Guang Hu, Jean Yee Hwa Yang, Raja Jothi:
  Knowledge-Based Analysis for Detecting Key Signaling Events from Time-Series Phosphoproteomics Data.
• 
  Brinda K. Vallat, Carlos J. Madrid-Aliste, András Fiser:
  Modularity of Protein Folds as a Tool for Template-Free Modeling of Structures.
• 
  Murat Alp, Vipan K. Parihar, Charles L. Limoli, Francis A. Cucinotta:
  Irradiation of Neurons with High-Energy Charged Particles: An In Silico Modeling Approach.
• 
  Eliseo Ferrante, Ali Emre Turgut, Edgar A. Duéñez-Guzmán, Marco Dorigo, Tom Wenseleers:
  Evolution of Self-Organized Task Specialization in Robot Swarms.
• 
  Arjun Bharioke, Dmitri B. Chklovskii:
  Automatic Adaptation to Fast Input Changes in a Time-Invariant Neural Circuit.
• 
  Patrícia Santos-Oliveira, António Correia, Tiago Rodrigues, Teresa M. Ribeiro-Rodrigues, Paulo Matafome, Juan Carlos Rodríguez-Manzaneque, Raquel Seiça, Henrique Girão, Rui D. M. Travasso:
  The Force at the Tip - Modelling Tension and Proliferation in Sprouting Angiogenesis.
• 
  Maxime Louet, Christian Seifert, Ulf Hensen, Frauke Gräter:
  Dynamic Allostery of the Catabolite Activator Protein Revealed by Interatomic Forces.
• 
  Po-Wei Chen, Luís L. Fonseca, Yusuf A. Hannun, Eberhard O. Voit:
  Dynamics of the Heat Stress Response of Ceramides with Different Fatty-Acyl Chain Lengths in Baker's Yeast.

Volume 11, Number 9, September 2015

Editorial

• 
  Santiago Schnell:
  Ten Simple Rules for a Computational Biologist's Laboratory Notebook.

Perspectives

• 
  Florian Markowetz:
  You Are Not Working for Me; I Am Working with You.
• 
  Alice Carolyn McHardy:
  How to Grow a Computational Biology Lab.
• 
  Michael A. Cerullo:
  The Problem with Phi: A Critique of Integrated Information Theory.
• 
  Thomas K. Karikari:
  Bioinformatics in Africa: The Rise of Ghana?

Research Articles

• 
  Naiqian Zhang, Haiyun Wang, Yun Fang, Jun Wang, Xiaoqi Zheng, Xiaole Shirley Liu:
  Predicting Anticancer Drug Responses Using a Dual-Layer Integrated Cell Line-Drug Network Model.
• 
  Gang Li, Karen E. Ross, Cecilia N. Arighi, Yifan Peng, Cathy H. Wu, K. Vijay-Shanker:
  miRTex: A Text Mining System for miRNA-Gene Relation Extraction.
• 
  Greg Jensen, Fabian Muñoz, Yelda Alkan, Vincent P. Ferrera, Herbert S. Terrace:
  Implicit Value Updating Explains Transitive Inference Performance: The Betasort Model.
• 
  Pete Riley, Michal Ben-Nun, Jon A. Linker, Angelia A. Cost, Jose L. Sanchez, Dylan B. George, David P. Bacon, Steven Riley:
  Early Characterization of the Severity and Transmissibility of Pandemic Influenza Using Clinical Episode Data from Multiple Populations.
• 
  Noah Ollikainen, René M. de Jong, Tanja Kortemme:
  Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity.
• 
  Vassilios N. Christopoulos, Paul R. Schrater:
  Dynamic Integration of Value Information into a Common Probability Currency as a Theory for Flexible Decision Making.
• 
  Suhani Nagpal, Satyam Tiwari, Koyeli Mapa, Lipi Thukral:
  Decoding Structural Properties of a Partially Unfolded Protein Substrate: En Route to Chaperone Binding.
• 
  Vipin Narang, Muhamad Azfar Ramli, Amit Singhal, Pavanish Kumar, Gennaro de Libero, Michael Poidinger, Christopher P. Monterola:
  Automated Identification of Core Regulatory Genes in Human Gene Regulatory Networks.
• 
  Jianfei Hu, Johnathan Neiswinger, Jin Zhang, Heng Zhu, Jiang Qian:
  Systematic Prediction of Scaffold Proteins Reveals New Design Principles in Scaffold-Mediated Signal Transduction.
• 
  Chakravarthy Marella, Andrew E. Torda, Dominik Schwudke:
  The LUX Score: A Metric for Lipidome Homology.
• 
  Julia C. Quindlen, Victor K. Lai, Victor H. Barocas:
  Multiscale Mechanical Model of the Pacinian Corpuscle Shows Depth and Anisotropy Contribute to the Receptor's Characteristic Response to Indentation.
• 
  Jasmine Foo, Lin L. Liu, Kevin Leder, Markus Riester, Yoh Iwasa, Christoph Lengauer, Franziska Michor:
  An Evolutionary Approach for Identifying Driver Mutations in Colorectal Cancer.
• 
  Héctor García Martín, Vinay Satish Kumar, Daniel Weaver, Amit Ghosh, Victor Chubukov, Aindrila Mukhopadhyay, Adam P. Arkin, Jay D. Keasling:
  A Method to Constrain Genome-Scale Models with ¹³C Labeling Data.
• 
  Marcos Economides, Zeb Kurth-Nelson, Annika Lübbert, Marc Guitart-Masip, Raymond J. Dolan:
  Model-Based Reasoning in Humans Becomes Automatic with Training.
• 
  Thembi Mdluli, Gregery T. Buzzard, Ann E. Rundell:
  Efficient Optimization of Stimuli for Model-Based Design of Experiments to Resolve Dynamical Uncertainty.
• 
  Ayal Lavi, Omri Perez, Uri Ashery:
  Shaping Neuronal Network Activity by Presynaptic Mechanisms.
• 
  Hannah Edwards, Charlotte M. Deane:
  Structural Bridges through Fold Space.
• 
  Stephan Köhler, Friederike Schmid, Giovanni Settanni:
  The Internal Dynamics of Fibrinogen and Its Implications for Coagulation and Adsorption.
• 
  Alexander Ullrich, Mathias A. Böhme, Johannes Schöneberg, Harald Depner, Stephan J. Sigrist, Frank Noé:
  Dynamical Organization of Syntaxin-1A at the Presynaptic Active Zone.
• 
  Sergei Maslov, Kim Sneppen:
  Diversity Waves in Collapse-Driven Population Dynamics.
• 
  Joseph Snider, Dongpyo Lee, Howard Poizner, Sergei Gepshtein:
  Prospective Optimization with Limited Resources.
• 
  Daniel Nichol, Peter Jeavons, Alexander G. Fletcher, Robert A. Bonomo, Philip K. Maini, Jerome L. Paul, Robert A. Gatenby, Alexander R. A. Anderson, Jacob G. Scott:
  Steering Evolution with Sequential Therapy to Prevent the Emergence of Bacterial Antibiotic Resistance.
• 
  Elizabeth A. Hobson, Simon DeDeo:
  Social Feedback and the Emergence of Rank in Animal Society.
• 
  Feixiong Cheng, Chuang Liu, Chen-Ching Lin, Junfei Zhao, Peilin Jia, Wen-Hsiung Li, Zhongming Zhao:
  A Gene Gravity Model for the Evolution of Cancer Genomes: A Study of 3, 000 Cancer Genomes across 9 Cancer Types.
• 
  Greet De Baets, Loic Van Doorn, Frederic Rousseau, Joost Schymkowitz:
  Increased Aggregation Is More Frequently Associated to Human Disease-Associated Mutations Than to Neutral Polymorphisms.
• 
  Claudio Altafini, Giuseppe Facchetti:
  Metabolic Adaptation Processes That Converge to Optimal Biomass Flux Distributions.
• 
  Marco Galardini, Matteo Brilli, Giulia Spini, Matteo Rossi, Bianca Roncaglia, Alessia Bani, Manuela Chiancianesi, Marco Moretto, Kristof Engelen, Giovanni Bacci, Francesco Pini, Emanuele G. Biondi, Marco Bazzicalupo, Alessio Mengoni:
  Evolution of Intra-specific Regulatory Networks in a Multipartite Bacterial Genome.
• 
  Elizabeth Ortiz-Gutiérrez, Karla García-Cruz, Eugenio Azpeitia, Aaron Castillo, María de la Paz Sánchez, Elena R. Álvarez-Buylla:
  A Dynamic Gene Regulatory Network Model That Recovers the Cyclic Behavior of Arabidopsis thaliana Cell Cycle.
• 
  Jonathan Glancy, Roderich Groß, James V. Stone, Stuart P. Wilson:
  A Self-Organising Model of Thermoregulatory Huddling.
• 
  Robert Becker, Stuart Knock, Petra Ritter, Viktor K. Jirsa:
  Relating Alpha Power and Phase to Population Firing and Hemodynamic Activity Using a Thalamo-cortical Neural Mass Model.
• 
  Katrin Böttger, Haralambos Hatzikirou, Anja Voss-Böhme, Elisabetta Ada Cavalcanti-Adam, Miguel A. Herrero, Andreas Deutsch:
  An Emerging Allee Effect Is Critical for Tumor Initiation and Persistence.
• 
  Vijay Rajagopal, Gregory Bass, Cameron G. Walker, David J. Crossman, Amorita Petzer, Anthony Hickey, Ivo Siekmann, Masahiko Hoshijima, Mark H. Ellisman, Edmund J. Crampin, Christian Soeller:
  Examination of the Effects of Heterogeneous Organization of RyR Clusters, Myofibrils and Mitochondria on Ca²⁺ Release Patterns in Cardiomyocytes.
• 
  Felix Effenberger, Jürgen Jost, Anna Levina:
  Self-organization in Balanced State Networks by STDP and Homeostatic Plasticity.
• 
  Amir Szitenberg, Max John, Mark L. Blaxter, David H. Lunt:
  ReproPhylo: An Environment for Reproducible Phylogenomics.
• 
  Imri Sofer, Sébastien M. Crouzet, Thomas Serre:
  Explaining the Timing of Natural Scene Understanding with a Computational Model of Perceptual Categorization.
• 
  Rebecca F. Alford, Julia Koehler Leman, Brian D. Weitzner, Amanda M. Duran, Drew C. Tilley, Assaf Elazar, Jeffrey J. Gray:
  An Integrated Framework Advancing Membrane Protein Modeling and Design.
• 
  Guido Montúfar, Keyan Ghazi-Zahedi, Nihat Ay:
  A Theory of Cheap Control in Embodied Systems.
• 
  Jiayu Wen, Erik Ladewig, Sol Shenker, Jaaved Mohammed, Eric C. Lai:
  Analysis of Nearly One Thousand Mammalian Mirtrons Reveals Novel Features of Dicer Substrates.
• 
  Rudy Clausen, Buyong Ma, Ruth Nussinov, Amarda Shehu:
  Mapping the Conformation Space of Wildtype and Mutant H-Ras with a Memetic, Cellular, and Multiscale Evolutionary Algorithm.
• 
  Sacha J. van Albada, Moritz Helias, Markus Diesmann:
  Scalability of Asynchronous Networks Is Limited by One-to-One Mapping between Effective Connectivity and Correlations.

Volume 11, Number 10, October 2015

Editorials

• 
  Amarda Shehu, Ruth Nussinov:
  Computational Methods for Exploration and Analysis of Macromolecular Structure and Dynamics.
• 
  Toni Kazic:
  Ten Simple Rules for Experiments' Provenance.
• 
  Richard de Grijs:
  Ten Simple Rules for Establishing International Research Collaborations.
• 
  Mark P. Simmons:
  Ten Simple Rules for Writing a Reply Paper.
• 
  David M. Shaw, Thomas C. Erren:
  Ten Simple Rules for Protecting Research Integrity.

Perspective

• 
  William K. Michener:
  Ten Simple Rules for Creating a Good Data Management Plan.

Research Articles

• 
  Hsin-Hung Li, Marisa Carrasco, David J. Heeger:
  Deconstructing Interocular Suppression: Attention and Divisive Normalization.
• 
  Laurence Aitchison, Dan Bang, Bahador Bahrami, Peter E. Latham:
  Doubly Bayesian Analysis of Confidence in Perceptual Decision-Making.
• 
  Serge Dmitrieff, François Nédélec:
  Membrane Mechanics of Endocytosis in Cells with Turgor.
• 
  Juan A. Delgado-SanMartin, Jennifer I. Hare, Alessandro P. S. de Moura, James W. T. Yates:
  Oxygen-Driven Tumour Growth Model: A Pathology-Relevant Mathematical Approach.
• 
  Christian L. Vestergaard, Mathieu Génois:
  Temporal Gillespie Algorithm: Fast Simulation of Contagion Processes on Time-Varying Networks.
• 
  Simon D. Angus, Jonathan Newton:
  Emergence of Shared Intentionality Is Coupled to the Advance of Cumulative Culture.
• 
  Peter K. Koo, Matthew Weitzman, Chandran R. Sabanaygam, Kenneth L. van Golen, Simon G. J. Mochrie:
  Extracting Diffusive States of Rho GTPase in Live Cells: Towards In Vivo Biochemistry.
• 
  Kushagra Singhal, Jocelyne Vreede, Alireza Mashaghi, Sander J. Tans, Peter G. Bolhuis:
  The Trigger Factor Chaperone Encapsulates and Stabilizes Partial Folds of Substrate Proteins.
• 
  Matthias S. Keil:
  Dendritic Pooling of Noisy Threshold Processes Can Explain Many Properties of a Collision-Sensitive Visual Neuron.
• 
  Mauricio Santillana, André T. Nguyen, Mark Dredze, Michael J. Paul, Elaine O. Nsoesie, John S. Brownstein:
  Combining Search, Social Media, and Traditional Data Sources to Improve Influenza Surveillance.
• 
  Nidhi Tyagi, Edward J. Farnell, Colin M. Fitzsimmons, Stephanie Ryan, Edridah M. Tukahebwa, Rick M. Maizels, David W. Dunne, Janet M. Thornton, Nicholas Furnham:
  Comparisons of Allergenic and Metazoan Parasite Proteins: Allergy the Price of Immunity.
• 
  Anja Winter, Ralf Schmid, Richard Bayliss:
  Structural Insights into Separase Architecture and Substrate Recognition through Computational Modelling of Caspase-Like and Death Domains.
• 
  Farras Abdelnour, Susanne G. Mueller, Ashish Raj:
  Relating Cortical Atrophy in Temporal Lobe Epilepsy with Graph Diffusion-Based Network Models.
• 
  Meekyum Olivia Kim, Patrick G. Blachly, James Andrew McCammon:
  Conformational Dynamics and Binding Free Energies of Inhibitors of BACE-1: From the Perspective of Protonation Equilibria.
• 
  Benfeard Williams II, Marino Convertino, Jhuma Das, Nikolay V. Dokholyan:
  ApoE4-specific Misfolded Intermediate Identified by Molecular Dynamics Simulations.
• 
  Rong Shen, Wei Han, Giacomo Fiorin, Shahidul M. Islam, Klaus Schulten, Benoît Roux:
  Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments.
• 
  Lane W. Votapka, Rommie E. Amaro:
  Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning.
• 
  Matteo Tiberti, Elena Papaleo, Tone Bengtsen, Wouter Boomsma, Kresten Lindorff-Larsen:
  ENCORE: Software for Quantitative Ensemble Comparison.
• 
  Predrag Kukic, Arvind Kannan, Maurits J. J. Dijkstra, Sanne Abeln, Carlo Camilloni, Michele Vendruscolo:
  Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations.
• 
  Sedeer el-Showk, Hanna Help-Rinta-Rahko, Tiina Blomster, Riccardo Siligato, Athanasius F. M. Marée, Ari Pekka Mähönen, Verônica A. Grieneisen:
  Parsimonious Model of Vascular Patterning Links Transverse Hormone Fluxes to Lateral Root Initiation: Auxin Leads the Way, while Cytokinin Levels Out.
• 
  Seren Soner, Pemra Ozbek, José Ignacio Garzón, Nir Ben-Tal, Turkan Haliloglu:
  DynaFace: Discrimination between Obligatory and Non-obligatory Protein-Protein Interactions Based on the Complex's Dynamics.
• 
  Priyanka Prakash, Abdallah Sayyed-Ahmad, Alemayehu A. Gorfe:
  pMD-Membrane: A Method for Ligand Binding Site Identification in Membrane-Bound Proteins.
• 
  Xiongwu Wu, Bernard R. Brooks:
  A Virtual Mixture Approach to the Study of Multistate Equilibrium: Application to Constant pH Simulation in Explicit Water.
• 
  Sivan Leviyang, Vitaly V. Ganusov:
  Broad CTL Response in Early HIV Infection Drives Multiple Concurrent CTL Escapes.
• 
  Jeffrey R. Brender, Yang Zhang:
  Predicting the Effect of Mutations on Protein-Protein Binding Interactions through Structure-Based Interface Profiles.
• 
  Daniel A. Keedy, James S. Fraser, Henry van den Bedem:
  Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit.
• 
  Manuel Wahle, Willy Wriggers:
  Multi-scale Visualization of Molecular Architecture Using Real-Time Ambient Occlusion in Sculptor.
• 
  Dieter Vanderelst, Marc W. Holderied, Herbert Peremans:
  Sensorimotor Model of Obstacle Avoidance in Echolocating Bats.
• 
  Armin Meier, Johannes Söding:
  Automatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling.
• 
  Joel Z. Leibo, Qianli Liao, Fabio Anselmi, Tomaso A. Poggio:
  The Invariance Hypothesis Implies Domain-Specific Regions in Visual Cortex.
• 
  Tobias Brosch, Heiko Neumann, Pieter R. Roelfsema:
  Reinforcement Learning of Linking and Tracing Contours in Recurrent Neural Networks.
• 
  Mingming Chen, Daqing Guo, Min Li, Tao Ma, Shengdun Wu, Jingling Ma, Yan Cui, Yang Xia, Peng Xu, Dezhong Yao:
  Critical Roles of the Direct GABAergic Pallido-cortical Pathway in Controlling Absence Seizures.
• 
  Àngel Gómez-Sicilia, Mateusz Sikora, Marek Cieplak, Mariano Carrión-Vázquez:
  An Exploration of the Universe of Polyglutamine Structures.
• 
  Dimitrije Markovic, Jan Gläscher, Peter Bossaerts, John P. O'Doherty, Stefan J. Kiebel:
  Modeling the Evolution of Beliefs Using an Attentional Focus Mechanism.
• 
  Philipp S. Orekhov, Daniel Klose, Armen Y. Mulkidjanian, Konstantin V. Shaitan, Martin Engelhard, Johann P. Klare, Heinz-Jürgen Steinhoff:
  Signaling and Adaptation Modulate the Dynamics of the Photosensoric Complex of Natronomonas pharaonis.
• 
  Simone Rizzetto, Corrado Priami, Attila Csikász-Nagy:
  Qualitative and Quantitative Protein Complex Prediction Through Proteome-Wide Simulations.
• 
  Paul C. Bressloff, Samuel R. Carroll:
  Laminar Neural Field Model of Laterally Propagating Waves of Orientation Selectivity.
• 
  Hirenkumar K. Makadia, James S. Schwaber, Rajanikanth Vadigepalli:
  Intracellular Information Processing through Encoding and Decoding of Dynamic Signaling Features.
• 
  Ioana Niculescu, Johannes Textor, Rob J. De Boer:
  Crawling and Gliding: A Computational Model for Shape-Driven Cell Migration.
• 
  Sean L. Seyler, Avishek Kumar, M. F. Thorpe, Oliver Beckstein:
  Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways.
• 
  Michael Chevalier, Ophelia S. Venturelli, Hana El-Samad:
  The Impact of Different Sources of Fluctuations on Mutual Information in Biochemical Networks.
• 
  Graeme Mitchison:
  The Shape of an Auxin Pulse, and What It Tells Us about the Transport Mechanism.
• 
  Xin Zeng, Bo Li, Rene Welch, Constanza Rojo, Ye Zheng, Colin N. Dewey, Sündüz Keles:
  Perm-seq: Mapping Protein-DNA Interactions in Segmental Duplication and Highly Repetitive Regions of Genomes with Prior-Enhanced Read Mapping.
• 
  Christian Rössert, Paul Dean, John Porrill:
  At the Edge of Chaos: How Cerebellar Granular Layer Network Dynamics Can Provide the Basis for Temporal Filters.
• 
  Eduard Porta-Pardo, Luz Garcia-Alonso, Thomas Hrabe, Joaquín Dopazo, Adam Godzik:
  A Pan-Cancer Catalogue of Cancer Driver Protein Interaction Interfaces.
• 
  David Bruce Borenstein, Peter Ringel, Marek Basler, Ned S. Wingreen:
  Established Microbial Colonies Can Survive Type VI Secretion Assault.
• 
  Santhosh Kannan Venkatesan, Kusumika Saha, Azmat Sohail, Walter Sandtner, Michael Freissmuth, Gerhard F. Ecker, Harald H. Sitte, Thomas Stockner:
  Refinement of the Central Steps of Substrate Transport by the Aspartate Transporter GltPh: Elucidating the Role of the Na2 Sodium Binding Site.
• 
  Robin van der Lee, Qian Feng, Martijn A. Langereis, Rob ter Horst, Radek Szklarczyk, Mihai G. Netea, Arno C. Andeweg, Frank J. M. van Kuppeveld, Martijn A. Huynen:
  Integrative Genomics-Based Discovery of Novel Regulators of the Innate Antiviral Response.
• 
  Niraj Kumar, Abhyudai Singh, Rahul V. Kulkarni:
  Transcriptional Bursting in Gene Expression: Analytical Results for General Stochastic Models.
• 
  Tristan Aumentado-Armstrong, Michael G. Metzen, Michael K. J. Sproule, Maurice J. Chacron:
  Electrosensory Midbrain Neurons Display Feature Invariant Responses to Natural Communication Stimuli.
• 
  Omer Ziv, Assaf Zaritsky, Yakey Yaffe, Naresh Mutukula, Reuven Edri, Yechiel Elkabetz:
  Quantitative Live Imaging of Human Embryonic Stem Cell Derived Neural Rosettes Reveals Structure-Function Dynamics Coupled to Cortical Development.
• 
  Hyuntae Na, Robert L. Jernigan, Guang Song:
  Bridging between NMA and Elastic Network Models: Preserving All-Atom Accuracy in Coarse-Grained Models.
• 
  Roland G. Huber, Hao Fan, Peter J. Bond:
  The Structural Basis for Activation and Inhibition of ZAP-70 Kinase Domain.
• 
  Radhakrishna Bettadapura, Muhibur Rasheed, Antje Vollrath, Chandrajit Bajaj:
  PF² fit: Polar Fast Fourier Matched Alignment of Atomistic Structures with 3D Electron Microscopy Maps.
• 
  Alexander D. Malkin, Robert P. Sheehan, Shibin Mathew, William J. Federspiel, Heinz Redl, Gilles Clermont:
  A Neutrophil Phenotype Model for Extracorporeal Treatment of Sepsis.
• 
  Daniel Soudry, Suraj Keshri, Patrick Stinson, Min-hwan Oh, Garud Iyengar, Liam Paninski:
  Efficient "Shotgun" Inference of Neural Connectivity from Highly Sub-sampled Activity Data.
• 
  Pablo Szekely, Yael Korem, Uri Moran, Avi E. Mayo, Uri Alon:
  The Mass-Longevity Triangle: Pareto Optimality and the Geometry of Life-History Trait Space.
• 
  Pengcheng Zhou, Shawn D. Burton, Adam C. Snyder, Matthew A. Smith, Nathaniel N. Urban, Robert E. Kass:
  Establishing a Statistical Link between Network Oscillations and Neural Synchrony.
• 
  Marinka Zitnik, Edward A. Nam, Christopher Dinh, Adam Kuspa, Gad Shaulsky, Blaz Zupan:
  Gene Prioritization by Compressive Data Fusion and Chaining.
• 
  Ian Krajbich, Todd A. Hare, Björn Bartling, Yosuke Morishima, Ernst Fehr:
  A Common Mechanism Underlying Food Choice and Social Decisions.
• 
  Andreas Henschel, Muhammad Zohaib Anwar, Vimitha Manohar:
  Comprehensive Meta-analysis of Ontology Annotated 16S rRNA Profiles Identifies Beta Diversity Clusters of Environmental Bacterial Communities.
• 
  Tiffany Kee, Pavel Sanda, Nitin Gupta, Mark Stopfer, Maxim Bazhenov:
  Feed-Forward versus Feedback Inhibition in a Basic Olfactory Circuit.
• 
  Jeewoen Shin, Thomas MacCarthy:
  Antagonistic Coevolution Drives Whack-a-Mole Sensitivity in Gene Regulatory Networks.
• 
  Alexandra Jacunski, Scott J. Dixon, Nicholas P. Tatonetti:
  Connectivity Homology Enables Inter-Species Network Models of Synthetic Lethality.
• 
  Dario Cuevas Rivera, Sebastian Bitzer, Stefan J. Kiebel:
  Modelling Odor Decoding in the Antennal Lobe by Combining Sequential Firing Rate Models with Bayesian Inference.
• 
  Bruce S. Gardiner, Kelvin Kian Loong Wong, Grand R. Joldes, Addison J. Rich, Chin Wee Tan, Antony W. Burgess, David W. Smith:
  Discrete Element Framework for Modelling Extracellular Matrix, Deformable Cells and Subcellular Components.
• 
  Michael A. DeJesus, Chaitra Ambadipudi, Richard Baker, Christopher M. Sassetti, Thomas R. Ioerger:
  TRANSIT - A Software Tool for Himar1 TnSeq Analysis.
• 
  Jason D. Wittenbach, Kristofer E. Bouchard, Michael S. Brainard, Dezhe Z. Jin:
  An Adapting Auditory-motor Feedback Loop Can Contribute to Generating Vocal Repetition.
• 
  Claire Colas, Christof Grewer, Nicholas James Otte, Armanda Gameiro, Thomas Albers, Kurnvir Singh, Helen Shere, Massimiliano Bonomi, Jeff Holst, Avner Schlessinger:
  Ligand Discovery for the Alanine-Serine-Cysteine Transporter (ASCT2, SLC1A5) from Homology Modeling and Virtual Screening.
• 
  Zhaoping Li, Zhe Li:
  Primary Visual Cortex as a Saliency Map: A Parameter-Free Prediction and Its Test by Behavioral Data.
• 
  Orit Adato, Noga Ninyo, Uri Gophna, Sagi Snir:
  Detecting Horizontal Gene Transfer between Closely Related Taxa.
• 
  Stanislav Nagy, Marc Goessling, Yali Amit, David Biron:
  A Generative Statistical Algorithm for Automatic Detection of Complex Postures.
• 
  Don-On Daniel Mak, King-Ho Cheung, Patrick Toglia, J. Kevin Foskett, Ghanim Ullah:
  Analyzing and Quantifying the Gain-of-Function Enhancement of IP₃ Receptor Gating by Familial Alzheimer's Disease-Causing Mutants in Presenilins.
• 
  Raya Ahmed, Liset Westera, Julia Drylewicz, Marjet Elemans, Yan Zhang, Elizabeth Kelly, Rajko Reljic, Kiki Tesselaar, Rob J. De Boer, Derek C. Macallan, José A. M. Borghans, Becca Asquith:
  Reconciling Estimates of Cell Proliferation from Stable Isotope Labeling Experiments.
• 
  Noushin Niknafs, Violeta Beleva Guthrie, Daniel Q. Naiman, Rachel Karchin:
  SubClonal Hierarchy Inference from Somatic Mutations: Automatic Reconstruction of Cancer Evolutionary Trees from Multi-region Next Generation Sequencing.
• 
  Yuri Pritykin, Dario Ghersi, Mona Singh:
  Genome-Wide Detection and Analysis of Multifunctional Genes.
• 
  Jan Karbowski:
  Cortical Composition Hierarchy Driven by Spine Proportion Economical Maximization or Wire Volume Minimization.
• 
  Min-Cheol Kim, Jordan Whisler, Yaron R. Silberberg, Roger D. Kamm, H. Harry Asada:
  Cell Invasion Dynamics into a Three Dimensional Extracellular Matrix Fibre Network.
• 
  Francisco G. Vital-Lopez, Jaques Reifman, Anders Wallqvist:
  Biofilm Formation Mechanisms of Pseudomonas aeruginosa Predicted via Genome-Scale Kinetic Models of Bacterial Metabolism.
• 
  Chris M. Stone, Nakul Chitnis:
  Implications of Heterogeneous Biting Exposure and Animal Hosts on Trypanosomiasis brucei gambiense Transmission and Control.

Volume 11, Number 11, November 2015

Education

• 
  Emile R. Chimusa, Mamana Mbiyavanga, Velaphi Masilela, Judit Kumuthini:
  "Broadband" Bioinformatics Skills Transfer with the Knowledge Transfer Programme (KTP): Educational Model for Upliftment and Sustainable Development.

Review

• 
  Miriam Grace, Marc-Thorsten Hütt:
  Regulation of Spatiotemporal Patterns by Biological Variability: General Principles and Applications to Dictyostelium discoideum.

Research Articles

• 
  Shuyi Ma, Kyle J. Minch, Tige R. Rustad, Samuel Hobbs, Suk-Lin Zhou, David R. Sherman, Nathan D. Price:
  Integrated Modeling of Gene Regulatory and Metabolic Networks in Mycobacterium tuberculosis.
• 
  Won-Min Song, Bin Zhang:
  Multiscale Embedded Gene Co-expression Network Analysis.
• 
  Jonathan W. Armond, Edward F. Harry, Andrew D. McAinsh, Nigel J. Burroughs:
  Inferring the Forces Controlling Metaphase Kinetochore Oscillations by Reverse Engineering System Dynamics.
• 
  Mikhail Shugay, Dmitriy V. Bagaev, Maria A. Turchaninova, Dmitriy A. Bolotin, Olga V. Britanova, Ekaterina V. Putintseva, Mikhail V. Pogorelyy, Vadim I. Nazarov, Ivan V. Zvyagin, Vitalina I. Kirgizova, Kirill I. Kirgizov, Elena V. Skorobogatova, Dmitry M. Chudakov:
  VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires.
• 
  Hisashi Ohtsuki, Yoh Iwasa, Martin A. Nowak:
  Reputation Effects in Public and Private Interactions.
• 
  Silvia Lovera, Maria Morando, Encarna Pucheta-Martinez, Jorge L. Martinez-Torrecuadrada, Giorgio Saladino, Francesco L. Gervasio:
  Towards a Molecular Understanding of the Link between Imatinib Resistance and Kinase Conformational Dynamics.
• 
  Minzhe Guo, Hui Wang, S. Steven Potter, Jeffrey A. Whitsett, Yan Xu:
  SINCERA: A Pipeline for Single-Cell RNA-Seq Profiling Analysis.
• 
  Alex Davies, Matthieu Louis, Barbara Webb:
  A Model of Drosophila Larva Chemotaxis.
• 
  Lin-Tai Da, Chao E, Baogen Duan, Chuanbiao Zhang, Xin Zhou, Jin Yu:
  A Jump-from-Cavity Pyrophosphate Ion Release Assisted by a Key Lysine Residue in T7 RNA Polymerase Transcription Elongation.
• 
  Maciej Jan Ejsmond, Jacek Radwan:
  Red Queen Processes Drive Positive Selection on Major Histocompatibility Complex (MHC) Genes.
• 
  Anna Rubinski, Noam E. Ziv:
  Remodeling and Tenacity of Inhibitory Synapses: Relationships with Network Activity and Neighboring Excitatory Synapses.
• 
  Andrea Maesani, Pavan Ramdya, Steeve Cruchet, Kyle Gustafson, Richard Benton, Dario Floreano:
  Fluctuation-Driven Neural Dynamics Reproduce Drosophila Locomotor Patterns.
• 
  Etienne Baratchart, Sébastien Benzekry, Andreas Bikfalvi, Thierry Colin, Lindsay S. Cooley, Raphäel Pineau, Emeline J. Ribot, Olivier Saut, Wilfried Souleyreau:
  Computational Modelling of Metastasis Development in Renal Cell Carcinoma.
• 
  Max S. Y. Lau, Glenn Marion, George Streftaris, Gavin J. Gibson:
  A Systematic Bayesian Integration of Epidemiological and Genetic Data.
• 
  Peter C. St. John, Francis J. Doyle III:
  Quantifying Stochastic Noise in Cultured Circadian Reporter Cells.
• 
  Robert P. Jenkins, Anja Hanisch, Cristian Soza-Ried, Erik Sahai, Julian Lewis:
  Stochastic Regulation of her1/7 Gene Expression Is the Source of Noise in the Zebrafish Somite Clock Counteracted by Notch Signalling.
• 
  Kimberly Glass, Michelle Girvan:
  Finding New Order in Biological Functions from the Network Structure of Gene Annotations.
• 
  Jia Li, Marie-Anne Poursat, Damien Drubay, Arnaud Motz, Zohra Saci, Antonin Morillon, Stefan Michiels, Daniel Gautheret:
  A Dual Model for Prioritizing Cancer Mutations in the Non-coding Genome Based on Germline and Somatic Events.
• 
  Chen Zhao, Aleksander S. Popel:
  Computational Model of MicroRNA Control of HIF-VEGF Pathway: Insights into the Pathophysiology of Ischemic Vascular Disease and Cancer.
• 
  Alberto Romagnoni, Jérôme Ribot, Daniel Bennequin, Jonathan Touboul:
  Parsimony, Exhaustivity and Balanced Detection in Neocortex.
• 
  Olivier J. N. Bertrand, Jens Peter Lindemann, Martin Egelhaaf:
  A Bio-inspired Collision Avoidance Model Based on Spatial Information Derived from Motion Detectors Leads to Common Routes.
• 
  Satohiro Tajima, Toru Yanagawa, Naotaka Fujii, Taro Toyoizumi:
  Untangling Brain-Wide Dynamics in Consciousness by Cross-Embedding.
• 
  Joanne L. Dunster, Francoise Mazet, Michael J. Fry, Jonathan M. Gibbins, Marcus J. Tindall:
  Regulation of Early Steps of GPVI Signal Transduction by Phosphatases: A Systems Biology Approach.
• 
  Jordi Fonollosa, Emre Neftci, Mikhail I. Rabinovich:
  Learning of Chunking Sequences in Cognition and Behavior.
• 
  Florian Raudies, Michael E. Hasselmo:
  Differences in Visual-Spatial Input May Underlie Different Compression Properties of Firing Fields for Grid Cell Modules in Medial Entorhinal Cortex.
• 
  Zhongyang Zhang, Ke Hao:
  SAAS-CNV: A Joint Segmentation Approach on Aggregated and Allele Specific Signals for the Identification of Somatic Copy Number Alterations with Next-Generation Sequencing Data.
• 
  Alejandro Ochoa, John D. Storey, Manuel Llinás, Mona Singh:
  Beyond the E-Value: Stratified Statistics for Protein Domain Prediction.
• 
  Manuel Schottdorf, Wolfgang Keil, David Coppola, Leonard E. White, Fred Wolf:
  Random Wiring, Ganglion Cell Mosaics, and the Functional Architecture of the Visual Cortex.
• 
  Donatien F. Chedom, Pablo R. Murcia, Chris D. Greenman:
  Inferring the Clonal Structure of Viral Populations from Time Series Sequencing.
• 
  Pablo Cordero, Rhiju Das:
  Rich RNA Structure Landscapes Revealed by Mutate-and-Map Analysis.
• 
  Benjamin D. Heavner, Nathan D. Price:
  Comparative Analysis of Yeast Metabolic Network Models Highlights Progress, Opportunities for Metabolic Reconstruction.
• 
  Stephen Nayfach, Patrick H. Bradley, Stacia K. Wyman, Timothy J. Laurent, Alexander G. Williams, Jonathan A. Eisen, Katherine S. Pollard, Thomas J. Sharpton:
  Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes.
• 
  Gabriel Madirolas, Gonzalo G. de Polavieja:
  Improving Collective Estimations Using Resistance to Social Influence.
• 
  James Rankin, Elyse Sussman, John Rinzel:
  Neuromechanistic Model of Auditory Bistability.
• 
  Gaurav Dwivedi, Margaret A. Gran, Pritha Bagchi, Melissa L. Kemp:
  Dynamic Redox Regulation of IL-4 Signaling.
• 
  Dmitry Svetlichnyy, Hana Imrichová, Mark Fiers, Zeynep Kalender Atak, Stein Aerts:
  Identification of High-Impact cis-Regulatory Mutations Using Transcription Factor Specific Random Forest Models.
• 
  Guido Gigante, Gustavo Deco, Shimon Marom, Paolo Del Giudice:
  Network Events on Multiple Space and Time Scales in Cultured Neural Networks and in a Stochastic Rate Model.
• 
  Peter Neri:
  The Elementary Operations of Human Vision Are Not Reducible to Template-Matching.
• 
  Marina Martinez-Garcia, Andrea Insabato, Mario Pannunzi, Jose L. Pardo-Vazquez, Carlos Acuña, Gustavo Deco:
  The Encoding of Decision Difficulty and Movement Time in the Primate Premotor Cortex.
• 
  Tri Hieu Nim, Le Luo, Jacob K. White, Marie-Véronique Clément, Lisa Tucker-Kellogg:
  Non-canonical Activation of Akt in Serum-Stimulated Fibroblasts, Revealed by Comparative Modeling of Pathway Dynamics.
• 
  Tian Hong, Kazuhide Watanabe, Catherine Ha Ta, Alvaro Villarreal-Ponce, Qing Nie, Xing Dai:
  An Ovol2-Zeb1 Mutual Inhibitory Circuit Governs Bidirectional and Multi-step Transition between Epithelial and Mesenchymal States.
• 
  Goker Erdogan, Ilker Yildirim, Robert A. Jacobs:
  From Sensory Signals to Modality-Independent Conceptual Representations: A Probabilistic Language of Thought Approach.
• 
  Sandeep Choubey, Jané Kondev, Alvaro Sanchez:
  Deciphering Transcriptional Dynamics In Vivo by Counting Nascent RNA Molecules.
• 
  Laura Hindersin, Arne Traulsen:
  Most Undirected Random Graphs Are Amplifiers of Selection for Birth-Death Dynamics, but Suppressors of Selection for Death-Birth Dynamics.
• 
  David Kappel, Stefan Habenschuss, Robert Legenstein, Wolfgang Maass:
  Network Plasticity as Bayesian Inference.
• 
  Mark A. Walker, Tobias Kohl, Stephan E. Lehnart, Joseph L. Greenstein, W. J. Lederer, Raimond L. Winslow:
  On the Adjacency Matrix of RyR2 Cluster Structures.
• 
  Kristin J. Adolfsen, Mark P. Brynildsen:
  A Kinetic Platform to Determine the Fate of Hydrogen Peroxide in Escherichia coli.
• 
  Peter Jedlicka, Lubica Benuskova, Wickliffe C. Abraham:
  A Voltage-Based STDP Rule Combined with Fast BCM-Like Metaplasticity Accounts for LTP and Concurrent "Heterosynaptic" LTD in the Dentate Gyrus In Vivo.
• 
  Jing Zhou, Camilo Aponte-Santamaría, Sebastian Sturm, Jakob Tómas Bullerjahn, Agnieszka Bronowska, Frauke Gräter:
  Mechanism of Focal Adhesion Kinase Mechanosensing.
• 
  Daniel Yakubovich, Shai Berlin, Uri Kahanovitch, Moran Rubinstein, Isabella Farhy-Tselnicker, Boaz Styr, Tal Keren-Raifman, Carmen W. Dessauer, Nathan Dascal:
  A Quantitative Model of the GIRK1/2 Channel Reveals That Its Basal and Evoked Activities Are Controlled by Unequal Stoichiometry of Gα and Gβγ.
• 
  Masato S. Abe, Masakazu Shimada:
  Lévy Walks Suboptimal under Predation Risk.
• 
  M. Senthil Kumar, Joshua B. Plotkin, Sridhar Hannenhalli:
  Regulated CRISPR Modules Exploit a Dual Defense Strategy of Restriction and Abortive Infection in a Model of Prokaryote-Phage Coevolution.
• 
  Max Hinne, Ronald J. Janssen, Tom Heskes, Marcel A. J. van Gerven:
  Bayesian Estimation of Conditional Independence Graphs Improves Functional Connectivity Estimates.
• 
  Joseph G. Makin, Benjamin K. Dichter, Philip N. Sabes:
  Learning to Estimate Dynamical State with Probabilistic Population Codes.
• 
  Samuel J. Gershman:
  A Unifying Probabilistic View of Associative Learning.
• 
  Jonathan Cannon, Nancy Kopell, Timothy J. Gardner, Jeffrey E. Markowitz:
  Neural Sequence Generation Using Spatiotemporal Patterns of Inhibition.
• 
  Sam Walcott, Neil M. Kad:
  Direct Measurements of Local Coupling between Myosin Molecules Are Consistent with a Model of Muscle Activation.
• 
  Makoto Ito, Kenji Doya:
  Parallel Representation of Value-Based and Finite State-Based Strategies in the Ventral and Dorsal Striatum.
• 
  David Bednar, Koen Beerens, Eva Sebestova, Jaroslav Bendl, Sagar D. Khare, Radka Chaloupkova, Zbynek Prokop, Jan Brezovsky, David Baker, Jirí Damborský:
  FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants.
• 
  David P. A. Cohen, Loredana Martignetti, Sylvie Robine, Emmanuel Barillot, Andrei Yu. Zinovyev, Laurence Calzone:
  Mathematical Modelling of Molecular Pathways Enabling Tumour Cell Invasion and Migration.

Volume 11, Number 12, December 2015

Review

• 
  Gil Ariel, Amir Ayali:
  Locust Collective Motion and Its Modeling.

Research Articles

• 
  Alice E. Milne, James R. Bell, William D. Hutchison, Frank van den Bosch, Paul D. Mitchell, David Crowder, Stephen Parnell, Andrew P. Whitmore:
  The Effect of Farmers' Decisions on Pest Control with Bt Crops: A Billion Dollar Game of Strategy.
• 
  Maximilian Puelma Touzel, Fred Wolf:
  Complete Firing-Rate Response of Neurons with Complex Intrinsic Dynamics.
• 
  Matthew Hall, Mark E. J. Woolhouse, Andrew Rambaut:
  Epidemic Reconstruction in a Phylogenetics Framework: Transmission Trees as Partitions of the Node Set.
• 
  Christoph Hartmann, Andreea Lazar, Bernhard Nessler, Jochen Triesch:
  Where's the Noise? Key Features of Spontaneous Activity and Neural Variability Arise through Learning in a Deterministic Network.
• 
  Tatjana Braun, Julia Koehler Leman, Oliver F. Lange:
  Combining Evolutionary Information and an Iterative Sampling Strategy for Accurate Protein Structure Prediction.
• 
  Dan Wilson, Jeff Moehlis:
  Clustered Desynchronization from High-Frequency Deep Brain Stimulation.
• 
  Jochen Kursawe, Pavel A. Brodskiy, Jeremiah J. Zartman, Ruth E. Baker, Alexander G. Fletcher:
  Capabilities and Limitations of Tissue Size Control through Passive Mechanical Forces.
• 
  Michael Fauth, Florentin Wörgötter, Christian Tetzlaff:
  Formation and Maintenance of Robust Long-Term Information Storage in the Presence of Synaptic Turnover.
• 
  Naoyuki Ohta, Kana Waki, Atsushi Mochizuki, Yutaka Satou:
  A Boolean Function for Neural Induction Reveals a Critical Role of Direct Intercellular Interactions in Patterning the Ectoderm of the Ascidian Embryo.
• 
  Mathieu Golos, Viktor K. Jirsa, Emmanuel Daucé:
  Multistability in Large Scale Models of Brain Activity.
• 
  Sunpeng Wang, Patricia Hottz, Mauro Schechter, Libin Rong:
  Modeling the Slow CD4+ T Cell Decline in HIV-Infected Individuals.
• 
  Wei Zhang, Jae-Woong Chang, Lilong Lin, Kay Minn, Baolin Wu, Jeremy Chien, Jeongsik Yong, Hui Zheng, Rui Kuang:
  Network-Based Isoform Quantification with RNA-Seq Data for Cancer Transcriptome Analysis.
• 
  Andreas Carlson, L. Mahadevan:
  Elastohydrodynamics and Kinetics of Protein Patterning in the Immunological Synapse.
• 
  Soma Ghosh, Nagasuma R. Chandra, Saraswathi Vishveshwara:
  Mechanism of Iron-Dependent Repressor (IdeR) Activation and DNA Binding: A Molecular Dynamics and Protein Structure Network Study.
• 
  Costas Mitsopoulos, Amanda C. Schierz, Paul Workman, Bissan Al-Lazikani:
  Distinctive Behaviors of Druggable Proteins in Cellular Networks.
• 
  Kevin Lloyd, Peter Dayan:
  Tamping Ramping: Algorithmic, Implementational, and Computational Explanations of Phasic Dopamine Signals in the Accumbens.
• 
  Jienian Yang, Maksim V. Plikus, Natalia L. Komarova:
  The Role of Symmetric Stem Cell Divisions in Tissue Homeostasis.
• 
  Henrik Ronellenfitsch, Jana Lasser, Douglas C. Daly, Eleni Katifori:
  Topological Phenotypes Constitute a New Dimension in the Phenotypic Space of Leaf Venation Networks.
• 
  Wolfram Möbius, Andrew W. Murray, David R. Nelson:
  How Obstacles Perturb Population Fronts and Alter Their Genetic Structure.
• 
  Taina T. Immonen, Jessica M. Conway, Ethan O. Romero-Severson, Alan S. Perelson, Thomas Leitner:
  Recombination Enhances HIV-1 Envelope Diversity by Facilitating the Survival of Latent Genomic Fragments in the Plasma Virus Population.
• 
  Alan Veliz-Cuba, Andrew J. Hirning, Adam A. Atanas, Faiza Hussain, Flavia Vancia, Kresimir Josic, Matthew R. Bennett:
  Sources of Variability in a Synthetic Gene Oscillator.
• 
  Elodie Laine, Alessandra Carbone:
  Local Geometry and Evolutionary Conservation of Protein Surfaces Reveal the Multiple Recognition Patches in Protein-Protein Interactions.
• 
  Takuya Isomura, Kiyoshi Kotani, Yasuhiko Jimbo:
  Cultured Cortical Neurons Can Perform Blind Source Separation According to the Free-Energy Principle.
• 
  Adam James Waite, Caroline Cannistra, Wenying Shou:
  Defectors Can Create Conditions That Rescue Cooperation.
• 
  R. Gonzalo Parra, Rocío Espada, Nina Verstraete, Diego U. Ferreiro:
  Structural and Energetic Characterization of the Ankyrin Repeat Protein Family.
• 
  S. S. Soumya, Animesh Gupta, Andrea Cugno, Luca Deseri, Kaushik Dayal, Dibyendu Das, Shamik Sen, Mandar M. Inamdar:
  Coherent Motion of Monolayer Sheets under Confinement and Its Pathological Implications.
• 
  James Kaminski, Molly K. Gibson, Eric A. Franzosa, Nicola Segata, Gautam Dantas, Curtis Huttenhower:
  High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED.
• 
  Matthew Ruffalo, Mehmet Koyutürk, Roded Sharan:
  Network-Based Integration of Disparate Omic Data To Identify "Silent Players" in Cancer.
• 
  Shiqiu Liu, Adam S. Smith, Yuting Gu, Jie Tan, C. Karen Liu, Greg Turk:
  Computer Simulations Imply Forelimb-Dominated Underwater Flight in Plesiosaurs.
• 
  Alex Pavlides, Stephen John Hogan, Rafal Bogacz:
  Computational Models Describing Possible Mechanisms for Generation of Excessive Beta Oscillations in Parkinson's Disease.
• 
  Ivar L. Thorson, Jean Liénard, Stephen V. David:
  The Essential Complexity of Auditory Receptive Fields.
• 
  Ankit N. Khambhati, Kathryn A. Davis, Brian S. Oommen, Stephanie H. Chen, Timothy H. Lucas, Brian Litt, Danielle S. Bassett:
  Dynamic Network Drivers of Seizure Generation, Propagation and Termination in Human Neocortical Epilepsy.
• 
  Zhichao Miao, Eric Westhof:
  A Large-Scale Assessment of Nucleic Acids Binding Site Prediction Programs.
• 
  Theo Arts, Robert S. Reneman, James B. Bassingthwaighte, Ger J. van der Vusse:
  Modeling Fatty Acid Transfer from Artery to Cardiomyocyte.
• 
  Lavisha Jindal, Eldon Emberly:
  Operational Principles for the Dynamics of the In Vitro ParA-ParB System.
• 
  Alberto Mazzoni, Henrik Lindén, Hermann Cuntz, Anders Lansner, Stefano Panzeri, Gaute T. Einevoll:
  Computing the Local Field Potential (LFP) from Integrate-and-Fire Network Models.
• 
  Fabiana A. Caetano, Brennan S. Dirk, Joshua H. K. Tam, P. Craig Cavanagh, Maria Goiko, Stephen S. G. Ferguson, Stephen H. Pasternak, Jimmy D. Dikeakos, John R. de Bruyn, Bryan Heit:
  MIiSR: Molecular Interactions in Super-Resolution Imaging Enables the Analysis of Protein Interactions, Dynamics and Formation of Multi-protein Structures.
• 
  Thomas E. Akam, Rui Costa, Peter Dayan:
  Simple Plans or Sophisticated Habits? State, Transition and Learning Interactions in the Two-Step Task.
• 
  Piotr J. Kamola, Yuko Nakano, Tomoko Takahashi, Paul A. Wilson, Kumiko Ui-Tei:
  The siRNA Non-seed Region and Its Target Sequences Are Auxiliary Determinants of Off-Target Effects.
• 
  Akli Ben Imeddourene, Ahmad Elbahnsi, Marc Gueroult, Christophe Oguey, Nicolas Foloppe, Brigitte Hartmann:
  Simulations Meet Experiment to Reveal New Insights into DNA Intrinsic Mechanics.
• 
  Frances Hutchings, Cheol E. Han, Simon S. Keller, Bernd Weber, Peter Neal Taylor, Marcus Kaiser:
  Predicting Surgery Targets in Temporal Lobe Epilepsy through Structural Connectome Based Simulations.
• 
  Thomas Buder, Andreas Deutsch, Barbara Klink, Anja Voss-Böhme:
  Model-Based Evaluation of Spontaneous Tumor Regression in Pilocytic Astrocytoma.
• 
  Varsha D. Badal, Petras J. Kundrotas, Ilya A. Vakser:
  Text Mining for Protein Docking.
• 
  Dominik R. Bach:
  Anxiety-Like Behavioural Inhibition Is Normative under Environmental Threat-Reward Correlations.
• 
  Liang Wang, Jie Zheng, Akiko Maehara, Chun Yang, Kristen Billiar, Zheyang Wu, Richard G. Bach, David Muccigrosso, Gary S. Mintz, Dalin Tang:
  Morphological and Stress Vulnerability Indices for Human Coronary Plaques and Their Correlations with Cap Thickness and Lipid Percent: An IVUS-Based Fluid-Structure Interaction Multi-patient Study.
• 
  Brian Odegaard, David R. Wozny, Ladan Shams:
  Biases in Visual, Auditory, and Audiovisual Perception of Space.
• 
  Stephan Eismann, Robert G. Endres:
  Protein Connectivity in Chemotaxis Receptor Complexes.
• 
  Brenda N. Vo, Christopher C. Drovandi, Anthony N. Pettitt, Graeme J. Pettet:
  Melanoma Cell Colony Expansion Parameters Revealed by Approximate Bayesian Computation.
• 
  István Bartha, Antonio Rausell, Paul J. McLaren, Pejman Mohammadi, Manuel Tardaguila, Nimisha Chaturvedi, Jacques Fellay, Amalio Telenti:
  The Characteristics of Heterozygous Protein Truncating Variants in the Human Genome.
• 
  Richard Moore, Hsu Kiang Ooi, Taek Kang, Leonidas Bleris, Lan Ma:
  MiR-192-Mediated Positive Feedback Loop Controls the Robustness of Stress-Induced p53 Oscillations in Breast Cancer Cells.
• 
  Ossnat Bar-Shira, Ronnie Maor, Gal Chechik:
  Gene Expression Switching of Receptor Subunits in Human Brain Development.
• 
  Sridevi Nagaraja, Jaques Reifman, Alexander Yu. Mitrophanov:
  Computational Identification of Mechanistic Factors That Determine the Timing and Intensity of the Inflammatory Response.
• 
  Kendra S. Burbank:
  Mirrored STDP Implements Autoencoder Learning in a Network of Spiking Neurons.
• 
  Marcelo Gomes Mattar, Michael W. Cole, Sharon L. Thompson-Schill, Danielle S. Bassett:
  A Functional Cartography of Cognitive Systems.
• 
  Pradeep Anand Ravindranath, Stefano Forli, David S. Goodsell, Arthur J. Olson, Michel F. Sanner:
  AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility.
• 
  Michela Riz, Morten Gram Pedersen:
  Mathematical Modeling of Interacting Glucose-Sensing Mechanisms and Electrical Activity Underlying Glucagon-Like Peptide 1 Secretion.
• 
  Shyam Kumar Sudhakar, Benjamin Torben-Nielsen, Erik De Schutter:
  Cerebellar Nuclear Neurons Use Time and Rate Coding to Transmit Purkinje Neuron Pauses.
• 
  Zev N. Kronenberg, Edward J. Osborne, Kelsey R. Cone, Brett J. Kennedy, Eric T. Domyan, Michael D. Shapiro, Nels C. Elde, Mark Yandell:
  Wham: Identifying Structural Variants of Biological Consequence.
• 
  Shree Hari Gautam, Thanh T. Hoang, Kylie McClanahan, Stephen K. Grady, Woodrow L. Shew:
  Maximizing Sensory Dynamic Range by Tuning the Cortical State to Criticality.
• 
  Gregory R. Johnson, Jieyue Li, Aabid Shariff, Gustavo K. Rohde, Robert F. Murphy:
  Automated Learning of Subcellular Variation among Punctate Protein Patterns and a Generative Model of Their Relation to Microtubules.