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 Adam 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.
• 
  Nathan Mih, Elizabeth Brunk, Aarash Bordbar, Bernhard O. Palsson:
  A Multi-scale Computational Platform to Mechanistically Assess the Effect of Genetic Variation on Drug Responses in Human Erythrocyte Metabolism.
• 
  Julia Rex, Ute Albrecht, Christian Ehlting, Maria Thomas, Ulrich M. Zanger, Oliver Sawodny, Dieter Häussinger, Michael Ederer, Ronny Feuer, Johannes G. Bode:
  Model-Based Characterization of Inflammatory Gene Expression Patterns of Activated Macrophages.
• 
  Amanda Buyan, Antreas C. Kalli, Mark S. P. Sansom:
  Multiscale Simulations Suggest a Mechanism for the Association of the Dok7 PH Domain with PIP-Containing Membranes.
• 
  Joshua Mayourian, Ruben M. Savizky, Eric A. Sobie, Kevin D. Costa:
  Modeling Electrophysiological Coupling and Fusion between Human Mesenchymal Stem Cells and Cardiomyocytes.
• 
  Dmitry D. Postnov, Donald J. Marsh, Dmitry E. Postnov, Thomas H. Braunstein, Niels-Henrik Holstein-Rathlou, Erik A. Martens, Olga V. Sosnovtseva:
  Modeling of Kidney Hemodynamics: Probability-Based Topology of an Arterial Network.
• 
  Michael Moutoussis, Raymond J. Dolan, Peter Dayan:
  How People Use Social Information to Find out What to Want in the Paradigmatic Case of Inter-temporal Preferences.
• 
  Fabian Fröhlich, Philipp Thomas, Atefeh Kazeroonian, Fabian J. Theis, Ramon Grima, Jan Hasenauer:
  Inference for Stochastic Chemical Kinetics Using Moment Equations and System Size Expansion.
• 
  Manikandan Narayanan, Andrew J. Martins, John S. Tsang:
  Robust Inference of Cell-to-Cell Expression Variations from Single- and K-Cell Profiling.
• 
  Yuheng Lu, Christina S. Leslie:
  Learning to Predict miRNA-mRNA Interactions from AGO CLIP Sequencing and CLASH Data.
• 
  Takahiro Ezaki, Yutaka Horita, Masanori Takezawa, Naoki Masuda:
  Reinforcement Learning Explains Conditional Cooperation and Its Moody Cousin.
• 
  Zheng Sun, Maksim V. Plikus, Natalia L. Komarova:
  Near Equilibrium Calculus of Stem Cells in Application to the Airway Epithelium Lineage.
• 
  Diego A. Vargas, Meng Sun, Khikmet Sadykov, Maria A. Kukuruzinska, Muhammad H. Zaman:
  The Integrated Role of Wnt/β-Catenin, N-Glycosylation, and E-Cadherin-Mediated Adhesion in Network Dynamics.
• 
  Emiliano Torre, Carlos Canova, Michael Denker, George L. Gerstein, Moritz Helias, Sonja Grün:
  ASSET: Analysis of Sequences of Synchronous Events in Massively Parallel Spike Trains.
• 
  Jose L. Herrera, Ravi Srinivasan, John S. Brownstein, Alison P. Galvani, Lauren Ancel Meyers:
  Disease Surveillance on Complex Social Networks.
• 
  Xing Chen, Biao Ren, Ming Chen, Quanxin Wang, Lixin Zhang, Guiying Yan:
  NLLSS: Predicting Synergistic Drug Combinations Based on Semi-supervised Learning.
• 
  Abbey B. Holt, Dan Wilson, Max Shinn, Jeff Moehlis, Theoden I. Netoff:
  Phasic Burst Stimulation: A Closed-Loop Approach to Tuning Deep Brain Stimulation Parameters for Parkinson's Disease.
• 
  Daniel Bennett, Stefan Bode, Maja Brydevall, Hayley Warren, Carsten Murawski:
  Intrinsic Valuation of Information in Decision Making under Uncertainty.
• 
  Pei-Chi Yang, Britton W. Boras, Mao-Tsuen Jeng, Steffen S. Docken, Timothy J. Lewis, Andrew D. McCulloch, Robert D. Harvey, Colleen E. Clancy:
  A Computational Modeling and Simulation Approach to Investigate Mechanisms of Subcellular cAMP Compartmentation.
• 
  Weitao Chen, Qing Nie, Tau-Mu Yi, Ching-Shan Chou:
  Modelling of Yeast Mating Reveals Robustness Strategies for Cell-Cell Interactions.
• 
  Deborah Chasman, Kevin B. Walters, Tiago J. S. Lopes, Amie J. Eisfeld, Yoshihiro Kawaoka, Sushmita Roy:
  Integrating Transcriptomic and Proteomic Data Using Predictive Regulatory Network Models of Host Response to Pathogens.
• 
  Edoardo Pasolli, Duy Tin Truong, Faizan Malik, Levi Waldron, Nicola Segata:
  Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights.
• 
  Cuncong Zhong, Anna Edlund, Youngik Yang, Jeffrey S. McLean, Shibu Yooseph:
  Metagenome and Metatranscriptome Analyses Using Protein Family Profiles.
• 
  Eva R. M. Joosten, Shihab A. Shamma, Christian Lorenzi, Peter Neri:
  Dynamic Reweighting of Auditory Modulation Filters.
• 
  Oren Shriki, Yaniv Sadeh, Jamie Ward:
  The Emergence of Synaesthesia in a Neuronal Network Model via Changes in Perceptual Sensitivity and Plasticity.
• 
  Rafal Bogacz, Eduardo Martin Moraud, Azzedine Abdi, Peter J. Magill, Jérôme Baufreton:
  Properties of Neurons in External Globus Pallidus Can Support Optimal Action Selection.
• 
  Gustaf Rydevik, Giles T. Innocent, Glenn Marion, Ross S. Davidson, Piran C. L. White, Charalambos Billinis, Paul Barrow, Peter P. C. Mertens, Dolores Gavier-Widén, Michael R. Hutchings:
  Using Combined Diagnostic Test Results to Hindcast Trends of Infection from Cross-Sectional Data.
• 
  Julian Weichsel, Phillip L. Geissler:
  The More the Tubular: Dynamic Bundling of Actin Filaments for Membrane Tube Formation.
• 
  Yizeng Li, Karl Grosh:
  The Coda of the Transient Response in a Sensitive Cochlea: A Computational Modeling Study.
• 
  Javier Estrada, Natalie Andrew, Daniel Gibson, Frederick Chang, Florian Gnad, Jeremy Gunawardena:
  Cellular Interrogation: Exploiting Cell-to-Cell Variability to Discriminate Regulatory Mechanisms in Oscillatory Signalling.
• 
  Brian A. Camley, Juliane Zimmermann, Herbert Levine, Wouter-Jan Rappel:
  Collective Signal Processing in Cluster Chemotaxis: Roles of Adaptation, Amplification, and Co-attraction in Collective Guidance.

Volume 12, Number 8, August 2016

Editorial

• 
  Rachel Karchin, Ruth Nussinov:
  Genome Landscapes of Disease: Strategies to Predict the Phenotypic Consequences of Human Germline and Somatic Variation.

Perspective

• 
  Bradley Voytek:
  The Virtuous Cycle of a Data Ecosystem.

Research Articles

• 
  Lior Kirsch, Gal Chechik:
  On Expression Patterns and Developmental Origin of Human Brain Regions.
• 
  Ruben G. A. van Heck, Mathias Ganter, Vítor A. P. Martins dos Santos, Jörg Stelling:
  Efficient Reconstruction of Predictive Consensus Metabolic Network Models.
• 
  Wouter Kool, Fiery Cushman, Samuel J. Gershman:
  When Does Model-Based Control Pay Off?
• 
  Jose Lugo-Martinez, Vikas Pejaver, Kymberleigh A. Pagel, Shantanu Jain, Matthew E. Mort, David N. Cooper, Sean D. Mooney, Predrag Radivojac:
  The Loss and Gain of Functional Amino Acid Residues Is a Common Mechanism Causing Human Inherited Disease.
• 
  Wanli You, Yu-ming M. Huang, Smitha Kizhake, Amarnath Natarajan, Chia-en A. Chang:
  Characterization of Promiscuous Binding of Phosphor Ligands to Breast-Cancer-Gene 1 (BRCA1) C-Terminal (BRCT): Molecular Dynamics, Free Energy, Entropy and Inhibitor Design.
• 
  Danika Lindsay, Colleen M. Garvey, Shannon M. Mumenthaler, Jasmine Foo:
  Leveraging Hypoxia-Activated Prodrugs to Prevent Drug Resistance in Solid Tumors.
• 
  William Letsou, Long Cai:
  Noncommutative Biology: Sequential Regulation of Complex Networks.
• 
  Mitchel Alioscha-Pérez, Carine Benadiba, Katty Goossens, Sandor Kasas, Giovanni Dietler, Ronnie Willaert, Hichem Sahli:
  A Robust Actin Filaments Image Analysis Framework.
• 
  Daphne Ezer, Victoria Moignard, Berthold Göttgens, Boris Adryan:
  Determining Physical Mechanisms of Gene Expression Regulation from Single Cell Gene Expression Data.
• 
  Chung-Chuan Lo, Xiao-Jing Wang:
  Conflict Resolution as Near-Threshold Decision-Making: A Spiking Neural Circuit Model with Two-Stage Competition for Antisaccadic Task.
• 
  Jeremiah D. Wander, Devapratim Sarma, Lise A. Johnson, Eberhard E. Fetz, Rajesh P. N. Rao, Jeffrey G. Ojemann, Felix Darvas:
  Cortico-Cortical Interactions during Acquisition and Use of a Neuroprosthetic Skill.
• 
  Anatoly Buchin, Sarah Rieubland, Michael Häusser, Boris S. Gutkin, Arnd Roth:
  Inverse Stochastic Resonance in Cerebellar Purkinje Cells.
• 
  Brendan Chambers, Jason N. MacLean:
  Higher-Order Synaptic Interactions Coordinate Dynamics in Recurrent Networks.
• 
  Seong-Kyun Kim, Hyoungkyu Kim, Jerald D. Kralik, Jaeseung Jeong:
  Vulnerability-Based Critical Neurons, Synapses, and Pathways in the Caenorhabditis elegans Connectome.
• 
  Charles Joly Beauparlant, Fabien C. Lamaze, Astrid Deschênes, Rawane Samb, Audrey Lemaçon, Pascal Belleau, Steve Bilodeau, Arnaud Droit:
  metagene Profiles Analyses Reveal Regulatory Element's Factor-Specific Recruitment Patterns.
• 
  Mohammad Soltani, Cesar Augusto Vargas Garcia, Duarte Antunes, Abhyudai Singh:
  Intercellular Variability in Protein Levels from Stochastic Expression and Noisy Cell Cycle Processes.
• 
  Jonas Reeb, Maximilian Hecht, Yannick Mahlich, Yana Bromberg, Burkhard Rost:
  Predicted Molecular Effects of Sequence Variants Link to System Level of Disease.
• 
  Pablo G. Cámara, Arnold J. Levine, Raúl Rabadán:
  Inference of Ancestral Recombination Graphs through Topological Data Analysis.
• 
  Bo-Xue Tian, C. Dale Poulter, Matthew P. Jacobson:
  Defining the Product Chemical Space of Monoterpenoid Synthases.
• 
  Neta Ravid Tannenbaum, Yoram Burak:
  Shaping Neural Circuits by High Order Synaptic Interactions.
• 
  Tamra Heberling, Lisa Davis, Jakub Gedeon, Charles Morgan, Tomás Gedeon:
  A Mechanistic Model for Cooperative Behavior of Co-transcribing RNA Polymerases.
• 
  Jorge Peña, Bin Wu, Jordi Arranz, Arne Traulsen:
  Evolutionary Games of Multiplayer Cooperation on Graphs.
• 
  Joeri B. G. van Wijngaarden, Riccardo Zucca, Simon Finnigan, Paul F. M. J. Verschure:
  The Impact of Cortical Lesions on Thalamo-Cortical Network Dynamics after Acute Ischaemic Stroke: A Combined Experimental and Theoretical Study.
• 
  Sreedhar S. Kumar, Jan Wülfing, Samora Okujeni, Joschka Boedecker, Martin A. Riedmiller, Ulrich Egert:
  Autonomous Optimization of Targeted Stimulation of Neuronal Networks.
• 
  Marcia C. Castro, Mathieu Maheu-Giroux, Christinah Chiyaka, Burton H. Singer:
  Malaria Incidence Rates from Time Series of 2-Wave Panel Surveys.
• 
  Holger Finger, Marlene Bönstrup, Bastian Cheng, Arnaud Messé, Claus C. Hilgetag, Götz Thomalla, Christian Gerloff, Peter König:
  Modeling of Large-Scale Functional Brain Networks Based on Structural Connectivity from DTI: Comparison with EEG Derived Phase Coupling Networks and Evaluation of Alternative Methods along the Modeling Path.
• 
  Paula A. Vasquez, Yuan Jin, Erik Palmer, David Hill, M. Gregory Forest:
  Modeling and Simulation of Mucus Flow in Human Bronchial Epithelial Cell Cultures - Part I: Idealized Axisymmetric Swirling Flow.
• 
  Diego Fasoli, Anna Cattani, Stefano Panzeri:
  The Complexity of Dynamics in Small Neural Circuits.
• 
  Jun Li, Jian Zhang, Jun Wang, Wenfei Li, Wei Wang:
  Structure Prediction of RNA Loops with a Probabilistic Approach.
• 
  Biman Jana, José N. Onuchic:
  Strain Mediated Adaptation Is Key for Myosin Mechanochemistry: Discovering General Rules for Motor Activity.
• 
  Ruth Merkle, Bernhard Steiert, Florian Salopiata, Sofia Depner, Andreas Raue, Nao Iwamoto, Max Schelker, Helge Hass, Marvin Wäsch, Martin E. Böhm, Oliver Mücke, Daniel B. Lipka, Christoph Plass, Wolf D. Lehmann, Clemens Kreutz, Jens Timmer, Marcel Schilling, Ursula Klingmüller:
  Identification of Cell Type-Specific Differences in Erythropoietin Receptor Signaling in Primary Erythroid and Lung Cancer Cells.
• 
  Karol A. Bacik, Michael T. Schaub, Mariano Beguerisse-Díaz, Yazan N. Billeh, Mauricio Barahona:
  Flow-Based Network Analysis of the Caenorhabditis elegans Connectome.
• 
  Daniel M. Lombardo, Flavio H. Fenton, Sanjiv M. Narayan, Wouter-Jan Rappel:
  Comparison of Detailed and Simplified Models of Human Atrial Myocytes to Recapitulate Patient Specific Properties.
• 
  Christopher J. Hasson, Zhaoran Zhang, Masaki O. Abe, Dagmar Sternad:
  Neuromotor Noise Is Malleable by Amplifying Perceived Errors.
• 
  Jonathan Rubin, Nachum Ulanovsky, Israel Nelken, Naftali Tishby:
  The Representation of Prediction Error in Auditory Cortex.
• 
  Daniel Hartleb, Florian Jarre, Martin J. Lercher:
  Improved Metabolic Models for E. coli and Mycoplasma genitalium from GlobalFit, an Algorithm That Simultaneously Matches Growth and Non-Growth Data Sets.
• 
  Ganna Rozhnova, Maarten F. Schim van der Loeff, Janneke C. M. Heijne, Mirjam E. Kretzschmar:
  Impact of Heterogeneity in Sexual Behavior on Effectiveness in Reducing HIV Transmission with Test-and-Treat Strategy.
• 
  Fei Liu, Shao-Wu Zhang, Weifeng Guo, Ze-Gang Wei, Luonan Chen:
  Inference of Gene Regulatory Network Based on Local Bayesian Networks.

Volume 12, Number 9, September 2016

Research Articles

• 
  Michael Schellenberger Costa, Arne Weigenand, Hong-Viet Victor Ngo, Lisa Marshall, Jan Born, Thomas Martinetz, Jens Christian Claussen:
  A Thalamocortical Neural Mass Model of the EEG during NREM Sleep and Its Response to Auditory Stimulation.
• 
  Anu G. Nair, Upinder S. Bhalla, Jeanette Hellgren Kotaleski:
  Role of DARPP-32 and ARPP-21 in the Emergence of Temporal Constraints on Striatal Calcium and Dopamine Integration.
• 
  John G. Mikhael, Rafal Bogacz:
  Learning Reward Uncertainty in the Basal Ganglia.
• 
  Mark N. Read, Jacqueline Bailey, Jon Timmis, Tatyana Chtanova:
  Leukocyte Motility Models Assessed through Simulation and Multi-objective Optimization-Based Model Selection.
• 
  Yann S. Dufour, Sébastien Gillet, Nicholas W. Frankel, Douglas B. Weibel, Thierry Emonet:
  Direct Correlation between Motile Behavior and Protein Abundance in Single Cells.
• 
  Abibatou Mbodj, Eleanor Hilary Gustafson, Lucia Ciglar, Guillaume Junion, Aitor González, Charles Girardot, Laurent Perrin, Eileen E. M. Furlong, Denis Thieffry:
  Qualitative Dynamical Modelling Can Formally Explain Mesoderm Specification and Predict Novel Developmental Phenotypes.
• 
  Laura Paparelli, Nikky Corthout, Benjamin Pavie, Devin L. Wakefield, Ragna Sannerud, Tijana Jovanovic-Talisman, Wim Annaert, Sebastian Munck:
  Inhomogeneity Based Characterization of Distribution Patterns on the Plasma Membrane.
• 
  Aharon Azulay, Eyal Itskovits, Alon Zaslaver:
  The C. elegans Connectome Consists of Homogenous Circuits with Defined Functional Roles.
• 
  Kang He, You Liang, Farnaz Abdollahi, Moria F. Bittmann, Konrad P. Körding, Kunlin Wei:
  The Statistical Determinants of the Speed of Motor Learning.
• 
  Sarah Feldt Muldoon, Fabio Pasqualetti, Shi Gu, Matthew Cieslak, Scott T. Grafton, Jean M. Vettel, Danielle S. Bassett:
  Stimulation-Based Control of Dynamic Brain Networks.
• 
  John Platig, Peter J. Castaldi, Dawn L. DeMeo, John Quackenbush:
  Bipartite Community Structure of eQTLs.
• 
  Nicholas Cain, Ramakrishnan Iyer, Christof Koch, Stefan Mihalas:
  The Computational Properties of a Simplified Cortical Column Model.
• 
  Yu-zhe Li, Ken Nakae, Shin Ishii, Honda Naoki:
  Uncertainty-Dependent Extinction of Fear Memory in an Amygdala-mPFC Neural Circuit Model.
• 
  Rolf J. F. Ypma, Edward T. Bullmore:
  Statistical Analysis of Tract-Tracing Experiments Demonstrates a Dense, Complex Cortical Network in the Mouse.
• 
  Xiaokan Guo, James Q. Boedicker:
  The Contribution of High-Order Metabolic Interactions to the Global Activity of a Four-Species Microbial Community.
• 
  Carolyn Zhang, Ryan Tsoi, Feilun Wu, Lingchong You:
  Processing Oscillatory Signals by Incoherent Feedforward Loops.
• 
  Patrick Fried, Máximo Sánchez-Aragón, Daniel Aguilar-Hidalgo, Birgitta Lehtinen, Fernando Casares, Dagmar Iber:
  A Model of the Spatio-temporal Dynamics of Drosophila Eye Disc Development.
• 
  Lorenzo Marcucci, Takumi Washio, Toshio Yanagida:
  Including Thermal Fluctuations in Actomyosin Stable States Increases the Predicted Force per Motor and Macroscopic Efficiency in Muscle Modelling.
• 
  Maria Kogadeeva, Nicola Zamboni:
  SUMOFLUX: A Generalized Method for Targeted 13C Metabolic Flux Ratio Analysis.
• 
  Florian C. Rieger, Peter Virnau:
  A Monte Carlo Study of Knots in Long Double-Stranded DNA Chains.
• 
  Feixiong Cheng, James L. Murray, Junfei Zhao, Jinsong Sheng, Zhongming Zhao, Donald H. Rubin:
  Systems Biology-Based Investigation of Cellular Antiviral Drug Targets Identified by Gene-Trap Insertional Mutagenesis.
• 
  William B. Ashworth, Nathan A. Davies, Ian David Lockhart Bogle:
  A Computational Model of Hepatic Energy Metabolism: Understanding Zonated Damage and Steatosis in NAFLD.
• 
  Shishi Luo, Jane A. Yu, Yun S. Song:
  Estimating Copy Number and Allelic Variation at the Immunoglobulin Heavy Chain Locus Using Short Reads.
• 
  Fabian Paul, Thomas R. Weikl:
  How to Distinguish Conformational Selection and Induced Fit Based on Chemical Relaxation Rates.
• 
  Edward Basso, Mamiko Arai, Yuri Dabaghian:
  Gamma Synchronization Influences Map Formation Time in a Topological Model of Spatial Learning.
• 
  Sheldon L. Reeves, Kelsey E. Fleming, Lin Zhang, Annalisa Scimemi:
  M-Track: A New Software for Automated Detection of Grooming Trajectories in Mice.
• 
  Joby John, Jonathan B. Dingwell, Joseph P. Cusumano:
  Error Correction and the Structure of Inter-Trial Fluctuations in a Redundant Movement Task.
• 
  Lars Lau Rakêt, Britta Grimme, Gregor Schöner, Christian Igel, Bo Markussen:
  Separating Timing, Movement Conditions and Individual Differences in the Analysis of Human Movement.
• 
  Eleni A. Kolokotroni, Dimitra D. Dionysiou, Christian Veith, Yoo-Jin Kim, Jörg Sabczynski, Astrid Franz, Aleksandar Grgic, Jan Palm, Rainer Bohle, Georgios S. Stamatakos:
  In Silico Oncology: Quantification of the In Vivo Antitumor Efficacy of Cisplatin-Based Doublet Therapy in Non-Small Cell Lung Cancer (NSCLC) through a Multiscale Mechanistic Model.
• 
  Harwin de Vries, Albert P. M. Wagelmans, Epco Hasker, Crispin Lumbala, Pascal Lutumba, Sake J. De Vlas, Joris van de Klundert:
  Forecasting Human African Trypanosomiasis Prevalences from Population Screening Data Using Continuous Time Models.
• 
  Yann Guyot, Bart Smeets, Tim Odenthal, Ramesh Subramani, Frank P. Luyten, Herman Ramon, Ioannis Papantoniou, Liesbet Geris:
  Immersed Boundary Models for Quantifying Flow-Induced Mechanical Stimuli on Stem Cells Seeded on 3D Scaffolds in Perfusion Bioreactors.
• 
  Hao Chen, Mai Chan Lau, Michael Thomas Wong, Evan W. Newell, Michael Poidinger, Jinmiao Chen:
  Cytofkit: A Bioconductor Package for an Integrated Mass Cytometry Data Analysis Pipeline.
• 
  Jinfang Zheng, Petras J. Kundrotas, Ilya A. Vakser, Shiyong Liu:
  Template-Based Modeling of Protein-RNA Interactions.
• 
  Naveen K. Vaidya, Ruy M. Ribeiro, Alan S. Perelson, Anil Kumar:
  Modeling the Effects of Morphine on Simian Immunodeficiency Virus Dynamics.
• 
  Jeanette Prinz, Ingo Vogt, Gianluca Adornetto, Mónica Campillos:
  A Novel Drug-Mouse Phenotypic Similarity Method Detects Molecular Determinants of Drug Effects.
• 
  Noam Auslander, Allon Wagner, Matthew A. Oberhardt, Eytan Ruppin:
  Data-Driven Metabolic Pathway Compositions Enhance Cancer Survival Prediction.
• 
  Aleena M. Notary, Matthew J. Westacott, Thomas H. Hraha, Marina Pozzoli, Richard K. P. Benninger:
  Decreases in Gap Junction Coupling Recovers Ca2+ and Insulin Secretion in Neonatal Diabetes Mellitus, Dependent on Beta Cell Heterogeneity and Noise.
• 
  Nicola De Maio, Chieh-Hsi Wu, Daniel J. Wilson:
  SCOTTI: Efficient Reconstruction of Transmission within Outbreaks with the Structured Coalescent.
• 
  Laurent Mesnard, Thangamani Muthukumar, Maren Burbach, Carol Li, Huimin Shang, Darshana Dadhania, John R. Lee, Vijay K. Sharma, Jenny Xiang, Caroline Suberbielle, Maryvonnick Carmagnat, Nacera Ouali, Eric Rondeau, John Friedewald, Michael M. Abecassis, Manikkam Suthanthiran, Fabien Campagne:
  Exome Sequencing and Prediction of Long-Term Kidney Allograft Function.
• 
  Stuart R. Young, Bruce S. Gardiner, Arash Mehdizadeh, Jonas Rubenson, Brian R. Umberger, David W. Smith:
  Adaptive Remodeling of Achilles Tendon: A Multi-scale Computational Model.
• 
  Carlos S. N. Brito, Wulfram Gerstner:
  Nonlinear Hebbian Learning as a Unifying Principle in Receptive Field Formation.
• 
  Grant Gillary, Ernst Niebur:
  The Edge of Stability: Response Times and Delta Oscillations in Balanced Networks.
• 
  Alex D. Washburne, Joshua W. Burby, Daniel Lacker:
  Novel Covariance-Based Neutrality Test of Time-Series Data Reveals Asymmetries in Ecological and Economic Systems.

Volume 12, Number 10, October 2016

Editorials

• 
  David T. Manallack, Elizabeth Yuriev:
  Ten Simple Rules for Developing a MOOC.
• 
  Edmund Hart, Pauline Barmby, David S. LeBauer, François Michonneau, Sarah Mount, Patrick Mulrooney, Timothée Poisot, Kara H. Woo, Naupaka Zimmerman, Jeffrey W. Hollister:
  Ten Simple Rules for Digital Data Storage.

Education

• 
  C. Brandon Ogbunugafor, Daniel L. Hartl:
  A New Take on John Maynard Smith's Concept of Protein Space for Understanding Molecular Evolution.

Research Articles

• 
  Qi Zheng, Elizabeth A. Grice:
  AlignerBoost: A Generalized Software Toolkit for Boosting Next-Gen Sequencing Mapping Accuracy Using a Bayesian-Based Mapping Quality Framework.
• 
  Neha Khetan, Chaitanya A. Athale:
  A Motor-Gradient and Clustering Model of the Centripetal Motility of MTOCs in Meiosis I of Mouse Oocytes.
• 
  Daniel Machado, Markus J. Herrgård, Isabel Rocha:
  Stoichiometric Representation of Gene-Protein-Reaction Associations Leverages Constraint-Based Analysis from Reaction to Gene-Level Phenotype Prediction.
• 
  Goar Sánchez-Sanz, Bartlomiej Tywoniuk, David Matallanas, David Romano, Lan K. Nguyen, Boris N. Kholodenko, Edina Rosta, Walter Kolch, Nicolae-Viorel Buchete:
  SARAH Domain-Mediated MST2-RASSF Dimeric Interactions.
• 
  Jianhui Tian, Cesar A. López, Cynthia A. Derdeyn, Morris S. Jones, Abraham Pinter, Bette T. Korber, S. Gnanakaran:
  Effect of Glycosylation on an Immunodominant Region in the V1V2 Variable Domain of the HIV-1 Envelope gp120 Protein.
• 
  Lauren J. Dupuis, Joost Lumens, Theo Arts, Tammo Delhaas:
  Mechano-chemical Interactions in Cardiac Sarcomere Contraction: A Computational Modeling Study.
• 
  Julia Reis, Jeffrey Shaman:
  Retrospective Parameter Estimation and Forecast of Respiratory Syncytial Virus in the United States.
• 
  Hansaim Lim, Aleksandar Poleksic, Yuan Yao, Hanghang Tong, Di He, Luke Zhuang, Patrick Meng, Lei Xie:
  Large-Scale Off-Target Identification Using Fast and Accurate Dual Regularized One-Class Collaborative Filtering and Its Application to Drug Repurposing.
• 
  René Dreos, Giovanna Ambrosini, Philipp Bucher:
  Influence of Rotational Nucleosome Positioning on Transcription Start Site Selection in Animal Promoters.
• 
  Guillaume Marrelec, Arnaud Messé, Alain Giron, David Rudrauf:
  Functional Connectivity's Degenerate View of Brain Computation.
• 
  Paula Villa Martín, Jorge Hidalgo, Rafael Rubio de Casas, Miguel A. Muñoz:
  Eco-evolutionary Model of Rapid Phenotypic Diversification in Species-Rich Communities.
• 
  Ayaka Kato, Kenji Morita:
  Forgetting in Reinforcement Learning Links Sustained Dopamine Signals to Motivation.
• 
  Hannah Bos, Markus Diesmann, Moritz Helias:
  Identifying Anatomical Origins of Coexisting Oscillations in the Cortical Microcircuit.
• 
  Mae L. Woods, Chris P. Barnes:
  Mechanistic Modelling and Bayesian Inference Elucidates the Variable Dynamics of Double-Strand Break Repair.
• 
  Braden A. W. Brinkman, Alison I. Weber, Fred Rieke, Eric Shea-Brown:
  How Do Efficient Coding Strategies Depend on Origins of Noise in Neural Circuits?
• 
  Guillermo Rodrigo, Juan F. Poyatos:
  Genetic Redundancies Enhance Information Transfer in Noisy Regulatory Circuits.
• 
  Douglas McLelland, Rufin VanRullen:
  Theta-Gamma Coding Meets Communication-through-Coherence: Neuronal Oscillatory Multiplexing Theories Reconciled.
• 
  Jumpei F. Yamagishi, Nen Saito, Kunihiko Kaneko:
  Symbiotic Cell Differentiation and Cooperative Growth in Multicellular Aggregates.
• 
  Duncan K. Ralph, Frederick A. Matsen IV:
  Likelihood-Based Inference of B Cell Clonal Families.
• 
  Richard A. Gray, Pras Pathmanathan:
  A Parsimonious Model of the Rabbit Action Potential Elucidates the Minimal Physiological Requirements for Alternans and Spiral Wave Breakup.
• 
  Lars Hahn, Chris-André Leimeister, Rachid Ounit, Stefano Lonardi, Burkhard Morgenstern:
  rasbhari: Optimizing Spaced Seeds for Database Searching, Read Mapping and Alignment-Free Sequence Comparison.
• 
  YoonSik Shim, Andrew Philippides, Kevin Staras, Phil Husbands:
  Unsupervised Learning in an Ensemble of Spiking Neural Networks Mediated by ITDP.
• 
  Daifeng Wang, Fei He, Sergei Maslov, Mark Gerstein:
  DREISS: Using State-Space Models to Infer the Dynamics of Gene Expression Driven by External and Internal Regulatory Networks.
• 
  Jason Karslake, Jeff Maltas, Peter Brumm, Kevin B. Wood:
  Population Density Modulates Drug Inhibition and Gives Rise to Potential Bistability of Treatment Outcomes for Bacterial Infections.
• 
  Qie He, Junfeng Zhu, David Dingli, Jasmine Foo, Kevin Leder:
  Optimized Treatment Schedules for Chronic Myeloid Leukemia.
• 
  Soya Shinkai, Tadasu Nozaki, Kazuhiro Maeshima, Yuichi Togashi:
  Dynamic Nucleosome Movement Provides Structural Information of Topological Chromatin Domains in Living Human Cells.
• 
  Matthieu Barbier, James R. Watson:
  The Spatial Dynamics of Predators and the Benefits and Costs of Sharing Information.
• 
  Ruben Perez-Carrasco, Pilar Guerrero, James Briscoe, Karen M. Page:
  Intrinsic Noise Profoundly Alters the Dynamics and Steady State of Morphogen-Controlled Bistable Genetic Switches.
• 
  Beibei Wang, Joshua Francis, Monika Sharma, Sean M. Law, Alexander V. Predeus, Michael Feig:
  Long-Range Signaling in MutS and MSH Homologs via Switching of Dynamic Communication Pathways.
• 
  Kerstin Reuter, Alexander Biehl, Laurena Koch, Volkhard Helms:
  PreTIS: A Tool to Predict Non-canonical 5' UTR Translational Initiation Sites in Human and Mouse.
• 
  Max Schelker, Caroline Maria Mair, Fabian Jolmes, Robert-William Welke, Edda Klipp, Andreas Herrmann, Max Flöttmann, Christian Sieben:
  Viral RNA Degradation and Diffusion Act as a Bottleneck for the Influenza A Virus Infection Efficiency.
• 
  Nathalie Van Humbeeck, Tom Putzeys, Johan Wagemans:
  Apparent Motion Suppresses Responses in Early Visual Cortex: A Population Code Model.
• 
  Joseph P. McKenna, Raghuram Dhumpa, Nikita Mukhitov, Michael G. Roper, Richard Bertram:
  Glucose Oscillations Can Activate an Endogenous Oscillator in Pancreatic Islets.
• 
  Alexander T. Dilthey, Pierre-Antoine Gourraud, Alexander J. Mentzer, Nezih Cereb, Zamin Iqbal, Gil McVean:
  High-Accuracy HLA Type Inference from Whole-Genome Sequencing Data Using Population Reference Graphs.
• 
  Alejandro Fernández Villaverde, Antonio Barreiro, Antonis Papachristodoulou:
  Structural Identifiability of Dynamic Systems Biology Models.
• 
  Allen Cheung:
  Probabilistic Learning by Rodent Grid Cells.
• 
  Marieke Jepma, Peter R. Murphy, Matthew R. Nassar, Mauricio Rangel-Gomez, Martijn Meeter, Sander Nieuwenhuis:
  Catecholaminergic Regulation of Learning Rate in a Dynamic Environment.
• 
  Hung-Yu Chang, Xuejin Li, He Li, George E. Karniadakis:
  MD/DPD Multiscale Framework for Predicting Morphology and Stresses of Red Blood Cells in Health and Disease.
• 
  Samuel M. D. Oliveira, Antti Häkkinen, Jason Lloyd-Price, Huy Tran, Vinodh Kandavalli, Andre S. Ribeiro:
  Temperature-Dependent Model of Multi-step Transcription Initiation in Escherichia coli Based on Live Single-Cell Measurements.

Volume 12, Number 11, November 2016

Editorial

• 
  Mohamed Helmy, Alexander Crits-Christoph, Gary D. Bader:
  Ten Simple Rules for Developing Public Biological Databases.

Research Articles

• 
  Hulda S. Haraldsdóttir, Ronan M. T. Fleming:
  Identification of Conserved Moieties in Metabolic Networks by Graph Theoretical Analysis of Atom Transition Networks.
• 
  Ayush Singhal, Michael Simmons, Zhiyong Lu:
  Text Mining Genotype-Phenotype Relationships from Biomedical Literature for Database Curation and Precision Medicine.
• 
  Nicol S. Harper, Oliver Schoppe, Ben D. B. Willmore, Zhanfeng Cui, Jan W. H. Schnupp, Andrew J. King:
  Network Receptive Field Modeling Reveals Extensive Integration and Multi-feature Selectivity in Auditory Cortical Neurons.
• 
  Florent Bocquelet, Thomas Hueber, Laurent Girin, Christophe Savariaux, Blaise Yvert:
  Real-Time Control of an Articulatory-Based Speech Synthesizer for Brain Computer Interfaces.
• 
  Mahdi Golkaram, Stefan Hellander, Brian Drawert, Linda R. Petzold:
  Macromolecular Crowding Regulates the Gene Expression Profile by Limiting Diffusion.
• 
  Max Tegmark:
  Improved Measures of Integrated Information.
• 
  Jason S. Prentice, Olivier Marre, Mark L. Ioffe, Adrianna Loback, Gasper Tkacik, Michael J. Berry II:
  Error-Robust Modes of the Retinal Population Code.
• 
  Shreyas Bhaban, Donatello Materassi, Mingang Li, Thomas Hays, Murti V. Salapaka:
  Interrogating Emergent Transport Properties for Molecular Motor Ensembles: A Semi-analytical Approach.
• 
  Denis S. Willett, Justin George, Nora S. Willett, Lukasz L. Stelinski, Stephen L. Lapointe:
  Machine Learning for Characterization of Insect Vector Feeding.
• 
  William J. Love, Kelson A. Zawack, James G. Booth, Yrjo T. Grhn, Cristina Lanzas:
  Markov Networks of Collateral Resistance: National Antimicrobial Resistance Monitoring System Surveillance Results from Escherichia coli Isolates, 2004-2012.
• 
  Yeeun Kim, Paul G. Higgs:
  Co-operation between Polymerases and Nucleotide Synthetases in the RNA World.
• 
  Jeffrey S. Seely, Matthew T. Kaufman, Stephen I. Ryu, Krishna V. Shenoy, John P. Cunningham, Mark M. Churchland:
  Tensor Analysis Reveals Distinct Population Structure that Parallels the Different Computational Roles of Areas M1 and V1.
• 
  Jason Mikiel-Hunter, Vibhakar C. Kotak, John Rinzel:
  High-Frequency Resonance in the Gerbil Medial Superior Olive.
• 
  Elad Noor, Avi I. Flamholz, Arren Bar-Even, Dan Davidi, Ron Milo, Wolfram Liebermeister:
  The Protein Cost of Metabolic Fluxes: Prediction from Enzymatic Rate Laws and Cost Minimization.
• 
  Kristyna Pluhackova, Stefan Gahbauer, Franziska Kranz, Tsjerk A. Wassenaar, Rainer A. Böckmann:
  Dynamic Cholesterol-Conditioned Dimerization of the G Protein Coupled Chemokine Receptor Type 4.
• 
  Jonathan A. Michaels, Benjamin Dann, Hansjörg Scherberger:
  Neural Population Dynamics during Reaching Are Better Explained by a Dynamical System than Representational Tuning.
• 
  David A. Van Valen, Takamasa Kudo, Keara M. Lane, Derek N. Macklin, Nicolas T. Quach, Mialy M. DeFelice, Inbal Maayan, Yu Tanouchi, Euan A. Ashley, Markus W. Covert:
  Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments.
• 
  Elizabeth N. Davison, Benjamin O. Turner, Kimberly J. Schlesinger, Michael B. Miller, Scott T. Grafton, Danielle S. Bassett, Jean M. Carlson:
  Individual Differences in Dynamic Functional Brain Connectivity across the Human Lifespan.
• 
  Roberto C. Sotero:
  Topology, Cross-Frequency, and Same-Frequency Band Interactions Shape the Generation of Phase-Amplitude Coupling in a Neural Mass Model of a Cortical Column.
• 
  George L. Sutphin, J. Matthew Mahoney, Keith S. Sheppard, David O. Walton, Ron Korstanje:
  WORMHOLE: Novel Least Diverged Ortholog Prediction through Machine Learning.
• 
  Sagi Snir, Bridgett M. Vonholdt, Matteo Pellegrini:
  A Statistical Framework to Identify Deviation from Time Linearity in Epigenetic Aging.
• 
  Sophia S. Liu, Adam J. Hockenberry, Andrea Lancichinetti, Michael C. Jewett, Luís A. Nunes Amaral:
  NullSeq: A Tool for Generating Random Coding Sequences with Desired Amino Acid and GC Contents.
• 
  Lefteris Koumakis, Alexandros Kanterakis, Evgenia Kartsaki, Maria Chatzimina, Michalis E. Zervakis, Manolis Tsiknakis, Despoina Vassou, Dimitris Kafetzopoulos, Kostas Marias, Vassilis Moustakis, George Potamias:
  MinePath: Mining for Phenotype Differential Sub-paths in Molecular Pathways.
• 
  Adam F. Prasanphanich, Douglas E. White, Margaret A. Gran, Melissa L. Kemp:
  Kinetic Modeling of ABCG2 Transporter Heterogeneity: A Quantitative, Single-Cell Analysis of the Side Population Assay.
• 
  Arno Onken, Jian K. Liu, P. P. Chamanthi R. Karunasekara, Ioannis Delis, Tim Gollisch, Stefano Panzeri:
  Using Matrix and Tensor Factorizations for the Single-Trial Analysis of Population Spike Trains.
• 
  Milen Nikolov, Caitlin A. Bever, Alexander Upfill-Brown, Busiku Hamainza, John M. Miller, Philip A. Eckhoff, Edward A. Wenger, Jaline Gerardin:
  Malaria Elimination Campaigns in the Lake Kariba Region of Zambia: A Spatial Dynamical Model.
• 
  Geir Halnes, Tuomo Mäki-Marttunen, Daniel X. Keller, Klas H. Pettersen, Ole A. Andreassen, Gaute T. Einevoll:
  Effect of Ionic Diffusion on Extracellular Potentials in Neural Tissue.
• 
  Rotem Ben-Shachar, Scott C. Schmidler, Katia Koelle:
  Drivers of Inter-individual Variation in Dengue Viral Load Dynamics.
• 
  Marzieh Ayati, Mehmet Koyutürk:
  PoCos: Population Covering Locus Sets for Risk Assessment in Complex Diseases.
• 
  Azmat Sohail, Kumaresan Jayaraman, Santhosh Kannan Venkatesan, Kamil Gotfryd, Markus Daerr, Ulrik Gether, Claus J. Loland, Klaus T. Wanner, Michael Freissmuth, Harald H. Sitte, Walter Sandtner, Thomas Stockner:
  The Environment Shapes the Inner Vestibule of LeuT.
• 
  Wan Yang, Donald R. Olson, Jeffrey Shaman:
  Forecasting Influenza Outbreaks in Boroughs and Neighborhoods of New York City.
• 
  Laura Riccardi, Paolo Mereghetti:
  Induced Fit in Protein Multimerization: The HFBI Case.
• 
  Fang-Cheng Yeh, Jean M. Vettel, Aarti Singh, Barnabás Póczos, Scott T. Grafton, Kirk I. Erickson, Wen-Yih Isaac Tseng, Timothy D. Verstynen:
  Quantifying Differences and Similarities in Whole-Brain White Matter Architecture Using Local Connectome Fingerprints.
• 
  Adaoha E. C. Ihekwaba, Ivan Mura, John Walshaw, Michael W. Peck, Gary C. Barker:
  An Integrative Approach to Computational Modelling of the Gene Regulatory Network Controlling Clostridium botulinum Type A1 Toxin Production.
• 
  Florian Aspart, Josef Ladenbauer, Klaus Obermayer:
  Extending Integrate-and-Fire Model Neurons to Account for the Effects of Weak Electric Fields and Input Filtering Mediated by the Dendrite.
• 
  Mona Habibi, Jörg Rottler, Steven S. Plotkin:
  As Simple As Possible, but Not Simpler: Exploring the Fidelity of Coarse-Grained Protein Models for Simulated Force Spectroscopy.
• 
  Kieran R. Campbell, Christopher Yau:
  Order Under Uncertainty: Robust Differential Expression Analysis Using Probabilistic Models for Pseudotime Inference.
• 
  Aleksandr V. Zhuravlev, Gennady A. Zakharov, Boris F. Shchegolev, Elena V. Savvateeva-Popova:
  Antioxidant Properties of Kynurenines: Density Functional Theory Calculations.
• 
  Bernardo Lino de Oliveira, Steven A. Niederer:
  A Biophysical Systems Approach to Identifying the Pathways of Acute and Chronic Doxorubicin Mitochondrial Cardiotoxicity.
• 
  Petri Takkala, Yi Zhu, Steven A. Prescott:
  Combined Changes in Chloride Regulation and Neuronal Excitability Enable Primary Afferent Depolarization to Elicit Spiking without Compromising its Inhibitory Effects.
• 
  Peter Rashkov, Ian P. Barrett, Robert E. Beardmore, Claus Bendtsen, Ivana Gudelj:
  Kinase Inhibition Leads to Hormesis in a Dual Phosphorylation-Dephosphorylation Cycle.
• 
  André F. Pereira, Daniel J. Hageman, Tomasz Garbowski, Christof Riedesel, Ulf Knothe, Dirk Zeidler, Melissa L. Knothe Tate:
  Creating High-Resolution Multiscale Maps of Human Tissue Using Multi-beam SEM.
• 
  Edgar D. Coelho, Joel P. Arrais, José Luís Oliveira:
  Computational Discovery of Putative Leads for Drug Repositioning through Drug-Target Interaction Prediction.
• 
  Kazunari Iwamoto, Yuki Shindo, Koichi Takahashi:
  Modeling Cellular Noise Underlying Heterogeneous Cell Responses in the Epidermal Growth Factor Signaling Pathway.
• 
  Elif Tekin, David Hunt, Mitchell G. Newberry, Van M. Savage:
  Do Vascular Networks Branch Optimally or Randomly across Spatial Scales?

Volume 12, Number 12, December 2016

Message from ISCB

• 
  Alastair M. Kilpatrick:
  The 5th ISCB Wikipedia Competition: Coming to a Classroom Near You?

Research Articles

• 
  Vasily A. Vakorin, Sam M. Doesburg, Leodante da Costa, Rakesh Jetly, Elizabeth W. Pang, Margot J. Taylor:
  Detecting Mild Traumatic Brain Injury Using Resting State Magnetoencephalographic Connectivity.
• 
  Thomas LaBar, Christoph Adami:
  Different Evolutionary Paths to Complexity for Small and Large Populations of Digital Organisms.
• 
  Laurence Aitchison, Nicola Corradi, Peter E. Latham:
  Zipf's Law Arises Naturally When There Are Underlying, Unobserved Variables.
• 
  Srikanth Ryali, Kaustubh Supekar, Tianwen Chen, John Kochalka, Weidong Cai, Jonathan Nicholas, Aarthi Padmanabhan, Vinod Menon:
  Temporal Dynamics and Developmental Maturation of Salience, Default and Central-Executive Network Interactions Revealed by Variational Bayes Hidden Markov Modeling.
• 
  Ryan C. Williamson, Benjamin R. Cowley, Ashok Litwin-Kumar, Brent Doiron, Adam Kohn, Matthew A. Smith, Byron M. Yu:
  Scaling Properties of Dimensionality Reduction for Neural Populations and Network Models.
• 
  Kari Y. Lam, Zachary M. Westrick, Christian L. Müller, Lionel A. Christiaen, Richard Bonneau:
  Fused Regression for Multi-source Gene Regulatory Network Inference.
• 
  Benjamin R. Cowley, Matthew A. Smith, Adam Kohn, Byron M. Yu:
  Stimulus-Driven Population Activity Patterns in Macaque Primary Visual Cortex.
• 
  Laurence Aitchison, Máté Lengyel:
  The Hamiltonian Brain: Efficient Probabilistic Inference with Excitatory-Inhibitory Neural Circuit Dynamics.
• 
  Sang Hoon Yeo, David W. Franklin, Daniel M. Wolpert:
  When Optimal Feedback Control Is Not Enough: Feedforward Strategies Are Required for Optimal Control with Active Sensing.
• 
  Angela Re, Levi Waldron, Alessandro Quattrone:
  Control of Gene Expression by RNA Binding Protein Action on Alternative Translation Initiation Sites.
• 
  Jennifer Scheidel, Leonie Amstein, Jörg Ackermann, Ivan Dikic, Ina Koch:
  In Silico Knockout Studies of Xenophagic Capturing of Salmonella.
• 
  Rahul Subramanian, Andrea L. Graham, Bryan T. Grenfell, Nimalan Arinaminpathy:
  Universal or Specific? A Modeling-Based Comparison of Broad-Spectrum Influenza Vaccines against Conventional, Strain-Matched Vaccines.
• 
  Jantien A. Backer, Jacco Wallinga:
  Spatiotemporal Analysis of the 2014 Ebola Epidemic in West Africa.
• 
  Marcin Zagórski, Zdzislaw Burda, Bartlomiej Waclaw:
  Beyond the Hypercube: Evolutionary Accessibility of Fitness Landscapes with Realistic Mutational Networks.
• 
  Brian Drawert, Andreas Hellander, Benjamin B. Bales, Debjani Banerjee, Giovanni Bellesia, Bernie J. Daigle Jr., Geoffrey Douglas, Mengyuan Gu, Anand Gupta, Stefan Hellander, Christopher B. Horuk, Dibyendu Nath, Aviral Takkar, Sheng Wu, Per Lötstedt, Chandra Krintz, Linda R. Petzold:
  Stochastic Simulation Service: Bridging the Gap between the Computational Expert and the Biologist.
• 
  Haixu Tang, Sujun Li, Yuzhen Ye:
  A Graph-Centric Approach for Metagenome-Guided Peptide and Protein Identification in Metaproteomics.
• 
  Philipp Schwedhelm, B. Suresh Krishna, Stefan Treue:
  An Extended Normalization Model of Attention Accounts for Feature-Based Attentional Enhancement of Both Response and Coherence Gain.
• 
  Andrew White, Malachi Tolman, Howard D. Thames, Hubert Rodney Withers, Kathy A. Mason, Mark K. Transtrum:
  The Limitations of Model-Based Experimental Design and Parameter Estimation in Sloppy Systems.
• 
  Debashis Barik, David A. Ball, Jean Peccoud, John J. Tyson:
  A Stochastic Model of the Yeast Cell Cycle Reveals Roles for Feedback Regulation in Limiting Cellular Variability.
• 
  James W. Baish, Christian Kunert, Timothy P. Padera, Lance L. Munn:
  Synchronization and Random Triggering of Lymphatic Vessel Contractions.
• 
  Ekaterina O. Morozova, Denis G. Zakharov, Boris S. Gutkin, Christopher C. Lapish, Alexey Kuznetsov:
  Dopamine Neurons Change the Type of Excitability in Response to Stimuli.
• 
  Anna Klimovskaia, Stefan Ganscha, Manfred Claassen:
  Sparse Regression Based Structure Learning of Stochastic Reaction Networks from Single Cell Snapshot Time Series.
• 
  James C. Schaff, Fei Gao, Li Ye, Igor L. Novak, Boris M. Slepchenko:
  Numerical Approach to Spatial Deterministic-Stochastic Models Arising in Cell Biology.
• 
  Renaud Bastien, Yasmine Meroz:
  The Kinematics of Plant Nutation Reveals a Simple Relation between Curvature and the Orientation of Differential Growth.
• 
  Dirk Alexander Kulawiak, Brian A. Camley, Wouter-Jan Rappel:
  Modeling Contact Inhibition of Locomotion of Colliding Cells Migrating on Micropatterned Substrates.
• 
  Kristen A. Marino, Diego Prada-Gracia, Davide Provasi, Marta Filizola:
  Impact of Lipid Composition and Receptor Conformation on the Spatio-temporal Organization of μ-Opioid Receptors in a Multi-component Plasma Membrane Model.
• 
  György Abrusán, Joseph A. Marsh:
  Alpha Helices Are More Robust to Mutations than Beta Strands.
• 
  Matthias Lechner, Mathias Schwarz, Madeleine Opitz, Erwin Frey:
  Hierarchical Post-transcriptional Regulation of Colicin E2 Expression in Escherichia coli.
• 
  Sahra Uygun, Cheng Peng, Melissa D. Lehti-Shiu, Robert L. Last, Shin-Han Shiu:
  Utility and Limitations of Using Gene Expression Data to Identify Functional Associations.
• 
  Marta Varela, Michael A. Colman, Jules C. Hancox, Oleg V. Aslanidi:
  Atrial Heterogeneity Generates Re-entrant Substrate during Atrial Fibrillation and Anti-arrhythmic Drug Action: Mechanistic Insights from Canine Atrial Models.
• 
  Ricardo Martínez-García, Corina E. Tarnita:
  Lack of Ecological and Life History Context Can Create the Illusion of Social Interactions in Dictyostelium discoideum.
• 
  Jacob D. Cooper, Benjamin Kerr:
  Evolution at 'Sutures' and 'Centers': Recombination Can Aid Adaptation of Spatially Structured Populations on Rugged Fitness Landscapes.
• 
  Matthew R. Huska, Martin Vingron:
  Improved Prediction of Non-methylated Islands in Vertebrates Highlights Different Characteristic Sequence Patterns.
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  Russell Gould, David M. Bassen, Anirikh Chakrabarti, Jeffrey D. Varner, Jonathan T. Butcher:
  Population Heterogeneity in the Epithelial to Mesenchymal Transition Is Controlled by NFAT and Phosphorylated Sp1.
• 
  Sébastien Raguideau, Sandra Plancade, Nicolas Pons, Marion Leclerc, Béatrice Laroche:
  Inferring Aggregated Functional Traits from Metagenomic Data Using Constrained Non-negative Matrix Factorization: Application to Fiber Degradation in the Human Gut Microbiota.
• 
  Andrew K. Smith, Brenden K. Petersen, Glen E. P. Ropella, Ryan C. Kennedy, Neil Kaplowitz, Murad Ookhtens, C. Anthony Hunt:
  Competing Mechanistic Hypotheses of Acetaminophen-Induced Hepatotoxicity Challenged by Virtual Experiments.
• 
  Jonathan Desponds, Huy Tran, Teresa Ferraro, Tanguy Lucas, Carmina Perez Romero, Aurelien Guillou, Cecile Fradin, Mathieu Coppey, Nathalie Dostatni, Aleksandra M. Walczak:
  Precision of Readout at the hunchback Gene: Analyzing Short Transcription Time Traces in Living Fly Embryos.
• 
  Guillaume Lajoie, Kevin K. Lin, Jean-Philippe Thivierge, Eric Shea-Brown:
  Encoding in Balanced Networks: Revisiting Spike Patterns and Chaos in Stimulus-Driven Systems.
• 
  Florent Meyniel, Maxime Maheu, Stanislas Dehaene:
  Human Inferences about Sequences: A Minimal Transition Probability Model.
• 
  Kawai Leung, Aylia Mohammadi, William S. Ryu, Ilya Nemenman:
  Stereotypical Escape Behavior in Caenorhabditis elegans Allows Quantification of Effective Heat Stimulus Level.
• 
  J. Patrick Pett, Anja Korencic, Felix Wesener, Achim Kramer, Hanspeter Herzel:
  Feedback Loops of the Mammalian Circadian Clock Constitute Repressilator.
• 
  Jatin Narula, Abhinav Tiwari, Oleg A. Igoshin:
  Role of Autoregulation and Relative Synthesis of Operon Partners in Alternative Sigma Factor Networks.
• 
  Ivana Gudelj, Margie Kinnersley, Peter Rashkov, Karen Schmidt, Frank Rosenzweig:
  Stability of Cross-Feeding Polymorphisms in Microbial Communities.
• 
  Aitor Blanco-Míguez, Jan P. Meier-Kolthoff, Alberto Gutiérrez-Jácome, Markus Göker, Florentino Fdez-Riverola, Borja Sánchez, Anália Lourenço:
  Improving Phylogeny Reconstruction at the Strain Level Using Peptidome Datasets.
• 
  Nadezda Kryuchkova-Mostacci, Marc Robinson-Rechavi:
  Tissue-Specificity of Gene Expression Diverges Slowly between Orthologs, and Rapidly between Paralogs.
• 
  Barry Bentley, Robyn Branicky, Christopher L. Barnes, Yee Lian Chew, Eviatar Yemini, Edward T. Bullmore, Petra E. Vértes, William R. Schafer:
  The Multilayer Connectome of Caenorhabditis elegans.
• 
  Won-Seok Hwang, Il-Buem Lee, Seok-Cheol Hong, Changbong Hyeon:
  Decoding Single Molecule Time Traces with Dynamic Disorder.
• 
  Song-Yao Zhang, Shao-Wu Zhang, Lian Liu, Jia Meng, Yufei Huang:
  m6A-Driver: Identifying Context-Specific mRNA m6A Methylation-Driven Gene Interaction Networks.
• 
  Simeon Carstens, Michael Nilges, Michael Habeck:
  Inferential Structure Determination of Chromosomes from Single-Cell Hi-C Data.
• 
  Yitav Glantz-Gashai, Tomer Meirson, Abraham O. Samson:
  Normal Modes Expose Active Sites in Enzymes.
• 
  Andrew F. Neuwald, Stephen F. Altschul:
  Inference of Functionally-Relevant N-acetyltransferase Residues Based on Statistical Correlations.
• 
  Michaël Dougoud, Laura Vinckenbosch, Christian Mazza, Beat Schwaller, László Pecze:
  The Effect of Gap Junctional Coupling on the Spatiotemporal Patterns of Ca2+ Signals and the Harmonization of Ca2+-Related Cellular Responses.
• 
  Matt J. Keeling, Thomas A. House, Alison J. Cooper, Lorenzo Pellis:
  Systematic Approximations to Susceptible-Infectious-Susceptible Dynamics on Networks.
• 
  Katharina Baum, Antonio Z. Politi, Bente Kofahl, Ralf Steuer, Jana Wolf:
  Feedback, Mass Conservation and Reaction Kinetics Impact the Robustness of Cellular Oscillations.
• 
  Renaud Berlemont