PLoS Computational Biology, Volume 10

Volume 10, Number 1, January 2014

Editorials

• 
  Weixiong Zhang:
  Ten Simple Rules for Writing Research Papers.
• 
  Ruth Nussinov:
  The Significance of the 2013 Nobel Prize in Chemistry and the Challenges Ahead.

Messages from ISCB

• 
  Kavisha Ramdayal, Miranda D. Stobbe, Tarun Mishra, Magali Michaut:
  Building the Future of Bioinformatics through Student-Facilitated Conferencing.
• 
  Reeta Rani Singhania, Dhatri Madduru, Pranathi Pappu, Sameera Panchangam, Renuka Suravajhala, Mohanalatha Chandrasekharan:
  The Making of the Women in Biology Forum (WiB) at Bioclues.

Education

• 
  Isabel Marques, Paulo Almeida, Renato J. Alves, Maria João Dias, Ana Godinho, José B. Pereira-Leal:
  Bioinformatics Projects Supporting Life-Sciences Learning in High Schools.

Perspective

• 
  Marc-Oliver Gewaltig, Robert C. Cannon:
  Current Practice in Software Development for Computational Neuroscience and How to Improve It.

Research Articles

• 
  Bin Hu, Hua-Xin Liao, S. Munir Alam, Byron Goldstein:
  Estimating the Probability of Polyreactive Antibodies 4E10 and 2F5 Disabling a gp41 Trimer after T Cell-HIV Adhesion.
• 
  Jonathan D. Drover:
  Timing over Tuning: Overcoming the Shortcomings of a Line Attractor during a Working Memory Task.
• 
  Paul Verbruggen, Tim Heinemann, Erik M. M. Manders, Gesa von Bornstaedt, Roel van Driel, Thomas Höfer:
  Robustness of DNA Repair through Collective Rate Control.
• 
  Areum Han, Peter Stoilov, Anthony J. Linares, Yu Zhou, Xiang-Dong Fu, Douglas L. Black:
  De Novo Prediction of PTBP1 Binding and Splicing Targets Reveals Unexpected Features of Its RNA Recognition and Function.
• 
  Omar Gutierrez-Arenas, Olivia Eriksson, Jeanette Hellgren Kotaleski:
  Segregation and Crosstalk of D1 Receptor-Mediated Activation of ERK in Striatal Medium Spiny Neurons upon Acute Administration of Psychostimulants.
• 
  Devin L. O'Connor, Adam Runions, Aaron Sluis, Jennifer Bragg, John P. Vogel, Przemyslaw Prusinkiewicz, Sarah Hake:
  A Division in PIN-Mediated Auxin Patterning during Organ Initiation in Grasses.
• 
  Geetu Tuteja, Karen Betancourt Moreira, Tisha Chung, Jenny Chen, Aaron M. Wenger, Gill Bejerano:
  Automated Discovery of Tissue-Targeting Enhancers and Transcription Factors from Binding Motif and Gene Function Data.
• 
  Arshan Nasir, Kyung Mo Kim, Gustavo Caetano-Anollés:
  Global Patterns of Protein Domain Gain and Loss in Superkingdoms.
• 
  Claude Gérard, Didier Gonze, Frédéric Lemaigre, Béla Novák:
  A Model for the Epigenetic Switch Linking Inflammation to Cell Transformation: Deterministic and Stochastic Approaches.
• 
  Jayanthi Santhanam, Lars Råberg, Andrew F. Read, Nicholas Jon Savill:
  Immune-Mediated Competition in Rodent Malaria Is Most Likely Caused by Induced Changes in Innate Immune Clearance of Merozoites.
• 
  Federico Comoglio, Renato Paro:
  Combinatorial Modeling of Chromatin Features Quantitatively Predicts DNA Replication Timing in Drosophila.
• 
  Rosalyn J. Moran, Mkael Symmonds, Raymond J. Dolan, Karl J. Friston:
  The Brain Ages Optimally to Model Its Environment: Evidence from Sensory Learning over the Adult Lifespan.
• 
  Geoffrey L. Johnston, Peter W. Gething, Simon I. Hay, David L. Smith, David A. Fidock:
  Modeling Within-Host Effects of Drugs on Plasmodium falciparum Transmission and Prospects for Malaria Elimination.
• 
  Biswa Sengupta, Simon Barry Laughlin, Jeremy Edward Niven:
  Consequences of Converting Graded to Action Potentials upon Neural Information Coding and Energy Efficiency.
• 
  Jean Daunizeau, Vincent Adam, Lionel Rigoux:
  VBA: A Probabilistic Treatment of Nonlinear Models for Neurobiological and Behavioural Data.
• 
  Zoltan Palmai, Christian Seifert, Frauke Gräter, Erika Balog:
  An Allosteric Signaling Pathway of Human 3-Phosphoglycerate Kinase from Force Distribution Analysis.
• 
  Zsuzsa Ákos, Róbert Beck, Máté Nagy, Tamás Vicsek, Enikö Kubinyi:
  Leadership and Path Characteristics during Walks Are Linked to Dominance Order and Individual Traits in Dogs.
• 
  Jia Chen, Haicen Yue, Qi Ouyang:
  Correlation between Oncogenic Mutations and Parameter Sensitivity of the Apoptosis Pathway Model.
• 
  Thibaut Jombart, Anne Cori, Xavier Didelot, Simon Cauchemez, Christophe Fraser, Neil M. Ferguson:
  Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data.
• 
  Matthias Rupp, Matthias R. Bauer, Rainer Wilcken, Andreas Lange, Michael Reutlinger, Frank M. Boeckler, Gisbert Schneider:
  Machine Learning Estimates of Natural Product Conformational Energies.
• 
  Nikos Vlassis, Maria Pires Pacheco, Thomas Sauter:
  Fast Reconstruction of Compact Context-Specific Metabolic Network Models.
• 
  Aidan I. Brown, Peter K. Kim, Andrew D. Rutenberg:
  PEX5 and Ubiquitin Dynamics on Mammalian Peroxisome Membranes.
• 
  Moritz Helias, Tom Tetzlaff, Markus Diesmann:
  The Correlation Structure of Local Neuronal Networks Intrinsically Results from Recurrent Dynamics.
• 
  Yi-Fei Huang, Geoffrey Brian Golding:
  Phylogenetic Gaussian Process Model for the Inference of Functionally Important Regions in Protein Tertiary Structures.
• 
  Kasper Jensen, Gianni Panagiotou, Irene Kouskoumvekaki:
  Integrated Text Mining and Chemoinformatics Analysis Associates Diet to Health Benefit at Molecular Level.
• 
  Jacob G. Scott, Anita B. Hjelmeland, Prakash Chinnaiyan, Alexander R. A. Anderson, David Basanta:
  Microenvironmental Variables Must Influence Intrinsic Phenotypic Parameters of Cancer Stem Cells to Affect Tumourigenicity.
• 
  John G. Koland:
  Coarse-Grained Molecular Simulation of Epidermal Growth Factor Receptor Protein Tyrosine Kinase Multi-Site Self-Phosphorylation.
• 
  Jaroslav Bendl, Jan Stourac, Ondrej Salanda, Antonín Pavelka, Eric D. Wieben, Jaroslav Zendulka, Jan Brezovsky, Jirí Damborský:
  PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations.
• 
  Ran Darshan, Arthur Leblois, David Hansel:
  Interference and Shaping in Sensorimotor Adaptations with Rewards.
• 
  David J. Klinke II:
  Induction of Wnt-Inducible Signaling Protein-1 Correlates with Invasive Breast Cancer Oncogenesis and Reduced Type 1 Cell-Mediated Cytotoxic Immunity: A Retrospective Study.
• 
  Behruz Bozorg, Pawel Krupinski, Henrik Jönsson:
  Stress and Strain Provide Positional and Directional Cues in Development.
• 
  W. Garrett Jenkinson, John K. Goutsias:
  Intrinsic Noise Induces Critical Behavior in Leaky Markovian Networks Leading to Avalanching.
• 
  Gesham Magombedze, Shigetoshi Eda, Vitaly V. Ganusov:
  Competition for Antigen between Th1 and Th2 Responses Determines the Timing of the Immune Response Switch during Mycobaterium avium Subspecies paratuberulosis Infection in Ruminants.
• 
  Thomas A. Dunton, Joseph E. Goose, David J. Gavaghan, Mark S. P. Sansom, James M. Osborne:
  The Free Energy Landscape of Dimerization of a Membrane Protein, NanC.
• 
  Sean T. Kelly, Jens Kremkow, Jianzhong Jin, Yushi Wang, Qi Wang, Jose-Manuel Alonso, Garrett B. Stanley:
  The Role of Thalamic Population Synchrony in the Emergence of Cortical Feature Selectivity.
• 
  Bratislav Misic, Olaf Sporns, Anthony Randal McIntosh:
  Communication Efficiency and Congestion of Signal Traffic in Large-Scale Brain Networks.
• 
  Nicole Bohme Carnegie, Rui Wang, Vladimir A. Novitsky, Victor De Gruttola:
  Linkage of Viral Sequences among HIV-Infected Village Residents in Botswana: Estimation of Linkage Rates in the Presence of Missing Data.
• 
  Shelly Mahlab, Michal Linial:
  Speed Controls in Translating Secretory Proteins in Eukaryotes - an Evolutionary Perspective.
• 
  Axel von Kamp, Steffen Klamt:
  Enumeration of Smallest Intervention Strategies in Genome-Scale Metabolic Networks.
• 
  Michela Riz, Matthias Braun, Morten Gram Pedersen:
  Mathematical Modeling of Heterogeneous Electrophysiological Responses in Human β-Cells.
• 
  Joshua Evan Auerbach, Josh C. Bongard:
  Environmental Influence on the Evolution of Morphological Complexity in Machines.
• 
  Aaron C. Miller, Linnea A. Polgreen, Philip Polgreen:
  Optimal Screening Strategies for Healthcare Associated Infections in a Multi-Institutional Setting.
• 
  Gasper Tkacik, Olivier Marre, Dario Amodei, Elad Schneidman, William Bialek, Michael J. Berry II:
  Searching for Collective Behavior in a Large Network of Sensory Neurons.
• 
  Roberta Santoro, Michelle Moerel, Federico De Martino, Rainer Goebel, Kâmil Ugurbil, Essa Yacoub, Elia Formisano:
  Encoding of Natural Sounds at Multiple Spectral and Temporal Resolutions in the Human Auditory Cortex.
• 
  Mehdi Adibi, James Scott McDonald, Colin W. G. Clifford, Ehsan Arabzadeh:
  Population Decoding in Rat Barrel Cortex: Optimizing the Linear Readout of Correlated Population Responses.
• 
  Guillem Casanovas, Anashua Banerji, Flavia d'Alessio, Martina U. Muckenthaler, Stefan Legewie:
  A Multi-Scale Model of Hepcidin Promoter Regulation Reveals Factors Controlling Systemic Iron Homeostasis.
• 
  Jacqueline M. Fulvio, C. Shawn Green, Paul R. Schrater:
  Task-Specific Response Strategy Selection on the Basis of Recent Training Experience.

Volume 10, Number 2, February 2014

Editorial

• 
  Katrina Pavelin, Sangya Pundir, Jennifer A. Cham:
  Ten Simple Rules for Running Interactive Workshops.

Message from ISCB

• 
  Segun A. Fatumo, Sayane Shome, Geoff MacIntyre:
  Workshops: A Great Way to Enhance and Supplement a Degree.

Perspectives

• 
  Wouter Boomsma, Jesper Ferkinghoff-Borg, Kresten Lindorff-Larsen:
  Combining Experiments and Simulations Using the Maximum Entropy Principle.
• 
  Tapesh Santra, Walter Kolch, Boris N. Kholodenko:
  Navigating the Multilayered Organization of Eukaryotic Signaling: A New Trend in Data Integration.
• 
  Chung-Jung Tsai, Ruth Nussinov:
  A Unified View of "How Allostery Works".

Research Articles

• 
  Lingxue Zhang, Seyoung Kim:
  Learning Gene Networks under SNP Perturbations Using eQTL Datasets.
• 
  Katherine C. H. Amrine, Wesley D. Swingley, David H. Ardell:
  tRNA Signatures Reveal a Polyphyletic Origin of SAR11 Strains among Alphaproteobacteria.
• 
  Yu Hu, Joel Zylberberg, Eric Shea-Brown:
  The Sign Rule and Beyond: Boundary Effects, Flexibility, and Noise Correlations in Neural Population Codes.
• 
  Thomas Garcia, Leonardo Gregory Brunnet, Silvia De Monte:
  Differential Adhesion between Moving Particles as a Mechanism for the Evolution of Social Groups.
• 
  Cristina Savin, Peter Dayan, Máté Lengyel:
  Optimal Recall from Bounded Metaplastic Synapses: Predicting Functional Adaptations in Hippocampal Area CA3.
• 
  Andrea Riba, Carla Bosia, Mariama El Baroudi, Laura Ollino, Michele Caselle:
  A Combination of Transcriptional and MicroRNA Regulation Improves the Stability of the Relative Concentrations of Target Genes.
• 
  Frederick A. Matsen IV, Christopher T. Small, Khanh Soliven, Gregory A. Engel, Mostafa M. Feeroz, Xiaoxing Wang, Karen L. Craig, M. Kamrul Hasan, Michael Emerman, Maxine L. Linial, Lisa Jones-Engel:
  A Novel Bayesian Method for Detection of APOBEC3-Mediated Hypermutation and Its Application to Zoonotic Transmission of Simian Foamy Viruses.
• 
  Pascal Carrivain, Maria Barbi, Jean-Marc Victor:
  In Silico Single-Molecule Manipulation of DNA with Rigid Body Dynamics.
• 
  James C. Gumbart, Morgan Beeby, Grant J. Jensen, Benoît Roux:
  Escherichia coli Peptidoglycan Structure and Mechanics as Predicted by Atomic-Scale Simulations.
• 
  Oliver W. Layton, N. Andrew Browning:
  A Unified Model of Heading and Path Perception in Primate MSTd.
• 
  Kerstin Hünniger, Teresa Lehnert, Kristin Bieber, Ronny Martin, Marc Thilo Figge, Oliver Kurzai:
  A Virtual Infection Model Quantifies Innate Effector Mechanisms and Candida albicans Immune Escape in Human Blood.
• 
  Oscar Lao, Fan Liu, Andreas Wollstein, Manfred Kayser:
  GAGA: A New Algorithm for Genomic Inference of Geographic Ancestry Reveals Fine Level Population Substructure in Europeans.
• 
  Elad Noor, Arren Bar-Even, Avi I. Flamholz, Ed Reznik, Wolfram Liebermeister, Ron Milo:
  Pathway Thermodynamics Highlights Kinetic Obstacles in Central Metabolism.
• 
  Anupam Chowdhury, Ali R. Zomorrodi, Costas D. Maranas:
  k-OptForce: Integrating Kinetics with Flux Balance Analysis for Strain Design.
• 
  Alan E. Bilsland, Katrina Stevenson, Yu Liu, Stacey Hoare, Claire J. Cairney, Jon Roffey, W. Nicol Keith:
  Mathematical Model of a Telomerase Transcriptional Regulatory Network Developed by Cell-Based Screening: Analysis of Inhibitor Effects and Telomerase Expression Mechanisms.
• 
  Shyam Srinivasan, Jia Sheng Hu, D. Spencer Currle, Ernest S. Fung, Wayne B. Hayes, Arthur D. Lander, Edwin S. Monuki:
  A BMP-FGF Morphogen Toggle Switch Drives the Ultrasensitive Expression of Multiple Genes in the Developing Forebrain.
• 
  Florian Lesaint, Olivier Sigaud, Shelly B. Flagel, Terry E. Robinson, Mehdi Khamassi:
  Modelling Individual Differences in the Form of Pavlovian Conditioned Approach Responses: A Dual Learning Systems Approach with Factored Representations.
• 
  Saliha Ece Acuner Ozbabacan, Attila Gürsoy, Ruth Nussinov, Ozlem Keskin:
  The Structural Pathway of Interleukin 1 (IL-1) Initiated Signaling Reveals Mechanisms of Oncogenic Mutations and SNPs in Inflammation and Cancer.
• 
  Zeina Shreif, Vipul Periwal:
  A Network Characteristic That Correlates Environmental and Genetic Robustness.
• 
  Markku Nurhonen, Kari Auranen:
  Optimal Serotype Compositions for Pneumococcal Conjugate Vaccination under Serotype Replacement.
• 
  Brian G. Pierce, Lance M. Hellman, Moushumi Hossain, Nishant K. Singh, Craig W. Vander Kooi, Zhiping Weng, Brian M. Baker:
  Computational Design of the Affinity and Specificity of a Therapeutic T Cell Receptor.
• 
  Germán A. Enciso, Douglas R. Kellogg, Arturo Vargas:
  Compact Modeling of Allosteric Multisite Proteins: Application to a Cell Size Checkpoint.
• 
  Peilin Jia, Zhongming Zhao:
  VarWalker: Personalized Mutation Network Analysis of Putative Cancer Genes from Next-Generation Sequencing Data.
• 
  Chad Liu, Chuan-Yuan Li, Fan Yuan:
  Mathematical Modeling of the Phoenix Rising Pathway.
• 
  Lili X. Peng, Monica T. Hsu, Massimiliano Bonomi, David A. Agard, Matthew P. Jacobson:
  The Free Energy Profile of Tubulin Straight-Bent Conformational Changes, with Implications for Microtubule Assembly and Drug Discovery.
• 
  Esa Pitkänen, Paula Jouhten, Jian Hou, Muhammad Fahad Syed, Peter Blomberg, Jana Kludas, Merja Oja, Liisa Holm, Merja Penttilä, Juho Rousu, Mikko Arvas:
  Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species.
• 
  Patrick W. Sheppard, Xiaoyun Sun, Mustafa Khammash, Rona G. Giffard:
  Overexpression of Heat Shock Protein 72 Attenuates NF-κB Activation Using a Combination of Regulatory Mechanisms in Microglia.

Volume 10, Number 3, March 2014

Editorial

• 
  James M. Osborne, Miguel O. Bernabeu, Maria Bruna, Ben Calderhead, Jonathan Cooper, Neil Dalchau, Sara-Jane Dunn, Alexander G. Fletcher, Robin Freeman, Derek Groen, Bernhard Knapp, Greg J. McInerny, Gary R. Mirams, Joe Pitt-Francis, Biswa Sengupta, David W. Wright, Christian A. Yates, David Gavaghan, Stephen Emmott, Charlotte M. Deane:
  Ten Simple Rules for Effective Computational Research.

Messages from ISCB

• 
  Sebastian J. Schultheiß, Joshua SungWoo Yang, Wataru Iwasaki, Shu-Hsi Lin, Angela Jean, Magali Michaut:
  Crossing Borders for Science.
• 
  Lonnie R. Welch, Fran Lewitter, Russell Schwartz, Catherine Brooksbank, Predrag Radivojac, Bruno A. Gaëta, Maria Victoria Schneider:
  Bioinformatics Curriculum Guidelines: Toward a Definition of Core Competencies.

Perspective

• 
  Jean Peccoud:
  If You Can't Measure It, You Can't Manage It.

Review

• 
  Nico J. D. Nagelkerke, Paul Arora, Prabhat Jha, Brian Williams, Lyle McKinnon, Sake J. De Vlas:
  The Rise and Fall of HIV in High-Prevalence Countries: A Challenge for Mathematical Modeling.

Research Articles

• 
  Florian Klimm, Danielle S. Bassett, Jean M. Carlson, Peter J. Mucha:
  Resolving Structural Variability in Network Models and the Brain.
• 
  Jianzhu Ma, Sheng Wang, Zhiyong Wang, Jinbo Xu:
  MRFalign: Protein Homology Detection through Alignment of Markov Random Fields.
• 
  Shaun Mahony, Matthew D. Edwards, Esteban O. Mazzoni, Richard I. Sherwood, Akshay Kakumanu, Carolyn A. Morrison, Hynek Wichterle, David K. Gifford:
  An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding.
• 
  Emily Berger, Deniz Yörükoglu, Jian Peng, Bonnie Berger:
  HapTree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data.
• 
  Ewa Szczurek, Niko Beerenwinkel:
  Modeling Mutual Exclusivity of Cancer Mutations.
• 
  Chase Cockrell, Scott Christley, Gary An:
  Investigation of Inflammation and Tissue Patterning in the Gut Using a Spatially Explicit General-Purpose Model of Enteric Tissue (SEGMEnT).
• 
  David Kappel, Bernhard Nessler, Wolfgang Maass:
  STDP Installs in Winner-Take-All Circuits an Online Approximation to Hidden Markov Model Learning.
• 
  Armin Töpfer, Tobias Marschall, Rowena A. Bull, Fabio Luciani, Alexander Schönhuth, Niko Beerenwinkel:
  Viral Quasispecies Assembly via Maximal Clique Enumeration.
• 
  Jian Zhou, Olga G. Troyanskaya:
  Global Quantitative Modeling of Chromatin Factor Interactions.
• 
  Wondimu Teka, Toma M. Marinov, Fidel Santamaría:
  Neuronal Spike Timing Adaptation Described with a Fractional Leaky Integrate-and-Fire Model.
• 
  Adrien Fauré, Barbara M. I. Vreede, Élio Sucena, Claudine Chaouiya:
  A Discrete Model of Drosophila Eggshell Patterning Reveals Cell-Autonomous and Juxtacrine Effects.
• 
  Fabian Konrath, Johannes Witt, Thomas Sauter, Dagmar Kulms:
  Identification of New IκBα Complexes by an Iterative Experimental and Mathematical Modeling Approach.
• 
  Alexandros Goulas, Matteo Bastiani, Gleb Bezgin, Harry B. M. Uylings, Alard Roebroeck, Peter Stiers:
  Comparative Analysis of the Macroscale Structural Connectivity in the Macaque and Human Brain.
• 
  Samanthe M. Lyons, Wenlong Xu, June Medford, Ashok Prasad:
  Loads Bias Genetic and Signaling Switches in Synthetic and Natural Systems.
• 
  Noah C. Benson, Omar H. Butt, David H. Brainard, Geoffrey Karl Aguirre:
  Correction of Distortion in Flattened Representations of the Cortical Surface Allows Prediction of V1-V3 Functional Organization from Anatomy.
• 
  Megan A. Cummins, Pavan J. Dalal, Marco Bugana, Stefano Severi, Eric A. Sobie:
  Comprehensive Analyses of Ventricular Myocyte Models Identify Targets Exhibiting Favorable Rate Dependence.
• 
  Colin J. Worby, Marc Lipsitch, William P. Hanage:
  Within-Host Bacterial Diversity Hinders Accurate Reconstruction of Transmission Networks from Genomic Distance Data.
• 
  Nguyen T. Nguyen, Xiaolin Zhang, Cathy Wu, Richard A. Lange, Robert J. Chilton, Merry L. Lindsey, Yufang Jin:
  Integrative Computational and Experimental Approaches to Establish a Post-Myocardial Infarction Knowledge Map.
• 
  Hazem Toutounji, Gordon Pipa:
  Spatiotemporal Computations of an Excitable and Plastic Brain: Neuronal Plasticity Leads to Noise-Robust and Noise-Constructive Computations.
• 
  Teresa Szczepinska, Jan Kutner, Michal Kopczynski, Krzysztof Pawlowski, Andrzej Dziembowski, Andrzej Kudlicki, Krzysztof Ginalski, Maga Rowicka:
  Probabilistic Approach to Predicting Substrate Specificity of Methyltransferases.
• 
  Lilach Soreq, Alessandro Guffanti, Nathan Salomonis, Alon Simchovitz, Zvi Israel, Hagai Bergman, Hermona Soreq:
  Long Non-Coding RNA and Alternative Splicing Modulations in Parkinson's Leukocytes Identified by RNA Sequencing.
• 
  Yili Zhang, Paul Smolen, Douglas A. Baxter, John H. Byrne:
  Computational Analyses of Synergism in Small Molecular Network Motifs.
• 
  Arnaud Messé, David Rudrauf, Habib Benali, Guillaume Marrelec:
  Relating Structure and Function in the Human Brain: Relative Contributions of Anatomy, Stationary Dynamics, and Non-stationarities.
• 
  Vladimir A. Kazeev, Mustafa Khammash, Michael Nip, Christoph Schwab:
  Direct Solution of the Chemical Master Equation Using Quantized Tensor Trains.
• 
  András György, Domitilla Del Vecchio:
  Modular Composition of Gene Transcription Networks.
• 
  Ramya Gamini, Wei Han, John E. Stone, Klaus Schulten:
  Assembly of Nsp1 Nucleoporins Provides Insight into Nuclear Pore Complex Gating.
• 
  Mingming Chen, Daqing Guo, Tiebin Wang, Wei Jing, Yang Xia, Peng Xu, Cheng Luo, Pedro A. Valdés-Sosa, Dezhong Yao:
  Bidirectional Control of Absence Seizures by the Basal Ganglia: A Computational Evidence.
• 
  Michael Pargett, Ann E. Rundell, Gregery T. Buzzard, David M. Umulis:
  Model-Based Analysis for Qualitative Data: An Application in Drosophila Germline Stem Cell Regulation.
• 
  Lars Ole Schwen, Markus Krauss, Christoph Niederalt, Felix Gremse, Fabian Kiessling, Andrea Schenk, Tobias Preusser, Lars Kuepfer:
  Spatio-Temporal Simulation of First Pass Drug Perfusion in the Liver.
• 
  Sepp Kollmorgen, Richard H. R. Hahnloser:
  Dynamic Alignment Models for Neural Coding.
• 
  James Lu, Katrin Hübner, M. Nazeem Nanjee, Eliot A. Brinton, Norman A. Mazer:
  An In-Silico Model of Lipoprotein Metabolism and Kinetics for the Evaluation of Targets and Biomarkers in the Reverse Cholesterol Transport Pathway.
• 
  Andrey Rzhetsky, Steven C. Bagley, Kanix Wang, Christopher S. Lyttle, Edwin H. Cook Jr., Russ B. Altman, Robert D. Gibbons:
  Environmental and State-Level Regulatory Factors Affect the Incidence of Autism and Intellectual Disability.
• 
  Saurabh Gombar, Thomas MacCarthy, Aviv Bergman:
  Epigenetics Decouples Mutational from Environmental Robustness. Did It Also Facilitate Multicellularity?
• 
  Md. Abul Hassan Samee, Saurabh Sinha:
  Quantitative Modeling of a Gene's Expression from Its Intergenic Sequence.
• 
  Jörn-Philipp Lies, Ralf M. Häfner, Matthias Bethge:
  Slowness and Sparseness Have Diverging Effects on Complex Cell Learning.
• 
  Partha S. Bhagavatula, Charles Claudianos, Michael R. Ibbotson, Mandyam V. Srinivasan:
  Behavioral Lateralization and Optimal Route Choice in Flying Budgerigars.
• 
  Alexandra Jilkine, Ryan N. Gutenkunst:
  Effect of Dedifferentiation on Time to Mutation Acquisition in Stem Cell-Driven Cancers.
• 
  Navneet Bung, Meenakshi Pradhan, Harini Srinivasan, Gopalakrishnan Bulusu:
  Structural Insights into E. coli Porphobilinogen Deaminase during Synthesis and Exit of 1-Hydroxymethylbilane.
• 
  Tatsunori B. Hashimoto, Matthew D. Edwards, David K. Gifford:
  Universal Count Correction for High-Throughput Sequencing.
• 
  Lit-Hsin Loo, Danai Laksameethanasan, Yi-Ling Tung:
  Quantitative Protein Localization Signatures Reveal an Association between Spatial and Functional Divergences of Proteins.

Correction

• 
  Correction: A Combination of Transcriptional and MicroRNA Regulation Improves the Stability of the Relative Concentrations of Target Genes.

Volume 10, Number 4, April 2014

Editorial

• 
  Alyssa Goodman, Alberto Pepe, Alexander W. Blocker, Christine L. Borgman, Kyle Cranmer, Mercè Crosas, Rosanne Di Stefano, Yolanda Gil, Paul Groth, Margaret L. Hedstrom, David W. Hogg, Vinay Kashyap, Ashish Mahabal, Aneta Siemiginowska, Aleksandra B. Slavkovic:
  Ten Simple Rules for the Care and Feeding of Scientific Data.

Message from ISCB

• 
  Christiana N. Fogg, Diane E. Kovats:
  ISMB 2014 - The Premier Conference for the World's Computational Biologists.

Education

• 
  Michelle D. Brazas, Fran Lewitter, Maria Victoria Schneider, Celia W. G. van Gelder, Patricia M. Palagi:
  A Quick Guide to Genomics and Bioinformatics Training for Clinical and Public Audiences.

Perspective

• 
  Segun A. Fatumo, Moses P. Adoga, Opeolu O. Ojo, Olugbenga Oluseun Oluwagbemi, Tolulope Adeoye, Itunuoluwa Ewejobi, Marion O. Adebiyi, Ezekiel F. Adebiyi, Clement Bewaji, Oyekanmi Nashiru:
  Computational Biology and Bioinformatics in Nigeria.

Review

• 
  Andrea Insabato, Laura Dempere-Marco, Mario Pannunzi, Gustavo Deco, Ranulfo Romo:
  The Influence of Spatiotemporal Structure of Noisy Stimuli in Decision Making.

Research Articles

• 
  Ke Tang, Jinfeng Zhang, Jie Liang:
  Fast Protein Loop Sampling and Structure Prediction Using Distance-Guided Sequential Chain-Growth Monte Carlo Method.
• 
  Leonardo L. Gollo, Claudio R. Mirasso, Olaf Sporns, Michael Breakspear:
  Mechanisms of Zero-Lag Synchronization in Cortical Motifs.
• 
  Qing-Miao Nie, Akio Togashi, Takeshi N. Sasaki, Mitsunori Takano, Masaki Sasai, Tomoki P. Terada:
  Coupling of Lever Arm Swing and Biased Brownian Motion in Actomyosin.
• 
  Wes Maciejewski, Feng Fu, Christoph Hauert:
  Evolutionary Game Dynamics in Populations with Heterogenous Structures.
• 
  Vincent Frappier, Rafael J. Najmanovich:
  A Coarse-Grained Elastic Network Atom Contact Model and Its Use in the Simulation of Protein Dynamics and the Prediction of the Effect of Mutations.
• 
  Aleksej Zelezniak, Steven Sheridan, Kiran Raosaheb Patil:
  Contribution of Network Connectivity in Determining the Relationship between Gene Expression and Metabolite Concentration Changes.
• 
  Adam M. Feist, Harish Nagarajan, Amelia-Elena Rotaru, Pier-Luc Tremblay, Tian Zhang, Kelly P. Nevin, Derek R. Lovley, Karsten Zengler:
  Constraint-Based Modeling of Carbon Fixation and the Energetics of Electron Transfer in Geobacter metallireducens.
• 
  Daniel Machado, Markus J. Herrgård:
  Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism.
• 
  Wan Yang, Alicia Karspeck, Jeffrey Shaman:
  Comparison of Filtering Methods for the Modeling and Retrospective Forecasting of Influenza Epidemics.
• 
  Franco M. Neri, Alex R. Cook, Gavin J. Gibson, Tim R. Gottwald, Christopher A. Gilligan:
  Bayesian Analysis for Inference of an Emerging Epidemic: Citrus Canker in Urban Landscapes.
• 
  Grace W. Tang, Russ B. Altman:
  Knowledge-based Fragment Binding Prediction.
• 
  Matteo Farinella, Daniel T. Ruedt, Padraig Gleeson, Frederic Lanore, R. Angus Silver:
  Glutamate-Bound NMDARs Arising from In Vivo-like Network Activity Extend Spatio-temporal Integration in a L5 Cortical Pyramidal Cell Model.
• 
  Thomas S. B. Schmidt, João F. Matias Rodrigues, Christian von Mering:
  Ecological Consistency of SSU rRNA-Based Operational Taxonomic Units at a Global Scale.
• 
  Hao Bai, Matthew D. Rolfe, Wenjing Jia, Simon Coakley, Robert K. Poole, Jeffrey Green, Mike Holcombe:
  Agent-Based Modeling of Oxygen-Responsive Transcription Factors in Escherichia coli.
• 
  Thomas Walenda, Thomas Stiehl, Hanna Braun, Julia Fröbel, Anthony D. Ho, Thomas Schroeder, Tamme W. Goecke, Björn Rath, Ulrich Germing, Anna K. Marciniak-Czochra, Wolfgang Wagner:
  Feedback Signals in Myelodysplastic Syndromes: Increased Self-Renewal of the Malignant Clone Suppresses Normal Hematopoiesis.
• 
  Roland F. Schwarz, Anne Trinh, Botond Sipos, James D. Brenton, Nick Goldman, Florian Markowetz:
  Phylogenetic Quantification of Intra-tumour Heterogeneity.
• 
  Man Chon U, Eric Talevich, Samiksha Katiyar, Khaled Rasheed, Natarajan Kannan:
  Prediction and Prioritization of Rare Oncogenic Mutations in the Cancer Kinome Using Novel Features and Multiple Classifiers.
• 
  Thomas D. Cuypers, Paulien Hogeweg:
  A Synergism between Adaptive Effects and Evolvability Drives Whole Genome Duplication to Fixation.
• 
  Hamed Nili, Cai Wingfield, Alexander Walther, Li Su, William D. Marslen-Wilson, Nikolaus Kriegeskorte:
  A Toolbox for Representational Similarity Analysis.
• 
  Robert Brown, Bogdan Pasaniuc:
  Enhanced Methods for Local Ancestry Assignment in Sequenced Admixed Individuals.
• 
  Bailu Si, Sandro Romani, Misha Tsodyks:
  Continuous Attractor Network Model for Conjunctive Position-by-Velocity Tuning of Grid Cells.
• 
  Lander Willem, Sean Stijven, Ekaterina Vladislavleva, Jan Broeckhove, Philippe Beutels, Niel Hens:
  Active Learning to Understand Infectious Disease Models and Improve Policy Making.
• 
  Bharath Ananthasubramaniam, Erik D. Herzog, Hanspeter Herzel:
  Timing of Neuropeptide Coupling Determines Synchrony and Entrainment in the Mammalian Circadian Clock.
• 
  Laetitia Canini, Jessica M. Conway, Alan S. Perelson, Fabrice Carrat:
  Impact of Different Oseltamivir Regimens on Treating Influenza A Virus Infection and Resistance Emergence: Insights from a Modelling Study.
• 
  David A. Rasmussen, Erik M. Volz, Katia Koelle:
  Phylodynamic Inference for Structured Epidemiological Models.
• 
  David J. McIver, John S. Brownstein:
  Wikipedia Usage Estimates Prevalence of Influenza-Like Illness in the United States in Near Real-Time.
• 
  Florent Meyniel, Lou Safra, Mathias Pessiglione:
  How the Brain Decides When to Work and When to Rest: Dissociation of Implicit-Reactive from Explicit-Predictive Computational Processes.
• 
  Lars Boukharta, Hugo Gutiérrez-de-Terán, Johan Åqvist:
  Computational Prediction of Alanine Scanning and Ligand Binding Energetics in G-Protein Coupled Receptors.
• 
  Ambuj Kumar, Rituraj Purohit:
  Use of Long Term Molecular Dynamics Simulation in Predicting Cancer Associated SNPs.
• 
  Dominik Wodarz, Ron Sorace, Natalia L. Komarova:
  Dynamics of Cellular Responses to Radiation.
• 
  Kirill Serkh, Daniel B. Forger:
  Optimal Schedules of Light Exposure for Rapidly Correcting Circadian Misalignment.
• 
  Kinya Hotta, Soumya Ranganathan, Ruchuan Liu, Fei Wu, Hiroaki Machiyama, Rong Gao, Hiroaki Hirata, Neelesh Soni, Takashi Ohe, Christopher W. V. Hogue, M. S. Madhusudhan, Yasuhiro Sawada:
  Biophysical Properties of Intrinsically Disordered p130Cas Substrate Domain - Implication in Mechanosensing.
• 
  Remco R. Bouckaert, Joseph Heled, Denise Kühnert, Timothy G. Vaughan, Chieh-Hsi Wu, Dong Xie, Marc A. Suchard, Andrew Rambaut, Alexei J. Drummond:
  BEAST 2: A Software Platform for Bayesian Evolutionary Analysis.
• 
  Jeffrey P. Perley, Judith Mikolajczak, Marietta L. Harrison, Gregery T. Buzzard, Ann E. Rundell:
  Multiple Model-Informed Open-Loop Control of Uncertain Intracellular Signaling Dynamics.
• 
  Bram Kuijper, Rufus A. Johnstone, Stuart Townley:
  The Evolution of Multivariate Maternal Effects.
• 
  Felix Campelo, Michael M. Kozlov:
  Sensing Membrane Stresses by Protein Insertions.
• 
  Bertrand Fontaine, José Luis Peña, Romain Brette:
  Spike-Threshold Adaptation Predicted by Membrane Potential Dynamics In Vivo.
• 
  Harriet L. Mills, Steven Riley:
  The Spatial Resolution of Epidemic Peaks.
• 
  Yunqiang Bian, Cheng Tan, Jun Wang, Yuebiao Sheng, Jian Zhang, Wei Wang:
  Atomistic Picture for the Folding Pathway of a Hybrid-1 Type Human Telomeric DNA G-quadruplex.
• 
  Sergio Ruiz-Carmona, Daniel Alvarez-Garcia, Nicolas Foloppe, A. Beatriz Garmendia-Doval, Szilveszter Juhos, Peter Schmidtke, Xavier Barril, Roderick E. Hubbard, S. David Morley:
  rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids.
• 
  Bram Vrancken, Andrew Rambaut, Marc A. Suchard, Alexei J. Drummond, Guy Baele, Inge Derdelinckx, Eric Van Wijngaerden, Anne-Mieke Vandamme, Kristel Van Laethem, Philippe Lemey:
  The Genealogical Population Dynamics of HIV-1 in a Large Transmission Chain: Bridging within and among Host Evolutionary Rates.
• 
  Avisek Das, Mert Gur, Mary Hongying Cheng, Sunhwan Jo, Ivet Bahar, Benoît Roux:
  Exploring the Conformational Transitions of Biomolecular Systems Using a Simple Two-State Anisotropic Network Model.
• 
  Paul J. McMurdie, Susan P. Holmes:
  Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible.
• 
  Marjet Elemans, Arnaud Florins, Luc Willems, Becca Asquith:
  Rates of CTL Killing in Persistent Viral Infection In Vivo.
• 
  Margarete Boos, Johannes Pritz, Simon Lange, Michael Belz:
  Leadership in Moving Human Groups.
• 
  Justin S. Hogg, Leonard A. Harris, Lori J. Stover, Niketh S. Nair, James R. Faeder:
  Exact Hybrid Particle/Population Simulation of Rule-Based Models of Biochemical Systems.
• 
  Dávid Samu, Anil K. Seth, Thomas Nowotny:
  Influence of Wiring Cost on the Large-Scale Architecture of Human Cortical Connectivity.
• 
  Gerard J. P. van Westen, Anna Gaulton, John P. Overington:
  Chemical, Target, and Bioactive Properties of Allosteric Modulation.

Corrections

• 
  Correction: Task-Based Core-Periphery Organization of Human Brain Dynamics.
• 
  Correction: Learning Gene Networks under SNP Perturbations Using eQTL Datasets.

Volume 10, Number 5, May 2014

Editorial

• 
  Bin Chen:
  Ten Simple Rules for Internship in a Pharmaceutical Company.

Messages from ISCB

• 
  Virginie Bernard, Sebastian J. Schultheiss, Magali Michaut:
  Learn from the Best.
• 
  Christiana N. Fogg, Diane E. Kovats:
  2014 ISCB Accomplishment by a Senior Scientist Award: Gene Myers.
• 
  Olugbenga Oluseun Oluwagbemi, Marion O. Adebiyi, Segun A. Fatumo, Geoff MacIntyre:
  Paving the Way Towards a Successful and Fulfilling Career in Computational Biology.

Review

• 
  Lei Xie, Xiaoxia Ge, Hepan Tan, Li Xie, Yinliang Zhang, Thomas Hart, Xiaowei Yang, Philip E. Bourne:
  Towards Structural Systems Pharmacology to Study Complex Diseases and Personalized Medicine.

Research Articles

• 
  Jisoo Park, Heather C. Wick, Daniel E. Kee, Keith Noto, Jill L. Maron, Donna K. Slonim:
  Finding Novel Molecular Connections between Developmental Processes and Disease.
• 
  Deborah Chasman, Brandi Gancarz, Linhui Hao, Michael Ferris, Paul Ahlquist, Mark Craven:
  Inferring Host Gene Subnetworks Involved in Viral Replication.
• 
  Matthew S. Graus, Carolyn Pehlke, Michael J. Wester, Lisa B. Davidson, Stanly L. Steinberg, Aaron K. Neumann:
  A New Tool to Quantify Receptor Recruitment to Cell Contact Sites during Host-Pathogen Interaction.
• 
  Neetika Nath, John B. O. Mitchell, Gustavo Caetano-Anollés:
  The Natural History of Biocatalytic Mechanisms.
• 
  Eric A. Yen, Aaron Tsay, Jérôme Waldispühl, Jackie Vogel:
  Exploration of the Dynamic Properties of Protein Complexes Predicted from Spatially Constrained Protein-Protein Interaction Networks.
• 
  Devin Greene, Kristina Crona:
  The Changing Geometry of a Fitness Landscape Along an Adaptive Walk.
• 
  Aistis Stankevicius, Quentin J. M. Huys, Aditi Kalra, Peggy Seriès:
  Optimism as a Prior Belief about the Probability of Future Reward.
• 
  Jussi T. Koivumäki, Gunnar Seemann, Mary M. Maleckar, Pasi Tavi:
  In Silico Screening of the Key Cellular Remodeling Targets in Chronic Atrial Fibrillation.
• 
  Tal Neiman, Yonatan Loewenstein:
  Spatial Generalization in Operant Learning: Lessons from Professional Basketball.
• 
  Rodolphe Thiébaut, Julia Drylewicz, Mélanie Prague, Christine Lacabaratz, Stéphanie Beq, Ana Jarne, Thérèse Croughs, Rafick-Pierre Sekaly, Michael M. Lederman, Irini Sereti, Daniel Commenges, Yves Lévy:
  Quantifying and Predicting the Effect of Exogenous Interleukin-7 on CD4⁺T Cells in HIV-1 Infection.
• 
  Julien Papaïx, Jeremy J. Burdon, Christian Lannou, Peter H. Thrall:
  Evolution of Pathogen Specialisation in a Host Metapopulation: Joint Effects of Host and Pathogen Dispersal.
• 
  Klas H. Pettersen, Scott M. Bugenhagen, Javaid Nauman, Daniel A. Beard, Stig W. Omholt:
  Arterial Stiffening Provides Sufficient Explanation for Primary Hypertension.
• 
  Kuang-Yui M. Chen, Jiaming Sun, Jason S. Salvo, David Baker, Patrick Barth:
  High-Resolution Modeling of Transmembrane Helical Protein Structures from Distant Homologues.
• 
  Oriol Güell, Francesc Sagués, M. Ángeles Serrano:
  Essential Plasticity and Redundancy of Metabolism Unveiled by Synthetic Lethality Analysis.
• 
  Drazen Petrov, Bojan Zagrovic:
  Are Current Atomistic Force Fields Accurate Enough to Study Proteins in Crowded Environments?
• 
  César Rennó-Costa, John E. Lisman, Paul F. M. J. Verschure:
  A Signature of Attractor Dynamics in the CA3 Region of the Hippocampus.
• 
  Dan Yamin, Arieh Gavious, Eyal Solnik, Nadav Davidovitch, Ran D. Balicer, Alison P. Galvani, Joseph S. Pliskin:
  An Innovative Influenza Vaccination Policy: Targeting Last Season's Patients.
• 
  Vitaly V. Ganusov, Jeremy Auerbach:
  Mathematical Modeling Reveals Kinetics of Lymphocyte Recirculation in the Whole Organism.
• 
  Ann M. Hermundstad, Kevin S. Brown, Danielle S. Bassett, Elissa M. Aminoff, Amy Frithsen, Arianne Johnson, Christine M. Tipper, Michael B. Miller, Scott T. Grafton, Jean M. Carlson:
  Structurally-Constrained Relationships between Cognitive States in the Human Brain.
• 
  Ciira Wa Maina, Antti Honkela, Filomena Matarese, Korbinian Grote, Hendrik G. Stunnenberg, George Reid, Neil D. Lawrence, Magnus Rattray:
  Inference of RNA Polymerase II Transcription Dynamics from Chromatin Immunoprecipitation Time Course Data.
• 
  Umeshkanta Singh Thounaojam, Jianxia Cui, Sharon E. Norman, Robert J. Butera, Carmen C. Canavier:
  Slow Noise in the Period of a Biological Oscillator Underlies Gradual Trends and Abrupt Transitions in Phasic Relationships in Hybrid Neural Networks.
• 
  Ignacio J. General, Ying Liu, Mandy E. Blackburn, Wenzhi Mao, Lila M. Gierasch, Ivet Bahar:
  ATPase Subdomain IA Is a Mediator of Interdomain Allostery in Hsp70 Molecular Chaperones.
• 
  Filippo Menolascina, Gianfranco Fiore, Emanuele Orabona, Luca De Stefano, Mike Ferry, Jeff Hasty, Mario di Bernardo, Diego di Bernardo:
  In-Vivo Real-Time Control of Protein Expression from Endogenous and Synthetic Gene Networks.
• 
  Nicolas Altemose, Karen H. Miga, Mauro Maggioni, Huntington F. Willard:
  Genomic Characterization of Large Heterochromatic Gaps in the Human Genome Assembly.
• 
  Sven Dähne, Niko Wilbert, Laurenz Wiskott:
  Slow Feature Analysis on Retinal Waves Leads to V1 Complex Cells.
• 
  Wendy J. Adams, James H. Elder:
  Effects of Specular Highlights on Perceived Surface Convexity.
• 
  Masafumi Oizumi, Larissa Albantakis, Giulio Tononi:
  From the Phenomenology to the Mechanisms of Consciousness: Integrated Information Theory 3.0.
• 
  Marc S. Sherman, Barak A. Cohen:
  A Computational Framework for Analyzing Stochasticity in Gene Expression.
• 
  Marcus J. Tindall, Angela Clerk:
  Modelling Negative Feedback Networks for Activating Transcription Factor 3 Predicts a Dominant Role for miRNAs in Immediate Early Gene Regulation.
• 
  Julian Tejada, Norberto Garcia-Cairasco, Antônio Carlos Roque-da-Silva:
  Combined Role of Seizure-Induced Dendritic Morphology Alterations and Spine Loss in Newborn Granule Cells with Mossy Fiber Sprouting on the Hyperexcitability of a Computer Model of the Dentate Gyrus.
• 
  Daphna Rothschild, Erez Dekel, Jean Hausser, Anat Bren, Guy Aidelberg, Pablo Szekely, Uri Alon:
  Linear Superposition and Prediction of Bacterial Promoter Activity Dynamics in Complex Conditions.
• 
  Sílvia G. Estácio, Heinrich Krobath, Diogo Vila-Viçosa, Miguel Machuqueiro, Eugene I. Shakhnovich, Patrícia F. N. Faísca:
  A Simulated Intermediate State for Folding and Aggregation Provides Insights into ΔN6 β₂-Microglobulin Amyloidogenic Behavior.
• 
  Mauricio Macossay-Castillo, Simone Kosol, Peter Tompa, Rita Pancsa:
  Synonymous Constraint Elements Show a Tendency to Encode Intrinsically Disordered Protein Segments.
• 
  Charles J. Wilson, David Barraza, Todd Troyer, Michael A. Farries:
  Predicting the Responses of Repetitively Firing Neurons to Current Noise.
• 
  Ronny Straube:
  Reciprocal Regulation as a Source of Ultrasensitivity in Two-Component Systems with a Bifunctional Sensor Kinase.
• 
  Ali Neishabouri, A. Aldo Faisal:
  Axonal Noise as a Source of Synaptic Variability.
• 
  Marko Jusup, Tadasu Matsuo, Yoh Iwasa:
  Barriers to Cooperation Aid Ideological Rigidity and Threaten Societal Collapse.
• 
  Rajesh Balagam, Douglas B. Litwin, Fabian Czerwinski, Mingzhai Sun, Heidi B. Kaplan, Joshua W. Shaevitz, Oleg A. Igoshin:
  Myxococcus xanthus Gliding Motors Are Elastically Coupled to the Substrate as Predicted by the Focal Adhesion Model of Gliding Motility.
• 
  Niklas Hübel, Eckehard Schöll, Markus A. Dahlem:
  Bistable Dynamics Underlying Excitability of Ion Homeostasis in Neuron Models.
• 
  Fabiano Baroni, Anthony N. Burkitt, David B. Grayden:
  Interplay of Intrinsic and Synaptic Conductances in the Generation of High-Frequency Oscillations in Interneuronal Networks with Irregular Spiking.
• 
  Fianne L. P. Sips, Christian A. Tiemann, Maaike H. Oosterveer, Albert K. Groen, Peter A. J. Hilbers, Natal A. W. van Riel:
  A Computational Model for the Analysis of Lipoprotein Distributions in the Mouse: Translating FPLC Profiles to Lipoprotein Metabolism.
• 
  Nan Zhao, Jing Ginger Han, Chi-Ren Shyu, Dmitry Korkin:
  Determining Effects of Non-synonymous SNPs on Protein-Protein Interactions using Supervised and Semi-supervised Learning.
• 
  Michael V. LeVine, Harel Weinstein:
  NbIT - A New Information Theory-Based Analysis of Allosteric Mechanisms Reveals Residues that Underlie Function in the Leucine Transporter LeuT.

Corrections

• 
  Correction: Quantitative Analysis of Glycerol Accumulation, Glycolysis and Growth under Hyper Osmotic Stress.
• 
  Correction: Long Non-Coding RNA and Alternative Splicing Modulations in Parkinson's Leukocytes Identified by RNA Sequencing.
• 
  Correction: Single Sample Expression-Anchored Mechanisms Predict Survival in Head and Neck Cancer.

Volume 10, Number 6, June 2014

Editorial

• 
  Philip E. Bourne:
  Ten Simple Rules for Approaching a New Job.

Message from ISCB

• 
  Christiana N. Fogg, Diane E. Kovats:
  International Society for Computational Biology Honors Dana Pe'er with Top Bioinformatics/Computational Biology Award for 2014.

Education

• 
  David B. Searls:
  A New Online Computational Biology Curriculum.

Research Articles

• 
  Shannon R. Moore, Gerald M. Saidel, Ulf Knothe, Melissa L. Knothe Tate:
  Mechanistic, Mathematical Model to Predict the Dynamics of Tissue Genesis in Bone Defects via Mechanical Feedback and Mediation of Biochemical Factors.
• 
  Noah C. Benson, Jeremy R. Manning, David H. Brainard:
  Unsupervised Learning of Cone Spectral Classes from Natural Images.
• 
  Jake M. Ferguson, Jessica B. Langebrake, Vincent L. Cannataro, Andres J. Garcia, Elizabeth A. Hamman, Maia Martcheva, Craig W. Osenberg:
  Optimal Sampling Strategies for Detecting Zoonotic Disease Epidemics.
• 
  Ankit Gupta, Corentin Briat, Mustafa Khammash:
  A Scalable Computational Framework for Establishing Long-Term Behavior of Stochastic Reaction Networks.
• 
  Sebastian Pechmann, Judith Frydman:
  Interplay between Chaperones and Protein Disorder Promotes the Evolution of Protein Networks.
• 
  Genevieve D. Erwin, Nir Oksenberg, Rebecca M. Truty, Dennis Kostka, Karl K. Murphy, Nadav Ahituv, Katherine S. Pollard, John A. Capra:
  Integrating Diverse Datasets Improves Developmental Enhancer Prediction.
• 
  Jaime Iranzo, Manuel J. Gómez, Francisco J. López de Saro, Susanna C. Manrubia:
  Large-Scale Genomic Analysis Suggests a Neutral Punctuated Dynamics of Transposable Elements in Bacterial Genomes.
• 
  Sergei V. Krivov, Hayley Fenton, Paul J. Goldsmith, Rajendra K. Prasad, Julie Fisher, Emanuele Paci:
  Optimal Reaction Coordinate as a Biomarker for the Dynamics of Recovery from Kidney Transplant.
• 
  Christian Diener, Gabriele Schreiber, Wolfgang Giese, Gabriel del Rio, Andreas Schröder, Edda Klipp:
  Yeast Mating and Image-Based Quantification of Spatial Pattern Formation.
• 
  Joe DeBartolo, Mikko Taipale, Amy E. Keating:
  Genome-Wide Prediction and Validation of Peptides That Bind Human Prosurvival Bcl-2 Proteins.
• 
  Yann S. Dufour, Xiongfei Fu, Luis Hernandez-Nunez, Thierry Emonet:
  Limits of Feedback Control in Bacterial Chemotaxis.
• 
  Doron Shem-Tov, Eran Halperin:
  Historical Pedigree Reconstruction from Extant Populations Using PArtitioning of RElatives (PREPARE).
• 
  Ellinor Haglund, Joanna I. Sulkowska, Jeffrey K. Noel, Heiko Lammert, José N. Onuchic, Patricia A. Jennings:
  Pierced Lasso Bundles Are a New Class of Knot-like Motifs.
• 
  Daniel J. Laydon, Anat Melamed, Aaron Sim, Nicolas A. Gillet, Kathleen Sim, Sam Darko, J. Simon Kroll, Daniel C. Douek, David A. Price, Charles R. M. Bangham, Becca Asquith:
  Quantification of HTLV-1 Clonality and TCR Diversity.
• 
  Mamiko Arai, Vicky Brandt, Yuri Dabaghian:
  The Effects of Theta Precession on Spatial Learning and Simplicial Complex Dynamics in a Topological Model of the Hippocampal Spatial Map.
• 
  Jerry S. Chen, Abygail M. Gumbayan, Robert W. Zeller, Joseph M. Mahaffy:
  An Expanded Notch-Delta Model Exhibiting Long-Range Patterning and Incorporating MicroRNA Regulation.
• 
  Nadine Töpfer, Federico Scossa, Alisdair R. Fernie, Zoran Nikoloski:
  Variability of Metabolite Levels Is Linked to Differential Metabolic Pathways in Arabidopsis's Responses to Abiotic Stresses.
• 
  Luigi Acerbi, Sethu Vijayakumar, Daniel M. Wolpert:
  On the Origins of Suboptimality in Human Probabilistic Inference.
• 
  Carlos Castro-Gonzalez, Miguel A. Luengo-Oroz, Louise Duloquin, Thierry Savy, Barbara Rizzi, Sophie Desnoulez, René Doursat, Yannick L. Kergosien, María J. Ledesma-Carbayo, Paul Bourgine, Nadine Peyriéras, Andrés Santos:
  A Digital Framework to Build, Visualize and Analyze a Gene Expression Atlas with Cellular Resolution in Zebrafish Early Embryogenesis.
• 
  Bo Hu, Yuhai Tu:
  Behaviors and Strategies of Bacterial Navigation in Chemical and Nonchemical Gradients.
• 
  Joshua T. Herbeck, John E. Mittler, Geoffrey S. Gottlieb, James I. Mullins:
  An HIV Epidemic Model Based on Viral Load Dynamics: Value in Assessing Empirical Trends in HIV Virulence and Community Viral Load.
• 
  Anca Doloc-Mihu, Ronald L. Calabrese:
  Identifying Crucial Parameter Correlations Maintaining Bursting Activity.
• 
  Borislav Savkovic, James A. Nichols, Donald Birkett, Tanya Applegate, Scott Ledger, Geoff Symonds, John M. Murray:
  A Quantitative Comparison of Anti-HIV Gene Therapy Delivered to Hematopoietic Stem Cells versus CD4+ T Cells.
• 
  Narjes Javaheri, Roland Dries, Jaap A. Kaandorp:
  Understanding the Sub-Cellular Dynamics of Silicon Transportation and Synthesis in Diatoms Using Population-Level Data and Computational Optimization.
• 
  Bruce Bobier, Terrence C. Stewart, Chris Eliasmith:
  A Unifying Mechanistic Model of Selective Attention in Spiking Neurons.
• 
  Ruth Barshir, Omer Shwartz, Ilan Y. Smoly, Esti Yeger Lotem:
  Comparative Analysis of Human Tissue Interactomes Reveals Factors Leading to Tissue-Specific Manifestation of Hereditary Diseases.
• 
  Julia R. Gog, Sébastien Ballesteros, Cécile Viboud, Lone Simonsen, Ottar N. Bjørnstad, Jeffrey Shaman, Dennis L. Chao, Farid Khan, Bryan T. Grenfell:
  Spatial Transmission of 2009 Pandemic Influenza in the US.
• 
  Noah Youngs, Duncan Penfold-Brown, Richard Bonneau, Dennis E. Shasha:
  Negative Example Selection for Protein Function Prediction: The NoGO Database.
• 
  Kevin J. Liu, Jingxuan Dai, Kathy Truong, Ying Song, Michael H. Kohn, Luay Nakhleh:
  An HMM-Based Comparative Genomic Framework for Detecting Introgression in Eukaryotes.
• 
  Daniel Silk, Paul D. W. Kirk, Chris P. Barnes, Tina Toni, Michael P. H. Stumpf:
  Model Selection in Systems Biology Depends on Experimental Design.
• 
  Martin H. Schaefer, Jae-Seong Yang, Luis Serrano, Christina Kiel:
  Protein Conservation and Variation Suggest Mechanisms of Cell Type-Specific Modulation of Signaling Pathways.
• 
  Guocai Chen, Michael J. Cairelli, Halil Kilicoglu, Dongwook Shin, Thomas C. Rindflesch:
  Augmenting Microarray Data with Literature-Based Knowledge to Enhance Gene Regulatory Network Inference.
• 
  Patricia Garcia-Cañadilla, Paula A. Rudenick, Fátima Crispi, Monica Cruz-Lemini, Georgina Palau-Caballero, Oscar Camara, Eduard Gratacós, Bart H. Bijnens:
  A Computational Model of the Fetal Circulation to Quantify Blood Redistribution in Intrauterine Growth Restriction.
• 
  Shira Rockowitz, Wen-Hui Lien, Erika Pedrosa, Gang Wei, Mingyan Lin, Keji Zhao, Herbert M. Lachman, Elaine Fuchs, Deyou Zheng:
  Comparison of REST Cistromes across Human Cell Types Reveals Common and Context-Specific Functions.
• 
  Michael J. McGeachie, Hsun-Hsien Chang, Scott T. Weiss:
  CGBayesNets: Conditional Gaussian Bayesian Network Learning and Inference with Mixed Discrete and Continuous Data.
• 
  Kristin Blacklock, Gennady M. Verkhivker:
  Computational Modeling of Allosteric Regulation in the Hsp90 Chaperones: A Statistical Ensemble Analysis of Protein Structure Networks and Allosteric Communications.
• 
  Junjie Wang, Lisa Tucker-Kellogg, Inn Chuan Ng, Ruirui Jia, P. S. Thiagarajan, Jacob K. White, Hanry Yu:
  The Self-Limiting Dynamics of TGF-β Signaling In Silico and In Vitro, with Negative Feedback through PPM1A Upregulation.
• 
  Ondrej Podlaha, Subhajyoti De, Mithat Gonen, Franziska Michor:
  Histone Modifications Are Associated with Transcript Isoform Diversity in Normal and Cancer Cells.
• 
  Qingrun Zhang, Quan Long, Jürg Ott:
  AprioriGWAS, a New Pattern Mining Strategy for Detecting Genetic Variants Associated with Disease through Interaction Effects.
• 
  Lorena Sigaut, John E. Pearson, Alejandro Colman-Lerner, Silvina Ponce Dawson:
  Messages Do Diffuse Faster than Messengers: Reconciling Disparate Estimates of the Morphogen Bicoid Diffusion Coefficient.
• 
  Xin Tang, Alireza Tofangchi, Sandeep V. Anand, Taher A. Saif:
  A Novel Cell Traction Force Microscopy to Study Multi-Cellular System.
• 
  Johanni Brea, Robert Urbanczik, Walter Senn:
  A Normative Theory of Forgetting: Lessons from the Fruit Fly.
• 
  Trygve Solstad, Hosam N. Yousif, Terrence J. Sejnowski:
  Place Cell Rate Remapping by CA3 Recurrent Collaterals.
• 
  Michael Kuhn, Anthony A. Hyman, Andreas Beyer:
  Coiled-Coil Proteins Facilitated the Functional Expansion of the Centrosome.
• 
  Steven W. Sowa, Michael Baldea, Lydia M. Contreras:
  Optimizing Metabolite Production Using Periodic Oscillations.

Corrections

• 
  Correction: Organism-Adapted Specificity of the Allosteric Regulation of Pyruvate Kinase in Lactic Acid Bacteria.
• 
  Correction: Collective Cell Motion in an Epithelial Sheet Can be Quantitatively Described by a Stochastic Interacting Particle Model.
• 
  Correction: Impact of Different Oseltamivir Regimens on Treating Influenza A Virus Infection and Resistance Emergence: Insights from a Modelling Study.

Volume 10, Number 7, July 2014

Message from ISCB

• 
  Jeroen de Ridder, Pieter Meysman, Olugbenga Oluseun Oluwagbemi, Thomas Abeel:
  Soft Skills: An Important Asset Acquired from Organizing Regional Student Group Activities.

Education Articles

• 
  Benjamin T. Miller, Rishi P. Singh, Vinushka Schalk, Yuri Pevzner, Jingjun Sun, Carrie S. Miller, Stefan Boresch, Toshiko Ichiye, Bernard R. Brooks, H. Lee Woodcock III:
  Web-Based Computational Chemistry Education with CHARMMing I: Lessons and Tutorial.
• 
  Frank C. Pickard IV, Benjamin T. Miller, Vinushka Schalk, Michael G. Lerner, H. Lee Woodcock III, Bernard R. Brooks:
  Web-Based Computational Chemistry Education with CHARMMing II: Coarse-Grained Protein Folding.
• 
  Bradley Scott Perrin Jr., Benjamin T. Miller, Vinushka Schalk, H. Lee Woodcock III, Bernard R. Brooks, Toshiko Ichiye:
  Web-Based Computational Chemistry Education with CHARMMing III: Reduction Potentials of Electron Transfer Proteins.

Research Articles

• 
  Benedict Anchang, Mary T. Do, Xi Zhao, Sylvia K. Plevritis:
  CCAST: A Model-Based Gating Strategy to Isolate Homogeneous Subpopulations in a Heterogeneous Population of Single Cells.
• 
  Santiago Esteban-Martín, Robert Bryn Fenwick, Jörgen Ådén, Benjamin P. Cossins, Carlos W. Bertoncini, Victor Guallar, Magnus Wolf-Watz, Xavier Salvatella:
  Correlated Inter-Domain Motions in Adenylate Kinase.
• 
  Stanca M. Ciupe, Ruy M. Ribeiro, Alan S. Perelson:
  Antibody Responses during Hepatitis B Viral Infection.
• 
  Robert Ton, Gustavo Deco, Andreas Daffertshofer:
  Structure-Function Discrepancy: Inhomogeneity and Delays in Synchronized Neural Networks.
• 
  Salim Akhter Chowdhury, Stanley E. Shackney, Kerstin Heselmeyer-Haddad, Thomas Ried, Alejandro A. Schäffer, Russell Schwartz:
  Algorithms to Model Single Gene, Single Chromosome, and Whole Genome Copy Number Changes Jointly in Tumor Phylogenetics.
• 
  Kathryn A. Loving, Andy Lin, Alan C. Cheng:
  Structure-Based Druggability Assessment of the Mammalian Structural Proteome with Inclusion of Light Protein Flexibility.
• 
  Jean-Luc Schwartz, Christophe Savariaux:
  No, There Is No 150 ms Lead of Visual Speech on Auditory Speech, but a Range of Audiovisual Asynchronies Varying from Small Audio Lead to Large Audio Lag.
• 
  Aniket Magarkar, Nawel Mele, Noha Abdel-Rahman, Sarah A. Butcher, Mika Torkkeli, Ritva Serimaa, Arja Paananen, Markus Linder, Alex Bunker:
  Hydrophobin Film Structure for HFBI and HFBII and Mechanism for Accelerated Film Formation.
• 
  Song Ke, Eugen N. Timin, Anna Stary-Weinzinger:
  Different Inward and Outward Conduction Mechanisms in Na_VMs Suggested by Molecular Dynamics Simulations.
• 
  Isaure Chauvot de Beauchêne, Ariane Allain, Nicolas Panel, Elodie Laine, Alain Trouvé, Patrice Dubreuil, Luba Tchertanov:
  Hotspot Mutations in KIT Receptor Differentially Modulate Its Allosterically Coupled Conformational Dynamics: Impact on Activation and Drug Sensitivity.
• 
  Gabriel Gonzalez, Brett Hannigan, William F. DeGrado:
  A Real-Time All-Atom Structural Search Engine for Proteins.
• 
  Christopher J. R. Illingworth, Andrej Fischer, Ville Mustonen:
  Identifying Selection in the Within-Host Evolution of Influenza Using Viral Sequence Data.
• 
  Sergey Hosid, Ilya Ioshikhes:
  Apoptotic Lymphocytes of H. sapiens Lose Nucleosomes in GC-Rich Promoters.
• 
  Junil Kim, Drieke Vandamme, Jeong-Rae Kim, Amaya Garcia Munoz, Walter Kolch, Kwang-Hyun Cho:
  Robustness and Evolvability of the Human Signaling Network.
• 
  Athanasia Papoutsi, Kyriaki Sidiropoulou, Panayiota Poirazi:
  Dendritic Nonlinearities Reduce Network Size Requirements and Mediate ON and OFF States of Persistent Activity in a PFC Microcircuit Model.
• 
  Tom Serge Weber, Irene Jaehnert, Christian Schichor, Michal Or-Guil, Jorge Carneiro:
  Quantifying the Length and Variance of the Eukaryotic Cell Cycle Phases by a Stochastic Model and Dual Nucleoside Pulse Labelling.
• 
  Hugo Gravato Marques, Arjun Bharadwaj, Fumiya Iida:
  From Spontaneous Motor Activity to Coordinated Behaviour: A Developmental Model.
• 
  Alessandro Attanasi, Andrea Cavagna, Lorenzo Del Castello, Irene Giardina, Stefania Melillo, Leonardo Parisi, Oliver Pohl, Bruno Rossaro, Edward Shen, Edmondo Silvestri, Massimiliano Viale:
  Collective Behaviour without Collective Order in Wild Swarms of Midges.
• 
  Ankur P. Parikh, Ross E. Curtis, Irene Kuhn, Sabine Becker-Weimann, Mina J. Bissell, Eric P. Xing, Wei Wu:
  Network Analysis of Breast Cancer Progression and Reversal Using a Tree-Evolving Network Algorithm.
• 
  Alessandro Barardi, Belén Sancristóbal, Jordi García-Ojalvo:
  Phase-Coherence Transitions and Communication in the Gamma Range between Delay-Coupled Neuronal Populations.
• 
  Rekin's Janky, Annelien Verfaillie, Hana Imrichová, Bram Van de Sande, Laura Standaert, Valerie Christiaens, Gert Hulselmans, Koen Herten, Marina Naval Sanchez, Delphine Potier, Dmitry Svetlichnyy, Zeynep Kalender Atak, Mark Fiers, Jean-Christophe Marine, Stein Aerts:
  iRegulon: From a Gene List to a Gene Regulatory Network Using Large Motif and Track Collections.
• 
  Anton Arkhipov, Yibing Shan, Eric T. Kim, David E. Shaw:
  Membrane Interaction of Bound Ligands Contributes to the Negative Binding Cooperativity of the EGF Receptor.
• 
  Assaf Zaritsky, Doron Kaplan, Inbal Hecht, Sari Natan, Lior Wolf, Nir S. Gov, Eshel Ben-Jacob, Ilan Tsarfaty:
  Propagating Waves of Directionality and Coordination Orchestrate Collective Cell Migration.
• 
  Antonio Rausell, Pejman Mohammadi, Paul J. McLaren, István Bartha, Ioannis Xenarios, Jacques Fellay, Amalio Telenti:
  Analysis of Stop-Gain and Frameshift Variants in Human Innate Immunity Genes.
• 
  Rubén Moreno-Bote:
  Poisson-Like Spiking in Circuits with Probabilistic Synapses.
• 
  Fabrizio Pucci, Marianne Rooman:
  Stability Curve Prediction of Homologous Proteins Using Temperature-Dependent Statistical Potentials.
• 
  Andrew McDavid, Lucas Dennis, Patrick Danaher, Greg Finak, Michael Krouse, Alice Wang, Philippa Webster, Joseph Beechem, Raphael Gottardo:
  Modeling Bi-modality Improves Characterization of Cell Cycle on Gene Expression in Single Cells.
• 
  Christophe Restif, Carolina Ibáñez-Ventoso, Mehul Nalin Vora, Suzhen Guo, Dimitris N. Metaxas, Monica Driscoll:
  CeleST: Computer Vision Software for Quantitative Analysis of C. elegans Swim Behavior Reveals Novel Features of Locomotion.
• 
  Karl Fogelmark, Carl Troein:
  Rethinking Transcriptional Activation in the Arabidopsis Circadian Clock.
• 
  Rocio Rebollido-Rios, Shyam Bandari, Christoph Wilms, Stanislav Jakuschev, Andrea Vortkamp, Kay Grobe, Daniel Hoffmann:
  Signaling Domain of Sonic Hedgehog as Cannibalistic Calcium-Regulated Zinc-Peptidase.
• 
  Mahmoud Ghandi, Dongwon Lee, Morteza Mohammad Noori, Michael A. Beer:
  Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features.
• 
  Richard Lonsdale, Sarah L. Rouse, Mark S. P. Sansom, Adrian J. Mulholland:
  A Multiscale Approach to Modelling Drug Metabolism by Membrane-Bound Cytochrome P450 Enzymes.
• 
  Adam M. Gifford, Yale E. Cohen, Alan A. Stocker:
  Characterizing the Impact of Category Uncertainty on Human Auditory Categorization Behavior.
• 
  Jacob D. Durrant, Rommie E. Amaro:
  LipidWrapper: An Algorithm for Generating Large-Scale Membrane Models of Arbitrary Geometry.
• 
  Eder Zavala, Tatiana T. Marquez-Lago:
  The Long and Viscous Road: Uncovering Nuclear Diffusion Barriers in Closed Mitosis.
• 
  Raphy Zarecki, Matthew A. Oberhardt, Leah Reshef, Uri Gophna, Eytan Ruppin:
  A Novel Nutritional Predictor Links Microbial Fastidiousness with Lowered Ubiquity, Growth Rate, and Cooperativeness.
• 
  Huiyong Sun, Youyong Li, Sheng Tian, Junmei Wang, Tingjun Hou:
  P-loop Conformation Governed Crizotinib Resistance in G2032R-Mutated ROS1 Tyrosine Kinase: Clues from Free Energy Landscape.
• 
  Alejandro Barrera, Ana Alastruey-Izquierdo, María J. Martín, Isabel Cuesta, Juan Antonio Vizcaíno:
  Analysis of the Protein Domain and Domain Architecture Content in Fungi and Its Application in the Search of New Antifungal Targets.
• 
  Allan Haldane, Michael Manhart, Alexandre V. Morozov:
  Biophysical Fitness Landscapes for Transcription Factor Binding Sites.
• 
  Habil Zare, Junfeng Wang, Alex Hu, Kris Weber, Joshua D. Smith, Deborah A. Nickerson, ChaoZhong Song, Daniela M. Witten, C. Anthony Blau, William Stafford Noble:
  Inferring Clonal Composition from Multiple Sections of a Breast Cancer.
• 
  Fredrik H. Karlsson, Intawat Nookaew, Jens Nielsen:
  Metagenomic Data Utilization and Analysis (MEDUSA) and Construction of a Global Gut Microbial Gene Catalogue.
• 
  Andrew E. Teschendorff, Xiaoping Liu, Helena Carén, Steve M. Pollard, Stephan Beck, Martin Widschwendter, Luonan Chen:
  The Dynamics of DNA Methylation Covariation Patterns in Carcinogenesis.
• 
  Suchin S. Gururangan, Alexander J. Sadovsky, Jason N. MacLean:
  Analysis of Graph Invariants in Functional Neocortical Circuitry Reveals Generalized Features Common to Three Areas of Sensory Cortex.
• 
  Michele Tizzoni, Paolo Bajardi, Adeline Decuyper, Guillaume Kon Kam King, Christian M. Schneider, Vincent D. Blondel, Zbigniew Smoreda, Marta C. González, Vittoria Colizza:
  On the Use of Human Mobility Proxies for Modeling Epidemics.
• 
  James B. Smadbeck, Kiat Hwa Chan, George A. Khoury, Bo Xue, Robert C. Robinson, Charlotte A. E. Hauser, Christodoulos A. Floudas:
  De Novo Design and Experimental Characterization of Ultrashort Self-Associating Peptides.
• 
  Federico Pedraja, Pedro Anibal Aguilera, Angel A. Caputi, Ruben Budelli:
  Electric Imaging through Evolution, a Modeling Study of Commonalities and Differences.
• 
  Marc Griesemer, Carissa Young, Anne S. Robinson, Linda R. Petzold:
  BiP Clustering Facilitates Protein Folding in the Endoplasmic Reticulum.
• 
  Urs Köster, Jascha Sohl-Dickstein, Charles M. Gray, Bruno A. Olshausen:
  Modeling Higher-Order Correlations within Cortical Microcolumns.
• 
  Jan Hasenauer, Christine Hasenauer, Tim Hucho, Fabian J. Theis:
  ODE Constrained Mixture Modelling: A Method for Unraveling Subpopulation Structures and Dynamics.
• 
  Lewis J. Martin, Ben Corry:
  Locating the Route of Entry and Binding Sites of Benzocaine and Phenytoin in a Bacterial Voltage Gated Sodium Channel.
• 
  Yong Wang, Chun Tang, Erkang Wang, Jin Wang:
  PolyUbiquitin Chain Linkage Topology Selects the Functions from the Underlying Binding Landscape.
• 
  James H. Kaufman, Justin Lessler, April Harry, Stefan Edlund, Kun Hu, Judith V. Douglas, Christian Thoens, Bernd Appel, Annemarie Käsbohrer, Matthias Filter:
  A Likelihood-Based Approach to Identifying Contaminated Food Products Using Sales Data: Performance and Challenges.
• 
  Hsuan-Chao Chiu, Roie Levy, Elhanan Borenstein:
  Emergent Biosynthetic Capacity in Simple Microbial Communities.
• 
  Daria A. Beshnova, Andrey G. Cherstvy, Yevhen Vainshtein, Vladimir B. Teif:
  Regulation of the Nucleosome Repeat Length In Vivo by the DNA Sequence, Protein Concentrations and Long-Range Interactions.
• 
  Peter Cassey, Andrew Heathcote, Scott D. Brown:
  Brain and Behavior in Decision-Making.
• 
  Alka A. Potdar, Joydeep Sarkar, Nupur K. Das, Paroma Ghosh, Miklos Gratzl, Paul L. Fox, Gerald M. Saidel:
  Computational Modeling and Analysis of Iron Release from Macrophages.
• 
  Bradley Kossmann, Ivaylo Ivanov:
  Alkylpurine Glycosylase D Employs DNA Sculpting as a Strategy to Extrude and Excise Damaged Bases.

Formal Comments

• 
  Param Priya Singh, Séverine Affeldt, Giulia Malaguti, Hervé Isambert:
  Human Dominant Disease Genes Are Enriched in Paralogs Originating from Whole Genome Duplication.
• 
  Wei-Hua Chen, Xing-Ming Zhao, Vera van Noort, Peer Bork:
  Comments on "Human Dominant Disease Genes Are Enriched in Paralogs Originating from Whole Genome Duplication".

Volume 10, Number 8, August 2014

Editorials

• 
  Sean Ekins, Ethan O. Perlstein:
  Ten Simple Rules of Live Tweeting at Scientific Conferences.
• 
  Qiang Cui, Ruth Nussinov:
  Making Biomolecular Simulations Accessible in the Post-Nobel Prize Era.

Message from ISCB

• 
  Tarun Mishra, R. Gonzalo Parra, Thomas Abeel:
  The Upside of Failure: How Regional Student Groups Learn from Their Mistakes.

Research Articles

• 
  Piero Dalle Pezze, Glyn Nelson, Elsje G. Otten, Viktor I. Korolchuk, Thomas B. L. Kirkwood, Thomas von Zglinicki, Daryl P. Shanley:
  Dynamic Modelling of Pathways to Cellular Senescence Reveals Strategies for Targeted Interventions.
• 
  Rui Xia, Selina Vattathil, Paul Scheet:
  Identification of Allelic Imbalance with a Statistical Model for Subtle Genomic Mosaicism.
• 
  Brian Y. Chen:
  VASP-E: Specificity Annotation with a Volumetric Analysis of Electrostatic Isopotentials.
• 
  Gang Zhao, Gitanjali Dharmadhikari, Kathrin Maedler, Michael Meyer-Hermann:
  Possible Role of Interleukin-1β in Type 2 Diabetes Onset and Implications for Anti-inflammatory Therapy Strategies.
• 
  Sébastien Benzekry, Clare Lamont, Afshin Beheshti, Amanda Tracz, John M. L. Ebos, Lynn Hlatky, Philip Hahnfeldt:
  Classical Mathematical Models for Description and Prediction of Experimental Tumor Growth.
• 
  Greg Finak, Jacob Frelinger, Wenxin Jiang, Evan W. Newell, John Ramey, Mark M. Davis, Spyros A. Kalams, Stephen C. De Rosa, Raphael Gottardo:
  OpenCyto: An Open Source Infrastructure for Scalable, Robust, Reproducible, and Automated, End-to-End Flow Cytometry Data Analysis.
• 
  Priscilla Ambrosi, Juan Sebastian Chahda, Hannah R. Koslen, Hillel J. Chiel, Claudia Mieko Mizutani:
  Modeling of the Dorsal Gradient across Species Reveals Interaction between Embryo Morphology and Toll Signaling Pathway during Evolution.
• 
  Gerald Hahn, Alejandro F. Bujan, Yves Frégnac, Ad Aertsen, Arvind Kumar:
  Communication through Resonance in Spiking Neuronal Networks.
• 
  Geir Villy Isaksen, Johan Åqvist, Bjørn Olav Brandsdal:
  Protein Surface Softness Is the Origin of Enzyme Cold-Adaptation of Trypsin.
• 
  Frantisek Honti, Stephen Meader, Caleb Webber:
  Unbiased Functional Clustering of Gene Variants with a Phenotypic-Linkage Network.
• 
  Ken Daigoro Yokoyama, Yang Zhang, Jian Ma:
  Tracing the Evolution of Lineage-Specific Transcription Factor Binding Sites in a Birth-Death Framework.
• 
  Jonathan Laudanski, Benjamin Torben-Nielsen, Idan Segev, Shihab Shamma:
  Spatially Distributed Dendritic Resonance Selectively Filters Synaptic Input.
• 
  Xiakun Chu, Jin Wang:
  Specificity and Affinity Quantification of Flexible Recognition from Underlying Energy Landscape Topography.
• 
  Andries J. van Tonder, Shilan Mistry, James E. Bray, Dorothea M. C. Hill, Alison J. Cody, Chris L. Farmer, Keith P. Klugman, Anne von Gottberg, Stephen D. Bentley, Julian Parkhill, Keith A. Jolley, Martin C. J. Maiden, Angela B. Brueggemann:
  Defining the Estimated Core Genome of Bacterial Populations Using a Bayesian Decision Model.
• 
  Cyril F. Reboul, James C. Whisstock, Michelle A. Dunstone:
  A New Model for Pore Formation by Cholesterol-Dependent Cytolysins.
• 
  Victor J. Barranca, Gregor Kovacic, Douglas Zhou, David Cai:
  Sparsity and Compressed Coding in Sensory Systems.
• 
  Alex H. Lang, Hu Li, James J. Collins, Pankaj Mehta:
  Epigenetic Landscapes Explain Partially Reprogrammed Cells and Identify Key Reprogramming Genes.
• 
  Yuan Zhang, Yanni Sun, James R. Cole:
  A Scalable and Accurate Targeted Gene Assembly Tool (SAT-Assembler) for Next-Generation Sequencing Data.
• 
  Kanghoon Jung, Hyeran Jang, Jerald D. Kralik, Jaeseung Jeong:
  Bursts and Heavy Tails in Temporal and Sequential Dynamics of Foraging Decisions.
• 
  Eizaburo Doi, Michael S. Lewicki:
  A Simple Model of Optimal Population Coding for Sensory Systems.
• 
  Samat Moldakarimov, Maxim Bazhenov, Terrence J. Sejnowski:
  Top-Down Inputs Enhance Orientation Selectivity in Neurons of the Primary Visual Cortex during Perceptual Learning.
• 
  Delphine Pessoa, Caetano Souto-Maior, Erida Gjini, Joao S. Lopes, Bruno Ceña, Cláudia T. Codeço, M. Gabriela M. Gomes:
  Unveiling Time in Dose-Response Models to Infer Host Susceptibility to Pathogens.
• 
  René F. M. van Oers, Elisabeth G. Rens, Danielle J. LaValley, Cynthia A. Reinhart-King, Roeland M. H. Merks:
  Mechanical Cell-Matrix Feedback Explains Pairwise and Collective Endothelial Cell Behavior In Vitro.
• 
  Huilei Xu, Yen-Sin Ang, Ana Sevilla, Ihor Lemischka, Avi Ma'ayan:
  Construction and Validation of a Regulatory Network for Pluripotency and Self-Renewal of Mouse Embryonic Stem Cells.
• 
  Anne-Florence Bitbol, David J. Schwab:
  Quantifying the Role of Population Subdivision in Evolution on Rugged Fitness Landscapes.
• 
  Alec Solway, Carlos Diuk, Natalia Córdova, Debbie Yee, Andrew G. Barto, Yael Niv, Matthew M. Botvinick:
  Optimal Behavioral Hierarchy.
• 
  Dov A. Pechenick, Joshua L. Payne, Jason H. Moore:
  Phenotypic Robustness and the Assortativity Signature of Human Transcription Factor Networks.
• 
  Miri Adler, Avi E. Mayo, Uri Alon:
  Logarithmic and Power Law Input-Output Relations in Sensory Systems with Fold-Change Detection.
• 
  Pengxing Cao, Xiahui Tan, Graham M. Donovan, Michael J. Sanderson, James Sneyd:
  A Deterministic Model Predicts the Properties of Stochastic Calcium Oscillations in Airway Smooth Muscle Cells.
• 
  Tetsuhiro S. Hatakeyama, Kunihiko Kaneko:
  Kinetic Memory Based on the Enzyme-Limited Competition.
• 
  Yujiang Wang, Marc Goodfellow, Peter Neal Taylor, Gerold Baier:
  Dynamic Mechanisms of Neocortical Focal Seizure Onset.
• 
  Seungyeul Yoo, Tao Huang, Joshua D. Campbell, Eunjee Lee, Zhidong Tu, Mark W. Geraci, Charles A. Powell, Eric E. Schadt, Avrum Spira, Jun Zhu:
  MODMatcher: Multi-Omics Data Matcher for Integrative Genomic Analysis.
• 
  Peter T. McHale, Arthur D. Lander:
  The Protective Role of Symmetric Stem Cell Division on the Accumulation of Heritable Damage.
• 
  Christopher A. Miller, Brian S. White, Nathan D. Dees, Malachi Griffith, John S. Welch, Obi L. Griffith, Ravi Vij, Michael H. Tomasson, Timothy A. Graubert, Matthew J. Walter, Matthew J. Ellis, William S. Schierding, John F. DiPersio, Timothy J. Ley, Elaine R. Mardis, Richard K. Wilson, Li Ding:
  SciClone: Inferring Clonal Architecture and Tracking the Spatial and Temporal Patterns of Tumor Evolution.
• 
  Umut Güçlü, Marcel A. J. van Gerven:
  Unsupervised Feature Learning Improves Prediction of Human Brain Activity in Response to Natural Images.
• 
  Alexis M. Dubreuil, Yali Amit, Nicolas Brunel:
  Memory Capacity of Networks with Stochastic Binary Synapses.
• 
  Erwan Hingant, Pascaline Fontes, Maria Teresa Alvarez-Martinez, Jacques-Damien Arnaud, Jean-Pierre Liautard, Laurent Pujo-Menjouet:
  A Micellar On-Pathway Intermediate Step Explains the Kinetics of Prion Amyloid Formation.
• 
  Bernhard Knapp, James Dunbar, Charlotte M. Deane:
  Large Scale Characterization of the LC13 TCR and HLA-B8 Structural Landscape in Reaction to 172 Altered Peptide Ligands: A Molecular Dynamics Simulation Study.
• 
  Cheemeng Tan, Robert Phillip Smith, Ming-Chi Tsai, Russell Schwartz, Lingchong You:
  Phenotypic Signatures Arising from Unbalanced Bacterial Growth.
• 
  Johannes Textor, Sarah E. Henrickson, Judith N. Mandl, Ulrich H. von Andrian, Jürgen Westermann, Rob J. De Boer, Joost B. Beltman:
  Random Migration and Signal Integration Promote Rapid and Robust T Cell Recruitment.
• 
  Nik J. Cunniffe, Francisco F. Laranjeira, Franco M. Neri, R. Erik DeSimone, Christopher A. Gilligan:
  Cost-Effective Control of Plant Disease When Epidemiological Knowledge Is Incomplete: Modelling Bahia Bark Scaling of Citrus.
• 
  Fang-Chieh Chou, Jan Lipfert, Rhiju Das:
  Blind Predictions of DNA and RNA Tweezers Experiments with Force and Torque.
• 
  Albert B. Kao, Noam Miller, Colin J. Torney, Andrew Hartnett, Iain D. Couzin:
  Collective Learning and Optimal Consensus Decisions in Social Animal Groups.
• 
  Shuo Gu, Daniel-Adriano Silva, Luming Meng, Alexander Yue, Xuhui Huang:
  Quantitatively Characterizing the Ligand Binding Mechanisms of Choline Binding Protein Using Markov State Model Analysis.
• 
  Jessica M. Conway, Alan S. Perelson:
  A Hepatitis C Virus Infection Model with Time-Varying Drug Effectiveness: Solution and Analysis.
• 
  Eric L. Haseltine, Sandra De Meyer, Inge Dierynck, Doug J. Bartels, Anne Ghys, Andrew Davis, Eileen Z. Zhang, Ann M. Tigges, Joan Spanks, Gaston Picchio, Tara L. Kieffer, James C. Sullivan:
  Modeling Viral Evolutionary Dynamics after Telaprevir-Based Treatment.
• 
  Jaclyn K. Mann, John P. Barton, Andrew L. Ferguson, Saleha Omarjee, Bruce D. Walker, Arup Chakraborty, Thumbi Ndung'u:
  The Fitness Landscape of HIV-1 Gag: Advanced Modeling Approaches and Validation of Model Predictions by In Vitro Testing.

Corrections

• 
  Correction: Exploring the Conformational Transitions of Biomolecular Systems Using a Simple Two-State Anisotropic Network Model.
• 
  Correction: A Computational Model of the Fetal Circulation to Quantify Blood Redistribution in Intrauterine Growth Restriction.
• 
  Correction: Exploration of the Dynamic Properties of Protein Complexes Predicted from Spatially Constrained Protein-Protein Interaction Networks.
• 
  Correction: The Self-Limiting Dynamics of TGF-β Signaling In Silico and In Vitro, with Negative Feedback through PPM1A Upregulation.

Volume 10, Number 9, September 2014

Editorial

• 
  Nicolas P. Rougier, Michael Droettboom, Philip E. Bourne:
  Ten Simple Rules for Better Figures.

Topic Page

• 
  Melanie I. Stefan, Thomas M. Bartol, Terrence J. Sejnowski, Mary B. Kennedy:
  Multi-state Modeling of Biomolecules.

Research Articles

• 
  David R. Blair, Kanix Wang, Svetlozar Nestorov, James A. Evans, Andrey Rzhetsky:
  Quantifying the Impact and Extent of Undocumented Biomedical Synonymy.
• 
  Apichat Suratanee, Martin H. Schaefer, Matthew J. Betts, Zita Soons, Heiko A. Mannsperger, Nathalie Harder, Marcus Oswald, Markus Gipp, Ellen Ramminger, Guillermo Marcus Martinez, Reinhard Männer, Karl Rohr, Erich E. Wanker, Robert B. Russell, Miguel A. Andrade-Navarro, Roland Eils, Rainer König:
  Characterizing Protein Interactions Employing a Genome-Wide siRNA Cellular Phenotyping Screen.
• 
  Stefano Luccioli, Eshel Ben-Jacob, Ari Barzilai, Paolo Bonifazi, Alessandro Torcini:
  Clique of Functional Hubs Orchestrates Population Bursts in Developmentally Regulated Neural Networks.
• 
  Jean-Baptiste Pettit, Raju Tomer, Kaia Achim, Sylvia Richardson, Lamiae Azizi, John C. Marioni:
  Identifying Cell Types from Spatially Referenced Single-Cell Expression Datasets.
• 
  David A. Sivak, Matt Thomson:
  Environmental Statistics and Optimal Regulation.
• 
  N. Lance Hepler, Konrad Scheffler, Steven Weaver, Ben Murrell, Douglas D. Richman, Dennis R. Burton, Pascal Poignard, Davey M. Smith, Sergei L. Kosakovsky Pond:
  IDEPI: Rapid Prediction of HIV-1 Antibody Epitopes and Other Phenotypic Features from Sequence Data Using a Flexible Machine Learning Platform.
• 
  Qing Xie, Qi Liu, Fengbiao Mao, Wanshi Cai, Honghu Wu, Mingcong You, Zhen Wang, Bingyu Chen, Zhongsheng Sun, Jinyu Wu:
  A Bayesian Framework to Identify Methylcytosines from High-Throughput Bisulfite Sequencing Data.
• 
  Rachel A. Mak-McCully, Stephen R. Deiss, Burke Q. Rosen, Ki-Young Jung, Terrence J. Sejnowski, Hélène Bastuji, Marc Rey, Sydney S. Cash, Maxim Bazhenov, Eric Halgren:
  Synchronization of Isolated Downstates (K-Complexes) May Be Caused by Cortically-Induced Disruption of Thalamic Spindling.
• 
  Sharlee Climer, Alan R. Templeton, Weixiong Zhang:
  Allele-Specific Network Reveals Combinatorial Interaction That Transcends Small Effects in Psoriasis GWAS.
• 
  Eric Libby, William Ratcliff, Michael Travisano, Ben Kerr:
  Geometry Shapes Evolution of Early Multicellularity.
• 
  Thea Hogan, Ulrich D. Kadolsky, Sim Tung, Benedict Seddon, Andrew J. Yates:
  Spatial Heterogeneity and Peptide Availability Determine CTL Killing Efficiency In Vivo.
• 
  Michal Brylinski:
  eMatchSite: Sequence Order-Independent Structure Alignments of Ligand Binding Pockets in Protein Models.
• 
  Stefan Nowak, Johannes Neidhart, Ivan G. Szendro, Joachim Krug:
  Multidimensional Epistasis and the Transitory Advantage of Sex.
• 
  Hojung Nam, Miguel Campodonico, Aarash Bordbar, Daniel R. Hyduke, Sangwoo Kim, Daniel C. Zielinski, Bernhard O. Palsson:
  A Systems Approach to Predict Oncometabolites via Context-Specific Genome-Scale Metabolic Networks.
• 
  Shunichi Kosugi, Hiroshi Yanagawa, Ryohei Terauchi, Satoshi Tabata:
  NESmapper: Accurate Prediction of Leucine-Rich Nuclear Export Signals Using Activity-Based Profiles.
• 
  Hong Yang, Elias W. Krumholz, Evan D. Brutinel, Nagendra P. Palani, Michael J. Sadowsky, Andrew M. Odlyzko, Jeffrey A. Gralnick, Igor G. L. Libourel:
  Genome-Scale Metabolic Network Validation of Shewanella oneidensis Using Transposon Insertion Frequency Analysis.
• 
  Sijia Huang, Cameron Yee, Travers Ching, Herbert Yu, Lana X. Garmire:
  A Novel Model to Combine Clinical and Pathway-Based Transcriptomic Information for the Prognosis Prediction of Breast Cancer.
• 
  James Dunbar, Bernhard Knapp, Angelika Fuchs, Jiye Shi, Charlotte M. Deane:
  Examining Variable Domain Orientations in Antigen Receptors Gives Insight into TCR-Like Antibody Design.
• 
  Peter R. Murphy, Joachim Vandekerckhove, Sander Nieuwenhuis:
  Pupil-Linked Arousal Determines Variability in Perceptual Decision Making.
• 
  Alex J. Cornish, Florian Markowetz:
  SANTA: Quantifying the Functional Content of Molecular Networks.
• 
  Penelope A. Hancock, Yasmin Rehman, Ian M. Hall, Obaghe Edeghere, Leon Danon, Thomas A. House, Matthew J. Keeling:
  Strategies for Controlling Non-Transmissible Infection Outbreaks Using a Large Human Movement Data Set.
• 
  Masato Yasui, Satomi Matsuoka, Masahiro Ueda:
  PTEN Hopping on the Cell Membrane Is Regulated via a Positively-Charged C2 Domain.
• 
  Krishnendu Chatterjee, Andreas Pavlogiannis, Ben Adlam, Martin A. Nowak:
  The Time Scale of Evolutionary Innovation.
• 
  Diana Chang, Alon Keinan:
  Principal Component Analysis Characterizes Shared Pathogenetics from Genome-Wide Association Studies.
• 
  Simone Vincenzi, Marc Mangel, Alain J. Crivelli, Stephan Munch, Hans J. Skaug:
  Determining Individual Variation in Growth and Its Implication for Life-History and Population Processes Using the Empirical Bayes Method.
• 
  Shaoyong Lu, Wenkang Huang, Qi Wang, Qiancheng Shen, Shuai Li, Ruth Nussinov, Jian Zhang:
  The Structural Basis of ATP as an Allosteric Modulator.
• 
  Jinyu Li, Giulia Rossetti, Jens Dreyer, Simone Raugei, Emiliano Ippoliti, Bernhard Lüscher, Paolo Carloni:
  Molecular Simulation-Based Structural Prediction of Protein Complexes in Mass Spectrometry: The Human Insulin Dimer.
• 
  Thu Thuy Nguyen, Jérémie Guedj, Elisabeth Chachaty, Jean de Gunzburg, Antoine Andremont, France Mentré:
  Mathematical Modeling of Bacterial Kinetics to Predict the Impact of Antibiotic Colonic Exposure and Treatment Duration on the Amount of Resistant Enterobacteria Excreted.
• 
  Gaetano Invernizzi, Matteo Tiberti, Matteo Lambrughi, Kresten Lindorff-Larsen, Elena Papaleo:
  Communication Routes in ARID Domains between Distal Residues in Helix 5 and the DNA-Binding Loops.
• 
  Sam Meyer, Guillaume Beslon:
  Torsion-Mediated Interaction between Adjacent Genes.
• 
  Tamás Székely Jr., Kevin Burrage, Marc Mangel, Michael B. Bonsall:
  Stochastic Dynamics of Interacting Haematopoietic Stem Cell Niche Lineages.
• 
  Marti Bernardo-Faura, Stefan Massen, Christine S. Falk, Nathan R. Brady, Roland Eils:
  Data-Derived Modeling Characterizes Plasticity of MAPK Signaling in Melanoma.
• 
  Sara Teller, Clara Granell, Manlio De Domenico, Jordi Soriano, Sergio Gómez, Alex Arenas:
  Emergence of Assortative Mixing between Clusters of Cultured Neurons.
• 
  Angela Simeone, Giovanni Marsico, Claudio Collinet, Thierry Galvez, Yannis Kalaidzidis, Marino Zerial, Andreas Beyer:
  Revealing Molecular Mechanisms by Integrating High-Dimensional Functional Screens with Protein Interaction Data.
• 
  Xiakun Chu, Fei Liu, Brian A. Maxwell, Yong Wang, Zucai Suo, Haijun Wang, Wei Han, Jin Wang:
  Dynamic Conformational Change Regulates the Protein-DNA Recognition: An Investigation on Binding of a Y-Family Polymerase to Its Target DNA.
• 
  Andreea Oliviana Diaconescu, Christoph Mathys, Lilian A. E. Weber, Jean Daunizeau, Lars Kasper, Ekaterina I. Lomakina, Ernst Fehr, Klaas E. Stephan:
  Inferring on the Intentions of Others by Hierarchical Bayesian Learning.
• 
  Erin M. Stuckey, Thomas A. Smith, Nakul Chitnis:
  Seasonally Dependent Relationships between Indicators of Malaria Transmission and Disease Provided by Mathematical Model Simulations.
• 
  Thomas H. Hraha, Matthew J. Westacott, Marina Pozzoli, Aleena M. Notary, P. Mason McClatchey, Richard K. P. Benninger:
  Phase Transitions in the Multi-cellular Regulatory Behavior of Pancreatic Islet Excitability.
• 
  Vassiliki Lila Koumandou, Sophia Kossida:
  Evolution of the F₀F₁ ATP Synthase Complex in Light of the Patchy Distribution of Different Bioenergetic Pathways across Prokaryotes.
• 
  Marnix H. Medema, Yared Paalvast, Don D. Nguyen, Alexey Melnik, Pieter C. Dorrestein, Eriko Takano, Rainer Breitling:
  Pep2Path: Automated Mass Spectrometry-Guided Genome Mining of Peptidic Natural Products.
• 
  Yun-Ching Chen, Christopher Douville, Cheng Wang, Noushin Niknafs, Grace H. T. Yeo, Violeta Beleva Guthrie, Hannah Carter, Peter D. Stenson, David N. Cooper, Biao Li, Sean D. Mooney, Rachel Karchin:
  A Probabilistic Model to Predict Clinical Phenotypic Traits from Genome Sequencing.
• 
  Amit Ghosh, Jerome P. Nilmeier, Daniel Weaver, Paul D. Adams, Jay D. Keasling, Aindrila Mukhopadhyay, Christopher J. Petzold, Héctor García Martín:
  A Peptide-Based Method for ¹³C Metabolic Flux Analysis in Microbial Communities.
• 
  Melissa M. Norström, Nazle M. Veras, Wei Huang, Mattia C. F. Prosperi, Jennifer Cook, Wendy Hartogensis, Frederick M. Hecht, Annika C. Karlsoon, Marco Salemi:
  Baseline CD4⁺ T Cell Counts Correlates with HIV-1 Synonymous Rate in HLA-B*5701 Subjects with Different Risk of Disease Progression.

Correction

• 
  Correction: Structure-Based Druggability Assessment of the Mammalian Structural Proteome with Inclusion of Light Protein Flexibility.

Volume 10, Number 10, October 2014

Editorial

• 
  Harriet Dashnow, Andrew Lonsdale, Philip E. Bourne:
  Ten Simple Rules for Writing a PLOS Ten Simple Rules Article.

Message from ISCB

• 
  Avinash Kumar Shanmugam, Geoff MacIntyre:
  Establishing and Managing a Global Student Network.

Perspective

• 
  Maxwell Lewis Neal, Michael T. Cooling, Lucian P. Smith, Christopher T. Thompson, Herbert M. Sauro, Brian E. Carlson, Daniel L. Cook, John H. Gennari:
  A Reappraisal of How to Build Modular, Reusable Models of Biological Systems.

Research Articles

• 
  Mary A. Rohrdanz, Wenwei Zheng, Bradley Lambeth, Jocelyne Vreede, Cecilia Clementi:
  Multiscale Approach to the Determination of the Photoactive Yellow Protein Signaling State Ensemble.
• 
  Rebecca Batorsky, Rinat A. Sergeev, Igor M. Rouzine:
  The Route of HIV Escape from Immune Response Targeting Multiple Sites Is Determined by the Cost-Benefit Tradeoff of Escape Mutations.
• 
  Gang Peng, Yu Fan, Wenyi Wang:
  FamSeq: A Variant Calling Program for Family-Based Sequencing Data Using Graphics Processing Units.
• 
  Munia Amin, Varun B. Kothamachu, Elisenda Feliu, Birgit E. Scharf, Steven L. Porter, Orkun S. Soyer:
  Phosphate Sink Containing Two-Component Signaling Systems as Tunable Threshold Devices.
• 
  Stinus Lindgreen, Sinan Ugur Umu, Alicia Sook-Wei Lai, Hisham Eldai, Wenting Liu, Stephanie McGimpsey, Nicole E. Wheeler, Patrick J. Biggs, Nick R. Thomson, Lars Barquist, Anthony M. Poole, Paul P. Gardner:
  Robust Identification of Noncoding RNA from Transcriptomes Requires Phylogenetically-Informed Sampling.
• 
  Sophia Rudorf, Michael Thommen, Marina V. Rodnina, Reinhard Lipowsky:
  Deducing the Kinetics of Protein Synthesis In Vivo from the Transition Rates Measured In Vitro.
• 
  Dirk De Vos, Kris Vissenberg, Jan Broeckhove, Gerrit T. S. Beemster:
  Putting Theory to the Test: Which Regulatory Mechanisms Can Drive Realistic Growth of a Root?
• 
  Nikola Ojkic, Javier López-Garrido, Kit Pogliano, Robert G. Endres:
  Bistable Forespore Engulfment in Bacillus subtilis by a Zipper Mechanism in Absence of the Cell Wall.
• 
  Allen Cheung:
  Estimating Location without External Cues.
• 
  Hai Fang:
  dcGOR: An R Package for Analysing Ontologies and Protein Domain Annotations.
• 
  Robert Legenstein, Wolfgang Maass:
  Ensembles of Spiking Neurons with Noise Support Optimal Probabilistic Inference in a Dynamically Changing Environment.
• 
  Boryana Doyle, Geoffrey Fudenberg, Maxim Imakaev, Leonid A. Mirny:
  Chromatin Loops as Allosteric Modulators of Enhancer-Promoter Interactions.
• 
  Diana Clausznitzer, Gabriele Micali, Silke Neumann, Victor Sourjik, Robert G. Endres:
  Predicting Chemical Environments of Bacteria from Receptor Signaling.
• 
  Christian L. Althaus, Beda Joos, Alan S. Perelson, Huldrych F. Günthard:
  Quantifying the Turnover of Transcriptional Subclasses of HIV-1-Infected Cells.
• 
  François Bertaux, Szymon Stoma, Dirk Drasdo, Grégory Batt:
  Modeling Dynamics of Cell-to-Cell Variability in TRAIL-Induced Apoptosis Explains Fractional Killing and Predicts Reversible Resistance.
• 
  Paraskevi Gkeka, Thomas Evangelidis, Maria Pavlaki, Vasiliki Lazani, Savvas Christoforidis, Bogos Agianian, Zoe Cournia:
  Investigating the Structure and Dynamics of the PIK3CA Wild-Type and H1047R Oncogenic Mutant.
• 
  Seth D. Axen, Onur Erbilgin, Cheryl A. Kerfeld:
  A Taxonomy of Bacterial Microcompartment Loci Constructed by a Novel Scoring Method.
• 
  Bahman Nasseroleslami, Christopher J. Hasson, Dagmar Sternad:
  Rhythmic Manipulation of Objects with Complex Dynamics: Predictability over Chaos.
• 
  Kei Moritsugu, Tohru Terada, Akinori Kidera:
  Energy Landscape of All-Atom Protein-Protein Interactions Revealed by Multiscale Enhanced Sampling.
• 
  Yue Li, Minggao Liang, Zhaolei Zhang:
  Regression Analysis of Combined Gene Expression Regulation in Acute Myeloid Leukemia.
• 
  Heidi Koldsø, David Shorthouse, Jean Hélie, Mark S. P. Sansom:
  Lipid Clustering Correlates with Membrane Curvature as Revealed by Molecular Simulations of Complex Lipid Bilayers.
• 
  Calvin J. Schneider, Hermann Cuntz, Ivan Soltesz:
  Linking Macroscopic with Microscopic Neuroanatomy Using Synthetic Neuronal Populations.
• 
  Roger C. Young, Peter Barendse:
  Linking Myometrial Physiology to Intrauterine Pressure; How Tissue-Level Contractions Create Uterine Contractions of Labor.
• 
  Nicole Voges, Antoine Chaffiol, Philippe Lucas, Dominique Martinez:
  Reactive Searching and Infotaxis in Odor Source Localization.
• 
  José A. Seoane, Colin Campbell, Ian N. M. Day, Juan P. Casas, Tom R. Gaunt:
  Canonical Correlation Analysis for Gene-Based Pleiotropy Discovery.
• 
  Matthew N. Benedict, Michael B. Mundy, Christopher S. Henry, Nicholas Chia, Nathan D. Price:
  Likelihood-Based Gene Annotations for Gap Filling and Quality Assessment in Genome-Scale Metabolic Models.
• 
  Markus Rehberg, Joachim B. Ritter, Udo Reichl:
  Glycolysis Is Governed by Growth Regime and Simple Enzyme Regulation in Adherent MDCK Cells.
• 
  Srivas Chennu, Paola Finoia, Evelyn Kamau, Judith Allanson, Guy B. Williams, Martin M. Monti, Valdas Noreika, Aurina Arnatkeviciute, Andrés Canales-Johnson, Francisco Olivares, Daniela Cabezas-Soto, David K. Menon, John D. Pickard, Adrian M. Owen, Tristan A. Bekinschtein:
  Spectral Signatures of Reorganised Brain Networks in Disorders of Consciousness.
• 
  Roy Malka, Francisco Feijó Delgado, Scott R. Manalis, John M. Higgins:
  In Vivo Volume and Hemoglobin Dynamics of Human Red Blood Cells.
• 
  Marco Mauri, Stefan Klumpp:
  A Model for Sigma Factor Competition in Bacterial Cells.
• 
  Christoph Feinauer, Marcin J. Skwark, Andrea Pagnani, Erik Aurell:
  Improving Contact Prediction along Three Dimensions.
• 
  Benedikt Obermayer, Erel Levine:
  Exploring the miRNA Regulatory Network Using Evolutionary Correlations.
• 
  Nicole Dölker, Maria W. Górna, Ludovico Sutto, Antonio S. Torralba, Giulio Superti-Furga, Francesco L. Gervasio:
  The SH2 Domain Regulates c-Abl Kinase Activation by a Cyclin-Like Mechanism and Remodulation of the Hinge Motion.
• 
  Frédéric Crevecoeur, Stephen H. Scott:
  Beyond Muscles Stiffness: Importance of State-Estimation to Account for Very Fast Motor Corrections.
• 
  Jonathan Barnoud, Giulia Rossi, Siewert J. Marrink, Luca Monticelli:
  Hydrophobic Compounds Reshape Membrane Domains.
• 
  Bo-Xue Tian, Frank H. Wallrapp, Gemma L. Holliday, Jeng-Yeong Chow, Patricia C. Babbitt, C. Dale Poulter, Matthew P. Jacobson:
  Predicting the Functions and Specificity of Triterpenoid Synthases: A Mechanism-Based Multi-intermediate Docking Approach.
• 
  Mariliis Tark-Dame, Hansjoerg Jerabek, Erik M. M. Manders, Dieter W. Heermann, Roel van Driel:
  Depletion of the Chromatin Looping Proteins CTCF and Cohesin Causes Chromatin Compaction: Insight into Chromatin Folding by Polymer Modelling.
• 
  Mary Hongying Cheng, Ivet Bahar:
  Complete Mapping of Substrate Translocation Highlights the Role of LeuT N-terminal Segment in Regulating Transport Cycle.
• 
  Inhae Kim, Heetak Lee, Seong Kyu Han, Sanguk Kim:
  Linear Motif-Mediated Interactions Have Contributed to the Evolution of Modularity in Complex Protein Interaction Networks.
• 
  Jinhua Liu, Xuelong Wang, Juan Li, Haifang Wang, Gang Wei, Jun Yan:
  Reconstruction of the Gene Regulatory Network Involved in the Sonic Hedgehog Pathway with a Potential Role in Early Development of the Mouse Brain.
• 
  Christian Lohse, Danielle S. Bassett, Kelvin O. Lim, Jean M. Carlson:
  Resolving Anatomical and Functional Structure in Human Brain Organization: Identifying Mesoscale Organization in Weighted Network Representations.
• 
  David Higgins, Michael Graupner, Nicolas Brunel:
  Memory Maintenance in Synapses with Calcium-Based Plasticity in the Presence of Background Activity.
• 
  Rafael Tapia-Rojo, Juan José Mazo, José Ángel Hernández, María Luisa Peleato, María F. Fillat, Fernando Falo:
  Mesoscopic Model and Free Energy Landscape for Protein-DNA Binding Sites: Analysis of Cyanobacterial Promoters.
• 
  Hendrik B. Tiedemann, Elida Schneltzer, Stefan Zeiser, Wolfgang Wurst, Johannes Beckers, Gerhard K. H. Przemeck, Martin Hrabé de Angelis:
  Fast Synchronization of Ultradian Oscillators Controlled by Delta-Notch Signaling with Cis-Inhibition.
• 
  Adiel Statman, Maya Kaufman, Amir Minerbi, Noam E. Ziv, Naama Brenner:
  Synaptic Size Dynamics as an Effectively Stochastic Process.
• 
  Shuai Liu, Pengfei Cai, Xianyu Piao, Nan Hou, Xiaosu Zhou, Chuang Wu, Heng Wang, Qijun Chen:
  Expression Profile of the Schistosoma japonicum Degradome Reveals Differential Protease Expression Patterns and Potential Anti-schistosomal Intervention Targets.
• 
  Andrew J. Fritz, Branislav Stojkovic, Hu Ding, Jinhui Xu, Sambit Bhattacharya, Ronald Berezney:
  Cell Type Specific Alterations in Interchromosomal Networks across the Cell Cycle.
• 
  Amos Korman, Efrat Greenwald, Ofer Feinerman:
  Confidence Sharing: An Economic Strategy for Efficient Information Flows in Animal Groups.
• 
  Nathalie Poupin, François Mariotti, Jean-François Huneau, Dominique Hermier, Hélène Fouillet:
  Natural Isotopic Signatures of Variations in Body Nitrogen Fluxes: A Compartmental Model Analysis.
• 
  Michael J. Prerau, Katie E. Hartnack, Gabriel Obregon-Henao, Aaron L. Sampson, Margaret Merlino, Karen Gannon, Matt T. Bianchi, Jeffrey M. Ellenbogen, Patrick L. Purdon:
  Tracking the Sleep Onset Process: An Empirical Model of Behavioral and Physiological Dynamics.
• 
  Tanggis Bohnuud, Dima Kozakov, Sandor Vajda:
  Evidence of Conformational Selection Driving the Formation of Ligand Binding Sites in Protein-Protein Interfaces.

Corrections

• 
  Correction: Beyond Muscles Stiffness: Importance of State-Estimation to Account for Very Fast Motor Corrections.
• 
  Correction: Environmental Statistics and Optimal Regulation.
• 
  Correction: Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism.
• 
  Correction: Inferring on the Intentions of Others by Hierarchical Bayesian Learning.

Volume 10, Number 11, November 2014

Editorial

• 
  Jennifer L. Martin:
  Ten Simple Rules to Achieve Conference Speaker Gender Balance.

Education Articles

• 
  Anya L. Goodman, Alex Dekhtyar:
  Teaching Bioinformatics in Concert.
• 
  Amir Rubinstein, Benny Chor:
  Computational Thinking in Life Science Education.

Research Articles

• 
  Mahdi Shafiei, Katherine A. Dunn, Hugh A. Chipman, Hong Gu, Joseph P. Bielawski:
  BiomeNet: A Bayesian Model for Inference of Metabolic Divergence among Microbial Communities.
• 
  Yasser Iturria-Medina, Roberto C. Sotero, Paule-Joanne Toussaint, Alan C. Evans:
  Epidemic Spreading Model to Characterize Misfolded Proteins Propagation in Aging and Associated Neurodegenerative Disorders.
• 
  Lei Huang, Dongsung Kim, Xiaojing Liu, Christopher R. Myers, Jason W. Locasale:
  Estimating Relative Changes of Metabolic Fluxes.
• 
  Michael Mak, Roger D. Kamm, Muhammad H. Zaman:
  Impact of Dimensionality and Network Disruption on Microrheology of Cancer Cells in 3D Environments.
• 
  Rava Azeredo da Silveira, Michael J. Berry II:
  High-Fidelity Coding with Correlated Neurons.
• 
  Tarja Äijänen, Artturi Koivuniemi, Matti Javanainen, Sami Rissanen, Tomasz Róg, Ilpo Vattulainen:
  How Anacetrapib Inhibits the Activity of the Cholesteryl Ester Transfer Protein? Perspective through Atomistic Simulations.
• 
  Nicholas Generous, Geoffrey Fairchild, Alina Deshpande, Sara Y. Del Valle, Reid Priedhorsky:
  Global Disease Monitoring and Forecasting with Wikipedia.
• 
  Arne Weigenand, Michael Schellenberger Costa, Hong-Viet Victor Ngo, Jens Christian Claussen, Thomas Martinetz:
  Characterization of K-Complexes and Slow Wave Activity in a Neural Mass Model.
• 
  Stefan Fürtinger, Joel C. Zinn, Kristina Simonyan:
  A Neural Population Model Incorporating Dopaminergic Neurotransmission during Complex Voluntary Behaviors.
• 
  Klas H. Pettersen, Henrik Lindén, Tom Tetzlaff, Gaute T. Einevoll:
  Power Laws from Linear Neuronal Cable Theory: Power Spectral Densities of the Soma Potential, Soma Membrane Current and Single-Neuron Contribution to the EEG.
• 
  Zhongyao Sun, Xiaofen Jin, Réka Albert, Sarah M. Assmann:
  Multi-level Modeling of Light-Induced Stomatal Opening Offers New Insights into Its Regulation by Drought.
• 
  Luca Ferreri, Mario Giacobini, Paolo Bajardi, Luigi Bertolotti, Luca Bolzoni, Valentina Tagliapietra, Annapaola Rizzoli, Roberto Rosà:
  Pattern of Tick Aggregation on Mice: Larger Than Expected Distribution Tail Enhances the Spread of Tick-Borne Pathogens.
• 
  Frederik Graw, Ashwin Balagopal, Abraham J. Kandathil, Stuart C. Ray, David L. Thomas, Ruy M. Ribeiro, Alan S. Perelson:
  Inferring Viral Dynamics in Chronically HCV Infected Patients from the Spatial Distribution of Infected Hepatocytes.
• 
  V. V. Hemanth Giri Rao, Shachi Gosavi:
  In the Multi-domain Protein Adenylate Kinase, Domain Insertion Facilitates Cooperative Folding while Accommodating Function at Domain Interfaces.
• 
  Leonardo Abdala Elias, Renato Naville Watanabe, André Fabio Kohn:
  Spinal Mechanisms May Provide a Combination of Intermittent and Continuous Control of Human Posture: Predictions from a Biologically Based Neuromusculoskeletal Model.
• 
  Flávio L. Pinheiro, Vítor V. Vasconcelos, Francisco C. Santos, Jorge M. Pacheco:
  Evolution of All-or-None Strategies in Repeated Public Goods Dilemmas.
• 
  Helmut Schmidt, George Petkov, Mark P. Richardson, John R. Terry:
  Dynamics on Networks: The Role of Local Dynamics and Global Networks on the Emergence of Hypersynchronous Neural Activity.
• 
  Ken Nakae, Yuji Ikegaya, Tomoe Ishikawa, Shigeyuki Oba, Hidetoshi Urakubo, Masanori Koyama, Shin Ishii:
  A Statistical Method of Identifying Interactions in Neuron-Glia Systems Based on Functional Multicell Ca2+ Imaging.
• 
  Sathej Gopalakrishnan, Hesam Montazeri, Stephan Menz, Niko Beerenwinkel, Wilhelm Huisinga:
  Estimating HIV-1 Fitness Characteristics from Cross-Sectional Genotype Data.
• 
  Aurélie Carlier, Nick van Gastel, Liesbet Geris, Geert Carmeliet, Hans Van Oosterwyck:
  Size Does Matter: An Integrative In Vivo-In Silico Approach for the Treatment of Critical Size Bone Defects.
• 
  Marcin J. Skwark, Daniele Raimondi, Mirco Michel, Arne Elofsson:
  Improved Contact Predictions Using the Recognition of Protein Like Contact Patterns.
• 
  Ivan V. Kazbanov, Richard H. Clayton, Martyn P. Nash, Chris P. Bradley, David J. Paterson, Martin P. Hayward, Peter Taggart, Alexander V. Panfilov:
  Effect of Global Cardiac Ischemia on Human Ventricular Fibrillation: Insights from a Multi-scale Mechanistic Model of the Human Heart.
• 
  Xavier Laurent, Nicolas Renault, Amaury Farce, Philippe Chavatte, Eric Henon:
  Relationships between Th1 or Th2 iNKT Cell Activity and Structures of CD1d-Antigen Complexes: Meta-analysis of CD1d-Glycolipids Dynamics Simulations.
• 
  Veronika Boskova, Sebastian Bonhoeffer, Tanja Stadler:
  Inference of Epidemiological Dynamics Based on Simulated Phylogenies Using Birth-Death and Coalescent Models.
• 
  Ryan Tasseff, Anjali Bheda-Malge, Teresa DiColandrea, Charles C. Bascom, Robert J. Isfort, Richard Gelinas:
  Mouse Hair Cycle Expression Dynamics Modeled as Coupled Mesenchymal and Epithelial Oscillators.
• 
  Seyed-Mahdi Khaligh-Razavi, Nikolaus Kriegeskorte:
  Deep Supervised, but Not Unsupervised, Models May Explain IT Cortical Representation.
• 
  Ricardo Pinho, Victor Garcia, Manuel Irimia, Marcus W. Feldman:
  Stability Depends on Positive Autoregulation in Boolean Gene Regulatory Networks.
• 
  Varsha Dhankani, J. Nathan Kutz, Joshua T. Schiffer:
  Herpes Simplex Virus-2 Genital Tract Shedding Is Not Predictable over Months or Years in Infected Persons.
• 
  Eran Elhaik, Dan Graur:
  A Comparative Study and a Phylogenetic Exploration of the Compositional Architectures of Mammalian Nuclear Genomes.
• 
  Junaid Hassan, Linda L. Bergaust, I. David Wheat, Lars R. Bakken:
  Low Probability of Initiating nirS Transcription Explains Observed Gas Kinetics and Growth of Bacteria Switching from Aerobic Respiration to Denitrification.
• 
  Thomas R. Caulfield, Fabienne C. Fiesel, Elisabeth L. Moussaud-Lamodière, Daniel F. A. R. Dourado, Samuel Flores, Wolfdieter Springer:
  Phosphorylation by PINK1 Releases the UBL Domain and Initializes the Conformational Opening of the E3 Ubiquitin Ligase Parkin.
• 
  Samuel Gershman, Angela Radulescu, Kenneth A. Norman, Yael Niv:
  Statistical Computations Underlying the Dynamics of Memory Updating.

Corrections

• 
  Correction: Reactive Searching and Infotaxis in Odor Source Localization.
• 
  Correction: Exploring the miRNA Regulatory Network Using Evolutionary Correlations.
• 
  Correction: An In-Silico Model of Lipoprotein Metabolism and Kinetics for the Evaluation of Targets and Biomarkers in the Reverse Cholesterol Transport Pathway.
• 
  Correction: A Likelihood-Based Approach to Identifying Contaminated Food Products Using Sales Data: Performance and Challenges.
• 
  Correction: Baseline CD4+ T Cell Counts Correlates with HIV-1 Synonymous Rate in HLA-B*5701 Subjects with Different Risk of Disease Progression.

Volume 10, Number 12, December 2014

Editorial

• 
  Jacopo Marino, Melanie I. Stefan, Sarah Blackford:
  Ten Simple Rules for Finishing Your PhD.

Education

• 
  Yang Ding, Meng Wang, Yao He, Adam Yongxin Ye, Xiaoxu Yang, Fenglin Liu, Yuqi Meng, Ge Gao, Liping Wei:
  "Bioinformatics: Introduction and Methods, " a Bilingual Massive Open Online Course (MOOC) as a New Example for Global Bioinformatics Education.

Research Articles

• 
  Christiaan H. van Dorp, Michiel van Boven, Rob J. De Boer:
  Immuno-epidemiological Modeling of HIV-1 Predicts High Heritability of the Set-Point Virus Load, while Selection for CTL Escape Dominates Virulence Evolution.
• 
  Adrian J. de Froment, Daniel I. Rubenstein, Simon A. Levin:
  An Extra Dimension to Decision-Making in Animals: The Three-way Trade-off between Speed, Effort per-Unit-Time and Accuracy.
• 
  Siddhartha Jain, Anthony Gitter, Ziv Bar-Joseph:
  Multitask Learning of Signaling and Regulatory Networks with Application to Studying Human Response to Flu.
• 
  Natalia Zabzina, Audrey Dussutour, Richard P. Mann, David J. T. Sumpter, Stamatios C. Nicolis:
  Symmetry Restoring Bifurcation in Collective Decision-Making.
• 
  Charles F. Cadieu, Ha Hong, Daniel Yamins, Nicolas Pinto, Diego Ardila, Ethan A. Solomon, Najib J. Majaj, James J. DiCarlo:
  Deep Neural Networks Rival the Representation of Primate IT Cortex for Core Visual Object Recognition.
• 
  Gilad Wallach, Jules Lallouette, Nitzan Herzog, Maurizio De Pittà, Eshel Ben-Jacob, Hugues Berry, Yael Hanein:
  Glutamate Mediated Astrocytic Filtering of Neuronal Activity.
• 
  Larissa Albantakis, Arend Hintze, Christof Koch, Christoph Adami, Giulio Tononi:
  Evolution of Integrated Causal Structures in Animats Exposed to Environments of Increasing Complexity.
• 
  Lakshmi Krishnan, Mounya Elhilali, Shihab A. Shamma:
  Segregating Complex Sound Sources through Temporal Coherence.
• 
  Robert Ietswaart, Florian Szardenings, Kenn Gerdes, Martin Howard:
  Competing ParA Structures Space Bacterial Plasmids Equally over the Nucleoid.
• 
  Songting Li, Nan Liu, Xiaohui Zhang, Douglas Zhou, David Cai:
  Bilinearity in Spatiotemporal Integration of Synaptic Inputs.
• 
  Ina Bisha, Alex Rodriguez, Alessandro Laio, Alessandra Magistrato:
  Metadynamics Simulations Reveal a Na⁺ Independent Exiting Path of Galactose for the Inward-Facing Conformation of vSGLT.
• 
  Christoph A. Haselwandter, Ned S. Wingreen:
  The Role of Membrane-Mediated Interactions in the Assembly and Architecture of Chemoreceptor Lattices.
• 
  Sven Jahnke, Raoul-Martin Memmesheimer, Marc Timme:
  Oscillation-Induced Signal Transmission and Gating in Neural Circuits.
• 
  Pablo Sartori, Léo Granger, Chiu Fan Lee, Jordan M. Horowitz:
  Thermodynamic Costs of Information Processing in Sensory Adaptation.
• 
  Lin Chen, Javad Noorbakhsh, Rhys M. Adams, Joseph Samaniego-Evans, Germaine Agollah, Dmitry Nevozhay, Jennie Kuzdzal-Fick, Pankaj Mehta, Gábor Balázsi:
  Two-Dimensionality of Yeast Colony Expansion Accompanied by Pattern Formation.
• 
  Tadashi Ando, Jeffrey Skolnick:
  Sliding of Proteins Non-specifically Bound to DNA: Brownian Dynamics Studies with Coarse-Grained Protein and DNA Models.
• 
  Krzysztof Puszynski, Alberto Gandolfi, Alberto d'Onofrio:
  The Pharmacodynamics of the p53-Mdm2 Targeting Drug Nutlin: The Role of Gene-Switching Noise.
• 
  Adviti Naik, Damjana Rozman, Ales Belic:
  SteatoNet: The First Integrated Human Metabolic Model with Multi-layered Regulation to Investigate Liver-Associated Pathologies.
• 
  Michael M. H. Graf, Zhixiong Lin, Urban Bren, Dietmar Haltrich, Wilfred F. van Gunsteren, Chris Oostenbrink:
  Pyranose Dehydrogenase Ligand Promiscuity: A Generalized Approach to Simulate Monosaccharide Solvation, Binding, and Product Formation.
• 
  Xiaolin Tang, Mourad Bendjennat, Saveez Saffarian:
  Vesicular Stomatitis Virus Polymerase's Strong Affinity to Its Template Suggests Exotic Transcription Models.
• 
  Ganesh Shahane, Chirag Parsania, Durba Sengupta, Manali Joshi:
  Molecular Insights into the Dynamics of Pharmacogenetically Important N-Terminal Variants of the Human β₂-Adrenergic Receptor.
• 
  Kelly C. Chang, Jason D. Bayer, Natalia A. Trayanova:
  Disrupted Calcium Release as a Mechanism for Atrial Alternans Associated with Human Atrial Fibrillation.
• 
  Krishna Praneeth Kilambi, Kavan Reddy, Jeffrey J. Gray:
  Protein-Protein Docking with Dynamic Residue Protonation States.
• 
  Ritwik K. Niyogi, Peter Shizgal, Peter Dayan:
  Some Work and Some Play: Microscopic and Macroscopic Approaches to Labor and Leisure.
• 
  Paraskevi Gkeka, Panagiotis Angelikopoulos, Lev Sarkisov, Zoe Cournia:
  Membrane Partitioning of Anionic, Ligand-Coated Nanoparticles Is Accompanied by Ligand Snorkeling, Local Disordering, and Cholesterol Depletion.
• 
  Alexandra Gavryushkina, David Welch, Tanja Stadler, Alexei J. Drummond:
  Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration.
• 
  Hua Cheng, R. Dustin Schaeffer, Yuxing Liao, Lisa N. Kinch, Jimin Pei, Shuoyong Shi, Bong-Hyun Kim, Nick V. Grishin:
  ECOD: An Evolutionary Classification of Protein Domains.
• 
  Gergely Boza, András Szilágyi, Ádám Kun, Mauro Santos, Eörs Szathmáry:
  Evolution of the Division of Labor between Genes and Enzymes in the RNA World.
• 
  Niklas Hübel, Markus A. Dahlem:
  Dynamics from Seconds to Hours in Hodgkin-Huxley Model with Time-Dependent Ion Concentrations and Buffer Reservoirs.
• 
  Christoph Zechner, Heinz Koeppl:
  Uncoupled Analysis of Stochastic Reaction Networks in Fluctuating Environments.
• 
  Evandro Ferrada:
  The Amino Acid Alphabet and the Architecture of the Protein Sequence-Structure Map. I. Binary Alphabets.
• 
  Ofri Raviv, Itay Lieder, Yonatan Loewenstein, Merav Ahissar:
  Contradictory Behavioral Biases Result from the Influence of Past Stimuli on Perception.
• 
  Norman E. Davey, Venkata P. Satagopam, Salvador Santiago-Mozos, Carlos Villacorta-Martin, Tanmay A. M. Bharat, Reinhard Schneider, John A. G. Briggs:
  The HIV Mutation Browser: A Resource for Human Immunodeficiency Virus Mutagenesis and Polymorphism Data.
• 
  Benjamin Lansdell, Kevin Ford, J. Nathan Kutz:
  A Reaction-Diffusion Model of Cholinergic Retinal Waves.
• 
  Mayu Sugiyama, Takashi Saitou, Hiroshi Kurokawa, Asako Sakaue-Sawano, Takeshi Imamura, Atsushi Miyawaki, Tadahiro Iimura:
  Live Imaging-Based Model Selection Reveals Periodic Regulation of the Stochastic G1/S Phase Transition in Vertebrate Axial Development.
• 
  Bill R. Miller III, Carol A. Parish, Eugene Y. Wu:
  Molecular Dynamics Study of the Opening Mechanism for DNA Polymerase I.
• 
  Julijana Gjorgjieva, Rebecca A. Mease, William J. Moody, Adrienne L. Fairhall:
  Intrinsic Neuronal Properties Switch the Mode of Information Transmission in Networks.
• 
  Matt J. Whitfield, Jonathon P. Luo, Wendy E. Thomas:
  Yielding Elastic Tethers Stabilize Robust Cell Adhesion.
• 
  Jean-Pierre Rospars, Alexandre Grémiaux, David Jarriault, Antoine Chaffiol, Christelle Monsempès, Nina Deisig, Sylvia Anton, Philippe Lucas, Dominique Martinez:
  Heterogeneity and Convergence of Olfactory First-Order Neurons Account for the High Speed and Sensitivity of Second-Order Neurons.
• 
  Yana Gofman, Charlotta Schärfe, Debora S. Marks, Turkan Haliloglu, Nir Ben-Tal:
  Structure, Dynamics and Implied Gating Mechanism of a Human Cyclic Nucleotide-Gated Channel.
• 
  Alex N. Nguyen Ba, Bob Strome, Jun Jie Hua, Jonathan Desmond, Isabelle Gagnon-Arsenault, Eric L. Weiss, Christian R. Landry, Alan M. Moses:
  Detecting Functional Divergence after Gene Duplication through Evolutionary Changes in Posttranslational Regulatory Sequences.
• 
  Bratislav Misic, Joaquín Goñi, Richard F. Betzel, Olaf Sporns, Anthony Randal McIntosh:
  A Network Convergence Zone in the Hippocampus.
• 
  Avital Brodt, Maya Botzman, Eyal David, Irit Gat-Viks:
  Dissecting Dynamic Genetic Variation That Controls Temporal Gene Response in Yeast.
• 
  Axel Kammerer, Christian Leibold:
  Hippocampal Remapping Is Constrained by Sparseness rather than Capacity.
• 
  Marie Devaine, Guillaume Hollard, Jean Daunizeau:
  The Social Bayesian Brain: Does Mentalizing Make a Difference When We Learn?
• 
  Roman Bauer, Frédéric Zubler, Sabina S. Pfister, Andreas Hauri, Michael Pfeiffer, Dylan R. Muir, Rodney J. Douglas:
  Developmental Self-Construction and -Configuration of Functional Neocortical Neuronal Networks.
• 
  Eline Boghaert, Derek C. Radisky, Celeste M. Nelson:
  Lattice-Based Model of Ductal Carcinoma In Situ Suggests Rules for Breast Cancer Progression to an Invasive State.
• 
  James F. Denton, Jose Lugo-Martinez, Abraham E. Tucker, Daniel R. Schrider, Wesley C. Warren, Matthew W. Hahn:
  Extensive Error in the Number of Genes Inferred from Draft Genome Assemblies.
• 
  A. Sofia F. Oliveira, João M. Damas, António M. Baptista, Cláudio M. Soares:
  Exploring O₂ Diffusion in A-Type Cytochrome c Oxidases: Molecular Dynamics Simulations Uncover Two Alternative Channels towards the Binuclear Site.
• 
  Marnix H. Medema, Peter Cimermancic, Andrej Sali, Eriko Takano, Michael A. Fischbach:
  A Systematic Computational Analysis of Biosynthetic Gene Cluster Evolution: Lessons for Engineering Biosynthesis.

Corrections

• 
  Correction: Limits of Feedback Control in Bacterial Chemotaxis.
• 
  Correction: Cell Type Specific Alterations in Interchromosomal Networks across the Cell Cycle.
• 
  Correction: Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features.