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PLoS Computational Biology, Volume 12

Volume 12, Number 1, January 2016

Editorial

• 
  Andrew Lonsdale, Jocelyn Sietsma Penington, Timothy Rice, Michael Walker, Harriet Dashnow:
  Ten Simple Rules for a Bioinformatics Journal Club.

Education

• 
  John D. Blischak, Emily R. Davenport, Greg Wilson:
  A Quick Introduction to Version Control with Git and GitHub.

Review

• 
  Ezio Bartocci, Pietro Liò:
  Computational Modeling, Formal Analysis, and Tools for Systems Biology.

Research Articles

• 
  Michael J. Hull, Stephen R. Soffe, David J. Willshaw, Alan Roberts:
  Modelling Feedback Excitation, Pacemaker Properties and Sensory Switching of Electrically Coupled Brainstem Neurons Controlling Rhythmic Activity.
• 
  Iman Farasat, Howard M. Salis:
  A Biophysical Model of CRISPR/Cas9 Activity for Rational Design of Genome Editing and Gene Regulation.
• 
  Gabriel A. Al-Ghalith, Emmanuel Montassier, Henry N. Ward, Dan Knight:
  NINJA-OPS: Fast Accurate Marker Gene Alignment Using Concatenated Ribosomes.
• 
  Kai J. Miller, Gerwin Schalk, Dora Hermes, Jeffrey G. Ojemann, Rajesh P. N. Rao:
  Spontaneous Decoding of the Timing and Content of Human Object Perception from Cortical Surface Recordings Reveals Complementary Information in the Event-Related Potential and Broadband Spectral Change.
• 
  Troy Day, Andrew F. Read:
  Does High-Dose Antimicrobial Chemotherapy Prevent the Evolution of Resistance?
• 
  Matthew A. Oberhardt, Raphy Zarecki, Leah Reshef, Fangfang Xia, Miquel Duran-Frigola, Rachel Schreiber, Christopher S. Henry, Nir Ben-Tal, Daniel J. Dwyer, Uri Gophna, Eytan Ruppin:
  Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5'-Phosphate Production in E. coli.
• 
  Olga Kononova, Joost Snijder, Yaroslav Kholodov, Kenneth A. Marx, Gijs J. L. Wuite, Wouter H. Roos, Valeri Barsegov:
  Fluctuating Nonlinear Spring Model of Mechanical Deformation of Biological Particles.
• 
  Isaure Chauvot de Beauchêne, Sjoerd Jacob de Vries, Martin Zacharias:
  Binding Site Identification and Flexible Docking of Single Stranded RNA to Proteins Using a Fragment-Based Approach.
• 
  Susanne Gerber, Martina Fröhlich, Hella Lichtenberg-Fraté, Sergey Shabala, Lana Shabala, Edda Klipp:
  A Thermodynamic Model of Monovalent Cation Homeostasis in the Yeast Saccharomyces cerevisiae.
• 
  Araks Martirosyan, Matteo Figliuzzi, Enzo Marinari, Andrea De Martino:
  Probing the Limits to MicroRNA-Mediated Control of Gene Expression.
• 
  Andrew R. Gallimore, A. Radu Aricescu, Michisuke Yuzaki, Radu Calinescu:
  A Computational Model for the AMPA Receptor Phosphorylation Master Switch Regulating Cerebellar Long-Term Depression.
• 
  Alexandre Ismail, Vincent Leroux, Myriam Smadja, Lucie Gonzalez, Murielle Lombard, Fabien Pierrel, Caroline Mellot-Draznieks, Marc Fontecave:
  Coenzyme Q Biosynthesis: Evidence for a Substrate Access Channel in the FAD-Dependent Monooxygenase Coq6.
• 
  Fernando P. Santos, Francisco C. Santos, Jorge M. Pacheco:
  Social Norms of Cooperation in Small-Scale Societies.
• 
  C. Brandon Ogbunugafor, C. Scott Wylie, Ibrahim Diakite, Daniel M. Weinreich, Daniel L. Hartl:
  Adaptive Landscape by Environment Interactions Dictate Evolutionary Dynamics in Models of Drug Resistance.
• 
  David Lamparter, Daniel Marbach, Rico Rueedi, Zoltán Kutalik, Sven Bergmann:
  Fast and Rigorous Computation of Gene and Pathway Scores from SNP-Based Summary Statistics.
• 
  Jacob G. Scott, Alexander G. Fletcher, Alexander R. A. Anderson, Philip K. Maini:
  Spatial Metrics of Tumour Vascular Organisation Predict Radiation Efficacy in a Computational Model.
• 
  Masafumi Oizumi, Shun-ichi Amari, Toru Yanagawa, Naotaka Fujii, Naotsugu Tsuchiya:
  Measuring Integrated Information from the Decoding Perspective.
• 
  Laura Fumanelli, Marco Ajelli, Stefano Merler, Neil M. Ferguson, Simon Cauchemez:
  Model-Based Comprehensive Analysis of School Closure Policies for Mitigating Influenza Epidemics and Pandemics.
• 
  Juan P. Bustamante, Leandro G. Radusky, Leonardo Boechi, Dario A. Estrin, Arjen ten Have, Marcelo A. Marti:
  Evolutionary and Functional Relationships in the Truncated Hemoglobin Family.
• 
  Keng Boon Wee, Raphael Tze Chuen Lee, Jing Lin, Zacharias Aloysius Dwi Pramono, Sebastian Maurer-Stroh:
  Discovery of Influenza A Virus Sequence Pairs and Their Combinations for Simultaneous Heterosubtypic Targeting that Hedge against Antiviral Resistance.
• 
  Srivas Chennu, Stuart O'Connor, Ram Adapa, David K. Menon, Tristan A. Bekinschtein:
  Brain Connectivity Dissociates Responsiveness from Drug Exposure during Propofol-Induced Transitions of Consciousness.
• 
  Jaline Gerardin, Caitlin A. Bever, Busiku Hamainza, John M. Miller, Philip A. Eckhoff, Edward A. Wenger:
  Optimal Population-Level Infection Detection Strategies for Malaria Control and Elimination in a Spatial Model of Malaria Transmission.
• 
  Lin Chao, Camilla Ulla Rang, Audrey Menegaz Proenca, Jasper Ubirajara Chao:
  Asymmetrical Damage Partitioning in Bacteria: A Model for the Evolution of Stochasticity, Determinism, and Genetic Assimilation.
• 
  Duncan K. Ralph, Frederick A. Matsen IV:
  Consistency of VDJ Rearrangement and Substitution Parameters Enables Accurate B Cell Receptor Sequence Annotation.
• 
  Akram Méndez, Luis Mendoza:
  A Network Model to Describe the Terminal Differentiation of B Cells.
• 
  Samira Yazdi, Matthias Stein, Fredrik Elinder, Magnus Andersson, Erik Lindahl:
  The Molecular Basis of Polyunsaturated Fatty Acid Interactions with the Shaker Voltage-Gated Potassium Channel.
• 
  Jennifer A. Hobbs, Regan Blythe Towal, Mitra J. Z. Hartmann:
  Evidence for Functional Groupings of Vibrissae across the Rodent Mystacial Pad.
• 
  Marco Agostino Deriu, Gianvito Grasso, Jack A. Tuszynski, Diego Gallo, Umberto Morbiducci, Andrea Danani:
  Josephin Domain Structural Conformations Explored by Metadynamics in Essential Coordinates.
• 
  Daniel D. Seaton, Jawahar Krishnan:
  Model-Based Analysis of Cell Cycle Responses to Dynamically Changing Environments.
• 
  Jayna Raghwani, Samir Bhatt, Oliver G. Pybus:
  Faster Adaptation in Smaller Populations: Counterintuitive Evolution of HIV during Childhood Infection.
• 
  Andrea N. Kravats, Sam Tonddast-Navaei, George Stan:
  Coarse-Grained Simulations of Topology-Dependent Mechanisms of Protein Unfolding and Translocation Mediated by ClpY ATPase Nanomachines.
• 
  Jessica M. Conway, Alan S. Perelson:
  Residual Viremia in Treated HIV⁺ Individuals.
• 
  Junaid Hassan, Zhi Qu, Linda L. Bergaust, Lars R. Bakken:
  Transient Accumulation of NO₂^- and N₂O during Denitrification Explained by Assuming Cell Diversification by Stochastic Transcription of Denitrification Genes.
• 
  Zhen Song, Alain Karma, James N. Weiss, Zhilin Qu:
  Long-Lasting Sparks: Multi-Metastability and Release Competition in the Calcium Release Unit Network.
• 
  In Jun Park, Andrew M. Hein, Yuriy V. Bobkov, Matthew A. Reidenbach, Barry W. Ache, José C. Príncipe:
  Neurally Encoding Time for Olfactory Navigation.
• 
  Roland Keller, Marcus Klein, Maria Thomas, Andreas Dräger, Ute Metzger, Markus F. Templin, Thomas O. Joos, Wolfgang E. Thasler, Andreas Zell, Ulrich M. Zanger:
  Coordinating Role of RXRα in Downregulating Hepatic Detoxification during Inflammation Revealed by Fuzzy-Logic Modeling.
• 
  Van Ngo, Yibo Wang, Stephan Haas, Sergei Yu Noskov, Robert A. Farley:
  K⁺ Block Is the Mechanism of Functional Asymmetry in Bacterial Na_v Channels.
• 
  Almudena Pino-Ángeles, John M. Leveritt III, Themis Lazaridis:
  Pore Structure and Synergy in Antimicrobial Peptides of the Magainin Family.
• 
  Maria E. Tomasso, Micheal J. Tarver, Deepa Devarajan, Steven T. Whitten:
  Hydrodynamic Radii of Intrinsically Disordered Proteins Determined from Experimental Polyproline II Propensities.

Volume 12, Number 2, February 2016

Editorials

• 
  PLOS Computational Biology 2015 Reviewer Thank You.
• 
  James Malone, Robert Stevens, Simon Jupp, Tom Hancocks, Helen E. Parkinson, Catherine Brooksbank:
  Ten Simple Rules for Selecting a Bio-ontology.

Message from ISCB

• 
  Nomi L. Harris, Peter J. A. Cock, Hilmar Lapp, Brad Chapman, Rob Davey, Christopher J. Fields, Karsten Hokamp, Monica C. Munoz-Torres:
  The 2015 Bioinformatics Open Source Conference (BOSC 2015).

Education

• 
  Jessica Hedge, Daniel J. Wilson:
  Practical Approaches for Detecting Selection in Microbial Genomes.

Perspectives

• 
  Nicola J. Mulder, Alan Christoffels, Tulio de Oliveira, Junaid Gamieldien, Scott Hazelhurst, Fourie Joubert, Judit Kumuthini, Ché S. Pillay, Jacky L. Snoep, Özlem Tastan Bishop, Nicki Tiffin:
  The Development of Computational Biology in South Africa: Successes Achieved and Lessons Learnt.
• 
  Niko Beerenwinkel, Chris D. Greenman, Jens Lagergren:
  Computational Cancer Biology: An Evolutionary Perspective.

Research Articles

• 
  William M. Jacobs, Tuomas P. J. Knowles, Daan Frenkel:
  Oligomers of Heat-Shock Proteins: Structures That Don't Imply Function.
• 
  Yasin Senbabaoglu, Selçuk Onur Sümer, Francisco Sánchez-Vega, Debra Bemis, Giovanni Ciriello, Nikolaus Schultz, Chris Sander:
  A Multi-Method Approach for Proteomic Network Inference in 11 Human Cancers.
• 
  Swami Iyer, Timothy Killingback:
  Evolution of Cooperation in Social Dilemmas on Complex Networks.
• 
  Beata Hat, Marek Kochanczyk, Marta N. Bogdal, Tomasz Lipniacki:
  Feedbacks, Bifurcations, and Cell Fate Decision-Making in the p53 System.
• 
  H. Francis Song, Guangyu R. Yang, Xiao-Jing Wang:
  Training Excitatory-Inhibitory Recurrent Neural Networks for Cognitive Tasks: A Simple and Flexible Framework.
• 
  Bertrand H. Lemasson, Colby J. Tanner, Eric Dimperio:
  A Sensory-Driven Trade-Off between Coordinated Motion in Social Prey and a Predator's Visual Confusion.
• 
  Caroline A. Lea-Carnall, Marcelo A. Montemurro, Nelson J. Trujillo-Barreto, Laura M. Parkes, Wael El-Deredy:
  Cortical Resonance Frequencies Emerge from Network Size and Connectivity.
• 
  David Angulo-Garcia, Joshua D. Berke, Alessandro Torcini:
  Cell Assembly Dynamics of Sparsely-Connected Inhibitory Networks: A Simple Model for the Collective Activity of Striatal Projection Neurons.
• 
  Skander Mensi, Olivier Hagens, Wulfram Gerstner, Christian Pozzorini:
  Enhanced Sensitivity to Rapid Input Fluctuations by Nonlinear Threshold Dynamics in Neocortical Pyramidal Neurons.
• 
  Andrew Chay, Ilaria Zamparo, Andreas Koschinski, Manuela Zaccolo, Kim T. Blackwell:
  Control of βAR- and N-methyl-D-aspartate (NMDA) Receptor-Dependent cAMP Dynamics in Hippocampal Neurons.
• 
  Joao A. Ascensao, Pratik Datta, Baris Hancioglu, Eduardo D. Sontag, Maria L. Gennaro, Oleg A. Igoshin:
  Non-monotonic Response to Monotonic Stimulus: Regulation of Glyoxylate Shunt Gene-Expression Dynamics in Mycobacterium tuberculosis.
• 
  Tiziano Dallavilla, Laurence Abrami, Patrick A. Sandoz, Georgios Savoglidis, Vassily Hatzimanikatis, F. Gisou van der Goot:
  Model-Driven Understanding of Palmitoylation Dynamics: Regulated Acylation of the Endoplasmic Reticulum Chaperone Calnexin.
• 
  Vahid Rahmati, Knut Kirmse, Dimitrije Markovic, Knut Holthoff, Stefan J. Kiebel:
  Inferring Neuronal Dynamics from Calcium Imaging Data Using Biophysical Models and Bayesian Inference.
• 
  Jordi van Gestel, Martin A. Nowak:
  Phenotypic Heterogeneity and the Evolution of Bacterial Life Cycles.
• 
  Juntao Liu, Guojun Li, Zheng Chang, Ting Yu, Bingqiang Liu, Rick McMullen, Pengyin Chen, Xiuzhen Huang:
  BinPacker: Packing-Based De Novo Transcriptome Assembly from RNA-seq Data.
• 
  Megan A. Greischar, Nicole Mideo, Andrew F. Read, Ottar N. Bjørnstad:
  Quantifying Transmission Investment in Malaria Parasites.
• 
  Thomas Miconi, Rufin VanRullen:
  A Feedback Model of Attention Explains the Diverse Effects of Attention on Neural Firing Rates and Receptive Field Structure.
• 
  Oren Shriki, Dovi Yellin:
  Optimal Information Representation and Criticality in an Adaptive Sensory Recurrent Neuronal Network.
• 
  Jingtao Lu, Michael-Rock Goldsmith, Christopher M. Grulke, Daniel T. Chang, Raina D. Brooks, Jeremy A. Leonard, Martin B. Phillips, Ethan D. Hypes, Matthew J. Fair, Rogelio Tornero-Velez, Jeffre Johnson, Curtis C. Dary, Yu-Mei Tan:
  Developing a Physiologically-Based Pharmacokinetic Model Knowledgebase in Support of Provisional Model Construction.
• 
  Benjamin Boucher, Anna Y. Lee, Michael T. Hallett, Sarah Jenna:
  Structural and Functional Characterization of a Caenorhabditis elegans Genetic Interaction Network within Pathways.
• 
  Ting Wang, Zhao Ren, Ying Ding, Zhou Fang, Zhe Sun, Matthew L. MacDonald, Robert A. Sweet, Jieru Wang, Wei Chen:
  FastGGM: An Efficient Algorithm for the Inference of Gaussian Graphical Model in Biological Networks.
• 
  Yong Liu, Min Wu, Chunyan Miao, Peilin Zhao, Xiaoli Li:
  Neighborhood Regularized Logistic Matrix Factorization for Drug-Target Interaction Prediction.
• 
  Nick Jagiella, Benedikt Müller, Margareta Müller, Irene E. Vignon-Clementel, Dirk Drasdo:
  Inferring Growth Control Mechanisms in Growing Multi-cellular Spheroids of NSCLC Cells from Spatial-Temporal Image Data.
• 
  Zohar Z. Bronfman, Noam Brezis, Marius Usher:
  Non-monotonic Temporal-Weighting Indicates a Dynamically Modulated Evidence-Integration Mechanism.
• 
  Paul Ardin, Fei Peng, Michael Mangan, Konstantinos Lagogiannis, Barbara Webb:
  Using an Insect Mushroom Body Circuit to Encode Route Memory in Complex Natural Environments.
• 
  Travis E. Gibson, Amir Bashan, Hong-Tai Cao, Scott T. Weiss, Yang-Yu Liu:
  On the Origins and Control of Community Types in the Human Microbiome.
• 
  Viljami R. Salmela, Linda Henriksson, Simo Vanni:
  Radial Frequency Analysis of Contour Shapes in the Visual Cortex.
• 
  Joshua M. Inouye, Francisco J. Valero Cuevas:
  Muscle Synergies Heavily Influence the Neural Control of Arm Endpoint Stiffness and Energy Consumption.
• 
  Daniel Miner, Jochen Triesch:
  Plasticity-Driven Self-Organization under Topological Constraints Accounts for Non-random Features of Cortical Synaptic Wiring.
• 
  Emily P. Harvey, Alona Ben-Tal:
  Robust Unidirectional Airflow through Avian Lungs: New Insights from a Piecewise Linear Mathematical Model.
• 
  Artémis Llamosi, Andrés M. González-Vargas, Cristian Versari, Eugenio Cinquemani, Giancarlo Ferrari-Trecate, Pascal Hersen, Grégory Batt:
  What Population Reveals about Individual Cell Identity: Single-Cell Parameter Estimation of Models of Gene Expression in Yeast.
• 
  Rory M. Donovan, José Juan Tapia, Devin P. Sullivan, James R. Faeder, Robert F. Murphy, Markus Dittrich, Daniel M. Zuckerman:
  Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories.
• 
  Benjamin D. Dalziel, Ottar N. Bjørnstad, Willem G. van Panhuis, Donald S. Burke, C. Jessica E. Metcalf, Bryan T. Grenfell:
  Persistent Chaos of Measles Epidemics in the Prevaccination United States Caused by a Small Change in Seasonal Transmission Patterns.
• 
  Hiromasa Takemura, Cesar F. Caiafa, Brian A. Wandell, Franco Pestilli:
  Ensemble Tractography.
• 
  Harendra Guturu, Sandeep Chinchali, Shoa L. Clarke, Gill Bejerano:
  Erosion of Conserved Binding Sites in Personal Genomes Points to Medical Histories.
• 
  Davi R. Ortega, Igor B. Zhulin:
  Evolutionary Genomics Suggests That CheV Is an Additional Adaptor for Accommodating Specific Chemoreceptors within the Chemotaxis Signaling Complex.
• 
  Steven W. Paugh, David R. Coss, Ju Bao, Lucas T. Laudermilk, Christy R. Grace, Antonio M. Ferreira, M. Brett Waddell, Granger Ridout, Deanna Naeve, Michael R. Leuze, Philip F. LoCascio, John C. Panetta, Mark R. Wilkinson, Ching-Hon Pui, Clayton W. Naeve, Edward C. Uberbacher, Erik J. Bonten, William E. Evans:
  MicroRNAs Form Triplexes with Double Stranded DNA at Sequence-Specific Binding Sites; a Eukaryotic Mechanism via which microRNAs Could Directly Alter Gene Expression.
• 
  Mathieu Schiess, Robert Urbanczik, Walter Senn:
  Somato-dendritic Synaptic Plasticity and Error-backpropagation in Active Dendrites.
• 
  Benedikt Frieg, Boris Görg, Nadine Homeyer, Verena Keitel, Dieter Häussinger, Holger Gohlke:
  Molecular Mechanisms of Glutamine Synthetase Mutations that Lead to Clinically Relevant Pathologies.
• 
  Leonid Chindelevitch, Caroline Colijn, Prashini Moodley, Douglas Wilson, Ted Cohen:
  ClassTR: Classifying Within-Host Heterogeneity Based on Tandem Repeats with Application to Mycobacterium tuberculosis Infections.
• 
  Javier Macía, Romilde Manzoni, Núria Conde-Pueyo, Arturo Urrios, Eulàlia de Nadal, Ricard V. Solé, Francesc Posas:
  Implementation of Complex Biological Logic Circuits Using Spatially Distributed Multicellular Consortia.
• 
  Ioannis Vlachos, Taskin Deniz, Ad Aertsen, Arvind Kumar:
  Recovery of Dynamics and Function in Spiking Neural Networks with Closed-Loop Control.
• 
  Victor Garcia, Marcus W. Feldman, Roland R. Regoes:
  Investigating the Consequences of Interference between Multiple CD8⁺ T Cell Escape Mutations in Early HIV Infection.
• 
  Yohan J. John, Basilis Zikopoulos, Daniel Bullock, Helen Barbas:
  The Emotional Gatekeeper: A Computational Model of Attentional Selection and Suppression through the Pathway from the Amygdala to the Inhibitory Thalamic Reticular Nucleus.
• 
  Jan O. Haerter, Namiko Mitarai, Kim Sneppen:
  Food Web Assembly Rules for Generalized Lotka-Volterra Equations.
• 
  Ivana Bozic, Jeffrey M. Gerold, Martin A. Nowak:
  Quantifying Clonal and Subclonal Passenger Mutations in Cancer Evolution.
• 
  Jon Lund Steffensen, Keith Dufault-Thompson, Ying Zhang:
  PSAMM: A Portable System for the Analysis of Metabolic Models.
• 
  Mathias Foo, David E. Somers, Pan-Jun Kim:
  Kernel Architecture of the Genetic Circuitry of the Arabidopsis Circadian System.

Volume 12, Number 3, March 2016

Message from ISCB

• 
  Bonnie Berger, Terry Gaasterland, Thomas Lengauer, Christine A. Orengo, Bruno Gaëta, Scott Markel, Alfonso Valencia:
  ISCB's Initial Reaction to The New England Journal of Medicine Editorial on Data Sharing.

Perspectives

• 
  Yoo-Ah Kim, Dong-Yeon Cho, Teresa M. Przytycka:
  Understanding Genotype-Phenotype Effects in Cancer via Network Approaches.
• 
  Christine Vogel:
  Systems Approaches to the Eukaryotic Stress Response.

Review

• 
  Sarina Grutsch, Sven Brüschweiler, Martin Tollinger:
  NMR Methods to Study Dynamic Allostery.

Research Articles

• 
  Vaclav Cvicek, William A. Goddard III, Ravinder Abrol:
  Structure-Based Sequence Alignment of the Transmembrane Domains of All Human GPCRs: Phylogenetic, Structural and Functional Implications.
• 
  Jeffrey J. Sutherland, Robert A. Jolly, Keith M. Goldstein, James L. Stevens:
  Assessing Concordance of Drug-Induced Transcriptional Response in Rodent Liver and Cultured Hepatocytes.
• 
  Sara Sheehan, Yun S. Song:
  Deep Learning for Population Genetic Inference.
• 
  Sandhya P. Tiwari, Nathalie Reuter:
  Similarity in Shape Dictates Signature Intrinsic Dynamics Despite No Functional Conservation in TIM Barrel Enzymes.
• 
  Maryna Kapustina, Denis Tsygankov, Jia Zhao, Timothy Wessler, Xiaofeng Yang, Alex Chen, Nathan Roach, Timothy C. Elston, Qi Wang, Ken Jacobson, M. Gregory Forest:
  Modeling the Excess Cell Surface Stored in a Complex Morphology of Bleb-Like Protrusions.
• 
  Mikhail Shubin, Artem Lebedev, Outi Lyytikäinen, Kari Auranen:
  Revealing the True Incidence of Pandemic A(H1N1)pdm09 Influenza in Finland during the First Two Seasons - An Analysis Based on a Dynamic Transmission Model.
• 
  Takeshi Nishimura, Futoshi Mori, Sho Hanida, Kiyoshi Kumahata, Shigeru Ishikawa, Kaouthar Samarat, Takako Miyabe-Nishiwaki, Misato Hayashi, Masaki Tomonaga, Juri Suzuki, Tetsuro Matsuzawa, Teruo Matsuzawa:
  Impaired Air Conditioning within the Nasal Cavity in Flat-Faced Homo.
• 
  J. Christian J. Ray, Michelle L. Wickersheim, Ameya P. Jalihal, Yusuf O. Adeshina, Tim F. Cooper, Gábor Balázsi:
  Cellular Growth Arrest and Persistence from Enzyme Saturation.
• 
  Nikita Chopra, Thomas E. Wales, Raji E. Joseph, Scott E. Boyken, John R. Engen, Robert L. Jernigan, Amy H. Andreotti:
  Dynamic Allostery Mediated by a Conserved Tryptophan in the Tec Family Kinases.
• 
  Tadeo E. Saldaño, Alexander Miguel Monzon, Gustavo D. Parisi, Sebastian Fernandez Alberti:
  Evolutionary Conserved Positions Define Protein Conformational Diversity.
• 
  Prakash Chandra Rathi, Alexander Fulton, Karl-Erich Jaeger, Holger Gohlke:
  Application of Rigidity Theory to the Thermostabilization of Lipase A from Bacillus subtilis.
• 
  Katharina A. Wilmes, Henning Sprekeler, Susanne Schreiber:
  Inhibition as a Binary Switch for Excitatory Plasticity in Pyramidal Neurons.
• 
  Andrew Mugler, Mark Kittisopikul, Luke Hayden, Jintao Liu, Chris H. Wiggins, Gürol M. Süel, Aleksandra M. Walczak:
  Noise Expands the Response Range of the Bacillus subtilis Competence Circuit.
• 
  Nicolas Dérian, Bertrand Bellier, Hang-Phuong Pham, Eliza Tsitoura, Dorothea Kazazi, Christophe Huret, Penelope Mavromara, David Klatzmann, Adrien Six:
  Early Transcriptome Signatures from Immunized Mouse Dendritic Cells Predict Late Vaccine-Induced T-Cell Responses.
• 
  Kelsey Chalmers, Elizabeth M. Kita, Ethan K. Scott, Geoffrey J. Goodhill:
  Quantitative Analysis of Axonal Branch Dynamics in the Developing Nervous System.
• 
  Bonnie Nijhof, Anna Castells-Nobau, Louis Wolf, Jolanda M. Scheffer-de Gooyert, Ignacio Monedero, Laura Torroja, Lluís Coromina, Jeroen A. W. M. van der Laak, Annette Schenck:
  A New Fiji-Based Algorithm That Systematically Quantifies Nine Synaptic Parameters Provides Insights into Drosophila NMJ Morphometry.
• 
  Sameeran Kunche, Huaming Yan, Anne L. Calof, John S. Lowengrub, Arthur D. Lander:
  Feedback, Lineages and Self-Organizing Morphogenesis.
• 
  G. Matthew Fricke, Kenneth Letendre, Melanie E. Moses, Judy L. Cannon:
  Persistence and Adaptation in Immunity: T Cells Balance the Extent and Thoroughness of Search.
• 
  Cevat Üstün:
  A Sensorimotor Model for Computing Intended Reach Trajectories.
• 
  Farshid S. Garmaroudi, Diane E. Handy, Yang-Yu Liu, Joseph Loscalzo:
  Systems Pharmacology and Rational Polypharmacy: Nitric Oxide-Cyclic GMP Signaling Pathway as an Illustrative Example and Derivation of the General Case.
• 
  Matthieu Gilson, Rubén Moreno-Bote, Adrián Ponce-Alvarez, Petra Ritter, Gustavo Deco:
  Estimation of Directed Effective Connectivity from fMRI Functional Connectivity Hints at Asymmetries of Cortical Connectome.
• 
  Dominique Cadosch, Pia Abel zur Wiesch, Roger D. Kouyos, Sebastian Bonhoeffer:
  The Role of Adherence and Retreatment in De Novo Emergence of MDR-TB.
• 
  Cristiano De Michele, Paolo De Los Rios, Giuseppe Foffi, Francesco Piazza:
  Simulation and Theory of Antibody Binding to Crowded Antigen-Covered Surfaces.
• 
  Jeroen Atsma, Femke Maij, Mathieu Koppen, David E. Irwin, W. Pieter Medendorp:
  Causal Inference for Spatial Constancy across Saccades.
• 
  Matthieu Jacobs, Nicolas Grégoire, William Couet, Jurgen B. Bulitta:
  Distinguishing Antimicrobial Models with Different Resistance Mechanisms via Population Pharmacodynamic Modeling.
• 
  Andreas Milias-Argeitis, Ana Paula Oliveira, Luca Gerosa, Laura Falter, Uwe Sauer, John Lygeros:
  Elucidation of Genetic Interactions in the Yeast GATA-Factor Network Using Bayesian Model Selection.
• 
  Anne Gabrielle Eva Collins, Michael Joshua Frank:
  Motor Demands Constrain Cognitive Rule Structures.
• 
  Jinzen Ikebe, Shun Sakuraba, Hidetoshi Kono:
  H3 Histone Tail Conformation within the Nucleosome and the Impact of K14 Acetylation Studied Using Enhanced Sampling Simulation.
• 
  Shane E. Gordon, Daniel K. Weber, Matthew T. Downton, John Wagner, Matthew A. Perugini:
  Dynamic Modelling Reveals 'Hotspots' on the Pathway to Enzyme-Substrate Complex Formation.
• 
  Andrej Kuritzin, Tabea G. Kischka, Jürgen Schmitz, Gennady Churakov:
  Incomplete Lineage Sorting and Hybridization Statistics for Large-Scale Retroposon Insertion Data.
• 
  Kenichi W. Okamoto, Fred Gould, Alun L. Lloyd:
  Integrating Transgenic Vector Manipulation with Clinical Interventions to Manage Vector-Borne Diseases.
• 
  Jeffrey K. Noel, Mariana Levi, Mohit Raghunathan, Heiko Lammert, Ryan L. Hayes, José N. Onuchic, Paul C. Whitford:
  SMOG 2: A Versatile Software Package for Generating Structure-Based Models.
• 
  Matthew K. Theisen, Jimmy G. Lafontaine Rivera, James C. Liao:
  Stability of Ensemble Models Predicts Productivity of Enzymatic Systems.
• 
  Artem Sokolov, Daniel E. Carlin, Evan O. Paull, Robert Baertsch, Joshua M. Stuart:
  Pathway-Based Genomics Prediction using Generalized Elastic Net.
• 
  Nils Giordano, Francis Mairet, Jean-Luc Gouzé, Johannes Geiselmann, Hidde de Jong:
  Dynamical Allocation of Cellular Resources as an Optimal Control Problem: Novel Insights into Microbial Growth Strategies.
• 
  Lies Boelen, Patrick K. O'Neill, Kathryn J. Quigley, Catherine J. Reynolds, Bernard Maillere, John H. Robinson, Ganjana Lertmemongkolchai, Daniel M. Altmann, Rosemary J. Boyton, Becca Asquith:
  BIITE: A Tool to Determine HLA Class II Epitopes from T Cell ELISpot Data.
• 
  Will D. Penny, Biswa Sengupta:
  Annealed Importance Sampling for Neural Mass Models.
• 
  André Schultz, Amina A. Qutub:
  Reconstruction of Tissue-Specific Metabolic Networks Using CORDA.
• 
  Enrico Guarnera, Igor N. Berezovsky:
  Structure-Based Statistical Mechanical Model Accounts for the Causality and Energetics of Allosteric Communication.
• 
  Baktash Babadi, L. F. Abbott:
  Stability and Competition in Multi-spike Models of Spike-Timing Dependent Plasticity.
• 
  Sam F. Greenbury, Steffen Schaper, Sebastian E. Ahnert, Ard A. Louis:
  Genetic Correlations Greatly Increase Mutational Robustness and Can Both Reduce and Enhance Evolvability.
• 
  Wondimu Teka, David B. Stockton, Fidel Santamaría:
  Power-Law Dynamics of Membrane Conductances Increase Spiking Diversity in a Hodgkin-Huxley Model.
• 
  Ramya Raviram, Pedro P. Rocha, Christian L. Müller, Emily R. Miraldi, Sana Badri, Yi Fu, Emily Swanzey, Charlotte Proudhon, Valentina Snetkova, Richard Bonneau, Jane A. Skok:
  4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments.
• 
  Michael D. Karcher, Julia A. Palacios, Trevor Bedford, Marc A. Suchard, Vladimir N. Minin:
  Quantifying and Mitigating the Effect of Preferential Sampling on Phylodynamic Inference.
• 
  Anat Kahan, Yoram Ben-Shaul:
  Extracting Behaviorally Relevant Traits from Natural Stimuli: Benefits of Combinatorial Representations at the Accessory Olfactory Bulb.

Volume 12, Number 4, April 2016

Topic Page

• 
  Natalia Szostak, Szymon Wasik, Jacek Blazewicz:
  Hypercycle.

Review

• 
  Tatiana Maximova, Ryan Moffatt, Buyong Ma, Ruth Nussinov, Amarda Shehu:
  Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics.

Research Articles

• 
  Samuel P. C. Brand, Kat S. Rock, Matt J. Keeling:
  The Interaction between Vector Life History and Short Vector Life in Vector-Borne Disease Transmission and Control.
• 
  Evgeni V. Nikolaev, Eduardo D. Sontag:
  Quorum-Sensing Synchronization of Synthetic Toggle Switches: A Design Based on Monotone Dynamical Systems Theory.
• 
  Raul Rodriguez-Esteban:
  A Drug-Centric View of Drug Development: How Drugs Spread from Disease to Disease.
• 
  Victor Trevino, Alberto Cassese, Zsuzsanna Nagy, Xiaodong Zhuang, John M. Herbert, Philipp Antzack, Kim Clarke, Nicholas Davies, Ayesha Rahman, Moray J. Campbell, Michele Guindani, Roy Bicknell, Marina Vannucci, Francesco Falciani:
  A Network Biology Approach Identifies Molecular Cross-Talk between Normal Prostate Epithelial and Prostate Carcinoma Cells.
• 
  Andrew Wight, Doo Yang, Ilya Ioshikhes, Andrew P. Makrigiannis:
  Nucleosome Presence at AML-1 Binding Sites Inversely Correlates with Ly49 Expression: Revelations from an Informatics Analysis of Nucleosomes and Immune Cell Transcription Factors.
• 
  Jonas Kubilius, Stefania Bracci, Hans P. Op de Beeck:
  Deep Neural Networks as a Computational Model for Human Shape Sensitivity.
• 
  Carles Foguet, Silvia Marin, Vitaly A. Selivanov, Eric Fanchon, Wai-Nang Paul Lee, Joan J. Guinovart, Pedro de Atauri, Marta Cascante:
  HepatoDyn: A Dynamic Model of Hepatocyte Metabolism That Integrates 13C Isotopomer Data.
• 
  Timothy S. Carpenter, Felice C. Lightstone:
  An Electrostatic Funnel in the GABA-Binding Pathway.
• 
  Jonas Schluter, Armin P. Schoech, Kevin R. Foster, Sara Mitri:
  The Evolution of Quorum Sensing as a Mechanism to Infer Kinship.
• 
  Konstantin Popov, James Komianos, Garegin A. Papoian:
  MEDYAN: Mechanochemical Simulations of Contraction and Polarity Alignment in Actomyosin Networks.
• 
  Enrico Sandro Colizzi, Paulien Hogeweg:
  Parasites Sustain and Enhance RNA-Like Replicators through Spatial Self-Organisation.
• 
  Ingrid Paine, Arnaud Chauviere, John Landua, Amulya Sreekumar, Vittorio Cristini, Jeffrey M. Rosen, Michael T. Lewis:
  A Geometrically-Constrained Mathematical Model of Mammary Gland Ductal Elongation Reveals Novel Cellular Dynamics within the Terminal End Bud.
• 
  Steven C. Bagley, Marina Sirota, Richard O. Chen, Atul J. Butte, Russ B. Altman:
  Constraints on Biological Mechanism from Disease Comorbidity Using Electronic Medical Records and Database of Genetic Variants.
• 
  Robert Kalescky, Hongyu Zhou, Jin Liu, Peng Tao:
  Rigid Residue Scan Simulations Systematically Reveal Residue Entropic Roles in Protein Allostery.
• 
  Rumen Kostadinov, Carlo C. Maley, Mary K. Kuhner:
  Bulk Genotyping of Biopsies Can Create Spurious Evidence for Hetereogeneity in Mutation Content.
• 
  Jolene Atia, Conor McCloskey, Anatoly S. Shmygol, David A. Rand, Hugo Antonius van den Berg, Andrew M. Blanks:
  Reconstruction of Cell Surface Densities of Ion Pumps, Exchangers, and Channels from mRNA Expression, Conductance Kinetics, Whole-Cell Calcium, and Current-Clamp Voltage Recordings, with an Application to Human Uterine Smooth Muscle Cells.
• 
  Mark Shein-Idelson, Gilad Cohen, Eshel Ben-Jacob, Yael Hanein:
  Modularity Induced Gating and Delays in Neuronal Networks.
• 
  Antonio L. C. Gomes, Harris H. Wang:
  The Role of Genome Accessibility in Transcription Factor Binding in Bacteria.
• 
  Eric Talevich, A. Hunter Shain, Thomas Botton, Boris C. Bastian:
  CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing.
• 
  Jie Wang, Shuli Xia, Brian Arand, Heng Zhu, Raghu Machiraju, Kun Huang, Hongkai Ji, Jiang Qian:
  Single-Cell Co-expression Analysis Reveals Distinct Functional Modules, Co-regulation Mechanisms and Clinical Outcomes.
• 
  Christian Diener, Georgina Garza Ramos Martínez, Daniel Moreno Blas, David A. Castillo González, Gerardo Corzo, Susana Castro-Obregon, Gabriel del Rio:
  Effective Design of Multifunctional Peptides by Combining Compatible Functions.
• 
  Kendall Gillies, Stephen M. Krone, James J. Nagler, Irvin R. Schultz:
  A Computational Model of the Rainbow Trout Hypothalamus-Pituitary-Ovary-Liver Axis.
• 
  Nurcan Tuncbag, Sara J. C. Gosline, Amanda J. Kedaigle, Anthony R. Soltis, Anthony Gitter, Ernest Fraenkel:
  Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package.
• 
  Melanie Laßek, Jens Weingarten, Martin Wegner, Benjamin F. Mueller, Marion Rohmer, Dominic Baeumlisberger, Tabiwang N. Arrey, Meike Hick, Jörg Ackermann, Amparo Acker-Palmer, Ina Koch, Ulrike Müller, Michael Karas, Walter Volknandt:
  APP Is a Context-Sensitive Regulator of the Hippocampal Presynaptic Active Zone.
• 
  Stephen Gang Wu, Yuxuan Wang, Wu Jiang, Tolutola Oyetunde, Ruilian Yao, Xuehong Zhang, Kazuyuki Shimizu, Yinjie J. Tang, Forrest Sheng Bao:
  Rapid Prediction of Bacterial Heterotrophic Fluxomics Using Machine Learning and Constraint Programming.
• 
  Paola Malerba, Giri P. Krishnan, Jean-Marc Fellous, Maxim Bazhenov:
  Hippocampal CA1 Ripples as Inhibitory Transients.
• 
  Sara Ballouz, Jesse A. Gillis:
  AuPairWise: A Method to Estimate RNA-Seq Replicability through Co-expression.
• 
  Brian Granger, Yi-Chien Chang, Yan Wang, Charles DeLisi, Daniel Segrè, Zhenjun Hu:
  Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0.
• 
  Yotam Luz, Maoz Shamir:
  Oscillations via Spike-Timing Dependent Plasticity in a Feed-Forward Model.
• 
  Nicolas Muller, Matthieu Piel, Vincent Calvez, Raphael Voituriez, Joana Gonçalves-Sá, Chin-Lin Guo, Xingyu Jiang, Andrew Murray, Nicolas Meunier:
  A Predictive Model for Yeast Cell Polarization in Pheromone Gradients.
• 
  Daniela Börnigen, Svitlana Tyekucheva, Xiaodong Wang, Jennifer R. Rider, Gwo-Shu Lee, Lorelei A. Mucci, Christopher Sweeney, Curtis Huttenhower:
  Computational Reconstruction of NFκB Pathway Interaction Mechanisms during Prostate Cancer.
• 
  Phuong Dao, Damian Wójtowicz, Steevenson Nelson, David Levens, Teresa M. Przytycka:
  Ups and Downs of Poised RNA Polymerase II in B-Cells.
• 
  Maulik K. Nariya, Johnny Israeli, Jack J. Shi, Eric J. Deeds:
  Mathematical Model for Length Control by the Timing of Substrate Switching in the Type III Secretion System.
• 
  Erida Gjini, Patricia H. Brito:
  Integrating Antimicrobial Therapy with Host Immunity to Fight Drug-Resistant Infections: Classical vs. Adaptive Treatment.
• 
  Wendy J. Adams:
  The Development of Audio-Visual Integration for Temporal Judgements.
• 
  Yohai Bar-Sinai, Jean-Daniel Julien, Eran Sharon, Shahaf Armon, Naomi Nakayama, Mokhtar Adda-Bedia, Arezki Boudaoud:
  Mechanical Stress Induces Remodeling of Vascular Networks in Growing Leaves.
• 
  Francesco Donnarumma, Domenico Maisto, Giovanni Pezzulo:
  Problem Solving as Probabilistic Inference with Subgoaling: Explaining Human Successes and Pitfalls in the Tower of Hanoi.
• 
  Lorenzo Asti, Guido Uguzzoni, Paolo Marcatili, Andrea Pagnani:
  Maximum-Entropy Models of Sequenced Immune Repertoires Predict Antigen-Antibody Affinity.
• 
  David N. Quan, Chen-Yu Tsao, Hsuan-Chen Wu, William E. Bentley:
  Quorum Sensing Desynchronization Leads to Bimodality and Patterned Behaviors.
• 
  Casimir Emako, Charlène Gayrard, Axel Buguin, Luís Neves de Almeida, Nicolas Vauchelet:
  Traveling Pulses for a Two-Species Chemotaxis Model.
• 
  Adam N. Sanborn, Ulrik R. Beierholm:
  Fast and Accurate Learning When Making Discrete Numerical Estimates.
• 
  Eben Kenah, Tom Britton, M. Elizabeth Halloran, Ira M. Longini Jr.:
  Molecular Infectious Disease Epidemiology: Survival Analysis and Algorithms Linking Phylogenies to Transmission Trees.
• 
  Simeone Marino, Hannah P. Gideon, Chang Gong, Shawn Mankad, John T. McCrone, Philana Ling Lin, Jennifer J. Linderman, JoAnne L. Flynn, Denise E. Kirschner:
  Computational and Empirical Studies Predict Mycobacterium tuberculosis-Specific T Cells as a Biomarker for Infection Outcome.
• 
  Yilun Zhang, Tatyana O. Sharpee:
  A Robust Feedforward Model of the Olfactory System.
• 
  Takumi Higaki, Natsumaro Kutsuna, Kae Akita, Hisako Takigawa-Imamura, Kenji Yoshimura, Takashi Miura:
  A Theoretical Model of Jigsaw-Puzzle Pattern Formation by Plant Leaf Epidermal Cells.
• 
  Andrew G. McDonald, Keith F. Tipton, Gavin P. Davey:
  A Knowledge-Based System for Display and Prediction of O-Glycosylation Network Behaviour in Response to Enzyme Knockouts.
• 
  Philipp J. Albert, Ulrich S. Schwarz:
  Dynamics of Cell Ensembles on Adhesive Micropatterns: Bridging the Gap between Single Cell Spreading and Collective Cell Migration.
• 
  Nafise Erfanian Saeedi, Peter J. Blamey, Anthony N. Burkitt, David B. Grayden:
  Learning Pitch with STDP: A Computational Model of Place and Temporal Pitch Perception Using Spiking Neural Networks.
• 
  Amit Upadhyay, Aaron D. Fleetwood, Ogun Adebali, Robert D. Finn, Igor B. Zhulin:
  Cache Domains That are Homologous to, but Different from PAS Domains Comprise the Largest Superfamily of Extracellular Sensors in Prokaryotes.
• 
  Robin N. Thompson, Christopher A. Gilligan, Nik J. Cunniffe:
  Detecting Presymptomatic Infection Is Necessary to Forecast Major Epidemics in the Earliest Stages of Infectious Disease Outbreaks.
• 
  Nick W. Ruktanonchai, Patrick De Leenheer, Andrew J. Tatem, Victor A. Alegana, T. Trevor Caughlin, Elisabeth Zu Erbach-Schoenberg, Christopher Lourenço, Corrine W. Ruktanonchai, David L. Smith:
  Identifying Malaria Transmission Foci for Elimination Using Human Mobility Data.
• 
  Maryam M. Shanechi, Amy L. Orsborn, Jose M. Carmena:
  Robust Brain-Machine Interface Design Using Optimal Feedback Control Modeling and Adaptive Point Process Filtering.
• 
  Daniel C. Kirouac, Jinyan Du, Johanna Lahdenranta, Matthew D. Onsum, Ulrik B. Nielsen, Birgit Schoeberl, Charlotte F. McDonagh:
  HER2+ Cancer Cell Dependence on PI3K vs. MAPK Signaling Axes Is Determined by Expression of EGFR, ERBB3 and CDKN1B.
• 
  Matias I. Maturana, Nicholas V. Apollo, Alex E. Hadjinicolaou, David J. Garrett, Shaun L. Cloherty, Tatiana Kameneva, David B. Grayden, Michael R. Ibbotson, Hamish Meffin:
  A Simple and Accurate Model to Predict Responses to Multi-electrode Stimulation in the Retina.
• 
  Kashif Mahfooz, Mahendra Singh, Robert Renden, John F. Wesseling:
  A Well-Defined Readily Releasable Pool with Fixed Capacity for Storing Vesicles at Calyx of Held.
• 
  Yael Steuerman, Irit Gat-Viks:
  Exploiting Gene-Expression Deconvolution to Probe the Genetics of the Immune System.
• 
  Ali Farshchiansadegh, Alejandro Melendez-Calderon, Rajiv Ranganathan, Todd D. Murphey, Ferdinando A. Mussa-Ivaldi:
  Sensory Agreement Guides Kinetic Energy Optimization of Arm Movements during Object Manipulation.

Volume 12, Number 5, May 2016

Message from ISCB

• 
  Lonnie R. Welch, Cath Brooksbank, Russell Schwartz, Sarah L. Morgan, Bruno A. Gaëta, Alastair M. Kilpatrick, Daniel Mietchen, Benjamin L. Moore, Nicola J. Mulder, Mark A. Pauley, William R. Pearson, Predrag Radivojac, Naomi Rosenberg, Anne G. Rosenwald, Gabriella Rustici, Tandy J. Warnow:
  Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB's Education Committee).

Perspectives

• 
  David L. Masica, Rachel Karchin:
  Towards Increasing the Clinical Relevance of In Silico Methods to Predict Pathogenic Missense Variants.
• 
  Erik van Nimwegen:
  Inferring Contacting Residues within and between Proteins: What Do the Probabilities Mean?
• 
  Erik Aurell:
  The Maximum Entropy Fallacy Redux?

Research Articles

• 
  Thom Griffith, Krasimira Tsaneva-Atanasova, Jack R. Mellor:
  Control of Ca2+ Influx and Calmodulin Activation by SK-Channels in Dendritic Spines.
• 
  Pascal Giehr, Charalampos Kyriakopoulos, Gabriella Ficz, Verena Wolf, Jörn Walter:
  The Influence of Hydroxylation on Maintaining CpG Methylation Patterns: A Hidden Markov Model Approach.
• 
  Hagai Lalazar, L. F. Abbott, Eilon Vaadia:
  Tuning Curves for Arm Posture Control in Motor Cortex Are Consistent with Random Connectivity.
• 
  Wenchao Zhang, Xinbin Dai, Qishan Wang, Shizhong Xu, Patrick Xuechun Zhao:
  PEPIS: A Pipeline for Estimating Epistatic Effects in Quantitative Trait Locus Mapping and Genome-Wide Association Studies.
• 
  Jaroslav Bendl, Milos Musil, Jan Stourac, Jaroslav Zendulka, Jirí Damborský, Jan Brezovsky:
  PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions.
• 
  Ana Zafra Ruano, Elisa Cilia, José R. Couceiro, Javier Ruiz Sanz, Joost Schymkowitz, Frederic Rousseau, Irene Luque, Tom Lenaerts:
  From Binding-Induced Dynamic Effects in SH3 Structures to Evolutionary Conserved Sectors.
• 
  Hannah E. Clapham, Than Ha Quyen, Duong Thi Hue Kien, Ilaria Dorigatti, Cameron P. Simmons, Neil M. Ferguson:
  Modelling Virus and Antibody Dynamics during Dengue Virus Infection Suggests a Role for Antibody in Virus Clearance.
• 
  Philip J. Tully, Henrik Lindén, Matthias H. Hennig, Anders Lansner:
  Spike-Based Bayesian-Hebbian Learning of Temporal Sequences.
• 
  Raphaël Mourad, Olivier Cuvier:
  Computational Identification of Genomic Features That Influence 3D Chromatin Domain Formation.
• 
  Thomas Heiberg, Espen Hagen, Geir Halnes, Gaute T. Einevoll:
  Biophysical Network Modelling of the dLGN Circuit: Different Effects of Triadic and Axonal Inhibition on Visual Responses of Relay Cells.
• 
  Joachim Hass, Loreen Hertäg, Daniel Durstewitz:
  A Detailed Data-Driven Network Model of Prefrontal Cortex Reproduces Key Features of In Vivo Activity.
• 
  Anwesha Bohler, Guanming Wu, Martina Kutmon, Leontius Adhika Pradhana, Susan L. Coort, Kristina Hanspers, Robin Haw, Alexander R. Pico, Chris T. A. Evelo:
  Reactome from a WikiPathways Perspective.
• 
  Tetsuro Funato, Yuki Yamamoto, Shinya Aoi, Takashi Imai, Toshio Aoyagi, Nozomi Tomita, Kazuo Tsuchiya:
  Evaluation of the Phase-Dependent Rhythm Control of Human Walking Using Phase Response Curves.
• 
  Sid Henriksen, Bruce G. Cumming, Jenny C. A. Read:
  A Single Mechanism Can Account for Human Perception of Depth in Mixed Correlation Random Dot Stereograms.
• 
  Jian Sun, James B. Hoying, Pierre Deymier, Donna D. Zhang, Pak Kin Wong:
  Cellular Architecture Regulates Collective Calcium Signaling and Cell Contractility.
• 
  Andrew F. Neuwald, Stephen F. Altschul:
  Bayesian Top-Down Protein Sequence Alignment with Inferred Position-Specific Gap Penalties.
• 
  Zizhang Sheng, Chaim A. Schramm, Mark Connors, Lynn Morris, John R. Mascola, Peter D. Kwong, Lawrence Shapiro:
  Effects of Darwinian Selection and Mutability on Rate of Broadly Neutralizing Antibody Evolution during HIV-1 Infection.
• 
  Josh Merel, David E. Carlson, Liam Paninski, John P. Cunningham:
  Neuroprosthetic Decoder Training as Imitation Learning.
• 
  Mark K. Transtrum, Peng Qiu:
  Bridging Mechanistic and Phenomenological Models of Complex Biological Systems.
• 
  John Wiedenhoeft, Eric Brugel, Alexander Schliep:
  Fast Bayesian Inference of Copy Number Variants using Hidden Markov Models with Wavelet Compression.
• 
  Benny Borremans, Niel Hens, Philippe Beutels, Herwig Leirs, Jonas Reijniers:
  Estimating Time of Infection Using Prior Serological and Individual Information Can Greatly Improve Incidence Estimation of Human and Wildlife Infections.
• 
  Hugo Jacquin, Amy Gilson, Eugene I. Shakhnovich, Simona Cocco, Rémi Monasson:
  Benchmarking Inverse Statistical Approaches for Protein Structure and Design with Exactly Solvable Models.
• 
  Jared Markowitz, Hugh M. Herr:
  Human Leg Model Predicts Muscle Forces, States, and Energetics during Walking.
• 
  Lisa M. Breckels, Sean B. Holden, David Wojnar, Claire M. Mulvey, Andy Christoforou, Arnoud Groen, Matthew W. B. Trotter, Oliver Kohlbacher, Kathryn S. Lilley, Laurent Gatto:
  Learning from Heterogeneous Data Sources: An Application in Spatial Proteomics.
• 
  Natalie S. Scholes, Robert O. J. Weinzierl:
  Molecular Dynamics of "Fuzzy" Transcriptional Activator-Coactivator Interactions.
• 
  Kit Curtius, Chao-Jen Wong, William D. Hazelton, Andrew M. Kaz, Amitabh Chak, Joseph E. Willis, William M. Grady, E. Georg Luebeck:
  A Molecular Clock Infers Heterogeneous Tissue Age Among Patients with Barrett's Esophagus.
• 
  Song Feng, Julien F. Ollivier, Orkun S. Soyer:
  Enzyme Sequestration as a Tuning Point in Controlling Response Dynamics of Signalling Networks.
• 
  Pengfei Tian, Robert B. Best:
  Structural Determinants of Misfolding in Multidomain Proteins.
• 
  Nicholas M. Timme, Shinya Ito, Maxym Myroshnychenko, Sunny Nigam, Masanori Shimono, Fang-Chin Yeh, Pawel Hottowy, Alan M. Litke, John M. Beggs:
  High-Degree Neurons Feed Cortical Computations.
• 
  Luke I. Rast, Igor M. Rouzine, Ganna Rozhnova, Lisa Bishop, Ariel D. Weinberger, Leor S. Weinberger:
  Conflicting Selection Pressures Will Constrain Viral Escape from Interfering Particles: Principles for Designing Resistance-Proof Antivirals.
• 
  Yougan Cheng, Hans Othmer:
  A Model for Direction Sensing in Dictyostelium discoideum: Ras Activity and Symmetry Breaking Driven by a Gβγ-Mediated, Gα2-Ric8 - Dependent Signal Transduction Network.
• 
  Tuoqi Liu, Jiajun Zhang, Tianshou Zhou:
  Effect of Interaction between Chromatin Loops on Cell-to-Cell Variability in Gene Expression.
• 
  Arthur Bernard, Jean-Baptiste André, Nicolas Bredèche:
  To Cooperate or Not to Cooperate: Why Behavioural Mechanisms Matter.
• 
  Alex J. Cope, Chelsea Sabo, Kevin N. Gurney, Eleni Vasilaki, James A. R. Marshall:
  A Model for an Angular Velocity-Tuned Motion Detector Accounting for Deviations in the Corridor-Centering Response of the Bee.
• 
  Jerome Kelleher, Alison M. Etheridge, Gilean McVean:
  Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes.
• 
  Maxim Grechkin, Benjamin A. Logsdon, Andrew J. Gentles, Su-In Lee:
  Identifying Network Perturbation in Cancer.
• 
  Alex D. Bird, Hermann Cuntz:
  Optimal Current Transfer in Dendrites.
• 
  Shashaank Vattikuti, Phyllis Thangaraj, Hua W. Xie, Stephen J. Gotts, Alex Martin, Carson C. Chow:
  Canonical Cortical Circuit Model Explains Rivalry, Intermittent Rivalry, and Rivalry Memory.
• 
  Joseph H. R. Hetmanski, Egor Zindy, Jean-Marc Schwartz, Patrick T. Caswell:
  A MAPK-Driven Feedback Loop Suppresses Rac Activity to Promote RhoA-Driven Cancer Cell Invasion.

Volume 12, Number 6, June 2016

Editorials

• 
  Robert E. Kass, Brian S. Caffo, Marie Davidian, Xiao-Li Meng, Bin Yu, Nancy Reid:
  Ten Simple Rules for Effective Statistical Practice.
• 
  Jin Liu, Ruth Nussinov:
  Allostery: An Overview of Its History, Concepts, Methods, and Applications.

Message from ISCB

• 
  Christiana N. Fogg, Diane E. Kovats:
  Program Bytes: Satellite Meetings, SIGs, and AKEs at ISMB 2016.

Education Articles

• 
  Bastian Schiffthaler, Myrto Kostadima, NGS Trainer Consortium, Nicolas Delhomme, Gabriella Rustici:
  Training in High-Throughput Sequencing: Common Guidelines to Enable Material Sharing, Dissemination, and Reusability.
• 
  Michelle D. Brazas, B. F. Francis Ouellette:
  Continuing Education Workshops in Bioinformatics Positively Impact Research and Careers.
• 
  Berk Ekmekci, Charles E. McAnany, Cameron Mura:
  An Introduction to Programming for Bioscientists: A Python-Based Primer.

Perspective

• 
  Frank J. Poelwijk, Vinod Krishna, Rama Ranganathan:
  The Context-Dependence of Mutations: A Linkage of Formalisms.

Review

• 
  Samuel Hertig, Naomi R. Latorraca, Ron O. Dror:
  Revealing Atomic-Level Mechanisms of Protein Allostery with Molecular Dynamics Simulations.

Research Articles

• 
  John D. O'Brien, Zamin Iqbal, Jason P. Wendler, Lucas Amenga-Etego:
  Inferring Strain Mixture within Clinical Plasmodium falciparum Isolates from Genomic Sequence Data.
• 
  Hui Liu, Gene E. Robinson, Eric Jakobsson:
  Conservation in Mammals of Genes Associated with Aggression-Related Behavioral Phenotypes in Honey Bees.
• 
  Anthony Szedlak, Nicholas Smith, Li Liu, Giovanni Paternostro, Carlo Piermarocchi:
  Evolutionary and Topological Properties of Genes and Community Structures in Human Gene Regulatory Networks.
• 
  Pintu Patra, Kimberley Kissoon, Isabel Cornejo, Heidi B. Kaplan, Oleg A. Igoshin:
  Colony Expansion of Socially Motile Myxococcus xanthus Cells Is Driven by Growth, Motility, and Exopolysaccharide Production.
• 
  Matteo Mori, Terence Hwa, Olivier C. Martin, Andrea De Martino, Enzo Marinari:
  Constrained Allocation Flux Balance Analysis.
• 
  X. Jessie Jeng, Z. John Daye, Wenbin Lu, Jung-Ying Tzeng:
  Rare Variants Association Analysis in Large-Scale Sequencing Studies at the Single Locus Level.
• 
  Thomas Eggert, Farrel R. Robinson, Andreas Straube:
  Modeling Inter-trial Variability of Saccade Trajectories: Effects of Lesions of the Oculomotor Part of the Fastigial Nucleus.
• 
  David Noren, Byron Long, Raquel Norel, Kahn Rhrissorrakrai, Kenneth R. Hess, Chenyue W. Hu, Alex Bisberg, André Schultz, Erik Engquist, Li Liu, Xihui Lin, Gregory M. Chen, Honglei Xie, Geoffrey A. M. Hunter, Paul C. Boutros, Oleg A. Stepanov, DREAM 9 AML-OPC Consortium, Thea Norman, Stephen H. Friend, Gustavo Stolovitzky, Steven M. Kornblau, Amina A. Qutub:
  A Crowdsourcing Approach to Developing and Assessing Prediction Algorithms for AML Prognosis.
• 
  Edward J. O'Brien, Jose Utrilla, Bernhard O. Palsson:
  Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments.
• 
  Ján Antolík, Sonja B. Hofer, James A. Bednar, Thomas D. Mrsic-Flogel:
  Model Constrained by Visual Hierarchy Improves Prediction of Neural Responses to Natural Scenes.
• 
  Elisa Boari de Lima, Wagner Meira Jr., Raquel Cardoso de Melo Minardi:
  Isofunctional Protein Subfamily Detection Using Data Integration and Spectral Clustering.
• 
  Oliver W. Layton, Brett R. Fajen:
  Competitive Dynamics in MSTd: A Mechanism for Robust Heading Perception Based on Optic Flow.
• 
  Carlo Albert, Sören Vogel, Roman Ashauer:
  Computationally Efficient Implementation of a Novel Algorithm for the General Unified Threshold Model of Survival (GUTS).
• 
  Rossana Mastrandrea, Alain Barrat:
  How to Estimate Epidemic Risk from Incomplete Contact Diaries Data?
• 
  Johanni Brea, Alexisz Tamás Gaál, Robert Urbanczik, Walter Senn:
  Prospective Coding by Spiking Neurons.
• 
  Olof Leimar, Sasha R. X. Dall, Peter Hammerstein, John M. McNamara:
  Genes as Cues of Relatedness and Social Evolution in Heterogeneous Environments.
• 
  Daniel L. Parton, Patrick B. Grinaway, Sonya M. Hanson, Kyle Beauchamp, John D. Chodera:
  Ensembler: Enabling High-Throughput Molecular Simulations at the Superfamily Scale.
• 
  Asa Thibodeau, Eladio J. Márquez, Oscar Luo, Yijun Ruan, Francesca Menghi, Dong-Guk Shin, Michael L. Stitzel, Paola Vera-Licona, Duygu Ucar:
  QuIN: A Web Server for Querying and Visualizing Chromatin Interaction Networks.
• 
  Aditya V. S. Ponnaluri, Luigi E. Perotti, Michael Liu, Zhilin Qu, James N. Weiss, Daniel B. Ennis, William S. Klug, Alan Garfinkel:
  Electrophysiology of Heart Failure Using a Rabbit Model: From the Failing Myocyte to Ventricular Fibrillation.
• 
  Raquel Bromberg, Nick V. Grishin, Zbyszek Otwinowski:
  Phylogeny Reconstruction with Alignment-Free Method That Corrects for Horizontal Gene Transfer.
• 
  Andra Waagmeester, Martina Kutmon, Anders Riutta, Ryan A. Miller, Egon L. Willighagen, Chris T. A. Evelo, Alexander R. Pico:
  Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources.
• 
  David A. Lee, Sayoni Das, Natalie L. Dawson, Dragana Dobrijevic, John Ward, Christine A. Orengo:
  Novel Computational Protocols for Functionally Classifying and Characterising Serine Beta-Lactamases.
• 
  Rupamanjari Majumder, Wanchana Jangsangthong, Iolanda Feola, Dirk L. Ypey, Daniël A. Pijnappels, Alexander V. Panfilov:
  A Mathematical Model of Neonatal Rat Atrial Monolayers with Constitutively Active Acetylcholine-Mediated K+ Current.
• 
  Daniel H. Huson, Sina Beier, Isabell Flade, Anna Górska, Mohamed El-Hadidi, Suparna Mitra, Hans-Joachim Ruscheweyh, Rewati Tappu:
  MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data.
• 
  Julio M. Belmonte, Maciej H. Swat, James A. Glazier:
  Filopodial-Tension Model of Convergent-Extension of Tissues.
• 
  Stefano Palminteri, Emma J. Kilford, Giorgio Coricelli, Sarah-Jayne Blakemore:
  The Computational Development of Reinforcement Learning during Adolescence.
• 
  Go Ashida, Jutta Kretzberg, Daniel J. Tollin:
  Roles for Coincidence Detection in Coding Amplitude-Modulated Sounds.
• 
  Sebastian Germerodt, Katrin Bohl, Anja Lück, Samay Pande, Anja Schröter, Christoph Kaleta, Stefan Schuster, Christian Kost:
  Pervasive Selection for Cooperative Cross-Feeding in Bacterial Communities.
• 
  Balázs Brankovics, Hao Zhang, Anne D. van Diepeningen, Theo A. J. van der Lee, Cees Waalwijk, G. Sybren de Hoog:
  GRAbB: Selective Assembly of Genomic Regions, a New Niche for Genomic Research.
• 
  Dominik Thalmeier, Marvin Uhlmann, Hilbert J. Kappen, Raoul-Martin Memmesheimer:
  Learning Universal Computations with Spikes.
• 
  Ingo Titze, Tobias Riede, Ted Mau:
  Predicting Achievable Fundamental Frequency Ranges in Vocalization Across Species.
• 
  Rebeca Campos-Sánchez, Marzia A. Cremona, Alessia Pini, Francesca Chiaromonte, Kateryna D. Makova:
  Integration and Fixation Preferences of Human and Mouse Endogenous Retroviruses Uncovered with Functional Data Analysis.
• 
  Karin Lundengård, Gunnar Cedersund, Sebastian Sten, Felix Leong, Alexander Smedberg, Fredrik Elinder, Maria Engström:
  Mechanistic Mathematical Modeling Tests Hypotheses of the Neurovascular Coupling in fMRI.
• 
  Zhuo Wang, Andrew T. Sornborger, Louis Tao:
  Graded, Dynamically Routable Information Processing with Synfire-Gated Synfire Chains.
• 
  Danilo Bzdok, Gaël Varoquaux, Olivier Grisel, Michael Eickenberg, Cyril Poupon, Bertrand Thirion:
  Formal Models of the Network Co-occurrence Underlying Mental Operations.
• 
  Chao Huang, Andrey Resnik, Tansu Celikel, Bernhard Englitz:
  Adaptive Spike Threshold Enables Robust and Temporally Precise Neuronal Encoding.
• 
  Xiao Fu, J. Scott Gens, James A. Glazier, Stephen A. Burns, Thomas J. Gast:
  Progression of Diabetic Capillary Occlusion: A Model.
• 
  Patrick Gemmell, Jotun Hein, Aris Katzourakis:
  Phylogenetic Analysis Reveals That ERVs "Die Young" but HERV-H Is Unusually Conserved.
• 
  Dario Corrada, Anatoly A. Soshilov, Michael S. Denison, Laura Bonati:
  Deciphering Dimerization Modes of PAS Domains: Computational and Experimental Analyses of the AhR: ARNT Complex Reveal New Insights Into the Mechanisms of AhR Transformation.
• 
  Adam Spiro, Ehud Shapiro:
  Accuracy of Answers to Cell Lineage Questions Depends on Single-Cell Genomics Data Quality and Quantity.
• 
  Ana-Maria Florescu, Pierre Therizols, Angelo Rosa:
  Large Scale Chromosome Folding Is Stable against Local Changes in Chromatin Structure.
• 
  Pierre Enel, Emmanuel Procyk, René Quilodrán, Peter Ford Dominey:
  Reservoir Computing Properties of Neural Dynamics in Prefrontal Cortex.
• 
  Zhihui Wang, Romica Kerketta, Yao-Li Chuang, Prashant Dogra, Joseph D. Butner, Terisse A. Brocato, Armin Day, Rong Xu, Haifa Shen, Eman Simbawa, A. S. Al-Fhaid, Samy Refahy Mahmoud, Steven A. Curley, Mauro Ferrari, Eugene J. Koay, Vittorio Cristini:
  Theory and Experimental Validation of a Spatio-temporal Model of Chemotherapy Transport to Enhance Tumor Cell Kill.
• 
  Henok Mengistu, Joost Huizinga, Jean-Baptiste Mouret, Jeff Clune:
  The Evolutionary Origins of Hierarchy.
• 
  Gudrun Schappacher-Tilp, Timothy Leonard, Gertrud Desch, Walter Herzog:
  Computing Average Passive Forces in Sarcomeres in Length-Ramp Simulations.
• 
  Da-Cang Huang, Jinfeng Wang, Ji-Xia Huang, Daniel Z. Sui, Hongyan Zhang, Mao-Gui Hu, Chengdong Xu:
  Towards Identifying and Reducing the Bias of Disease Information Extracted from Search Engine Data.
• 
  Stojan Jovanovic, Stefan Rotter:
  Interplay between Graph Topology and Correlations of Third Order in Spiking Neuronal Networks.
• 
  Yu Toyoshima, Terumasa Tokunaga, Osamu Hirose, Manami Kanamori, Takayuki Teramoto, Moon Sun Jang, Sayuri Kuge, Takeshi Ishihara, Ryo Yoshida, Yuichi Iino:
  Accurate Automatic Detection of Densely Distributed Cell Nuclei in 3D Space.
• 
  Ren-Hua Chung, Wei-Yun Tsai, Chen-Yu Kang, Po-Ju Yao, Hui-Ju Tsai, Chia-Hsiang Chen:
  FamPipe: An Automatic Analysis Pipeline for Analyzing Sequencing Data in Families for Disease Studies.
• 
  Gentian Buzi, Mustafa Khammash:
  Implementation Considerations, Not Topological Differences, Are the Main Determinants of Noise Suppression Properties in Feedback and Incoherent Feedforward Circuits.
• 
  Jérôme Wong-Ng, Anna Melbinger, Antonio Celani, Massimo Vergassola:
  The Role of Adaptation in Bacterial Speed Races.
• 
  Olivier Rivoire, Kimberly A. Reynolds, Rama Ranganathan:
  Evolution-Based Functional Decomposition of Proteins.
• 
  Arun Chandramohan, Srinath Krishnamurthy, Andreas Larsson, Paer Nordlund, Anna Jansson, Ganesh S. Anand:
  Predicting Allosteric Effects from Orthosteric Binding in Hsp90-Ligand Interactions: Implications for Fragment-Based Drug Design.
• 
  K. Aurelia Ball, Jeffrey R. Johnson, Mary K. Lewinski, John Guatelli, Erik Verschueren, Nevan J. Krogan, Matthew P. Jacobson:
  Non-degradative Ubiquitination of Protein Kinases.
• 
  Kumari Sonal Choudhary, Neha Rohatgi, Skarphedinn Halldorsson, Eirikur Briem, Thorarinn Gudjonsson, Steinn Gudmundsson, Ottar Rolfsson:
  EGFR Signal-Network Reconstruction Demonstrates Metabolic Crosstalk in EMT.
• 
  Tobias Sikosek, Heinrich Krobath, Hue Sun Chan:
  Theoretical Insights into the Biophysics of Protein Bi-stability and Evolutionary Switches.
• 
  George A. Tsianos, Lisa N. MacFadden:
  Validated Predictions of Metabolic Energy Consumption for Submaximal Effort Movement.
• 
  Margaritis Voliotis, Philipp Thomas, Ramon Grima, Clive G. Bowsher:
  Stochastic Simulation of Biomolecular Networks in Dynamic Environments.

Volume 12, Number 7, July 2016

Editorials

• 
  Greg J. McInerny:
  Ten Simple Rules for Curating and Facilitating Small Workshops.
• 
  Ke Yuan, Lei Cai, Siu Ping Ngok, Li Ma, Crystal M. Botham:
  Ten Simple Rules for Writing a Postdoctoral Fellowship.
• 
  Yasset Pérez-Riverol, Laurent Gatto, Rui Wang, Timo Sachsenberg, Julian Uszkoreit, Felipe da Veiga Leprevost, Christian Fufezan, Tobias Ternent, Stephen J. Eglen, Daniel S. Katz, Tom J. Pollard, Alexander Konovalov, Robert M. Flight, Kai Blin, Juan Antonio Vizcaíno:
  Ten Simple Rules for Taking Advantage of Git and GitHub.
• 
  Ruth Nussinov, Jason A. Papin:
  Computing Biology.

Message from ISCB

• 
  Christiana N. Fogg, Diane E. Kovats:
  2016 ISCB Innovator Award: Serafim Batzoglou.

Topic Page

• 
  Jeffrey B. Joy, Richard H. Liang, Rosemary M. McCloskey, T. Nguyen, Art F. Y. Poon:
  Ancestral Reconstruction.

Research Articles

• 
  Victor Hanson-Smith, Alexander Johnson:
  PhyloBot: A Web Portal for Automated Phylogenetics, Ancestral Sequence Reconstruction, and Exploration of Mutational Trajectories.
• 
  Juliana S. Bernardes, Gerson Zaverucha, Catherine Vaquero, Alessandra Carbone:
  Improvement in Protein Domain Identification Is Reached by Breaking Consensus, with the Agreement of Many Profiles and Domain Co-occurrence.
• 
  Michela Candotti, Modesto Orozco:
  The Differential Response of Proteins to Macromolecular Crowding.
• 
  Chuan Gao, Ian C. McDowell, Shiwen Zhao, Christopher D. Brown, Barbara E. Engelhardt:
  Context Specific and Differential Gene Co-expression Networks via Bayesian Biclustering.
•