PLoS Computational Biology, Volume 13

Volume 13, Number 1, January 2017

Editorials

• 
  Ruth Nussinov, Jason A. Papin, Ilya A. Vakser:
  Computing the Dynamic Supramolecular Structural Proteome.
• 
  Mary Regina Boland, Konrad J. Karczewski, Nicholas P. Tatonetti:
  Ten Simple Rules to Enable Multi-site Collaborations through Data Sharing.
• 
  Markus List, Peter Ebert, Felipe Albrecht:
  Ten Simple Rules for Developing Usable Software in Computational Biology.

Perspective

• 
  Luca Cardelli, Rosa D. Hernansaiz-Ballesteros, Neil Dalchau, Attila Csikász-Nagy:
  Efficient Switches in Biology and Computer Science.

Review

• 
  Abby Tabor, Michael A. Thacker, G. Lorimer Moseley, Konrad P. Körding:
  Pain: A Statistical Account.

Research Articles

• 
  Stuart P. Wilson:
  Self-organised criticality in the evolution of a thermodynamic model of rodent thermoregulatory huddling.
• 
  Max Hinne, Annet Meijers, Rembrandt Bakker, Paul H. E. Tiesinga, Morten Mørup, Marcel A. J. van Gerven:
  The missing link: Predicting connectomes from noisy and partially observed tract tracing data.
• 
  Te Wu, Long Wang, Feng Fu:
  Coevolutionary dynamics of phenotypic diversity and contingent cooperation.
• 
  Cox Lwaka Tamba, Yuan-Li Ni, Yuan-Ming Zhang:
  Iterative sure independence screening EM-Bayesian LASSO algorithm for multi-locus genome-wide association studies.
• 
  Richard John Wheeler:
  Use of chiral cell shape to ensure highly directional swimming in trypanosomes.
• 
  Hoyon Hwang, Jiou Wang:
  Effect of mutation mechanisms on variant composition and distribution in Caenorhabditis elegans.
• 
  Gaurav Bajpai, Ishutesh Jain, Mandar M. Inamdar, Dibyendu Das, Ranjith Padinhateeri:
  Binding of DNA-bending non-histone proteins destabilizes regular 30-nm chromatin structure.
• 
  Nikolay Chenkov, Henning Sprekeler, Richard Kempter:
  Memory replay in balanced recurrent networks.
• 
  Weikang Wang, Kuan Tao, Jing Wang, Gen Yang, Qi Ouyang, Yugang Wang, Lei Zhang, Feng Liu:
  Exploring the inhibitory effect of membrane tension on cell polarization.
• 
  Shenshen Wang:
  Optimal Sequential Immunization Can Focus Antibody Responses against Diversity Loss and Distraction.
• 
  Qixuan Wang, William R. Holmes, Julian Sosnik, Thomas F. Schilling, Qing Nie:
  Cell Sorting and Noise-Induced Cell Plasticity Coordinate to Sharpen Boundaries between Gene Expression Domains.
• 
  Ilan Y. Smoly, Netta Shemesh, Michal Ziv-Ukelson, Anat Ben-Zvi, Esti Yeger Lotem:
  An Asymmetrically Balanced Organization of Kinases versus Phosphatases across Eukaryotes Determines Their Distinct Impacts.
• 
  Austin W. T. Chiang, Walt Y. L. Wu, Ting Wang, Ming-Jing Hwang:
  Identification of Entry Factors Involved in Hepatitis C Virus Infection Based on Host-Mimicking Short Linear Motifs.
• 
  Sylvain Prigent, Clémence Frioux, Simon M. Dittami, Sven Thiele, Abdelhalim Larhlimi, Guillaume Collet, Fabien Gutknecht, Jeanne Got, Damien Eveillard, Jérémie Bourdon, Frédéric Plewniak, Thierry Tonon, Anne Siegel:
  Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks.
• 
  Hsiao-Han Chang, Colin J. Worby, Adoke Yeka, Joaniter Nankabirwa, Moses R. Kamya, Sarah G. Staedke, Grant Dorsey, Maxwell Murphy, Daniel E. Neafsey, Anna E. Jeffreys, Christina Hubbart, Kirk A. Rockett, Roberto Amato, Dominic Kwiatkowski, Caroline O. Buckee, Bryan Greenhouse:
  THE REAL McCOIL: A method for the concurrent estimation of the complexity of infection and SNP allele frequency for malaria parasites.
• 
  Gianluigi Rossi, Giulio A. De Leo, Stefano Pongolini, Silvano Natalini, Luca Zarenghi, Matteo Ricchi, Luca Bolzoni:
  The Potential Role of Direct and Indirect Contacts on Infection Spread in Dairy Farm Networks.
• 
  Marie Amalric, Liping Wang, Pierre Pica, Santiago Figueira, Mariano Sigman, Stanislas Dehaene:
  The language of geometry: Fast comprehension of geometrical primitives and rules in human adults and preschoolers.
• 
  Vasileios Vavourakis, Peter A. Wijeratne, Rebecca Shipley, Marilena Loizidou, Triantafyllos Stylianopoulos, David J. Hawkes:
  A Validated Multiscale In-Silico Model for Mechano-sensitive Tumour Angiogenesis and Growth.
• 
  Mina A. Khoei, Guillaume S. Masson, Laurent U. Perrinet:
  The Flash-Lag Effect as a Motion-Based Predictive Shift.
• 
  Stewart Heitmann, Michael Rule, Wilson Truccolo, Bard Ermentrout:
  Optogenetic Stimulation Shifts the Excitability of Cerebral Cortex from Type I to Type II: Oscillation Onset and Wave Propagation.
• 
  David Lamparter, Daniel Marbach, Rico Rueedi, Sven Bergmann, Zoltán Kutalik:
  Genome-Wide Association between Transcription Factor Expression and Chromatin Accessibility Reveals Regulators of Chromatin Accessibility.
• 
  Mohammadkarim Saeedghalati, Farnoush Farahpour, Bettina Budeus, Anja Lange, Astrid M. Westendorf, Marc Seifert, Ralf Küppers, Daniel Hoffmann:
  Quantitative Comparison of Abundance Structures of Generalized Communities: From B-Cell Receptor Repertoires to Microbiomes.
• 
  Veronika Koren, Sophie Denève:
  Computational Account of Spontaneous Activity as a Signature of Predictive Coding.
• 
  Antonella Paladino, Monica Civera, Laura Belvisi, Giorgio Colombo:
  High Affinity vs. Native Fibronectin in the Modulation of αvβ3 Integrin Conformational Dynamics: Insights from Computational Analyses and Implications for Molecular Design.
• 
  Fabian Fröhlich, Barbara Kaltenbacher, Fabian J. Theis, Jan Hasenauer:
  Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks.
• 
  Oliver Pohl, Marius Hintsche, Zahra Alirezaeizanjani, Maximilian Seyrich, Carsten Beta, Holger Stark:
  Inferring the Chemotactic Strategy of P. putida and E. coli Using Modified Kramers-Moyal Coefficients.
• 
  William R. Holmes, Nabora de Mochel, Qixuan Wang, Huijing Du, Tao Peng, Michael Chiang, Olivier Cinquin, Ken Cho, Qing Nie:
  Gene Expression Noise Enhances Robust Organization of the Early Mammalian Blastocyst.
• 
  Tamara Carla Bidone, Wonyeong Jung, Daniel Maruri, Carlos Borau, Roger D. Kamm, Taeyoon Kim:
  Morphological Transformation and Force Generation of Active Cytoskeletal Networks.
• 
  Tanmay A. Gokhale, Jong M. Kim, Robert D. Kirkton, Nenad Bursac, Craig S. Henriquez:
  Modeling an Excitable Biosynthetic Tissue with Inherent Variability for Paired Computational-Experimental Studies.
• 
  Heiner Stuke, Hannes Stuke, Veith Andreas Weilnhammer, Katharina Schmack:
  Psychotic Experiences and Overhasty Inferences Are Related to Maladaptive Learning.
• 
  Ignacio A. Rodriguez-Brenes, Andrew Hofacre, Hung Fan, Dominik Wodarz:
  Complex Dynamics of Virus Spread from Low Infection Multiplicities: Implications for the Spread of Oncolytic Viruses.
• 
  Erik Andrews, Yue Wang, Tian Xia, Wenqing Cheng, Chao Cheng:
  Contextual Refinement of Regulatory Targets Reveals Effects on Breast Cancer Prognosis of the Regulome.
• 
  Edward S. Lee, Paul G. Thomas, Jeff E. Mold, Andrew J. Yates:
  Identifying T Cell Receptors from High-Throughput Sequencing: Dealing with Promiscuity in TCRα and TCRβ Pairing.
• 
  Iris Reuveni, Sourav Ghosh, Edi Barkai:
  Real Time Multiplicative Memory Amplification Mediated by Whole-Cell Scaling of Synaptic Response in Key Neurons.
• 
  Hilje M. Doekes, Christophe Fraser, Katrina A. Lythgoe:
  Effect of the Latent Reservoir on the Evolution of HIV at the Within- and Between-Host Levels.
• 
  Oded Barzelay, Miriam Furst, Omri Barak:
  A New Approach to Model Pitch Perception Using Sparse Coding.
• 
  Bethany Levick, Andy South, Ian M. Hastings:
  A Two-Locus Model of the Evolution of Insecticide Resistance to Inform and Optimise Public Health Insecticide Deployment Strategies.
• 
  Aysima Hacisuleyman, Burak Erman:
  Entropy Transfer between Residue Pairs and Allostery in Proteins: Quantifying Allosteric Communication in Ubiquitin.
• 
  Christian Donner, Klaus Obermayer, Hideaki Shimazaki:
  Approximate Inference for Time-Varying Interactions and Macroscopic Dynamics of Neural Populations.
• 
  Gabrielle Stetz, Gennady M. Verkhivker:
  Computational Analysis of Residue Interaction Networks and Coevolutionary Relationships in the Hsp70 Chaperones: A Community-Hopping Model of Allosteric Regulation and Communication.
• 
  Alireza Yazdani, He Li, Jay D. Humphrey, George E. Karniadakis:
  A General Shear-Dependent Model for Thrombus Formation.
• 
  Christoph Zimmer, Reza Yaesoubi, Ted Cohen:
  A Likelihood Approach for Real-Time Calibration of Stochastic Compartmental Epidemic Models.
• 
  Yaroslav Pollak, Sarah Goldberg, Roee Amit:
  A Looping-Based Model for Quenching Repression.
• 
  Federica Giardina, Ethan O. Romero-Severson, Jan Albert, Tom Britton, Thomas Leitner:
  Inference of Transmission Network Structure from HIV Phylogenetic Trees.
• 
  Christopher M. Siwy, Christopher Lockhart, Dmitri K. Klimov:
  Is the Conformational Ensemble of Alzheimer's Aβ10-40 Peptide Force Field Dependent?
• 
  Kaitlyn M. Gayvert, Omar Aly, James Platt, Marcus W. Bosenberg, David F. Stern, Olivier Elemento:
  A Computational Approach for Identifying Synergistic Drug Combinations.
• 
  Eric Jonas, Konrad Paul Körding:
  Could a Neuroscientist Understand a Microprocessor?
• 
  Luc E. Coffeng, Cornelus Hermsen, Robert W. Sauerwein, Sake J. De Vlas:
  The Power of Malaria Vaccine Trials Using Controlled Human Malaria Infection.
• 
  James M. Kunert, Joshua L. Proctor, Steven L. Brunton, J. Nathan Kutz:
  Spatiotemporal Feedback and Network Structure Drive and Encode Caenorhabditis elegans Locomotion.
• 
  Andrea Insabato, Mario Pannunzi, Gustavo Deco:
  Multiple Choice Neurodynamical Model of the Uncertain Option Task.
• 
  Emanuel J. V. Gonçalves, Zrinka Raguz Nakic, Mattia Zampieri, Omar Wagih, David Ochoa, Uwe Sauer, Pedro Beltrão, Julio Saez-Rodriguez:
  Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast.
• 
  Mihaela Enculescu, Christoph Metzendorf, Richard Sparla, Maximilian Hahnel, Johannes G. Bode, Martina U. Muckenthaler, Stefan Legewie:
  Modelling Systemic Iron Regulation during Dietary Iron Overload and Acute Inflammation: Role of Hepcidin-Independent Mechanisms.
• 
  Martina Michalikova, Michiel W. H. Remme, Richard Kempter:
  Spikelets in Pyramidal Neurons: Action Potentials Initiated in the Axon Initial Segment That Do Not Activate the Soma.
• 
  Pia Abel zur Wiesch, Fabrizio Clarelli, Ted Cohen:
  Using Chemical Reaction Kinetics to Predict Optimal Antibiotic Treatment Strategies.
• 
  Nicholas A. Rossi, Mary J. Dunlop:
  Customized Regulation of Diverse Stress Response Genes by the Multiple Antibiotic Resistance Activator MarA.
• 
  Sheng Wang, Siqi Sun, Zhen Li, Renyu Zhang, Jinbo Xu:
  Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model.
• 
  Kristin Verena Kaltdorf, Katja Schulze, Frederik Helmprobst, Philip Kollmannsberger, Thomas Dandekar, Christian Stigloher:
  FIJI Macro 3D ART VeSElecT: 3D Automated Reconstruction Tool for Vesicle Structures of Electron Tomograms.
• 
  James M. Kunert, Pedro D. Maia, J. Nathan Kutz:
  Functionality and Robustness of Injured Connectomic Dynamics in C. elegans: Linking Behavioral Deficits to Neural Circuit Damage.
• 
  Hualou Liang, Hongbin Wang:
  Structure-Function Network Mapping and Its Assessment via Persistent Homology.
• 
  Elyse H. Norton, Stephen M. Fleming, Nathaniel D. Daw, Michael S. Landy:
  Suboptimal Criterion Learning in Static and Dynamic Environments.
• 
  Chen Zhao, Jeffrey S. Isenberg, Aleksander S. Popel:
  Transcriptional and Post-Transcriptional Regulation of Thrombospondin-1 Expression: A Computational Model.

Volume 13, Number 2, February 2017

Editorials

• 
  Julia V. Ponomarenko, Romina Garrido, Roderic Guigó:
  Ten Simple Rules on How to Organize a Scientific Retreat.
• 
  Dyoni M. de Oliveira, Marcos Silveira Buckeridge, Wanderley Dantas dos Santos:
  Ten Simple Rules for Developing a Successful Research Proposal in Brazil.

Research Articles

• 
  Sophie K. Kay, Heather A. Harrington, Sarah Shepherd, Keith Brennan, Trevor Dale, James M. Osborne, David J. Gavaghan, Helen M. Byrne:
  The role of the Hes1 crosstalk hub in Notch-Wnt interactions of the intestinal crypt.
• 
  Miguel A. Fortuna, Luis Zaman, Charles Ofria, Andreas Wagner:
  The genotype-phenotype map of an evolving digital organism.
• 
  Yihao Zhang, Krithika Abiraman, He Li, David M. Pierce, Anastasios V. Tzingounis, George Lykotrafitis:
  Modeling of the axon membrane skeleton structure and implications for its mechanical properties.
• 
  Qian Qin, Jianxing Feng:
  Imputation for transcription factor binding predictions based on deep learning.
• 
  Felipe Gerhard, Moritz Deger, Wilson Truccolo:
  On the stability and dynamics of stochastic spiking neuron models: Nonlinear Hawkes process and point process GLMs.
• 
  Arno Klein, Satrajit S. Ghosh, Forrest Sheng Bao, Joachim Giard, Yrjö Häme, Eliezer Stavsky, Noah Lee, Brian Rossa, Martin Reuter, Elias Chaibub Neto, Anisha Keshavan:
  Mindboggling morphometry of human brains.
• 
  Alice R. Walker, Pavel Silvestrov, Tina A. Müller, Robert H. Podolsky, Gregory Dyson, Robert P. Hausinger, Gerardo Andrés Cisneros:
  ALKBH7 Variant Related to Prostate Cancer Exhibits Altered Substrate Binding.
• 
  Zachary S. L. Foster, Thomas J. Sharpton, Niklaus J. Grünwald:
  Metacoder: An R package for visualization and manipulation of community taxonomic diversity data.
• 
  Sean M. Gibbons, Sean M. Kearney, Chris S. Smillie, Eric J. Alm:
  Two dynamic regimes in the human gut microbiome.
• 
  Dongjun Chung, Hang J. Kim, Hongyu Zhao:
  graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture.
• 
  Jan Ewald, Martin Bartl, Thomas Dandekar, Christoph Kaleta:
  Optimality principles reveal a complex interplay of intermediate toxicity and kinetic efficiency in the regulation of prokaryotic metabolism.
• 
  Vinal V. Lakhani, Timothy C. Elston:
  Testing the limits of gradient sensing.
• 
  Naomi V. Bradbury, William J. M. Probert, Katriona Shea, Michael C. Runge, Christopher Fonnesbeck, Matt J. Keeling, Matthew J. Ferrari, Michael J. Tildesley:
  Quantifying the Value of Perfect Information in Emergency Vaccination Campaigns.
• 
  John F. Magnotti, Michael S. Beauchamp:
  A Causal Inference Model Explains Perception of the McGurk Effect and Other Incongruent Audiovisual Speech.
• 
  Jung-Min Han, Akihiko Tanimura, Vivien Kirk, James Sneyd:
  A mathematical model of calcium dynamics in HSY cells.
• 
  Franca Schmid, Philbert S. Tsai, David Kleinfeld, Patrick Jenny, Bruno Weber:
  Depth-dependent flow and pressure characteristics in cortical microvascular networks.
• 
  Mark P. Little, Jolyon H. Hendry:
  Mathematical models of tissue stem and transit target cell divisions and the risk of radiation- or smoking-associated cancer.
• 
  Alexander Miguel Monzon, Diego J. Zea, María Silvina Fornasari, Tadeo E. Saldaño, Sebastian Fernandez Alberti, Silvio C. E. Tosatto, Gustavo D. Parisi:
  Conformational diversity analysis reveals three functional mechanisms in proteins.
• 
  James M. Osborne, Alexander G. Fletcher, Joe Pitt-Francis, Philip K. Maini, David J. Gavaghan:
  Comparing individual-based approaches to modelling the self-organization of multicellular tissues.
• 
  Dong-Ping Yang, Hai-Jun Zhou, Changsong Zhou:
  Co-emergence of multi-scale cortical activities of irregular firing, oscillations and avalanches achieves cost-efficient information capacity.
• 
  Didac Santesmasses, Marco Mariotti, Roderic Guigó:
  Computational identification of the selenocysteine tRNA (tRNASec) in genomes.
• 
  Franziska Oschmann, Konstantin Mergenthaler, Evelyn Jungnickel, Klaus Obermayer:
  Spatial separation of two different pathways accounting for the generation of calcium signals in astrocytes.
• 
  Miguel Fribourg, Diomedes E. Logothetis, Javier González-Maeso, Stuart C. Sealfon, Belén Galocha-Iragüen, Fernando Las-Heras Andrés, Vladimir Brezina:
  Elucidation of molecular kinetic schemes from macroscopic traces using system identification.
• 
  Pierre Millard, Kieran Smallbone, Pedro Mendes:
  Metabolic regulation is sufficient for global and robust coordination of glucose uptake, catabolism, energy production and growth in Escherichia coli.
• 
  Vivek Charu, Scott Zeger, Julia R. Gog, Ottar N. Bjørnstad, Stephen Kissler, Lone Simonsen, Bryan T. Grenfell, Cécile Viboud:
  Human mobility and the spatial transmission of influenza in the United States.
• 
  Angela F. Harper, Janelle B. Leuthaeuser, Patricia C. Babbitt, John H. Morris, Thomas E. Ferrin, Leslie B. Poole, Jacquelyn S. Fetrow:
  An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins.
• 
  István Bartha, Paul J. McLaren, Chanson J. Brumme, P. Richard Harrigan, Amalio Telenti, Jacques Fellay:
  Estimating the Respective Contributions of Human and Viral Genetic Variation to HIV Control.
• 
  Tracey M. Filzen, Peter S. Kutchukian, Jeffrey D. Hermes, Jing Li, Matthew Tudor:
  Representing high throughput expression profiles via perturbation barcodes reveals compound targets.
• 
  Jarred R. Mondoñedo, Béla Suki:
  Predicting Structure-Function Relations and Survival following Surgical and Bronchoscopic Lung Volume Reduction Treatment of Emphysema.
• 
  Yen-Fu Chen, Hsiu-Chuan Lin, Kai-Neng Chuang, Chih-Hsu Lin, Hsueh-Chi S. Yen, Chen-Hsiang Yeang:
  A quantitative model for the rate-limiting process of UGA alternative assignments to stop and selenocysteine codons.
• 
  Hojjat Bazzazi, Aleksander S. Popel:
  Computational investigation of sphingosine kinase 1 (SphK1) and calcium dependent ERK1/2 activation downstream of VEGFR2 in endothelial cells.
• 
  Johannes Burge, Priyank Jaini:
  Accuracy Maximization Analysis for Sensory-Perceptual Tasks: Computational Improvements, Filter Robustness, and Coding Advantages for Scaled Additive Noise.
• 
  Daniel Magee, Marc A. Suchard, Matthew Scotch:
  Bayesian phylogeography of influenza A/H3N2 for the 2014-15 season in the United States using three frameworks of ancestral state reconstruction.
• 
  William Poole, Kalle Leinonen, Ilya Shmulevich, Theo A. Knijnenburg, Brady Bernard:
  Multiscale mutation clustering algorithm identifies pan-cancer mutational clusters associated with pathway-level changes in gene expression.
• 
  David Henriques, Alejandro Fernández Villaverde, Miguel Rocha, Julio Saez-Rodriguez, Julio R. Banga:
  Data-driven reverse engineering of signaling pathways using ensembles of dynamic models.
• 
  Julia Chifman, Seda Arat, Zhiyong Deng, Erica Lemler, James C. Pino, Leonard A. Harris, Michael A. Kochen, Carlos F. Lopez, Steven A. Akman, Frank M. Torti, Suzy V. Torti, Reinhard C. Laubenbacher:
  Activated Oncogenic Pathway Modifies Iron Network in Breast Epithelial Cells: A Dynamic Modeling Perspective.
• 
  Luca Ponzoni, Giulia Rossetti, Luca Maggi, Alejandro Giorgetti, Paolo Carloni, Cristian Micheletti:
  Unifying view of mechanical and functional hotspots across class A GPCRs.
• 
  Stephanie Evans, Kieran Alden, Lourdes Cucurull-Sanchez, Christopher Larminie, Mark C. Coles, Marika C. Kullberg, Jon Timmis:
  ASPASIA: A toolkit for evaluating the effects of biological interventions on SBML model behaviour.
• 
  Mark Roper, Chrisantha Fernando, Lars Chittka:
  Insect Bio-inspired Neural Network Provides New Evidence on How Simple Feature Detectors Can Enable Complex Visual Generalization and Stimulus Location Invariance in the Miniature Brain of Honeybees.
• 
  Miguel Won, Manuel Marques-Pita, Carlota Louro, Joana Gonçalves-Sá:
  Early and Real-Time Detection of Seasonal Influenza Onset.
• 
  Berta Verd, Anton Crombach, Johannes Jaeger:
  Dynamic Maternal Gradients Control Timing and Shift-Rates for Drosophila Gap Gene Expression.
• 
  Olga K. Kamneva:
  Genome composition and phylogeny of microbes predict their co-occurrence in the environment.
• 
  Jerome M. Karp, Samuel Sparks, David Cowburn:
  Effects of FGFR2 kinase activation loop dynamics on catalytic activity.
• 
  Guillaume Lajoie, Nedialko I. Krouchev, John F. Kalaska, Adrienne L. Fairhall, Eberhard E. Fetz:
  Correlation-based model of artificially induced plasticity in motor cortex by a bidirectional brain-computer interface.
• 
  Christoph Thiel, Henrik Cordes, Lorenzo Fabbri, Hélène Eloise Aschmann, Vanessa Baier, Ines Smit, Francis Atkinson, Lars Mathias Blank, Lars Kuepfer:
  A Comparative Analysis of Drug-Induced Hepatotoxicity in Clinically Relevant Situations.
• 
  Jannis Schuecker, Maximilian Schmidt, Sacha J. van Albada, Markus Diesmann, Moritz Helias:
  Fundamental Activity Constraints Lead to Specific Interpretations of the Connectome.

Volume 13, Number 3, March 2017

Editorials

• 
  Matthew Zook, Solon Barocas, danah boyd, Kate Crawford, Emily Keller, Seeta Peña Gangadharan, Alyssa Goodman, Rachelle Hollander, Barbara König, Jacob Metcalf, Arvind Narayanan, Alondra Nelson, Frank Pasquale:
  Ten simple rules for responsible big data research.
• 
  Christopher J. Lortie:
  Ten simple rules for short and swift presentations.
• 
  Bruno A. Gaëta, Javier De Las Rivas, Paul Horton, Pieter Meysman, Nicola J. Mulder, Paolo Romano, Lonnie R. Welch:
  Ten simple rules for forming a scientific professional society.
• 
  PLOS Computational Biology 2016 Reviewer and Editorial Board Thank You.

Research Articles

• 
  Jeffrey Chen, Thomas MacCarthy:
  The preferred nucleotide contexts of the AID/APOBEC cytidine deaminases have differential effects when mutating retrotransposon and virus sequences compared to host genes.
• 
  Sergey G. Aleksin, Kaiyu Zheng, Dmitri A. Rusakov, Leonid Savtchenko:
  ARACHNE: A neural-neuroglial network builder with remotely controlled parallel computing.
• 
  Bin Huang, Mingyang Lu, Dongya Jia, Eshel Ben-Jacob, Herbert Levine, José N. Onuchic:
  Interrogating the topological robustness of gene regulatory circuits by randomization.
• 
  Sang Woo Park, Benjamin M. Bolker:
  Effects of contact structure on the transient evolution of HIV virulence.
• 
  Charles Rocabert, Carole Knibbe, Jessika Consuegra, Dominique Schneider, Guillaume Beslon:
  Beware batch culture: Seasonality and niche construction predicted to favor bacterial adaptive diversification.
• 
  Polydefkis Diamantis, Oliver T. Unke, Markus Meuwly:
  Migration of small ligands in globins: Xe diffusion in truncated hemoglobin N.
• 
  Marie Devaine, Jean Daunizeau:
  Learning about and from others' prudence, impatience or laziness: The computational bases of attitude alignment.
• 
  Daniele Caligiore, Francesco Mannella, Michael A. Arbib, Gianluca Baldassarre:
  Dysfunctions of the basal ganglia-cerebellar-thalamo-cortical system produce motor tics in Tourette syndrome.
• 
  Swati Jain, Jonathan D. Jou, Ivelin S. Georgiev, Bruce Randall Donald:
  A critical analysis of computational protein design with sparse residue interaction graphs.
• 
  Walter Basile, Oxana Sachenkova, Sara Light, Arne Elofsson:
  High GC content causes orphan proteins to be intrinsically disordered.
• 
  David A. Rasmussen, Roger D. Kouyos, Huldrych F. Günthard, Tanja Stadler:
  Phylodynamics on local sexual contact networks.
• 
  Matthew J. Betts, Oliver Wichmann, Mathias Utz, Timon Andre, Evangelia Petsalaki, Pablo Minguez, Luca Parca, Frederick P. Roth, Anne-Claude Gavin, Peer Bork, Robert B. Russell:
  Systematic identification of phosphorylation-mediated protein interaction switches.
• 
  Mahamar Dicko, Pierre Saramito, Guy B. Blanchard, Claire M. Lye, Bénédicte Sanson, Jocelyn Étienne:
  Geometry can provide long-range mechanical guidance for embryogenesis.
• 
  Zhu-Hong You, Zhi-an Huang, Zexuan Zhu, Guiying Yan, Zheng-Wei Li, Zhenkun Wen, Xing Chen:
  PBMDA: A novel and effective path-based computational model for miRNA-disease association prediction.
• 
  Kiwon Jang, Kwoneel Kim, Ara Cho, Insuk Lee, Jung Kyoon Choi:
  Network perturbation by recurrent regulatory variants in cancer.
• 
  Anush Chiappino-Pepe, Stepan Tymoshenko, Meriç Ataman, Dominique Soldati-Favre, Vassily Hatzimanikatis:
  Bioenergetics-based modeling of Plasmodium falciparum metabolism reveals its essential genes, nutritional requirements, and thermodynamic bottlenecks.
• 
  Binwu Zhao, Martien A. Cohen Stuart, Carol K. Hall:
  Navigating in foldonia: Using accelerated molecular dynamics to explore stability, unfolding and self-healing of the β-solenoid structure formed by a silk-like polypeptide.
• 
  Michiel J. M. Niesen, Connie Y. Wang, Reid C. Van Lehn, Thomas Miller III:
  Structurally detailed coarse-grained model for Sec-facilitated co-translational protein translocation and membrane integration.
• 
  Lindsay E. Clegg, Feilim Mac Gabhann:
  A computational analysis of in vivo VEGFR activation by multiple co-expressed ligands.
• 
  Alexander Byers Brummer, Van M. Savage, Brian J. Enquist:
  A general model for metabolic scaling in self-similar asymmetric networks.
• 
  Aurélien Naldi, Romain M. Larive, Urszula Czerwinska, Serge Urbach, Philippe Montcourrier, Christian Roy, Jérôme Solassol, Gilles Freiss, Peter J. Coopman, Ovidiu Radulescu:
  Reconstruction and signal propagation analysis of the Syk signaling network in breast cancer cells.
• 
  Cibele Vieira Falkenberg, Evren U. Azeloglu, Mark Stothers, Thomas J. Deerinck, Yibang Chen, John C. He, Mark H. Ellisman, James C. Hone, Ravi Iyengar, Leslie M. Loew:
  Fragility of foot process morphology in kidney podocytes arises from chaotic spatial propagation of cytoskeletal instability.
• 
  Daniel Howsmon, Uwe Kruger, Stepan Melnyk, S. Jill James, Juergen Hahn:
  Classification and adaptive behavior prediction of children with autism spectrum disorder based upon multivariate data analysis of markers of oxidative stress and DNA methylation.
• 
  Joris Paijmans, David K. Lubensky, Pieter Rein ten Wolde:
  A thermodynamically consistent model of the post-translational Kai circadian clock.
• 
  Johannes Friedrich, Pengcheng Zhou, Liam Paninski:
  Fast online deconvolution of calcium imaging data.
• 
  Tohar S. Yarden, Israel Nelken:
  Stimulus-specific adaptation in a recurrent network model of primary auditory cortex.
• 
  Jonathan T. Young, Tetsuhiro S. Hatakeyama, Kunihiko Kaneko:
  Dynamics robustness of cascading systems.
• 
  Andrew F. Brouwer, Rafael Meza, Marisa C. Eisenberg:
  Parameter estimation for multistage clonal expansion models from cancer incidence data: A practical identifiability analysis.
• 
  Xuejin Li, E. Du, Ming Dao, Subra Suresh, George E. Karniadakis:
  Patient-specific modeling of individual sickle cell behavior under transient hypoxia.
• 
  Julien Vibert, Veronique Thomas-Vaslin:
  Modelling T cell proliferation: Dynamics heterogeneity depending on cell differentiation, age, and genetic background.
• 
  David C. Farrow, Logan C. Brooks, Sangwon Hyun, Ryan J. Tibshirani, Donald S. Burke, Roni Rosenfeld:
  A human judgment approach to epidemiological forecasting.
• 
  Mauricio González-Forero, Timm Faulwasser, Laurent Lehmann:
  A model for brain life history evolution.
• 
  Krzysztof J. Gorgolewski, Fidel Alfaro-Almagro, Tibor Auer, Pierre Bellec, Mihai Capota, M. Mallar Chakravarty, Nathan William Churchill, Alexander Li Cohen, R. Cameron Craddock, Gabriel A. Devenyi, Anders Eklund, Oscar Esteban, Guillaume Flandin, Satrajit S. Ghosh, J. Swaroop Guntupalli, Mark Jenkinson, Anisha Keshavan, Gregory Kiar, Franziskus Liem, Pradeep Reddy Raamana, David Raffelt, Christopher John Steele, Pierre-Olivier Quirion, Robert E. Smith, Stephen C. Strother, Gaël Varoquaux, Yida Wang, Tal Yarkoni, Russell A. Poldrack:
  BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods.
• 
  Rashmi Priya, Guillermo A. Gomez, Srikanth Budnar, Bipul R. Acharya, András Czirók, Alpha S. Yap, Zoltan Neufeld:
  Bistable front dynamics in a contractile medium: Travelling wave fronts and cortical advection define stable zones of RhoA signaling at epithelial adherens junctions.
• 
  Junjiajia Long, Steven W. Zucker, Thierry Emonet:
  Feedback between motion and sensation provides nonlinear boost in run-and-tumble navigation.
• 
  James T. Yurkovich, Laurence Yang, Bernhard O. Palsson:
  Biomarkers are used to predict quantitative metabolite concentration profiles in human red blood cells.
• 
  Emma Saulnier, Olivier Gascuel, Samuel Alizon:
  Inferring epidemiological parameters from phylogenies using regression-ABC: A comparative study.
• 
  Matthew B. Biggs, Jason A. Papin:
  Managing uncertainty in metabolic network structure and improving predictions using EnsembleFBA.
• 
  Amir Bitran, Wei-Yin Chiang, Erel Levine, Mara Prentiss:
  Mechanisms of fast and stringent search in homologous pairing of double-stranded DNA.
• 
  Carlos Pulido-Quetglas, Estel Aparicio-Prat, Carme Arnan, Taisia Polidori, Toni Hermoso, Emilio Palumbo, Julia V. Ponomarenko, Roderic Guigó, Rory Johnson:
  Scalable Design of Paired CRISPR Guide RNAs for Genomic Deletion.
• 
  Erick Andres Perez-Alday, Michael A. Colman, Philip Langley, Henggui Zhang:
  Novel non-invasive algorithm to identify the origins of re-entry and ectopic foci in the atria from 64-lead ECGs: A computational study.
• 
  Etay Hay, Petra Ritter, Nancy J. Lobaugh, Anthony R. McIntosh:
  Multiregional integration in the brain during resting-state fMRI activity.
• 
  Susmita Roy, Heiko Lammert, Ryan L. Hayes, Bin Chen, Regan LeBlanc, T. Kwaku Dayie, José N. Onuchic, Karissa Y. Sanbonmatsu:
  A magnesium-induced triplex pre-organizes the SAM-II riboswitch.
• 
  Paul M. Bays, Ben A. Dowding:
  Fidelity of the representation of value in decision-making.

Volume 13, Number 4, April 2017

Editorial

• 
  Morgan L. Taschuk, Greg Wilson:
  Ten simple rules for making research software more robust.

Review

• 
  Steffen Klamt, Georg Regensburger, Matthias P. Gerstl, Christian Jungreuthmayer, Stefan Schuster, Radhakrishnan Mahadevan, Jürgen Zanghellini, Stefan Müller:
  From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints.

Research Articles

• 
  Andrea K. Barreiro, Cheng Ly:
  When do correlations increase with firing rates in recurrent networks?
• 
  Charles K. Fisher, Thierry Mora, Aleksandra M. Walczak:
  Variable habitat conditions drive species covariation in the human microbiota.
• 
  David J. Albers, Matthew E. Levine, Bruce J. Gluckman, Henry N. Ginsberg, George Hripcsak, Lena Mamykina:
  Personalized glucose forecasting for type 2 diabetes using data assimilation.
• 
  Yunpeng Cai, Wei Zheng, Jin Yao, Yujie Yang, Volker Mai, Qi Mao, Yijun Sun:
  ESPRIT-Forest: Parallel clustering of massive amplicon sequence data in subquadratic time.
• 
  Jonas Ranft, Leandro G. Almeida, Pamela C. Rodriguez, Antoine Triller, Vincent Hakim:
  An aggregation-removal model for the formation and size determination of post-synaptic scaffold domains.
• 
  Jörn Diedrichsen, Nikolaus Kriegeskorte:
  Representational models: A common framework for understanding encoding, pattern-component, and representational-similarity analysis.
• 
  Xiuli Chen, Kieran Mohr, Joseph M. Galea:
  Predicting explorative motor learning using decision-making and motor noise.
• 
  Francesca Mastrogiuseppe, Srdjan Ostojic:
  Intrinsically-generated fluctuating activity in excitatory-inhibitory networks.
• 
  Abdellali Kelil, Benjamin Dubreuil, Emmanuel D. Levy, Stephen W. Michnick:
  Exhaustive search of linear information encoding protein-peptide recognition.
• 
  Mónica L. García-Gómez, Eugenio Azpeitia, Elena R. Álvarez-Buylla:
  A dynamic genetic-hormonal regulatory network model explains multiple cellular behaviors of the root apical meristem of Arabidopsis thaliana.
• 
  Thomas A. Peterson, Iris Ivy M. Gauran, Junyong Park, DoHwan Park, Maricel G. Kann:
  Oncodomains: A protein domain-centric framework for analyzing rare variants in tumor samples.
• 
  Georgia Melagraki, Evangelos Ntougkos, Vagelis Rinotas, Christos Papaneophytou, Georgios Leonis, Thomas M. Mavromoustakos, George Kontopidis, Eleni Douni, Antreas Afantitis, George Kollias:
  Cheminformatics-aided discovery of small-molecule Protein-Protein Interaction (PPI) dual inhibitors of Tumor Necrosis Factor (TNF) and Receptor Activator of NF-κB Ligand (RANKL).
• 
  Tilo Schwalger, Moritz Deger, Wulfram Gerstner:
  Towards a theory of cortical columns: From spiking neurons to interacting neural populations of finite size.
• 
  Joel Zylberberg, Alexandre Pouget, Peter E. Latham, Eric Shea-Brown:
  Robust information propagation through noisy neural circuits.
• 
  Claus Fritzemeier, Daniel Hartleb, Balázs Szappanos, Balázs Papp, Martin J. Lercher:
  Erroneous energy-generating cycles in published genome scale metabolic networks: Identification and removal.
• 
  Imane Boudellioua, Rozaimi B. Mahamad Razali, Maxat Kulmanov, Yasmeen Hashish, Vladimir B. Bajic, Eva Goncalves-Serra, Nadia Schoenmakers, Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf:
  Semantic prioritization of novel causative genomic variants.
• 
  Anish K. Simhal, Cecilia Aguerrebere, Forrest Collman, Joshua T. Vogelstein, Kristina D. Micheva, Richard J. Weinberg, Stephen J. Smith, Guillermo Sapiro:
  Probabilistic fluorescence-based synapse detection.
• 
  Dipjyoti Das, Supravat Dey, Robert C. Brewster, Sandeep Choubey:
  Effect of transcription factor resource sharing on gene expression noise.
• 
  Serena Bradde, Marija Vucelja, Tiberiu Tesileanu, Vijay Balasubramanian:
  Dynamics of adaptive immunity against phage in bacterial populations.
• 
  Yonatan Savir, Alexander Martynov, Michael Springer:
  Achieving global perfect homeostasis through transporter regulation.
• 
  Vijay Singh, Ilya Nemenman:
  Simple biochemical networks allow accurate sensing of multiple ligands with a single receptor.
• 
  Mireya Plass, Simon H. Rasmussen, Anders Krogh:
  Highly accessible AU-rich regions in 3' untranslated regions are hotspots for binding of regulatory factors.
• 
  Yann Zerlaut, Alain Destexhe:
  Heterogeneous firing responses predict diverse couplings to presynaptic activity in mice layer V pyramidal neurons.
• 
  Martin Pirkl, Madeline Diekmann, Marlies van der Wees, Niko Beerenwinkel, Holger Fröhlich, Florian Markowetz:
  Inferring modulators of genetic interactions with epistatic nested effects models.
• 
  Xiaoliang Yang, Zihua Wang, Zhichu Xiang, Dan Li, Zhiyuan Hu, Wei Cui, Lingling Geng, Qiaojun Fang:
  Peptide probes derived from pertuzumab by molecular dynamics modeling for HER2 positive tumor imaging.
• 
  Nicolas Gauvrit, Hector Zenil, Fernando Soler-Toscano, Jean-Paul Delahaye, Peter C. Brugger:
  Human behavioral complexity peaks at age 25.
• 
  Tobias U. Hauser, Michael Moutoussis, Reto Iannaccone, Silvia Brem, Susanne Walitza, Renate Drechsler, Peter Dayan, Raymond J. Dolan:
  Increased decision thresholds enhance information gathering performance in juvenile Obsessive-Compulsive Disorder (OCD).
• 
  Lenna X. Peterson, Amitava Roy, Charles Christoffer, Genki Terashi, Daisuke Kihara:
  Modeling disordered protein interactions from biophysical principles.
• 
  Fayyaz ul Amir Afsar Minhas, Eric D. Ross, Asa Ben-Hur:
  Amino acid composition predicts prion activity.
• 
  Andrew F. Brouwer, Mark H. Weir, Marisa C. Eisenberg, Rafael Meza, Joseph N. S. Eisenberg:
  Dose-response relationships for environmentally mediated infectious disease transmission models.
• 
  Mindaugas Snipas, Lina Rimkute, Tadas Kraujalis, Kestutis Maciunas, Feliksas F. Bukauskas:
  Functional asymmetry and plasticity of electrical synapses interconnecting neurons through a 36-state model of gap junction channel gating.
• 
  Eduardo D. Sontag:
  Dynamic compensation, parameter identifiability, and equivariances.
• 
  Kostas Kouvaris, Jeff Clune, Loizos Kounios, Markus Brede, Richard A. Watson:
  How evolution learns to generalise: Using the principles of learning theory to understand the evolution of developmental organisation.
• 
  Iman Habibi, Raymond Cheong, Tomasz Lipniacki, Andre Levchenko, Effat S. Emamian, Ali Abdi:
  Computation and measurement of cell decision making errors using single cell data.
• 
  Wan Yang, Liang Wen, Shen-Long Li, Kai Chen, Wen-Yi Zhang, Jeffrey Shaman:
  Geospatial characteristics of measles transmission in China during 2005-2014.
• 
  Tom Sumner, Richard J. Orton, Darren M. Green, Rowland R. Kao, Simon Gubbins:
  Quantifying the roles of host movement and vector dispersal in the transmission of vector-borne diseases of livestock.
• 
  Ofir Shukron, David Holcman:
  Transient chromatin properties revealed by polymer models and stochastic simulations constructed from Chromosomal Capture data.
• 
  Wen-Ting Chu, Jane Clarke, Sarah L. Shammas, Jin Wang:
  Role of non-native electrostatic interactions in the coupled folding and binding of PUMA with Mcl-1.
• 
  Viveca Lindahl, Alessandra Villa, Berk Hess:
  Sequence dependency of canonical base pair opening in the DNA double helix.
• 
  Anne-Claire M. F. Martines, Karen van Eunen, Dirk-Jan Reijngoud, Barbara M. Bakker:
  The promiscuous enzyme medium-chain 3-keto-acyl-CoA thiolase triggers a vicious cycle in fatty-acid beta-oxidation.
• 
  Irene Otero-Muras, Pencho Yordanov, Jörg Stelling:
  Chemical Reaction Network Theory elucidates sources of multistability in interferon signaling.
• 
  Hildur Knutsdottir, Cole Zmurchok, Dhananjay Bhaskar, Eirikur Palsson, Damian Dalle Nogare, Ajay B. Chitnis, Leah Edelstein-Keshet:
  Polarization and migration in the zebrafish posterior lateral line system.

Volume 13, Number 5, May 2017

Editorials

• 
  Samuel Demharter, Nicholas Pearce, Kylie Beattie, Isabel Frost, Jinwoo Leem, Alistair Martin, Robert Oppenheimer, Cristian Regep, Tammo Rukat, Alexander Skates, Nicola Trendel, David J. Gavaghan, Charlotte M. Deane, Bernhard Knapp:
  Ten simple rules for surviving an interdisciplinary PhD.
• 
  Megan Yu, Yu-Min Kuo:
  Ten simple rules to make the most out of your undergraduate research career.
• 
  Philip E. Bourne, Jessica K. Polka, Ronald D. Vale, Robert Kiley:
  Ten simple rules to consider regarding preprint submission.

Education

• 
  Björn A. Grüning, Eric Rasche, Boris Rebolledo-Jaramillo, Carl Eberhard, Torsten Houwaart, John Chilton, Nate Coraor, Rolf Backofen, James Taylor, Anton Nekrutenko:
  Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers.

Topic Page

• 
  Rohan Lowe, Neil J. Shirley, Mark Bleackley, Stephen Dolan, Thomas Shafee:
  Transcriptomics technologies.

Research Articles

• 
  Wesley P. Clawson, Nathaniel C. Wright, Ralf Wessel, Woodrow L. Shew:
  Adaptation towards scale-free dynamics improves cortical stimulus discrimination at the cost of reduced detection.
• 
  Semidán Robaina-Estévez, Zoran Nikoloski:
  On the effects of alternative optima in context-specific metabolic model predictions.
• 
  Poppy Miller, Jonathan Marshall, Nigel French, Chris P. Jewell:
  sourceR: Classification and source attribution of infectious agents among heterogeneous populations.
• 
  Pierre Bonnin, Norbert Kern, Neil T. Young, Ian Stansfield, M. Carmen Romano:
  Novel mRNA-specific effects of ribosome drop-off on translation rate and polysome profile.
• 
  Luca Ambrogioni, Marcel A. J. van Gerven, Eric Maris:
  Dynamic decomposition of spatiotemporal neural signals.
• 
  Yogi A. Patel, Ansel George, Alan D. Dorval II, John A. White, David J. Christini, Robert J. Butera:
  Hard real-time closed-loop electrophysiology with the Real-Time eXperiment Interface (RTXI).
• 
  Florian Berger, A. J. Hudspeth:
  Chemomechanical regulation of myosin Ic cross-bridges: Deducing the elastic properties of an ensemble from single-molecule mechanisms.
• 
  Tomi Suomi, Fatemeh Seyednasrollah, Maria K. Jaakkola, Thomas Faux, Laura L. Elo:
  ROTS: An R package for reproducibility-optimized statistical testing.
• 
  Tad Dallas, Andrew W. Park, John M. Drake:
  Predicting cryptic links in host-parasite networks.
• 
  Rita Bhui, Heather N. Hayenga:
  An agent-based model of leukocyte transendothelial migration during atherogenesis.
• 
  Gerald Hahn, Adrián Ponce-Alvarez, Cyril Monier, Giacomo Benvenuti, Arvind Kumar, Frédéric Chavane, Gustavo Deco, Yves Frégnac:
  Spontaneous cortical activity is transiently poised close to criticality.
• 
  Raphaël Mourad, Lang Li, Olivier Cuvier:
  Uncovering direct and indirect molecular determinants of chromatin loops using a computational integrative approach.
• 
  Rodrigo D. Requião, Luiza Fernandes, Henrique José Araujo de Souza, Silvana Rossetto, Tatiana Domitrovic, Fernando L. Palhano:
  Protein charge distribution in proteomes and its impact on translation.
• 
  Eugen Bauer, Johannes Zimmermann, Federico Baldini, Ines Thiele, Christoph Kaleta:
  BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities.
• 
  Ali Nematbakhsh, Wenzhao Sun, Pavel A. Brodskiy, Aboutaleb Amiri, Cody Narciso, Zhiliang Xu, Jeremiah J. Zartman, Mark S. Alber:
  Multi-scale computational study of the mechanical regulation of cell mitotic rounding in epithelia.
• 
  Gabriel F. Dorlhiac, Clyde Fare, Jasper J. van Thor:
  PyLDM - An open source package for lifetime density analysis of time-resolved spectroscopic data.
• 
  Jeffrey P. Nguyen, Ashley N. Linder, George S. Plummer, Joshua W. Shaevitz, Andrew M. Leifer:
  Automatically tracking neurons in a moving and deforming brain.
• 
  Don Klinkenberg, Jantien A. Backer, Xavier Didelot, Caroline Colijn, Jacco Wallinga:
  Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks.
• 
  Zachary R. Sailer, Michael J. Harms:
  High-order epistasis shapes evolutionary trajectories.
• 
  Siu Hung Joshua Chan, Margaret N. Simons, Costas D. Maranas:
  SteadyCom: Predicting microbial abundances while ensuring community stability.
• 
  Jin Hyun Ju, Sushila A. Shenoy, Ronald G. Crystal, Jason G. Mezey:
  An independent component analysis confounding factor correction framework for identifying broad impact expression quantitative trait loci.
• 
  Veith Andreas Weilnhammer, Heiner Stuke, Guido Hesselmann, Philipp Sterzer, Katharina Schmack:
  A predictive coding account of bistable perception - a model-based fMRI study.
• 
  Andreas Tuerk, Gregor Wiktorin, Serhat Güler:
  Mixture models reveal multiple positional bias types in RNA-Seq data and lead to accurate transcript concentration estimates.
• 
  Benjamin Risse, Dimitri Berh, Nils Otto, Christian Klämbt, Xiaoyi Jiang:
  FIMTrack: An open source tracking and locomotion analysis software for small animals.
• 
  Thomas O. Richardson, Jonas Liechti, Nathalie Stroeymeyt, Sebastian Bonhoeffer, Laurent Keller:
  Short-term activity cycles impede information transmission in ant colonies.
• 
  Thomas H. B. FitzGerald, Dorothea Hämmerer, Karl J. Friston, Shu-Chen Li, Raymond J. Dolan:
  Sequential inference as a mode of cognition and its correlates in fronto-parietal and hippocampal brain regions.
• 
  Mikhail Kolmogorov, Eamonn Kennedy, Zhuxin Dong, Gregory Timp, Pavel A. Pevzner:
  Single-molecule protein identification by sub-nanopore sensors.
• 
  Alexander Franks, Edoardo M. Airoldi, Nikolai Slavov:
  Post-transcriptional regulation across human tissues.
• 
  Nicolás Tomasini, Paula Gabriela Ragone, Sébastien Gourbière, Juan Pablo Aparicio, Patricio Diosque:
  Epidemiological modeling of Trypanosoma cruzi: Low stercorarian transmission and failure of host adaptive immunity explain the frequency of mixed infections in humans.
• 
  Eghbal A. Hosseini, Katrina P. Nguyen, Wilsaan M. Joiner:
  The decay of motor adaptation to novel movement dynamics reveals an asymmetry in the stability of motion state-dependent learning.
• 
  Julie L. Chaney, Aaron Steele, Rory Carmichael, Anabel Rodriguez, Alicia T. Specht, Kim Ngo, Jun Li, Scott J. Emrich, Patricia L. Clark:
  Widespread position-specific conservation of synonymous rare codons within coding sequences.
• 
  Christopher M. Jakobson, Danielle Tullman-Ercek, Marilyn F. Slininger, Niall M. Mangan:
  A systems-level model reveals that 1, 2-Propanediol utilization microcompartments enhance pathway flux through intermediate sequestration.
• 
  Mikhail Shugay, Andrew R. Zaretsky, Dmitriy A. Shagin, Irina A. Shagina, Ivan A. Volchenkov, Andrew A. Shelenkov, Mikhail Y. Lebedin, Dmitriy V. Bagaev, Sergey A. Lukyanov, Dmitry M. Chudakov:
  MAGERI: Computational pipeline for molecular-barcoded targeted resequencing.
• 
  William R. Holmes, Jinseok Park, Andre Levchenko, Leah Edelstein-Keshet:
  A mathematical model coupling polarity signaling to cell adhesion explains diverse cell migration patterns.
• 
  Silvan C. Quax, Ole Jensen, Paul H. E. Tiesinga:
  Top-down control of cortical gamma-band communication via pulvinar induced phase shifts in the alpha rhythm.
• 
  Yujiang Wang, Andrew J. Trevelyan, Antonio Valentín, Gonzalo Alarcón, Peter Neal Taylor, Marcus Kaiser:
  Mechanisms underlying different onset patterns of focal seizures.
• 
  Robert C. Jackson, Giovanni Y. Di Veroli, Siang-Boon Koh, Ian Goldlust, Frances M. Richards, Duncan I. Jodrell:
  Modelling of the cancer cell cycle as a tool for rational drug development: A systems pharmacology approach to cyclotherapy.
• 
  Yusuke Matsui, Atsushi Niida, Ryutaro Uchi, Koshi Mimori, Satoru Miyano, Teppei Shimamura:
  phyC: Clustering cancer evolutionary trees.
• 
  Nimrod Shaham, Yoram Burak:
  Slow diffusive dynamics in a chaotic balanced neural network.
• 
  Ying Li, Xueya Zhou, Zichao Zhai, Tingting Li:
  Co-occurring protein phosphorylation are functionally associated.
• 
  Thaddeus Cybulski, Edward S. Boyden, George M. Church, Keith E. J. Tyo, Konrad P. Körding:
  Nucleotide-time alignment for molecular recorders.

Volume 13, Number 6, June 2017

Messages from ISCB

• 
  Christiana N. Fogg, Diane E. Kovats, Bonnie Berger:
  2017 ISCB Accomplishment by a Senior Scientist Award given to Pavel Pevzner.
• 
  Christiana N. Fogg, Diane E. Kovats, Bonnie Berger:
  2017 Outstanding Contributions to ISCB Award: Fran Lewitter.
• 
  Christiana N. Fogg, Diane E. Kovats, Bonnie Berger:
  2017 ISCB Overton Prize awarded to Christoph Bock.
• 
  Christiana N. Fogg, Diane E. Kovats, Bonnie Berger:
  2017 ISCB Innovator Award: Aviv Regev.

Education

• 
  C. Victor Jongeneel, Ovokeraye Achinike-Oduaran, Ezekiel F. Adebiyi, Marion O. Adebiyi, Seun Adeyemi, Bola Akanle, Shaun Aron, Efejiro Ashano, Hocine Bendou, Gerrit Botha, Emile R. Chimusa, Ananyo Choudhury, Ravikiran Donthu, Jenny Drnevich, Oluwadamilare Falola, Christopher J. Fields, Scott Hazelhurst, Liesl Hendry, Itunuoluwa Isewon, Radhika S. Khetani, Judit Kumuthini, Magambo Phillip Kimuda, Lerato E. Magosi, Liudmila S. Mainzer, Suresh Maslamoney, Mamana Mbiyavanga, Ayton Meintjes, Danny Mugutso, Phelelani T. Mpangase, Richard Munthali, Victoria Nembaware, Andrew Ndhlovu, Trust Odia, Adaobi Okafor, Olaleye Oladipo, Sumir Panji, Venesa Pillay, Gloria Rendon, Dhriti Sengupta, Nicola J. Mulder:
  Assessing computational genomics skills: Our experience in the H3ABioNet African bioinformatics network.

Perspective

• 
  Greg Wilson, Jennifer Bryan, Karen Cranston, Justin Kitzes, Lex Nederbragt, Tracy K. Teal:
  Good enough practices in scientific computing.

Reviews

• 
  Xiangxiang Zeng, Wei Lin, Maozu Guo, Quan Zou:
  A comprehensive overview and evaluation of circular RNA detection tools.
• 
  Yuriy Sverchkov, Mark Craven:
  A review of active learning approaches to experimental design for uncovering biological networks.

Research Articles

• 
  Shaohuan Wu, Ke Li, Yingshu Li, Tong Zhao, Ting Li, Yu-Fei Yang, Wenfeng Qian:
  Independent regulation of gene expression level and noise by histone modifications.
• 
  Daniel L. Barton, Silke Henkes, Cornelis J. Weijer, Rastko Sknepnek:
  Active Vertex Model for cell-resolution description of epithelial tissue mechanics.
• 
  Yan Zhang, Shantao Li, Alexej Abyzov, Mark B. Gerstein:
  Landscape and variation of novel retroduplications in 26 human populations.
• 
  Miquel Duran-Frigola, Lydia Siragusa, Eytan Ruppin, Xavier Barril, Gabriele Cruciani, Patrick Aloy:
  Detecting similar binding pockets to enable systems polypharmacology.
• 
  Peyman Khorsand, Alireza Soltani:
  Optimal structure of metaplasticity for adaptive learning.
• 
  Aliza B. Rubenstein, Manasi A. Pethe, Sagar D. Khare:
  MFPred: Rapid and accurate prediction of protein-peptide recognition multispecificity using self-consistent mean field theory.
• 
  Marine Le Morvan, Andrei Yu. Zinovyev, Jean-Philippe Vert:
  NetNorM: Capturing cancer-relevant information in somatic exome mutation data with gene networks for cancer stratification and prognosis.
• 
  Gabriel Koch Ocker, Kresimir Josic, Eric Shea-Brown, Michael A. Buice:
  Linking structure and activity in nonlinear spiking networks.
• 
  Moritz Augustin, Josef Ladenbauer, Fabian Baumann, Klaus Obermayer:
  Low-dimensional spike rate models derived from networks of adaptive integrate-and-fire neurons: Comparison and implementation.
• 
  Peter Marx, Peter Antal, Bence Bolgár, Gyorgy Bagdy, Bill Deakin, Gabriella Juhász:
  Comorbidities in the diseasome are more apparent than real: What Bayesian filtering reveals about the comorbidities of depression.
• 
  Stefano Castellana, Caterina Fusilli, Gianluigi Mazzoccoli, Tommaso Biagini, Daniele Capocefalo, Massimo Carella, Angelo L. Vescovi, Tommaso Mazza:
  High-confidence assessment of functional impact of human mitochondrial non-synonymous genome variations by APOGEE.
• 
  Mathieu Ouellet, Gérald Guillebaud, Valerie Gervais, David Lupien St-Pierre, Marc Germain:
  A novel algorithm identifies stress-induced alterations in mitochondrial connectivity and inner membrane structure from confocal images.
• 
  Rasmus Magnusson, Guido Pio Mariotti, Mattias Köpsén, William Lövfors, Danuta R. Gawel, Rebecka Jörnsten, Jörg Linde, Torbjörn E. M. Nordling, Elin Nyman, Sylvie Schulze, Colm E. Nestor, Huan Zhang, Gunnar Cedersund, Mikael Benson, Andreas Tjärnberg, Mika Gustafsson:
  LASSIM - A network inference toolbox for genome-wide mechanistic modeling.
• 
  Jhuma Das, Andrei A. Aleksandrov, Liying Cui, Lihua He, John R. Riordan, Nikolay V. Dokholyan:
  Transmembrane helical interactions in the CFTR channel pore.
• 
  Hadi Maboudi, Hideaki Shimazaki, Martin Giurfa, Lars Chittka:
  Olfactory learning without the mushroom bodies: Spiking neural network models of the honeybee lateral antennal lobe tract reveal its capacities in odour memory tasks of varied complexities.
• 
  Maxwell B. Wang, Julia P. Owen, Pratik Mukherjee, Ashish Raj:
  Brain network eigenmodes provide a robust and compact representation of the structural connectome in health and disease.
• 
  Jens Christian Claussen, Jurgita Skieceviciene, Jun Wang, Philipp Rausch, Tom H. Karlsen, Wolfgang Lieb, John F. Baines, Andre Franke, Marc-Thorsten Hütt:
  Boolean analysis reveals systematic interactions among low-abundance species in the human gut microbiome.
• 
  Noga Mosheiff, Haggai Agmon, Avraham Moriel, Yoram Burak:
  An efficient coding theory for a dynamic trajectory predicts non-uniform allocation of entorhinal grid cells to modules.
• 
  David L. Gibbs, Ilya Shmulevich:
  Solving the influence maximization problem reveals regulatory organization of the yeast cell cycle.
• 
  En-Yu Lai, Yi-Hau Chen, Kun-Pin Wu:
  A knowledge-based T2-statistic to perform pathway analysis for quantitative proteomic data.
• 
  Michael A. Colman, Haibo Ni, Bo Liang, Nicole Schmitt, Henggui Zhang:
  In silico assessment of genetic variation in KCNA5 reveals multiple mechanisms of human atrial arrhythmogenesis.
• 
  Matthew Chalk, Paul Masset, Sophie Denève, Boris S. Gutkin:
  Sensory noise predicts divisive reshaping of receptive fields.
• 
  Meng Ke, Yafei Yuan, Xin Jiang, Nieng Yan, Haipeng Gong:
  Molecular determinants for the thermodynamic and functional divergence of uniporter GLUT1 and proton symporter XylE.
• 
  Darshan W. Bryner, Stephen Criscione, Andrew Leith, Quyen Huynh, Fred W. Huffer, Nicola Neretti:
  GINOM: A statistical framework for assessing interval overlap of multiple genomic features.
• 
  Rocío Espada, R. Gonzalo Parra, Thierry Mora, Aleksandra M. Walczak, Diego U. Ferreiro:
  Inferring repeat-protein energetics from evolutionary information.
• 
  Samira Abbasi, Amber E. Hudson, Selva K. Maran, Ying Cao, Ataollah Abbasi, Detlef H. Heck, Dieter Jaeger:
  Robust transmission of rate coding in the inhibitory Purkinje cell to cerebellar nuclei pathway in awake mice.
• 
  Qiwen Hu, Eun Ji Kim, Jian Feng, Gregory R. Grant, Elizabeth A. Heller:
  Histone posttranslational modifications predict specific alternative exon subtypes in mammalian brain.
• 
  Dominic G. Whittaker, Haibo Ni, Aziza El Harchi, Jules C. Hancox, Henggui Zhang:
  Atrial arrhythmogenicity of KCNJ2 mutations in short QT syndrome: Insights from virtual human atria.
• 
  Patrick Löffler, Samuel Schmitz, Enrico Hupfeld, Reinhard Sterner, Rainer Merkl:
  Rosetta: MSF: a modular framework for multi-state computational protein design.
• 
  Tobias Kühn, Moritz Helias:
  Locking of correlated neural activity to ongoing oscillations.
• 
  David W. Rogers, Marvin A. Böttcher, Arne Traulsen, Duncan Greig:
  Ribosome reinitiation can explain length-dependent translation of messenger RNA.
• 
  Sonia Cortassa, Steven J. Sollott, Miguel Antonio Aon:
  Mitochondrial respiration and ROS emission during β-oxidation in the heart: An experimental-computational study.
• 
  Andreas Kühne, Urs Mayr, Daniel C. Sévin, Manfred Claassen, Nicola Zamboni:
  Metabolic network segmentation: A probabilistic graphical modeling approach to identify the sites and sequential order of metabolic regulation from non-targeted metabolomics data.
• 
  Ryan R. Wick, Louise M. Judd, Claire L. Gorrie, Kathryn E. Holt:
  Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads.
• 
  Yiming Hu, Qiongshi Lu, Ryan Powles, Xinwei Yao, Can Yang, Fang Fang, Xinran Xu, Hongyu Zhao:
  Leveraging functional annotations in genetic risk prediction for human complex diseases.
• 
  Raony G. C. C. L. Cardenas, Natália Duarte Linhares, Raquel L. Ferreira, Sérgio D. Junho Pena:
  Mendel, MD: A user-friendly open-source web tool for analyzing WES and WGS in the diagnosis of patients with Mendelian disorders.
• 
  Gen Kurosawa, Atsuko Fujioka, Satoshi Koinuma, Atsushi Mochizuki, Yasufumi Shigeyoshi:
  Temperature-amplitude coupling for stable biological rhythms at different temperatures.
• 
  Diego A. Gutnisky, Jianing Yu, Samuel Andrew Hires, Minh-Son To, Michael Ross Bale, Karel Svoboda, David Golomb:
  Mechanisms underlying a thalamocortical transformation during active tactile sensation.
• 
  Sebastián A. Romano, Verónica Pérez-Schuster, Adrien Jouary, Jonathan Boulanger-Weill, Alessia Candeo, Thomas Pietri, Germán Sumbre:
  An integrated calcium imaging processing toolbox for the analysis of neuronal population dynamics.
• 
  Mattias Frånberg, Rona J. Strawbridge, Anders Hamsten, PROCARDIS consortium, Ulf de Faire, Jens Lagergren, Bengt Sennblad:
  Fast and general tests of genetic interaction for genome-wide association studies.
• 
  Caroline Baroukh, Violette Turon, Olivier Bernard:
  Dynamic metabolic modeling of heterotrophic and mixotrophic microalgal growth on fermentative wastes.
• 
  Jae Kyoung Kim, Eduardo D. Sontag:
  Reduction of multiscale stochastic biochemical reaction networks using exact moment derivation.
• 
  David M. Fox, Hua-an Tseng, Tomasz G. Smolinski, Horacio G. Rotstein, Farzan Nadim:
  Mechanisms of generation of membrane potential resonance in a neuron with multiple resonant ionic currents.
• 
  Jim R. Potvin, Andrew J. Fuglevand:
  A motor unit-based model of muscle fatigue.
• 
  Anthony R. Bradley, Alexander S. Rose, Antonín Pavelka, Yana Valasatava, Jose M. Duarte, Andreas Prlic, Peter W. Rose:
  MMTF - An efficient file format for the transmission, visualization, and analysis of macromolecular structures.
• 
  Sheng Wang, Jian Peng:
  Network-assisted target identification for haploinsufficiency and homozygous profiling screens.
• 
  Daniel Durstewitz:
  A state space approach for piecewise-linear recurrent neural networks for identifying computational dynamics from neural measurements.
• 
  Nargesalsadat Dorratoltaj, Achla Marathe, Bryan L. Lewis, Samarth Swarup, Stephen G. Eubank, Kaja M. Abbas:
  Epidemiological and economic impact of pandemic influenza in Chicago: Priorities for vaccine interventions.
• 
  Patricia Wollstadt, Kristin K. Sellers, Lucas Rudelt, Viola Priesemann, Axel Hutt, Flavio Fröhlich, Michael Wibral:
  Breakdown of local information processing may underlie isoflurane anesthesia effects.

Volume 13, Number 7, July 2017

Research Articles

• 
  Murodzhon Akhmedov, Amanda J. Kedaigle, Renan Escalante Chong, Roberto Montemanni, Francesco Bertoni, Ernest Fraenkel, Ivo Kwee:
  PCSF: An R-package for network-based interpretation of high-throughput data.
• 
  John H. C. Palmer, Adam Keane, Pulin Gong:
  Learning and executing goal-directed choices by internally generated sequences in spiking neural circuits.
• 
  Oliver J. Maclaren, Aimée Parker, Carmen Pin, Simon R. Carding, Alastair J. M. Watson, Alexander G. Fletcher, Helen M. Byrne, Philip K. Maini:
  A hierarchical Bayesian model for understanding the spatiotemporal dynamics of the intestinal epithelium.
• 
  Ethan Oblak, Jarrod A. Lewis-Peacock, James S. Sulzer:
  Self-regulation strategy, feedback timing and hemodynamic properties modulate learning in a simulated fMRI neurofeedback environment.
• 
  Joshua G. A. Cashaback, Heather R. McGregor, Ayman Mohatarem, Paul L. Gribble:
  Dissociating error-based and reinforcement-based loss functions during sensorimotor learning.
• 
  Saeed Omidi, Mihaela Zavolan, Mikhail Pachkov, Jeremie Breda, Severin Berger, Erik van Nimwegen:
  Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors.
• 
  Zixuan Cang, Guo-Wei Wei:
  TopologyNet: Topology based deep convolutional and multi-task neural networks for biomolecular property predictions.
• 
  Vehpi Yildirim, Suryakiran Vadrevu, Benjamin Thompson, Leslie S. Satin, Richard Bertram:
  Upregulation of an inward rectifying K+ channel can rescue slow Ca2+ oscillations in K(ATP) channel deficient pancreatic islets.
• 
  Xinxian Shao, Andrew Mugler, Justin Kim, Ha Jun Jeong, Bruce R. Levin, Ilya Nemenman:
  Growth of bacteria in 3-d colonies.
• 
  Davide Lonardoni, Hayder Amin, Stefano Di Marco, Alessandro Maccione, Luca Berdondini, Thierry Nieus:
  Recurrently connected and localized neuronal communities initiate coordinated spontaneous activity in neuronal networks.
• 
  Lukas Bartonek, Bojan Zagrovic:
  mRNA/protein sequence complementarity and its determinants: The impact of affinity scales.
• 
  Peter K. Eastman, Jason M. Swails, John D. Chodera, Robert McGibbon, Yutong Zhao, Kyle Beauchamp, Lee-Ping Wang, Andrew C. Simmonett, Matthew P. Harrigan, Chaya D. Stern, Rafal P. Wiewiora, Bernard R. Brooks, Vijay S. Pande:
  OpenMM 7: Rapid development of high performance algorithms for molecular dynamics.
• 
  Christopher Finn McQuaid, Frank van den Bosch, Anna Szyniszewska, Titus Alicai, Anthony Pariyo, Patrick Chiza Chikoti, Christopher A. Gilligan:
  Spatial dynamics and control of a crop pathogen with mixed-mode transmission.
• 
  Johan D. Carlin, Nikolaus Kriegeskorte:
  Adjudicating between face-coding models with individual-face fMRI responses.
• 
  Haruo Hosoya, Aapo Hyvärinen:
  A mixture of sparse coding models explaining properties of face neurons related to holistic and parts-based processing.
• 
  Giorgos Minas, David A. Rand:
  Long-time analytic approximation of large stochastic oscillators: Simulation, analysis and inference.
• 
  Bin Shao, Haiyu Yuan, Rongfei Zhang, Xuan Wang, Shuwen Zhang, Qi Ouyang, Nan Hao, Chunxiong Luo:
  Reconstructing the regulatory circuit of cell fate determination in yeast mating response.
• 
  Joanna Jedrzejewska-Szmek, Vincent Luczak, Ted Abel, Kim T. Blackwell:
  β-adrenergic signaling broadly contributes to LTP induction.
• 
  Koon-Kiu Yan, Shaoke Lou, Mark Gerstein:
  MrTADFinder: A network modularity based approach to identify topologically associating domains in multiple resolutions.
• 
  Warren D. Anderson, Danielle DeCicco, James S. Schwaber, Rajanikanth Vadigepalli:
  A data-driven modeling approach to identify disease-specific multi-organ networks driving physiological dysregulation.
• 
  Carla Aimé, Jean-Baptiste André, Michel Raymond:
  Grandmothering and cognitive resources are required for the emergence of menopause and extensive post-reproductive lifespan.
• 
  Shihao Yang, Samuel C. Kou, Fred Lu, John S. Brownstein, Nicholas Brooke, Mauricio Santillana:
  Advances in using Internet searches to track dengue.
• 
  James R. H. Cooke, Arjan C. ter Horst, Robert J. van Beers, W. Pieter Medendorp:
  Effect of depth information on multiple-object tracking in three dimensions: A probabilistic perspective.
• 
  Meriç Ataman, Vassily Hatzimanikatis:
  lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target metabolites.
• 
  Meriç Ataman, Daniel F. Hernandez Gardiol, Georgios Fengos, Vassily Hatzimanikatis:
  redGEM: Systematic reduction and analysis of genome-scale metabolic reconstructions for development of consistent core metabolic models.
• 
  François Serra, Davide Baù, Mike Goodstadt, David Castillo, Guillaume J. Filion, Marc A. Martí-Renom:
  Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors.
• 
  Yang Li, Alexis A. Jourdain, Sarah E. Calvo, Jun S. Liu, Vamsi K. Mootha:
  CLIC, a tool for expanding biological pathways based on co-expression across thousands of datasets.
• 
  Marta Lukacisinová, Sebastian Novak, Tiago Paixão:
  Stress-induced mutagenesis: Stress diversity facilitates the persistence of mutator genes.
• 
  Joni Vuorio, Ilpo Vattulainen, Hector Martinez-Seara:
  Atomistic fingerprint of hyaluronan-CD44 binding.
• 
  Connor Sharp, James E. Bray, Nicholas G. Housden, Martin C. J. Maiden, Colin Kleanthous:
  Diversity and distribution of nuclease bacteriocins in bacterial genomes revealed using Hidden Markov Models.
• 
  Nick Fyson, Jerry King, Thomas Belcher, Andrew Preston, Caroline Colijn:
  A curated genome-scale metabolic model of Bordetella pertussis metabolism.
• 
  András Szabó, Roeland M. H. Merks:
  Blood vessel tortuosity selects against evolution of aggressive tumor cells in confined tissue environments: A modeling approach.
• 
  Laurent Mackay, Hana Zemkova, Stanko S. Stojilkovic, Arthur Sherman, Anmar Khadra:
  Deciphering the regulation of P2X4 receptor channel gating by ivermectin using Markov models.
• 
  Mathieu Bottier, Sylvain Blanchon, Gabriel Pelle, Emilie Bequignon, Daniel Isabey, André Coste, Estelle Escudier, James B. Grotberg, Jean-François Papon, Marcel Filoche, Bruno Louis:
  A new index for characterizing micro-bead motion in a flow induced by ciliary beating: Part I, experimental analysis.
• 
  Mathieu Bottier, Marta Peña Fernández, Gabriel Pelle, Daniel Isabey, Bruno Louis, James B. Grotberg, Marcel Filoche:
  A new index for characterizing micro-bead motion in a flow induced by ciliary beating: Part II, modeling.
• 
  Aseel Shomar, Lukas Geyrhofer, Noam E. Ziv, Naama Brenner:
  Cooperative stochastic binding and unbinding explain synaptic size dynamics and statistics.
• 
  Gamze Gürsoy, Yun Xu, Jie Liang:
  Spatial organization of the budding yeast genome in the cell nucleus and identification of specific chromatin interactions from multi-chromosome constrained chromatin model.
• 
  Sang-Woo Lee, Yoshihiro Morishita:
  Possible roles of mechanical cell elimination intrinsic to growing tissues from the perspective of tissue growth efficiency and homeostasis.
• 
  Franz Hamilton, Alun L. Lloyd, Kevin B. Flores:
  Hybrid modeling and prediction of dynamical systems.
• 
  Muhammet Uzuntarla, Ernest Barreto, Joaquín J. Torres:
  Inverse stochastic resonance in networks of spiking neurons.
• 
  Cesare V. Parise, Marc O. Ernst:
  Noise, multisensory integration, and previous response in perceptual disambiguation.
• 
  Wilsaan M. Joiner, Gary C. Sing, Maurice A. Smith:
  Temporal specificity of the initial adaptive response in motor adaptation.
• 
  Shuxiang Ruan, Gary D. Stormo:
  Inherent limitations of probabilistic models for protein-DNA binding specificity.
• 
  Roman A. Sandler, Dustin Fetterhoff, Robert E. Hampson, Sam A. Deadwyler, Vasilis Z. Marmarelis:
  Cannabinoids disrupt memory encoding by functionally isolating hippocampal CA1 from CA3.
• 
  Hua-Qing Wu, Mei-Ling Cheng, Jin-Mei Lai, Hsuan-Hui Wu, Meng-Chun Chen, Wen-Huan Liu, Wu-Hsiung Wu, Peter Mu-Hsin Chang, Chi-Ying F. Huang, Ann-Ping Tsou, Ming-Shi Shiao, Feng-Sheng Wang:
  Flux balance analysis predicts Warburg-like effects of mouse hepatocyte deficient in miR-122a.
• 
  Mikhail V. Pogorelyy, Yuval Elhanati, Quentin Marcou, Anastasiia L. Sycheva, Ekaterina Komech, Vadim I. Nazarov, Olga V. Britanova, Dmitry M. Chudakov, Ilgar Z. Mamedov, Yuri B. Lebedev, Thierry Mora, Aleksandra M. Walczak:
  Persisting fetal clonotypes influence the structure and overlap of adult human T cell receptor repertoires.
• 
  Jonathan Diamond, Daniel M. Wolpert, J. Randall Flanagan:
  Rapid target foraging with reach or gaze: The hand looks further ahead than the eye.
• 
  Kamran Kaveh, Yutaka Takahashi, Michael Farrar, Guy Storme, Marcucci Guido, Jamie Piepenburg, Jackson Penning, Jasmine Foo, Kevin Leder, Susanta K. Hui:
  Combination therapeutics of Nilotinib and radiation in acute lymphoblastic leukemia as an effective method against drug-resistance.
• 
  William Gilpin, Marcus W. Feldman:
  A phase transition induces chaos in a predator-prey ecosystem with a dynamic fitness landscape.
• 
  Magdalena Zwierzyna, John P. Overington:
  Classification and analysis of a large collection of in vivo bioassay descriptions.
• 
  Xiaoping Liu, Xiao Chang, Rui Liu, Xiangtian Yu, Luonan Chen, Kazuyuki Aihara:
  Quantifying critical states of complex diseases using single-sample dynamic network biomarkers.
• 
  Dariusz Matlak, Ewa Szczurek:
  Epistasis in genomic and survival data of cancer patients.
• 
  Pekka Marttinen, William P. Hanage:
  Speciation trajectories in recombining bacterial species.
• 
  Alexandra Vormberg, Felix Effenberger, Julia Muellerleile, Hermann Cuntz:
  Universal features of dendrites through centripetal branch ordering.
• 
  Juliana C. Wortman, Marcos Nahmad, Pengcheng Zhang, Arthur D. Lander, Clare C. Yu:
  Expanding signaling-molecule wavefront model of cell polarization in the Drosophila wing primordium.

Volume 13, Number 8, August 2017

Editorials

• 
  Toby P. Aicher, Dániel L. Barabási, Benjamin D. Harris, Ajay Nadig, Kaitlin L. Williams:
  Ten simple rules for getting the most out of a summer laboratory internship.
• 
  Chiara Bruckmann, Endre Sebestyén:
  Ten simple rules to initiate and run a postdoctoral association.

Education

• 
  Laura R. Emery, Sarah L. Morgan:
  The application of project-based learning in bioinformatics training.

Research Articles

• 
  Michael A. Colman, Christian Pinali, Andrew W. Trafford, Henggui Zhang, Ashraf Kitmitto:
  A computational model of spatio-temporal cardiac intracellular calcium handling with realistic structure and spatial flux distribution from sarcoplasmic reticulum and t-tubule reconstructions.
• 
  Lore Thaler, Galen M. Reich, Xinyu Zhang, Dinghe Wang, Graeme E. Smith, Tao Zeng, Raja Syamsul Azmir Raja Abdullah, Mikhail Cherniakov, Christopher J. Baker, Daniel Kish, Michail Antoniou:
  Mouth-clicks used by blind expert human echolocators - signal description and model based signal synthesis.
• 
  Mohamed A. Ghadie, Luke Lambourne, Marc Vidal, Yu Xia:
  Domain-based prediction of the human isoform interactome provides insights into the functional impact of alternative splicing.
• 
  Idan Alter, Loren Gragert, Stephanie Fingerson, Martin Maiers, Yoram Louzoun:
  HLA class I haplotype diversity is consistent with selection for frequent existing haplotypes.
• 
  Alexander J. Mastin, Frank van den Bosch, Timothy R. Gottwald, Vasthi Alonso Chávez, Stephen Parnell:
  A method of determining where to target surveillance efforts in heterogeneous epidemiological systems.
• 
  Jairo A. Navarrete, Pablo Dartnell:
  Towards a category theory approach to analogy: Analyzing re-representation and acquisition of numerical knowledge.
• 
  Vikranth R. Bejjanki, Rava Azeredo da Silveira, Jonathan D. Cohen, Nicholas B. Turk-Browne:
  Noise correlations in the human brain and their impact on pattern classification.
• 
  Vickie Li, Santiago Herce Castañón, Joshua A. Solomon, Hildward Vandormael, Christopher Summerfield:
  Robust averaging protects decisions from noise in neural computations.
• 
  Peter J. Hellyer, Claudia Clopath, Angie A. Kehagia, Federico E. Turkheimer, Robert Leech:
  From homeostasis to behavior: Balanced activity in an exploration of embodied dynamic environmental-neural interaction.
• 
  Mark G. F. Sun, Philip M. Kim:
  Data driven flexible backbone protein design.
• 
  Narimane Nekkab, Pascal Astagneau, Laura Temime, Pascal Crépey:
  Spread of hospital-acquired infections: A comparison of healthcare networks.
• 
  Christopher B. Massa, Angela M. Groves, Smita U. Jaggernauth, Debra L. Laskin, Andrew J. Gow:
  Histologic and biochemical alterations predict pulmonary mechanical dysfunction in aging mice with chronic lung inflammation.
• 
  Michal Bassani-Sternberg, Chloé Chong, Philippe Guillaume, Marthe Solleder, HuiSong Pak, Philippe O. Gannon, Lana E. Kandalaft, George Coukos, David Gfeller:
  Deciphering HLA-I motifs across HLA peptidomes improves neo-antigen predictions and identifies allostery regulating HLA specificity.
• 
  Matías A. Goldin, Gabriel B. Mindlin:
  Temperature manipulation of neuronal dynamics in a forebrain motor control nucleus.
• 
  Jonas Liechti, Gabriel E. Leventhal, Sebastian Bonhoeffer:
  Host population structure impedes reversion to drug sensitivity after discontinuation of treatment.
• 
  Daniel R. Amor, Raúl Montañez, Salva Duran-Nebreda, Ricard V. Solé:
  Spatial dynamics of synthetic microbial mutualists and their parasites.
• 
  Wesley M. Botello-Smith, Abdelaziz Alsamarah, Payal Chatterjee, Chen Xie, Jerome J. Lacroix, Jijun Hao, Yun Lyna Luo:
  Polymodal allosteric regulation of Type 1 Serine/Threonine Kinase Receptors via a conserved electrostatic lock.
• 
  Remo Monti, Iros Barozzi, Marco Osterwalder, Elizabeth Lee, Momoe Kato, Tyler H. Garvin, Ingrid Plajzer-Frick, Catherine S. Pickle, Jennifer A. Akiyama, Veena Afzal, Niko Beerenwinkel, Diane E. Dickel, Axel Visel, Len A. Pennacchio:
  Limb-Enhancer Genie: An accessible resource of accurate enhancer predictions in the developing limb.
• 
  Xin Chen, Jeffrey M. Beck, John M. Pearson:
  Neuron's eye view: Inferring features of complex stimuli from neural responses.
• 
  David Amar, Ron Shamir, Daniel Yekutieli:
  Extracting replicable associations across multiple studies: Empirical Bayes algorithms for controlling the false discovery rate.
• 
  Lingfei Wang, Tom Michoel:
  Efficient and accurate causal inference with hidden confounders from genome-transcriptome variation data.
• 
  Julia Fukuyama, Laurie Rumker, Kris Sankaran, Pratheepa Jeganathan, Les Dethlefsen, David A. Relman, Susan P. Holmes:
  Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment.
• 
  Elsje Pienaar, Jansy Sarathy, Brendan Prideaux, Jillian Dietzold, Véronique Dartois, Denise E. Kirschner, Jennifer J. Linderman:
  Comparing efficacies of moxifloxacin, levofloxacin and gatifloxacin in tuberculosis granulomas using a multi-scale systems pharmacology approach.
• 
  Marinho A. Lopes, Mark P. Richardson, Eugenio Abela, Christian Rummel, Kaspar Schindler, Marc Goodfellow, John R. Terry:
  An optimal strategy for epilepsy surgery: Disruption of the rich-club?
• 
  Maike K. Aurich, Ronan M. T. Fleming, Ines Thiele:
  A systems approach reveals distinct metabolic strategies among the NCI-60 cancer cell lines.
• 
  Stefano Palminteri, Germain Lefebvre, Emma J. Kilford, Sarah-Jayne Blakemore:
  Confirmation bias in human reinforcement learning: Evidence from counterfactual feedback processing.
• 
  Honda Naoki:
  Revisiting chemoaffinity theory: Chemotactic implementation of topographic axonal projection.
• 
  Alexander V. Maltsev, Victor A. Maltsev, Michael D. Stern:
  Stabilization of diastolic calcium signal via calcium pump regulation of complex local calcium releases and transient decay in a computational model of cardiac pacemaker cell with individual release channels.
• 
  Anna Cichonska, Balaguru Ravikumar, Elina Parri, Sanna Timonen, Tapio Pahikkala, Antti Airola, Krister Wennerberg, Juho Rousu, Tero Aittokallio:
  Computational-experimental approach to drug-target interaction mapping: A case study on kinase inhibitors.
• 
  Grégory Dumont, Alexandre Payeur, André Longtin:
  A stochastic-field description of finite-size spiking neural networks.
• 
  Johannes Friedrich, Weijian Yang, Daniel Soudry, Yu Mu, Misha B. Ahrens, Rafael Yuste, Darcy S. Peterka, Liam Paninski:
  Multi-scale approaches for high-speed imaging and analysis of large neural populations.
• 
  Tjibbe Donker, Timo Smieszek, Katherine L. Henderson, Alan P. Johnson, A. Sarah Walker, Julie V. Robotham:
  Measuring distance through dense weighted networks: The case of hospital-associated pathogens.
• 
  Eilon Sharon, Hao Shi, Sandhya Kharbanda, Winston Koh, Lance R. Martin, Kiran K. Khush, Hannah A. Valantine, Jonathan K. Pritchard, Iwijn De Vlaminck:
  Quantification of transplant-derived circulating cell-free DNA in absence of a donor genotype.
• 
  Jinyuan Yan, Maxime Deforet, Kerry E. Boyle, Rayees Rahman, Raymond Liang, Chinweike Okegbe, Lars E. P. Dietrich, Weigang Qiu, João B. Xavier:
  Bow-tie signaling in c-di-GMP: Machine learning in a simple biochemical network.
• 
  Eduardo A. Aponte, Dario Schöbi, Klaas E. Stephan, Jakob Heinzle:
  The Stochastic Early Reaction, Inhibition, and late Action (SERIA) model for antisaccades.
• 
  Quan Wang, Constantin A. Rothkopf, Jochen Triesch:
  A model of human motor sequence learning explains facilitation and interference effects based on spike-timing dependent plasticity.
• 
  Philippe Gambette, Leo van Iersel, Mark Jones, Manuel Lafond, Fabio Pardi, Céline Scornavacca:
  Rearrangement moves on rooted phylogenetic networks.

Volume 13, Number 9, September 2017

Editorials

• 
  Brett Mensh, Konrad P. Körding:
  Ten simple rules for structuring papers.
• 
  Kristyn S. Masters, Pamela K. Kreeger:
  Ten simple rules for developing a mentor-mentee expectations document.
• 
  Ernesto Ruelas Inzunza, Gabriela I. Salazar-Rivera, Magdiel Láinez, María Guadalupe Ruiz-Gómez, Carlo A. Domínguez-Eusebio, Griselda Cristóbal-Sánchez, Issaac A. Teodosio Faustino, Edel Pérez-López, Meagan L. Campbell, Marcus Vinicius Merfa, Ivonne Tatiana Latorre Beltrán, Fernanda Armas, Claudio Mota-Vargas:
  Ten simple rules for successfully completing a graduate degree in Latin America.
• 
  Ruth Nussinov, Jason A. Papin:
  How can computation advance microbiome research?

Education

• 
  Rafael Hernández-de-Diego, Etienne P. de Villiers, Tomas Klingström, Hadrien Gourlé, Ana Conesa, Erik Bongcam-Rudloff:
  The eBioKit, a stand-alone educational platform for bioinformatics.

Research Articles

• 
  Pavel Sanda, Steven Skorheim, Maxim Bazhenov:
  Multi-layer network utilizing rewarded spike time dependent plasticity to learn a foraging task.
• 
  Chiara Damiani, Riccardo Colombo, Daniela Gaglio, Fabrizia Mastroianni, Dario Pescini, Hans V. Westerhoff, Giancarlo Mauri, Marco Vanoni, Lilia Alberghina:
  A metabolic core model elucidates how enhanced utilization of glucose and glutamine, with enhanced glutamine-dependent lactate production, promotes cancer cell growth: The WarburQ effect.
• 
  Julie J. Lee, Mehdi Keramati:
  Flexibility to contingency changes distinguishes habitual and goal-directed strategies in humans.
• 
  Marianne Bauer, Isabella R. Graf, Vudtiwat Ngampruetikorn, Greg J. Stephens, Erwin Frey:
  Exploiting ecology in drug pulse sequences in favour of population reduction.
• 
  André Voigt, Katja Nowick, Eivind Almaas:
  A composite network of conserved and tissue specific gene interactions reveals possible genetic interactions in glioma.
• 
  Vanessa Dumeaux, Bjørn Fjukstad, Hans E. Fjosne, Jan-Ole Frantzen, Marit Muri Holmen, Enno Rodegerdts, Ellen Schlichting, Anne-Lise Børresen-Dale, Lars Ailo Bongo, Eiliv Lund, Michael T. Hallett:
  Interactions between the tumor and the blood systemic response of breast cancer patients.
• 
  Michiel van Boven, Jan van de Kassteele, Marjolein J. Korndewal, Christiaan H. van Dorp, Mirjam E. Kretzschmar, Fiona van der Klis, Hester E. de Melker, Ann C. Vossen, Debbie van Baarle:
  Infectious reactivation of cytomegalovirus explaining age- and sex-specific patterns of seroprevalence.
• 
  Stefan M. Kallenberger, Anne L. Unger, Stefan Legewie, Konstantinos Lymperopoulos, Ursula Klingmüller, Roland Eils, Dirk-Peter Herten:
  Correlated receptor transport processes buffer single-cell heterogeneity.
• 
  Evan M. Russek, Ida Momennejad, Matthew M. Botvinick, Samuel J. Gershman, Nathaniel D. Daw:
  Predictive representations can link model-based reinforcement learning to model-free mechanisms.
• 
  Kyle P. Blum, Boris Lamotte d'Incamps, Daniel Zytnicki, Lena H. Ting:
  Force encoding in muscle spindles during stretch of passive muscle.
• 
  Cai Wingfield, Li Su, Xunying Liu, Chao Zhang, Philip C. Woodland, Andrew Thwaites, Elisabeth Fonteneau, William D. Marslen-Wilson:
  Relating dynamic brain states to dynamic machine states: Human and machine solutions to the speech recognition problem.
• 
  Harang Ju, Costa M. Colbert, William B. Levy:
  Limited synapse overproduction can speed development but sometimes with long-term energy and discrimination penalties.
• 
  Willem de Haan, Elisabeth C. W. van Straaten, Alida A. Gouw, Cornelis J. Stam:
  Altering neuronal excitability to preserve network connectivity in a computational model of Alzheimer's disease.
• 
  Mark D. McDonnell, Bruce P. Graham:
  Phase changes in neuronal postsynaptic spiking due to short term plasticity.
• 
  Shyam Kumar Sudhakar, Sungho Hong, Ivan Raikov, Rodrigo Publio, Claus Lang, Thomas G. Close, Daqing Guo, Mario Negrello, Erik De Schutter:
  Spatiotemporal network coding of physiological mossy fiber inputs by the cerebellar granular layer.
• 
  Jean-Louis Dinh, Etienne Farcot, Charlie Hodgman:
  The logic of the floral transition: Reverse-engineering the switch controlling the identity of lateral organs.
• 
  Jan Humplik, Gasper Tkacik:
  Probabilistic models for neural populations that naturally capture global coupling and criticality.
• 
  Kaido Lepik, Tarmo Annilo, Viktorija Kukuskina, eQTLGen Consortium, Kai Kisand, Zoltán Kutalik, Pärt Peterson, Hedi Peterson:
  C-reactive protein upregulates the whole blood expression of CD59 - an integrative analysis.
• 
  Paul Villoutreix, Joakim Andén, Bomyi Lim, Hang Lu, Ioannis G. Kevrekidis, Amit Singer, Stanislav Y. Shvartsman:
  Synthesizing developmental trajectories.
• 
  Alexey A. Gritsenko, Shira Weingarten-Gabbay, Shani Elias-Kirma, Ronit Nir, Dick de Ridder, Eran Segal:
  Sequence features of viral and human Internal Ribosome Entry Sites predictive of their activity.
• 
  Yuewu Liu, Xiufen Zou:
  Mathematical modeling and quantitative analysis of HIV-1 Gag trafficking and polymerization.
• 
  Mudassar Iqbal, Neil Doherty, Anna M. L. Page, Saara N. A. Qazi, Ishan Ajmera, Peter A. Lund, Theodore Kypraios, David J. Scott, Philip J. Hill, Dov J. Stekel:
  Reconstructing promoter activity from Lux bioluminescent reporters.
• 
  Kirill Lykov, Yasaman Nematbakhsh, Menglin Shang, Chwee Teck Lim, Igor V. Pivkin:
  Probing eukaryotic cell mechanics via mesoscopic simulations.
• 
  Sirin Yonucu, Defne Yiotalmaz, Colin Phipps, Mehmet Burcin Unlu, Mohammad Kohandel:
  Quantifying the effects of antiangiogenic and chemotherapy drug combinations on drug delivery and treatment efficacy.
• 
  Burcu Tepekule, Hildegard Uecker, Isabel Derungs, Antoine Frénoy, Sebastian Bonhoeffer:
  Modeling antibiotic treatment in hospitals: A systematic approach shows benefits of combination therapy over cycling, mixing, and mono-drug therapies.
• 
  Jianfei Hu, Eli Boritz, William Wylie, Daniel C. Douek:
  Stochastic principles governing alternative splicing of RNA.
• 
  María E. Soler-Oliva, José A. Guerrero-Martínez, Valentina Bachetti, José C. Reyes:
  Analysis of the relationship between coexpression domains and chromatin 3D organization.
• 
  Kiesha Prem, Alex R. Cook, Mark Jit:
  Projecting social contact matrices in 152 countries using contact surveys and demographic data.
• 
  Shintaroh Kubo, Wenfei Li, Shoji Takada:
  Allosteric conformational change cascade in cytoplasmic dynein revealed by structure-based molecular simulations.
• 
  Xiaosheng Luo, Liufang Xu, Bo Han, Jin Wang:
  Funneled potential and flux landscapes dictate the stabilities of both the states and the flow: Fission yeast cell cycle.
• 
  Petter Holme, Nelly Litvak:
  Cost-efficient vaccination protocols for network epidemiology.
• 
  Siri Camee van Keulen, Ursula Rothlisberger:
  Exploring the inhibition mechanism of adenylyl cyclase type 5 by n-terminal myristoylated Gαi1.
• 
  Jaideep Joshi, Iain D. Couzin, Simon A. Levin, Vishwesha Guttal:
  Mobility can promote the evolution of cooperation via emergent self-assortment dynamics.
• 
  Piyush Labhsetwar, Marcelo C. R. Melo, John A. Cole, Zaida Luthey-Schulten:
  Population FBA predicts metabolic phenotypes in yeast.
• 
  Yanju Liu, Sheryl M. Gracewski, Jong-Hoon Nam:
  Two passive mechanical conditions modulate power generation by the outer hair cells.
• 
  Kevin D. Murray, Christfried Webers, Cheng Soon Ong, Justin O. Borevitz, Norman Warthmann:
  kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity.
• 
  Minseung Kim, Ameen Eetemadi, Ilias Tagkopoulos:
  DeepPep: Deep proteome inference from peptide profiles.
• 
  Abed Ghanbari, Aleksey Malyshev, Maxim Volgushev, Ian H. Stevenson:
  Estimating short-term synaptic plasticity from pre- and postsynaptic spiking.
• 
  Pietro Balbi, Paolo Massobrio, Jeanette Hellgren Kotaleski:
  A single Markov-type kinetic model accounting for the macroscopic currents of all human voltage-gated sodium channel isoforms.
• 
  Richard B. Greaves, Sabine Dietmann, Austin Smith, Susan Stepney, Julianne D. Halley:
  A conceptual and computational framework for modelling and understanding the non-equilibrium gene regulatory networks of mouse embryonic stem cells.
• 
  Volker Hofmann, Maurice J. Chacron:
  Differential receptive field organizations give rise to nearly identical neural correlations across three parallel sensory maps in weakly electric fish.

Volume 13, Number 10, October 2017

Editorials

• 
  Trey Ideker, Ruth Nussinov:
  Network approaches and applications in biology.
• 
  William Stafford Noble:
  Ten simple rules for writing a response to reviewers.
• 
  Philip E. Bourne:
  Ten simple rules in considering a career in academia versus government.

Education Articles

• 
  Lindsay Barone, Jason Williams, David Micklos:
  Unmet needs for analyzing biological big data: A survey of 704 NSF principal investigators.
• 
  Andreas Handel:
  Learning infectious disease epidemiology in a modern framework.
• 
  Kim T. Gurwitz, Shaun Aron, Sumir Panji, Suresh Maslamoney, Pedro L. Fernandes, David P. Judge, Amel Ghouila, Jean-Baka Domelevo Entfellner, Fatma Z. Guerfali, Colleen Saunders, Ahmed Mansour Alzohairy, Samson P. Salifu, Rehab Ahmed, Ruben Cloete, Jonathan K. Kayondo, Deogratius Ssemwanga, Nicola J. Mulder, H3ABioNet Consortium:
  Designing a course model for distance-based online bioinformatics training in Africa: The H3ABioNet experience.

Review

• 
  Emine Guven-Maiorov, Chung-Jung Tsai, Ruth Nussinov:
  Structural host-microbiota interaction networks.

Research Articles

• 
  Alex Finnegan, Jun S. Song:
  Maximum entropy methods for extracting the learned features of deep neural networks.
• 
  Giray Enkavi, Heikki Mikkolainen, Burçin Güngör, Elina Ikonen, Ilpo Vattulainen:
  Concerted regulation of npc2 binding to endosomal/lysosomal membranes by bis(monoacylglycero)phosphate and sphingomyelin.
• 
  Vijay Vedula, Juhyun Lee, Hao Xu, C.-C. Jay Kuo, Tzung K. Hsiai, Alison L. Marsden:
  A method to quantify mechanobiologic forces during zebrafish cardiac development using 4-D light sheet imaging and computational modeling.
• 
  Max S. Y. Lau, Gavin J. Gibson, Hola Adrakey, Amanda McClelland, Steven Riley, Jon Zelner, George Streftaris, Sebastian Funk, C. Jessica E. Metcalf, Benjamin D. Dalziel, Bryan T. Grenfell:
  A mechanistic spatio-temporal framework for modelling individual-to-individual transmission - With an application to the 2014-2015 West Africa Ebola outbreak.
• 
  Ryan Thomas Philips, Mriganka Sur, V. Srinivasa Chakravarthy:
  The influence of astrocytes on the width of orientation hypercolumns in visual cortex: A computational perspective.
• 
  Kris V. Parag, Glenn Vinnicombe:
  Point process analysis of noise in early invertebrate vision.
• 
  Guoshi Li, Craig S. Henriquez, Flavio Fröhlich:
  Unified thalamic model generates multiple distinct oscillations with state-dependent entrainment by stimulation.
• 
  Andrew J. K. Phillips, Elizabeth B. Klerman, James P. Butler:
  Modeling the adenosine system as a modulator of cognitive performance and sleep patterns during sleep restriction and recovery.
• 
  Ekaterina Kotelnikova, Narsis Aftab Kiani, Elena Abad, Elena H. Martinez-Lapiscina, Magí Andorrà, Irati Zubizarreta, Irene Pulido-Valdeolivas, Inna Pertsovskaya, Leonidas G. Alexopoulos, Tomas Olsson, Roland Martin, Friedemann Paul, Jesper Tegnér, Jordi García-Ojalvo, Pablo Villoslada:
  Dynamics and heterogeneity of brain damage in multiple sclerosis.
• 
  Shreejoy J. Tripathy, Lilah Toker, Brenna Li, Cindy-Lee Crichlow, Dmitry Tebaykin, B. Ogan Mancarci, Paul Pavlidis:
  Transcriptomic correlates of neuron electrophysiological diversity.
• 
  Nicolas E. Martin, Siddharth Malik, Nicolas Calimet, Jean-Pierre Changeux, Marco Cecchini:
  Un-gating and allosteric modulation of a pentameric ligand-gated ion channel captured by molecular dynamics.
• 
  James Rankin, Frédéric Chavane:
  Neural field model to reconcile structure with function in primary visual cortex.
• 
  Amir Houshang Bahrami, Mary G. Lin, Xuefeng Ren, James H. Hurley, Gerhard Hummer:
  Scaffolding the cup-shaped double membrane in autophagy.
• 
  John Joseph Valletta, Mario Recker:
  Identification of immune signatures predictive of clinical protection from malaria.
• 
  Anna Hake, Nico Pfeifer:
  Prediction of HIV-1 sensitivity to broadly neutralizing antibodies shows a trend towards resistance over time.
• 
  Cynthia Sandor, Nicola L. Beer, Caleb Webber:
  Diverse type 2 diabetes genetic risk factors functionally converge in a phenotype-focused gene network.
• 
  Theodore Roman, Lu Xie, Russell Schwartz:
  Automated deconvolution of structured mixtures from heterogeneous tumor genomic data.
• 
  Claire N. Bedbrook, Kevin K. Yang, Austin J. Rice, Viviana Gradinaru, Frances H. Arnold:
  Machine learning to design integral membrane channelrhodopsins for efficient eukaryotic expression and plasma membrane localization.
• 
  Timothy N. Rubin, Oluwasanmi Koyejo, Krzysztof J. Gorgolewski, Michael N. Jones, Russell A. Poldrack, Tal Yarkoni:
  Decoding brain activity using a large-scale probabilistic functional-anatomical atlas of human cognition.
• 
  Jaron T. Colas, Wolfgang M. Pauli, Tobias Larsen, J. Michael Tyszka, John P. O'Doherty:
  Distinct prediction errors in mesostriatal circuits of the human brain mediate learning about the values of both states and actions: evidence from high-resolution fMRI.
• 
  Kalinga Pavan T. Silva, Prithiviraj Chellamuthu, James Q. Boedicker:
  Quantifying the strength of quorum sensing crosstalk within microbial communities.
• 
  Akshay Kakumanu, Silvia Velasco, Esteban O. Mazzoni, Shaun Mahony:
  Deconvolving sequence features that discriminate between overlapping regulatory annotations.
• 
  Spencer J. Fox, Joel C. Miller, Lauren Ancel Meyers:
  Seasonality in risk of pandemic influenza emergence.
• 
  Mengjia Xu, Dimitrios P. Papageorgiou, Sabia Z. Abidi, Ming Dao, Hong Zhao, George E. Karniadakis:
  A deep convolutional neural network for classification of red blood cells in sickle cell anemia.
• 
  Roman Shevchuk, Jochen S. Hub:
  Bayesian refinement of protein structures and ensembles against SAXS data using molecular dynamics.
• 
  Cen Wan, Jonathan G. Lees, Federico Minneci, Christine A. Orengo, David T. Jones:
  Analysis of temporal transcription expression profiles reveal links between protein function and developmental stages of Drosophila melanogaster.
• 
  Nan Lin, Yun Zhu, Ruzong Fan, Momiao Xiong:
  A quadratically regularized functional canonical correlation analysis for identifying the global structure of pleiotropy with NGS data.
• 
  Shiran Abadi, Winston X. Yan, David Amar, Itay Mayrose:
  A machine learning approach for predicting CRISPR-Cas9 cleavage efficiencies and patterns underlying its mechanism of action.
• 
  Evelina Gabasova, John E. Reid, Lorenz Wernisch:
  Clusternomics: Integrative context-dependent clustering for heterogeneous datasets.
• 
  Niklas Hübel, Mahshid S. Hosseini-Zare, Jokubas Ziburkus, Ghanim Ullah:
  The role of glutamate in neuronal ion homeostasis: A case study of spreading depolarization.
• 
  Phuong Dao, Yoo-Ah Kim, Damian Wójtowicz, Sanna Madan, Roded Sharan, Teresa M. Przytycka:
  BeWith: A Between-Within method to discover relationships between cancer modules via integrated analysis of mutual exclusivity, co-occurrence and functional interactions.
• 
  Kevin Drew, Christian L. Müller, Richard Bonneau, Edward M. Marcotte:
  Identifying direct contacts between protein complex subunits from their conditional dependence in proteomics datasets.
• 
  Bo Wang, Lin Huang, Yuke Zhu, Anshul Kundaje, Serafim Batzoglou, Anna Goldenberg:
  Vicus: Exploiting local structures to improve network-based analysis of biological data.
• 
  Yao Shen, Mariano J. Alvarez, Brygida C. Bisikirska, Alexander Lachmann, Ronald Realubit, Sergey Pampou, Jorida Coku, Charles Karan, Andrea Califano:
  Systematic, network-based characterization of therapeutic target inhibitors.
• 
  Daniel E. Carlin, Barry Demchak, Dexter Pratt, Eric Sage, Trey Ideker:
  Network propagation in the cytoscape cyberinfrastructure.
• 
  Aziz M. Mezlini, Anna Goldenberg:
  Incorporating networks in a probabilistic graphical model to find drivers for complex human diseases.
• 
  Kevin S. Bonham, Melanie I. Stefan:
  Women are underrepresented in computational biology: An analysis of the scholarly literature in biology, computer science and computational biology.
• 
  Mark L. Ioffe, Michael J. Berry II:
  The structured 'low temperature' phase of the retinal population code.
• 
  Jiawen Chen, Steven C. Almo, Yinghao Wu:
  General principles of binding between cell surface receptors and multi-specific ligands: A computational study.
• 
  Alex D. M. Dewar, Antoine Wystrach, Andrew Philippides, Paul Graham:
  Neural coding in the visual system of Drosophila melanogaster: How do small neural populations support visually guided behaviours?
• 
  Peter Ashcroft, Markus G. Manz, Sebastian Bonhoeffer:
  Clonal dominance and transplantation dynamics in hematopoietic stem cell compartments.
• 
  Thomas G. Fai, Alejandra Leo-Macias, David L. Stokes, Charles S. Peskin:
  Image-based model of the spectrin cytoskeleton for red blood cell simulation.
• 
  Emre Akbas, Miguel P. Eckstein:
  Object detection through search with a foveated visual system.
• 
  Agne Tilunaite, Wayne Croft, Noah Russell, Tomas C. Bellamy, Rüdiger Thul:
  A Bayesian approach to modelling heterogeneous calcium responses in cell populations.
• 
  Gudrun Gygli, Maria Fátima Lucas, Victor Guallar, Willem J. H. van Berkel:
  The ins and outs of vanillyl alcohol oxidase: Identification of ligand migration paths.
• 
  Kensuke Arai, Robert E. Kass:
  Inferring oscillatory modulation in neural spike trains.
• 
  Francesco Rigoli, Christoph Mathys, Karl J. Friston, Raymond J. Dolan:
  A unifying Bayesian account of contextual effects in value-based choice.
• 
  Jaymar Soriano, Takatomi Kubo, Takao Inoue, Hiroyuki Kida, Toshitaka Yamakawa, Michiyasu Suzuki, Kazushi Ikeda:
  Differential temperature sensitivity of synaptic and firing processes in a neural mass model of epileptic discharges explains heterogeneous response of experimental epilepsy to focal brain cooling.
• 
  Marina E. Wosniack, Marcos C. Santos, Ernesto P. Raposo, Gandhi M. Viswanathan, Marcos G. E. da Luz:
  The evolutionary origins of Lévy walk foraging.
• 
  Carsten Conradi, Elisenda Feliu, Maya Mincheva, Carsten Wiuf:
  Identifying parameter regions for multistationarity.
• 
  Marcel Nonnenmacher, Christian Behrens, Philipp Berens, Matthias Bethge, Jakob H. Macke:
  Signatures of criticality arise from random subsampling in simple population models.
• 
  Tiziano D'Albis, Richard Kempter:
  A single-cell spiking model for the origin of grid-cell patterns.
• 
  Andrea K. Barreiro, Shree Hari Gautam, Woodrow L. Shew, Cheng Ly:
  A theoretical framework for analyzing coupled neuronal networks: Application to the olfactory system.
• 
  Yaron Orenstein, David Pellow, Guillaume Marçais, Ron Shamir, Carl Kingsford:
  Designing small universal k-mer hitting sets for improved analysis of high-throughput sequencing.
• 
  Vadim Puller, Richard A. Neher, Jan Albert:
  Estimating time of HIV-1 infection from next-generation sequence diversity.
• 
  Thomas Heidlauf, Thomas Klotz, Christian Rode, Tobias Siebert, Oliver Röhrle:
  A continuum-mechanical skeletal muscle model including actin-titin interaction predicts stable contractions on the descending limb of the force-length relation.
• 
  Vahid Rostami, PierGianLuca Porta Mana, Sonja Grün, Moritz Helias:
  Bistability, non-ergodicity, and inhibition in pairwise maximum-entropy models.
• 
  Louis Verny, Nadir Sella, Séverine Affeldt, Param Priya Singh, Hervé Isambert:
  Learning causal networks with latent variables from multivariate information in genomic data.

Volume 13, Number 11, November 2017

Research Articles

• 
  Sushant Patkar, Assaf Magen, Roded Sharan, Sridhar Hannenhalli:
  A network diffusion approach to inferring sample-specific function reveals functional changes associated with breast cancer.
• 
  Alejandro Fernández Villaverde, Julio R. Banga:
  Dynamical compensation and structural identifiability of biological models: Analysis, implications, and reconciliation.
• 
  Suzan Farhang-Sardroodi, Amir Hossein Darooneh, Moladad Nikbakht, Natalia L. Komarova, Mohammad Kohandel:
  The effect of spatial randomness on the average fixation time of mutants.
• 
  Ruolin Liu, Julie A. Dickerson:
  Strawberry: Fast and accurate genome-guided transcript reconstruction and quantification from RNA-Seq.
• 
  Alexis T. Baria, Brian Maniscalco, Biyu J. He:
  Initial-state-dependent, robust, transient neural dynamics encode conscious visual perception.
• 
  Yuriy Pichugin, Jorge Peña, Paul B. Rainey, Arne Traulsen:
  Fragmentation modes and the evolution of life cycles.
• 
  Alizée Lopez-Persem, Lionel Rigoux, Sacha Bourgeois-Gironde, Jean Daunizeau, Mathias Pessiglione:
  Choose, rate or squeeze: Comparison of economic value functions elicited by different behavioral tasks.
• 
  Daniel Monsivais, Asim Ghosh, Kunal Bhattacharya, Robin I. M. Dunbar, Kimmo Kaski:
  Tracking urban human activity from mobile phone calling patterns.
• 
  Li Jiang, Luca Giuggioli, Andrea Perna, Ramón Escobedo, Valentin Lecheval, Clément Sire, Zhangang Han, Guy Theraulaz:
  Identifying influential neighbors in animal flocking.
• 
  Stefan Albert, Katharina Schmack, Philipp Sterzer, Gaby Schneider:
  A hierarchical stochastic model for bistable perception.
• 
  David J. Price, Alexandre Breuzé, Richard Dybowski, Piero Mastroeni, Olivier Restif:
  An efficient moments-based inference method for within-host bacterial infection dynamics.
• 
  Edwin van Leeuwen, Petra Klepac, Dominic Thorrington, Richard Pebody, Marc Baguelin:
  fluEvidenceSynthesis: An R package for evidence synthesis based analysis of epidemiological outbreaks.
• 
  Franciszek Rakowski, Jan Karbowski:
  Optimal synaptic signaling connectome for locomotory behavior in Caenorhabditis elegans: Design minimizing energy cost.
• 
  Stefano Anzellotti, Alfonso Caramazza, Rebecca Saxe:
  Multivariate pattern dependence.
• 
  Ronny Straube, Meera Shah, Dietrich Flockerzi, Dieter A. Wolf:
  Trade-off and flexibility in the dynamic regulation of the cullin-RING ubiquitin ligase repertoire.
• 
  Anthony Szedlak, Spencer Sims, Nicholas Smith, Giovanni Paternostro, Carlo Piermarocchi:
  Cell cycle time series gene expression data encoded as cyclic attractors in Hopfield systems.
• 
  Zoltan Neufeld, William von Witt, Dora Lakatos, Jiaming Wang, Balazs Hegedus, András Czirók:
  The role of Allee effect in modelling post resection recurrence of glioblastoma.
• 
  Jeffrey Shaman, Sasikiran Kandula, Wan Yang, Alicia Karspeck:
  The use of ambient humidity conditions to improve influenza forecast.
• 
  Mark A. Walker, Viatcheslav Gurev, John Jeremy Rice, Joseph L. Greenstein, Raimond L. Winslow:
  Estimating the probabilities of rare arrhythmic events in multiscale computational models of cardiac cells and tissue.
• 
  Emma H. Schwager, Himel Mallick, Steffen Ventz, Curtis Huttenhower:
  A Bayesian method for detecting pairwise associations in compositional data.
• 
  Guo-Shi Li, Thomas A. Cleland:
  A coupled-oscillator model of olfactory bulb gamma oscillations.
• 
  Masoud Nickaeen, Igor L. Novak, Stephanie Pulford, Aaron Rumack, Jamie Brandon, Boris M. Slepchenko, Alex Mogilner:
  A free-boundary model of a motile cell explains turning behavior.
• 
  Rosemary M. McCloskey, Art F. Y. Poon:
  A model-based clustering method to detect infectious disease transmission outbreaks from sequence variation.
• 
  John A. P. Sekar, José Juan Tapia, James R. Faeder:
  Automated visualization of rule-based models.
• 
  Philip M. Tan, Kyle S. Buchholz, Jeffrey H. Omens, Andrew D. McCulloch, Jeffrey J. Saucerman:
  Predictive model identifies key network regulators of cardiomyocyte mechano-signaling.
• 
  Gonzalo E. Mena, Lauren E. Grosberg, Sasidhar Madugula, Pawel Hottowy, Alan M. Litke, John P. Cunningham, E. J. Chichilnisky, Liam Paninski:
  Electrical stimulus artifact cancellation and neural spike detection on large multi-electrode arrays.
• 
  Jorge Fernandez-de-Cossío-Diaz, Kalet Leon, Roberto Mulet:
  Characterizing steady states of genome-scale metabolic networks in continuous cell cultures.
• 
  Thomas Coudrat, John Simms, Arthur Christopoulos, Denise Wootten, Patrick M. Sexton:
  Improving virtual screening of G protein-coupled receptors via ligand-directed modeling.
• 
  Yun-Ching Chen, Valer Gotea, Gennady Margolin, Laura Elnitski:
  Significant associations between driver gene mutations and DNA methylation alterations across many cancer types.
• 
  Richard D. Smith, Jing Lu, Heather A. Carlson:
  Are there physicochemical differences between allosteric and competitive ligands?
• 
  Yanli Wang, Wing-Cheong Lo, Ching-Shan Chou:
  A modeling study of budding yeast colony formation and its relationship to budding pattern and aging.
• 
  Tetsuhiro S. Hatakeyama, Chikara Furusawa:
  Metabolic dynamics restricted by conserved carriers: Jamming and feedback.
• 
  Marie Devaine, Aurore San-Galli, Cinzia Trapanese, Giulia Bardino, Christelle Hano, Michel Saint Jalme, Sébastien Bouret, Shelly Masi, Jean Daunizeau:
  Reading wild minds: A computational assay of Theory of Mind sophistication across seven primate species.
• 
  Michael F. Sloma, David H. Mathews:
  Base pair probability estimates improve the prediction accuracy of RNA non-canonical base pairs.
• 
  Shaima Hashem, Matteo Tiberti, Arianna Fornili:
  Allosteric modulation of cardiac myosin dynamics by omecamtiv mecarbil.
• 
  Emyr Bakker, Kun Tian, Luciano Mutti, Constantinos Demonacos, Jean-Marc Schwartz, Marija Krstic-Demonacos:
  Insight into glucocorticoid receptor signalling through interactome model analysis.
• 
  Daniel R. Romano, Matthew C. Pharris, Neal M. Patel, Tamara Kinzer-Ursem:
  Competitive tuning: Competition's role in setting the frequency-dependence of Ca2+-dependent proteins.
• 
  Teresa K. Yamana, Sasikiran Kandula, Jeffrey Shaman:
  Individual versus superensemble forecasts of seasonal influenza outbreaks in the United States.
• 
  Florian Rohart, Benoît Gautier, Amrit Singh, Kim-Anh Lê Cao:
  mixOmics: An R package for 'omics feature selection and multiple data integration.
• 
  André Luzardo, Eduardo Alonso, Esther Mondragón:
  A Rescorla-Wagner drift-diffusion model of conditioning and timing.

Volume 13, Number 12, December 2017

Editorials

• 
  Diego A. Forero, Sandra Lopez-Leon, George P. Patrinos:
  Ten simple rules for international short-term research stays.
• 
  Crystal M. Botham, Joshua A. Arribere, Sky W. Brubaker, Kevin T. Beier:
  Ten simple rules for writing a career development award proposal.

Education

• 
  Rebecca F. Alford, Andrew Leaver-Fay, Lynda Gonzales, Erin L. Dolan, Jeffrey J. Gray:
  A cyber-linked undergraduate research experience in computational biomolecular structure prediction and design.

Research Articles

• 
  Rico Rueedi, Roger Mallol, Johannes Raffler, David Lamparter, Nele Friedrich, Peter Vollenweider, Gérard Waeber, Gabi Kastenmüller, Zoltán Kutalik, Sven Bergmann:
  Metabomatching: Using genetic association to identify metabolites in proton NMR spectroscopy.
• 
  Bryan T. Weinstein, Maxim O. Lavrentovich, Wolfram Möbius, Andrew W. Murray, David R. Nelson:
  Genetic drift and selection in many-allele range expansions.
• 
  Vincent Jacob, Christelle Monsempès, Jean-Pierre Rospars, Jean-Baptiste Masson, Philippe Lucas:
  Olfactory coding in the turbulent realm.
• 
  Toru Niina, Giovanni B. Brandani, Cheng Tan, Shoji Takada:
  Sequence-dependent nucleosome sliding in rotation-coupled and uncoupled modes revealed by molecular simulations.
• 
  Patrick Meyer, Pallab Maity, Andre Burkovski, Julian D. Schwab, Christoph Müssel, Karmveer Singh, Filipa F. Ferreira, Linda Krug, Harald J. Maier, Meinhard Wlaschek, Thomas Wirth, Hans A. Kestler, Karin Scharffetter-Kochanek:
  A model of the onset of the senescence associated secretory phenotype after DNA damage induced senescence.
• 
  Siwei Wang, Alexander Borst, Noga Zaslavsky, Naftali Tishby, Idan Segev:
  Efficient encoding of motion is mediated by gap junctions in the fly visual system.
• 
  Oleksandr Ostrenko, Pietro Incardona, Rajesh Ramaswamy, Lutz Brusch, Ivo F. Sbalzarini:
  pSSAlib: The partial-propensity stochastic chemical network simulator.
• 
  Kaitlin E. Frasier, Marie A. Roch, Melissa S. Soldevilla, Sean M. Wiggins, Lance P. Garrison, John A. Hildebrand:
  Automated classification of dolphin echolocation click types from the Gulf of Mexico.
• 
  Sanjay Sonney, Jeremy Leipzig, Marie T. Lott, Shiping Zhang, Vincent Procaccio, Douglas C. Wallace, Neal Sondheimer:
  Predicting the pathogenicity of novel variants in mitochondrial tRNA with MitoTIP.
• 
  Austin E. Soplata, Michelle M. McCarthy, Jason S. Sherfey, Shane Lee, Patrick L. Purdon, Emery N. Brown, Nancy Kopell:
  Thalamocortical control of propofol phase-amplitude coupling.
• 
  Tom Dupré la Tour, Lucille Tallot, Laetitia Grabot, Valérie Doyère, Virginie van Wassenhove, Yves Grenier, Alexandre Gramfort:
  Non-linear auto-regressive models for cross-frequency coupling in neural time series.
• 
  Nadav Ben-Shushan, Misha Tsodyks:
  Stabilizing patterns in time: Neural network approach.
• 
  Amit Yashar, Rachel N. Denison:
  Feature reliability determines specificity and transfer of perceptual learning in orientation search.
• 
  Gábor Erdös, Tamás Szaniszló, Mátyás Pajkos, Borbála Hajdu-Soltész, Bence Kiss, Gábor Pál, László Nyitray, Zsuzsanna Dosztányi:
  Novel linear motif filtering protocol reveals the role of the LC8 dynein light chain in the Hippo pathway.
• 
  Dylan R. Muir, Patricia Molina-Luna, Morgane M. Roth, Fritjof Helmchen, Björn Kampa:
  Specific excitatory connectivity for feature integration in mouse primary visual cortex.
• 
  Xinxin Wang, Anders E. Carlsson:
  A master equation approach to actin polymerization applied to endocytosis in yeast.
• 
  Tsvetomira Radeva, Anna R. Dornhaus, Nancy A. Lynch, Radhika Nagpal, Hsin-Hao Su:
  Costs of task allocation with local feedback: Effects of colony size and extra workers in social insects and other multi-agent systems.
• 
  Shyr-Shea Chang, Shenyinying Tu, Kyung In Baek, Andrew Pietersen, Yu-Hsiu Liu, Van M. Savage, Sheng-Ping L. Hwang, Tzung K. Hsiai, Marcus L. Roper:
  Optimal occlusion uniformly partitions red blood cells fluxes within a microvascular network.
• 
  Christoph Baldow, Sebastian Salentin, Michael Schroeder, Ingo Roeder, Ingmar Glauche:
  MAGPIE: Simplifying access and execution of computational models in the life sciences.
• 
  William M. McFadden, Patrick M. McCall, Margaret L. Gardel, Edwin M. Munro:
  Filament turnover tunes both force generation and dissipation to control long-range flows in a model actomyosin cortex.
• 
  Andrea Tacchetti, Leyla Isik, Tomaso A. Poggio:
  Invariant recognition drives neural representations of action sequences.
• 
  James N. Ingram, Mohsen Sadeghi, J. Randall Flanagan, Daniel M. Wolpert:
  An error-tuned model for sensorimotor learning.
• 
  Zhengnan Huang, Hongjiu Zhang, Jonathan Boss, Stephen A. Goutman, Bhramar Mukherjee, Ivo D. Dinov, Yuanfang Guan:
  Complete hazard ranking to analyze right-censored data: An ALS survival study.
• 
  Alexander Martynov, Konstantin Severinov, Iaroslav Ispolatov:
  Optimal number of spacers in CRISPR arrays.
• 
  Xing Chen, Li Huang:
  LRSSLMDA: Laplacian Regularized Sparse Subspace Learning for MiRNA-Disease Association prediction.
• 
  Loan Huynh, Chris Neale, Régis Pomès, Hue Sun Chan:
  Molecular recognition and packing frustration in a helical protein.
• 
  Maria C. Quintero, Robert W. Putnam, Juan M. Cordovez:
  Theoretical perspectives on central chemosensitivity: CO2/H+-sensitive neurons in the locus coeruleus.
• 
  Thomas D. Gaddy, Qianhui Wu, Alyssa D. Arnheim, Stacey D. Finley:
  Mechanistic modeling quantifies the influence of tumor growth kinetics on the response to anti-angiogenic treatment.
• 
  Ye Henry Li, Dangna Li, Nikolay Samusik, Xiaowei Wang, Leying Guan, Garry P. Nolan, Wing Hung Wong:
  Scalable multi-sample single-cell data analysis by Partition-Assisted Clustering and Multiple Alignments of Networks.
• 
  Go Ashida, Daniel J. Tollin, Jutta Kretzberg:
  Physiological models of the lateral superior olive.
• 
  Nawsad Alam, Oriel Goldstein, Bing Xia, Kathryn A. Porter, Dima Kozakov, Ora Schueler-Furman:
  High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock.
• 
  Takaho Tsuchiya, Masashi Fujii, Naoki Matsuda, Katsuyuki Kunida, Shinsuke Uda, Hiroyuki Kubota, Katsumi Konishi, Shinya Kuroda:
  System identification of signaling dependent gene expression with different time-scale data.
• 
  Chieh Lo, Radu Marculescu:
  MPLasso: Inferring microbial association networks using prior microbial knowledge.
• 
  Jinglin Li, Jens Peter Lindemann, Martin Egelhaaf:
  Local motion adaptation enhances the representation of spatial structure at EMD arrays.

Corrections

• 
  Correction: Signatures of criticality arise from random subsampling in simple population models.
• 
  Correction: Identifying influential neighbors in animal flocking.
• 
  Correction: Sequential inference as a mode of cognition and its correlates in fronto-parietal and hippocampal brain regions.
• 
  Correction: Reading wild minds: A computational assay of Theory of Mind sophistication across seven primate species.
• 
  Correction: Dynamic Maternal Gradients Control Timing and Shift-Rates for Drosophila Gap Gene Expression.