Journal: PLoS Computational Biology

Volume 11, Issue 9

0 -- 0Vassilios N. Christopoulos, Paul R. Schrater. Dynamic Integration of Value Information into a Common Probability Currency as a Theory for Flexible Decision Making
0 -- 0Ayal Lavi, Omri Perez, Uri Ashery. Shaping Neuronal Network Activity by Presynaptic Mechanisms
0 -- 0Feixiong Cheng, Chuang Liu, Chen-Ching Lin, Junfei Zhao, Peilin Jia, Wen-Hsiung Li, Zhongming Zhao. A Gene Gravity Model for the Evolution of Cancer Genomes: A Study of 3, 000 Cancer Genomes across 9 Cancer Types
0 -- 0Imri Sofer, Sébastien M. Crouzet, Thomas Serre. Explaining the Timing of Natural Scene Understanding with a Computational Model of Perceptual Categorization
0 -- 0Gang Li, Karen E. Ross, Cecilia N. Arighi, Yifan Peng, Cathy H. Wu, K. Vijay-Shanker. miRTex: A Text Mining System for miRNA-Gene Relation Extraction
0 -- 0Rudy Clausen, Buyong Ma, Ruth Nussinov, Amarda Shehu. Mapping the Conformation Space of Wildtype and Mutant H-Ras with a Memetic, Cellular, and Multiscale Evolutionary Algorithm
0 -- 0Michael A. Cerullo. The Problem with Phi: A Critique of Integrated Information Theory
0 -- 0Felix Effenberger, Jürgen Jost, Anna Levina. Self-organization in Balanced State Networks by STDP and Homeostatic Plasticity
0 -- 0Guido Montufar, Keyan Ghazi-Zahedi, Nihat Ay. A Theory of Cheap Control in Embodied Systems
0 -- 0Marcos Economides, Zeb Kurth-Nelson, Annika Lübbert, Marc Guitart-Masip, Raymond J. Dolan. Model-Based Reasoning in Humans Becomes Automatic with Training
0 -- 0Jasmine Foo, Lin L. Liu, Kevin Leder, Markus Riester, Yoh Iwasa, Christoph Lengauer, Franziska Michor. An Evolutionary Approach for Identifying Driver Mutations in Colorectal Cancer
0 -- 0Elizabeth A. Hobson, Simon Dedeo. Social Feedback and the Emergence of Rank in Animal Society
0 -- 0Elizabeth Ortiz-Gutiérrez, Karla García-Cruz, Eugenio Azpeitia, Aaron Castillo, María de la Paz Sánchez, Elena R. Alvarez-Buylla. Arabidopsis thaliana Cell Cycle
0 -- 0Greet De Baets, Loic Van Doorn, Frederic Rousseau, Joost Schymkowitz. Increased Aggregation Is More Frequently Associated to Human Disease-Associated Mutations Than to Neutral Polymorphisms
0 -- 0Vipin Narang, Muhamad Azfar Ramli, Amit Singhal, Pavanish Kumar, Gennaro de Libero, Michael Poidinger, Christopher P. Monterola. Automated Identification of Core Regulatory Genes in Human Gene Regulatory Networks
0 -- 0Pete Riley, Michal Ben-Nun, Jon A. Linker, Angelia A. Cost, Jose L. Sanchez, Dylan George, David P. Bacon, Steven Riley. Early Characterization of the Severity and Transmissibility of Pandemic Influenza Using Clinical Episode Data from Multiple Populations
0 -- 0Jonathan Glancy, Roderich Groß, James V. Stone, Stuart P. Wilson. A Self-Organising Model of Thermoregulatory Huddling
0 -- 0Joseph Snider, Dongpyo Lee, Howard Poizner, Sergei Gepshtein. Prospective Optimization with Limited Resources
0 -- 0Julia C. Quindlen, Victor K. Lai, Victor H. Barocas. Multiscale Mechanical Model of the Pacinian Corpuscle Shows Depth and Anisotropy Contribute to the Receptor's Characteristic Response to Indentation
0 -- 0Claudio Altafini, Giuseppe Facchetti. Metabolic Adaptation Processes That Converge to Optimal Biomass Flux Distributions
0 -- 0Sacha J. van Albada, Moritz Helias, Markus Diesmann. Scalability of Asynchronous Networks Is Limited by One-to-One Mapping between Effective Connectivity and Correlations
0 -- 0Jiayu Wen, Erik Ladewig, Sol Shenker, Jaaved Mohammed, Eric C. Lai. Analysis of Nearly One Thousand Mammalian Mirtrons Reveals Novel Features of Dicer Substrates
0 -- 0Amir Szitenberg, Max John, Mark L. Blaxter, David H. Lunt. ReproPhylo: An Environment for Reproducible Phylogenomics
0 -- 0Stephan Köhler, Friederike Schmid, Giovanni Settanni. The Internal Dynamics of Fibrinogen and Its Implications for Coagulation and Adsorption
0 -- 0Chakravarthy Marella, Andrew E. Torda, Dominik Schwudke. The LUX Score: A Metric for Lipidome Homology
0 -- 0Héctor García Martín, Vinay Satish Kumar, Daniel Weaver, Amit Ghosh, Victor Chubukov, Aindrila Mukhopadhyay, Adam Arkin, Jay D. Keasling. 13C Labeling Data
0 -- 0Marco Galardini, Matteo Brilli, Giulia Spini, Matteo Rossi, Bianca Roncaglia, Alessia Bani, Manuela Chiancianesi, Marco Moretto, Kristof Engelen, Giovanni Bacci, Francesco Pini, Emanuele G. Biondi, Marco Bazzicalupo, Alessio Mengoni. Evolution of Intra-specific Regulatory Networks in a Multipartite Bacterial Genome
0 -- 0Naiqian Zhang, Haiyun Wang, Yun Fang, Jun Wang, Xiaoqi Zheng, X. Shirley Liu. Predicting Anticancer Drug Responses Using a Dual-Layer Integrated Cell Line-Drug Network Model
0 -- 0Santiago Schnell. Ten Simple Rules for a Computational Biologist's Laboratory Notebook
0 -- 0Katrin Böttger, Haralambos Hatzikirou, Anja Voss-Böhme, Elisabetta Ada Cavalcanti-Adam, Miguel A. Herrero, Andreas Deutsch. An Emerging Allee Effect Is Critical for Tumor Initiation and Persistence
0 -- 0Greg Jensen, Fabian Muñoz, Yelda Alkan, Vincent P. Ferrera, Herbert S. Terrace. Implicit Value Updating Explains Transitive Inference Performance: The Betasort Model
0 -- 0Thomas K. Karikari. Bioinformatics in Africa: The Rise of Ghana?
0 -- 0Jianfei Hu, Johnathan Neiswinger, Jin Zhang, Heng Zhu, Jiang Qian. Systematic Prediction of Scaffold Proteins Reveals New Design Principles in Scaffold-Mediated Signal Transduction
0 -- 0Vijay Rajagopal, Gregory Bass, Cameron G. Walker, David J. Crossman, Amorita Petzer, Anthony Hickey, Ivo Siekmann, Masahiko Hoshijima, Mark H. Ellisman, Edmund J. Crampin, Christian Soeller. 2+ Release Patterns in Cardiomyocytes
0 -- 0Florian Markowetz. You Are Not Working for Me; I Am Working with You
0 -- 0Noah Ollikainen, René M. de Jong, Tanja Kortemme. Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity
0 -- 0Sergei Maslov, Kim Sneppen. Diversity Waves in Collapse-Driven Population Dynamics
0 -- 0Daniel Nichol, Peter Jeavons, Alexander G. Fletcher, Robert A. Bonomo, Philip K. Maini, Jerome L. Paul, Robert A. Gatenby, Alexander R. A. Anderson, Jacob G. Scott. Steering Evolution with Sequential Therapy to Prevent the Emergence of Bacterial Antibiotic Resistance
0 -- 0Alexander Ullrich, Mathias A. Böhme, Johannes Schöneberg, Harald Depner, Stephan J. Sigrist, Frank Noé. Dynamical Organization of Syntaxin-1A at the Presynaptic Active Zone
0 -- 0Alice Carolyn McHardy. How to Grow a Computational Biology Lab
0 -- 0Hannah Edwards, Charlotte M. Deane. Structural Bridges through Fold Space
0 -- 0Rebecca F. Alford, Julia Koehler Leman, Brian Weitzner, Amanda M. Duran, Drew C. Tilley, Assaf Elazar, Jeffrey J. Gray. An Integrated Framework Advancing Membrane Protein Modeling and Design
0 -- 0Suhani Nagpal, Satyam Tiwari, Koyeli Mapa, Lipi Thukral. Decoding Structural Properties of a Partially Unfolded Protein Substrate: En Route to Chaperone Binding
0 -- 0Robert Becker, Stuart Knock, Petra Ritter, Viktor K. Jirsa. Relating Alpha Power and Phase to Population Firing and Hemodynamic Activity Using a Thalamo-cortical Neural Mass Model
0 -- 0Thembi Mdluli, Gregery T. Buzzard, Ann E. Rundell. Efficient Optimization of Stimuli for Model-Based Design of Experiments to Resolve Dynamical Uncertainty

Volume 11, Issue 8

0 -- 0Alex McAvoy, Christoph Hauert. Asymmetric Evolutionary Games
0 -- 0Ghanim Ullah, Yina Wei, Markus A. Dahlem, Martin Wechselberger, Steven J. Schiff. The Role of Cell Volume in the Dynamics of Seizure, Spreading Depression, and Anoxic Depolarization
0 -- 0Chris G. Antonopoulos, Shambhavi Srivastava, Sandro E. de S. Pinto, Murilo S. Baptista. Do Brain Networks Evolve by Maximizing Their Information Flow Capacity?
0 -- 0Kirill Lykov, Xuejin Li, Huan Lei, Igor V. Pivkin, George E. Karniadakis. Inflow/Outflow Boundary Conditions for Particle-Based Blood Flow Simulations: Application to Arterial Bifurcations and Trees
0 -- 0Ariel Afek, Hila Cohen, Shiran Barber-Zucker, Raluca Gordân, David B. Lukatsky. Nonconsensus Protein Binding to Repetitive DNA Sequence Elements Significantly Affects Eukaryotic Genomes
0 -- 0Claudia Schillings, Mikael Sunnåker, Jörg Stelling, Christoph Schwab. Efficient Characterization of Parametric Uncertainty of Complex (Bio)chemical Networks
0 -- 0Zing Tsung-Yeh Tsai, Shin-Han Shiu, Huai-Kuang Tsai. Contribution of Sequence Motif, Chromatin State, and DNA Structure Features to Predictive Models of Transcription Factor Binding in Yeast
0 -- 0Shaun S. Sanders, Dale D. O. Martin, Stefanie L. Butland, Mathieu Lavallée-Adam, Diego Calzolari, Chris Kay, John R. Yates III, Michael R. Hayden. Curation of the Mammalian Palmitoylome Indicates a Pivotal Role for Palmitoylation in Diseases and Disorders of the Nervous System and Cancers
0 -- 0James P. Roach, Eshel Ben-Jacob, Leonard M. Sander, Michal R. Zochowski. Formation and Dynamics of Waves in a Cortical Model of Cholinergic Modulation
0 -- 0Liping Xiong, Ganhui Lan. An Optimal Free Energy Dissipation Strategy of the MinCDE Oscillator in Regulating Symmetric Bacterial Cell Division
0 -- 0Brinda K. Vallat, Carlos J. Madrid-Aliste, András Fiser. Modularity of Protein Folds as a Tool for Template-Free Modeling of Structures
0 -- 0Roland F. Schwarz, Robyn Branicky, Laura J. Grundy, William R. Schafer, André E. X. Brown. elegans Locomotion
0 -- 0Gabriel Koch Ocker, Ashok Litwin-Kumar, Brent Doiron. Self-Organization of Microcircuits in Networks of Spiking Neurons with Plastic Synapses
0 -- 0Hiroo Kenzaki, Shoji Takada. Partial Unwrapping and Histone Tail Dynamics in Nucleosome Revealed by Coarse-Grained Molecular Simulations
0 -- 0Murat Alp, Vipan K. Parihar, Charles L. Limoli, Francis A. Cucinotta. In Silico Modeling Approach
0 -- 0Logan C. Brooks, David C. Farrow, Sangwon Hyun, Ryan J. Tibshirani, Roni Rosenfeld. Flexible Modeling of Epidemics with an Empirical Bayes Framework
0 -- 0Tim Genewein, Eduard Hez, Zeynab Razzaghpanah, Daniel A. Braun. Structure Learning in Bayesian Sensorimotor Integration
0 -- 0Liat Rockah-Shmuel, Ágnes Tóth-Petróczy, Dan S. Tawfik. Systematic Mapping of Protein Mutational Space by Prolonged Drift Reveals the Deleterious Effects of Seemingly Neutral Mutations
0 -- 0Po-Wei Chen, Luís L. Fonseca, Yusuf A. Hannun, Eberhard O. Voit. Dynamics of the Heat Stress Response of Ceramides with Different Fatty-Acyl Chain Lengths in Baker's Yeast
0 -- 0Jonas Paulsen, Odin Gramstad, Philippe Collas. Manifold Based Optimization for Single-Cell 3D Genome Reconstruction
0 -- 0John R. Houser, Craig Barnhart, Daniel R. Boutz, Sean M. Carroll, Aurko Dasgupta, Joshua K. Michener, Brittany D. Needham, Ophelia Papoulas, Viswanadham Sridhara, Dariya K. Sydykova, Christopher J. Marx, M. Stephen Trent, Jeffrey E. Barrick, Edward M. Marcotte, Claus O. Wilke. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation
0 -- 0Deborah A. Striegel, Manami Hara, Vipul Periwal. The Beta Cell in Its Cluster: Stochastic Graphs of Beta Cell Connectivity in the Islets of Langerhans
0 -- 0James E. M. Bennett, Wyeth Bair. Refinement and Pattern Formation in Neural Circuits by the Interaction of Traveling Waves with Spike-Timing Dependent Plasticity
0 -- 0Alexey A. Gritsenko, Marc Hulsman, Marcel J. T. Reinders, Dick de Ridder. Unbiased Quantitative Models of Protein Translation Derived from Ribosome Profiling Data
0 -- 0Shuai Yuan, H. Richard Johnston, Guosheng Zhang, Yun Li, Yi-Juan Hu, Zhaohui S. Qin. One Size Doesn't Fit All - RefEditor: Building Personalized Diploid Reference Genome to Improve Read Mapping and Genotype Calling in Next Generation Sequencing Studies
0 -- 0Arjun Bharioke, Dmitri B. Chklovskii. Automatic Adaptation to Fast Input Changes in a Time-Invariant Neural Circuit
0 -- 0Chuan Xue, Blerta Shtylla, Anthony Brown. A Stochastic Multiscale Model That Explains the Segregation of Axonal Microtubules and Neurofilaments in Neurological Diseases
0 -- 0Assaf Amitai, Mathias Toulouze, Karine Dubrana, David Holcman. Analysis of Single Locus Trajectories for Extracting In Vivo Chromatin Tethering Interactions
0 -- 0Sayed-Rzgar Hosseini, Aditya Barve, Andreas Wagner. 15 Central Carbon Metabolisms Reveals an Organization Conducive to Metabolic Innovation
0 -- 0Rajesh Balagam, Oleg A. Igoshin. Myxococcus xanthus Bacteria
0 -- 0Mitchell G. Newberry, Daniel B. Ennis, Van M. Savage. Testing Foundations of Biological Scaling Theory Using Automated Measurements of Vascular Networks
0 -- 0James Tamerius, Cécile Viboud, Jeffrey Shaman, Gerardo Chowell. Impact of School Cycles and Environmental Forcing on the Timing of Pandemic Influenza Activity in Mexican States, May-December 2009
0 -- 0Sander Land, Steven A. Niederer. A Spatially Detailed Model of Isometric Contraction Based on Competitive Binding of Troponin I Explains Cooperative Interactions between Tropomyosin and Crossbridges
0 -- 0Patrícia Santos-Oliveira, António Correia, Tiago Rodrigues, Teresa M. Ribeiro-Rodrigues, Paulo Matafome, Juan Carlos Rodríguez-Manzaneque, Raquel Seiça, Henrique Girão, Rui D. M. Travasso. The Force at the Tip - Modelling Tension and Proliferation in Sprouting Angiogenesis
0 -- 0Chengsheng Zhu, Tom O. Delmont, Timothy M. Vogel, Yana Bromberg. Functional Basis of Microorganism Classification
0 -- 0Tadashi Miyamoto, Chikara Furusawa, Kunihiko Kaneko. Pluripotency, Differentiation, and Reprogramming: A Gene Expression Dynamics Model with Epigenetic Feedback Regulation
0 -- 0Pengxing Cao, Ada W. C. Yan, Jane Marie Heffernan, Stephen Petrie, Robert G. Moss, Louise A. Carolan, Teagan A. Guarnaccia, Anne Kelso, Ian G. Barr, Jodie McVernon, Karen L. Laurie, James M. McCaw. Innate Immunity and the Inter-exposure Interval Determine the Dynamics of Secondary Influenza Virus Infection and Explain Observed Viral Hierarchies
0 -- 0Cahit Dalgicdir, Christoph Globisch, Christine Peter, Mehmet Sayar. Tipping the Scale from Disorder to Alpha-helix: Folding of Amphiphilic Peptides in the Presence of Macroscopic and Molecular Interfaces
0 -- 0Maxime Louet, Christian Seifert, Ulf Hensen, Frauke Gräter. Dynamic Allostery of the Catabolite Activator Protein Revealed by Interatomic Forces
0 -- 0Pengyi Yang, Xiaofeng Zheng, Vivek Jayaswal, Guang Hu, Jean Yee Hwa Yang, Raja Jothi. Knowledge-Based Analysis for Detecting Key Signaling Events from Time-Series Phosphoproteomics Data
0 -- 0Zachary A. King, Andreas Dräger, Ali Ebrahim, Nikolaus Sonnenschein, Nathan E. Lewis, Bernhard O. Palsson. Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways
0 -- 0Malachi Griffith, Jason R. Walker, Nicholas C. Spies, Benjamin J. Ainscough, Obi L. Griffith. Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud
0 -- 0Huijing Du, Qing Nie, William R. Holmes. The Interplay between Wnt Mediated Expansion and Negative Regulation of Growth Promotes Robust Intestinal Crypt Structure and Homeostasis
0 -- 0Songjian Lu, Kevin N. Lu, Shi-Yuan Cheng, Bo Hu, Xiaojun Ma, Nicholas Nystrom, Xinghua Lu. Identifying Driver Genomic Alterations in Cancers by Searching Minimum-Weight, Mutually Exclusive Sets
0 -- 0Eliseo Ferrante, Ali Emre Turgut, Edgar A. Duéñez-Guzmán, Marco Dorigo, Tom Wenseleers. Evolution of Self-Organized Task Specialization in Robot Swarms
0 -- 0Paul M. Harrison, Laurent Badel, Mark J. Wall, Magnus J. E. Richardson. Experimentally Verified Parameter Sets for Modelling Heterogeneous Neocortical Pyramidal-Cell Populations
0 -- 0Sebastian Bitzer, Jelle Bruineberg, Stefan J. Kiebel. A Bayesian Attractor Model for Perceptual Decision Making
0 -- 0Alireza Alemi, Carlo Baldassi, Nicolas Brunel, Riccardo Zecchina. A Three-Threshold Learning Rule Approaches the Maximal Capacity of Recurrent Neural Networks
0 -- 0Jeffrey R. Johnson, Silvia D. Santos, Tasha Johnson, Ursula Pieper, Marta Strumillo, Omar Wagih, Andrej Sali, Nevan J. Krogan, Pedro Beltrão. Xenopus laevis Oocytes
0 -- 0Åsmund Flobak, Anaïs Baudot, Elisabeth Remy, Liv Thommesen, Denis Thieffry, Martin Kuiper, Astrid Lægreid. Discovery of Drug Synergies in Gastric Cancer Cells Predicted by Logical Modeling
0 -- 0Adrián Ponce-Alvarez, Biyu J. He, Patric Hagmann, Gustavo Deco. Task-Driven Activity Reduces the Cortical Activity Space of the Brain: Experiment and Whole-Brain Modeling
0 -- 0Marc Breit, Michael Netzer, Klaus Weinberger, Christian Baumgartner. Modeling and Classification of Kinetic Patterns of Dynamic Metabolic Biomarkers in Physical Activity

Volume 11, Issue 7

0 -- 0Chris Neale, Nilmadhab Chakrabarti, Pawel Pomorski, Emil F. Pai, Régis Pomès. Hydrophobic Gating of Ion Permeation in Magnesium Channel CorA
0 -- 0Kartik Subramanian, Mark R. Paul, John J. Tyson. Caulobacter crescentus: A Theoretical Investigation of Alternative Models
0 -- 0Mengchen Zhu, Christopher J. Rozell. Modeling Inhibitory Interneurons in Efficient Sensory Coding Models
0 -- 0Bethany L. Dearlove, Simon D. W. Frost. Measuring Asymmetry in Time-Stamped Phylogenies
0 -- 0Malachi Griffith, Obi L. Griffith, Scott M. Smith, Avinash Ramu, Matthew B. Callaway, Anthony M. Brummett, Michael J. Kiwala, Adam C. Coffman, Allison A. Regier, Benjamin J. Oberkfell, Gabriel E. Sanderson, Thomas P. Mooney, Nathaniel G. Nutter, Edward A. Belter, Feiyu Du, Robert L. Long, Travis E. Abbott, Ian T. Ferguson, David L. Morton, Mark M. Burnett, James V. Weible, Joshua B. Peck, Adam Dukes, Joshua F. McMichael, Justin T. Lolofie, Brian R. Derickson, Jasreet Hundal, Zachary L. Skidmore, Benjamin J. Ainscough, Nathan D. Dees, William S. Schierding, Cyriac Kandoth, Kyung H. Kim, Charles Lu, Christopher C. Harris, Nicole Maher, Christopher A. Maher, Vincent J. Magrini, Benjamin S. Abbott, Ken Chen, Eric Clark, Indraniel Das, Xian Fan, Amy E. Hawkins, Todd G. Hepler, Todd N. Wylie, Shawn M. Leonard, William E. Schroeder, Xiaoqi Shi, Lynn K. Carmichael, Matthew R. Weil, Richard W. Wohlstadter, Gary Stiehr, Michael D. McLellan, Craig S. Pohl, Christopher A. Miller, Daniel C. Koboldt, Jason R. Walker, James M. Eldred, David E. Larson, David J. Dooling, Li Ding, Elaine R. Mardis, Richard K. Wilson. Genome Modeling System: A Knowledge Management Platform for Genomics
0 -- 0Ruth Nussinov, Sebastian Bonhoeffer, Jason A. Papin, Olaf Sporns. From "What Is?" to "What Isn't?" Computational Biology
0 -- 0Olivier Marre, Vicente Botella-Soler, Kristina D. Simmons, Thierry Mora, Gasper Tkacik, Michael J. Berry II. High Accuracy Decoding of Dynamical Motion from a Large Retinal Population
0 -- 0Qinglong Zeng, Jeet Sukumaran, Steven H. Wu, Allen G. Rodrigo. Neutral Models of Microbiome Evolution
0 -- 0Elizabeth L. Sander, J. Timothy Wootton, Stefano Allesina. What Can Interaction Webs Tell Us About Species Roles?
0 -- 0Daniel Harnack, Miha Pelko, Antoine Chaillet, Yacine Chitour, Mark C. W. van Rossum. Stability of Neuronal Networks with Homeostatic Regulation
0 -- 0Bethany Percha, Russ B. Altman. Learning the Structure of Biomedical Relationships from Unstructured Text
0 -- 0Marharyta Petukh, Minghui Li, Emil Alexov. Predicting Binding Free Energy Change Caused by Point Mutations with Knowledge-Modified MM/PBSA Method
0 -- 0John Walmsley, Theo Arts, Nicolas Derval, Pierre Bordachar, Hubert Cochet, Sylvain Ploux, Frits W. Prinzen, Tammo Delhaas, Joost Lumens. Fast Simulation of Mechanical Heterogeneity in the Electrically Asynchronous Heart Using the MultiPatch Module
0 -- 0Weston Cox, Brian J. Fischer. Optimal Prediction of Moving Sound Source Direction in the Owl
0 -- 0Amy Wesolowski, Wendy Prudhomme O'Meara, Nathan Eagle, Andrew J. Tatem, Caroline O. Buckee. Evaluating Spatial Interaction Models for Regional Mobility in Sub-Saharan Africa
0 -- 0Thomas Hoffmann, Angela M. Krackhardt, Iris Antes. Quantitative Analysis of the Association Angle between T-cell Receptor Vα/Vβ Domains Reveals Important Features for Epitope Recognition
0 -- 0Blake T. Thomas, Davis W. Blalock, William B. Levy. Adaptive Synaptogenesis Constructs Neural Codes That Benefit Discrimination
0 -- 0Dimitar V. Pachov, Henry van den Bedem. Nullspace Sampling with Holonomic Constraints Reveals Molecular Mechanisms of Protein Gαs
0 -- 0Param Priya Singh, Jatin Arora, Hervé Isambert. Identification of Ohnolog Genes Originating from Whole Genome Duplication in Early Vertebrates, Based on Synteny Comparison across Multiple Genomes
0 -- 0Saket Navlakha, Alison L. Barth, Ziv Bar-Joseph. Decreasing-Rate Pruning Optimizes the Construction of Efficient and Robust Distributed Networks
0 -- 0Jian K. Liu, Tim Gollisch. Spike-Triggered Covariance Analysis Reveals Phenomenological Diversity of Contrast Adaptation in the Retina
0 -- 0Yann Sweeney, Jeanette Hellgren Kotaleski, Matthias H. Hennig. A Diffusive Homeostatic Signal Maintains Neural Heterogeneity and Responsiveness in Cortical Networks
0 -- 0Jan M. Ache, Volker Dürr. A Computational Model of a Descending Mechanosensory Pathway Involved in Active Tactile Sensing
0 -- 0Joshua J. Hamilton, Montserrat Calixto Contreras, Jennifer L. Reed. 2 Transfer in a Methanogenic, Syntrophic Community
0 -- 0Alexander M. Sevy, Tim M. Jacobs, James E. Crowe Jr., Jens Meiler. Design of Protein Multi-specificity Using an Independent Sequence Search Reduces the Barrier to Low Energy Sequences
0 -- 0Wan Yang, Benjamin J. Cowling, Eric H. Y. Lau, Jeffrey Shaman. Forecasting Influenza Epidemics in Hong Kong
0 -- 0Lu Zhang, Daniel-Adriano Silva, Fátima Pardo Avila, Dong Wang, Xuhui Huang. Structural Model of RNA Polymerase II Elongation Complex with Complete Transcription Bubble Reveals NTP Entry Routes
0 -- 0Yael Korem, Pablo Szekely, Yuval Hart, Hila Sheftel, Jean Hausser, Avi E. Mayo, Michael E. Rothenberg, Tomer Kalisky, Uri Alon. Geometry of the Gene Expression Space of Individual Cells
0 -- 0Truong D. Nguyen-Huu, Chinmaya Gupta, Bo Ma, William Ott, Kresimir Josic, Matthew R. Bennett. Timing and Variability of Galactose Metabolic Gene Activation Depend on the Rate of Environmental Change
0 -- 0Michael T. Schaub, Yazan N. Billeh, Costas A. Anastassiou, Christof Koch, Mauricio Barahona. Emergence of Slow-Switching Assemblies in Structured Neuronal Networks
0 -- 0Tong Li, Malgorzata B. Tracka, Shahid Uddin, Jose Casas-Finet, Donald J. Jacobs, Dennis R. Livesay. Rigidity Emerges during Antibody Evolution in Three Distinct Antibody Systems: Evidence from QSFR Analysis of Fab Fragments
0 -- 0Richard R. Stein, Debora S. Marks, Chris Sander. Inferring Pairwise Interactions from Biological Data Using Maximum-Entropy Probability Models
0 -- 0Hanlun Jiang, Fu Kit Sheong, Lizhe Zhu, Xin Gao, Julie Bernauer, Xuhui Huang. Markov State Models Reveal a Two-Step Mechanism of miRNA Loading into the Human Argonaute Protein: Selective Binding followed by Structural Re-arrangement
0 -- 0Tomohiro Tanaka, Naoto Hori, Shoji Takada. How Co-translational Folding of Multi-domain Protein Is Affected by Elongation Schedule: Molecular Simulations
0 -- 0Omri Harish, David Hansel. Asynchronous Rate Chaos in Spiking Neuronal Circuits
0 -- 0Daniel S. Himmelstein, Sergio E. Baranzini. Heterogeneous Network Edge Prediction: A Data Integration Approach to Prioritize Disease-Associated Genes
0 -- 0Marijn B. Martens, Tansu Celikel, Paul H. E. Tiesinga. A Developmental Switch for Hebbian Plasticity
0 -- 0César A. Ramírez-Sarmiento, Jeffrey K. Noel, Sandro L. Valenzuela, Irina Artsimovitch. Interdomain Contacts Control Native State Switching of RfaH on a Dual-Funneled Landscape

Volume 11, Issue 6

0 -- 0Robert C. Wilson, Yael Niv. Is Model Fitting Necessary for Model-Based fMRI?
0 -- 0J. Brendan Ritchie, David A. Tovar, Thomas A. Carlson. Emerging Object Representations in the Visual System Predict Reaction Times for Categorization
0 -- 0Ahmed T. Ayoub, Mariusz Klobukowski, Jack A. Tuszynski. Detailed Per-residue Energetic Analysis Explains the Driving Force for Microtubule Disassembly
0 -- 0Hanae Shimo, Satya Nanda Vel Arjunan, Hiroaki Machiyama, Taiko Nishino, Makoto Suematsu, Hideaki Fujita, Masaru Tomita, Koichi Takahashi. Particle Simulation of Oxidation Induced Band 3 Clustering in Human Erythrocytes
0 -- 0Kerry E. Boyle, Hilary Monaco, Dave van Ditmarsch, Maxime Deforet, João B. Xavier. Integration of Metabolic and Quorum Sensing Signals Governing the Decision to Cooperate in a Bacterial Social Trait
0 -- 0Andrew E. Brennan, Maurice A. Smith. The Decay of Motor Memories Is Independent of Context Change Detection
0 -- 0Lishibanya Mohapatra, Bruce L. Goode, Jané Kondev. Antenna Mechanism of Length Control of Actin Cables
0 -- 0Mariana Esther Martinez-Sanchez, Luis Mendoza, Carlos Villarreal, Elena R. Alvarez-Buylla. A Minimal Regulatory Network of Extrinsic and Intrinsic Factors Recovers Observed Patterns of CD4+ T Cell Differentiation and Plasticity
0 -- 0Juan A. Bueren-Calabuig, Julien Michel. Elucidation of Ligand-Dependent Modulation of Disorder-Order Transitions in the Oncoprotein MDM2
0 -- 0Daisuke Ohshima, Kyoko Arimoto-Matsuzaki, Taichiro Tomida, Mutsuhiro Takekawa, Kazuhisa Ichikawa. Spatio-temporal Dynamics and Mechanisms of Stress Granule Assembly
0 -- 0Assaf Zvuloni, Yael Artzy-Randrup, Guy Katriel, Yossi Loya, Lewi Stone. Modeling the Impact of White-Plague Coral Disease in Climate Change Scenarios
0 -- 0Andreas Hula, P. Read Montague, Peter Dayan. Monte Carlo Planning Method Estimates Planning Horizons during Interactive Social Exchange
0 -- 0Jingchun Sun, Min Zhao, Peilin Jia, Lily Wang, Yonghui Wu, Carissa Iverson, Yubo Zhou, Erica A. Bowton, Dan M. Roden, Joshua C. Denny, Melinda C. Aldrich, Hua Xu, Zhongming Zhao. Deciphering Signaling Pathway Networks to Understand the Molecular Mechanisms of Metformin Action
0 -- 0Xiaoke Ma, Long Gao, Georgios Karamanlidis, Peng Gao, Chi Fung Lee, Lorena Garcia-Menendez, Rong Tian, Kai Tan. Revealing Pathway Dynamics in Heart Diseases by Analyzing Multiple Differential Networks
0 -- 0Vicente Reyes-Puerta, Suam Kim, Jyh-Jang Sun, Barbara Imbrosci, Werner Kilb, Heiko J. Luhmann. High Stimulus-Related Information in Barrel Cortex Inhibitory Interneurons
0 -- 0Pierre Broly, Jean-Louis Deneubourg. Behavioural Contagion Explains Group Cohesion in a Social Crustacean
0 -- 0Lindsay Wendel Clegg, Feilim Mac Gabhann. Site-Specific Phosphorylation of VEGFR2 Is Mediated by Receptor Trafficking: Insights from a Computational Model
0 -- 0Josh S. Merel, Donald M. Pianto, John P. Cunningham, Liam Paninski. Encoder-Decoder Optimization for Brain-Computer Interfaces
0 -- 0Imen Lassadi, Alain Kamgoué, Isabelle Goiffon, Nicolas Tanguy-le-Gac, Kerstin Bystricky. Differential Chromosome Conformations as Hallmarks of Cellular Identity Revealed by Mathematical Polymer Modeling
0 -- 0Christian Pozzorini, Skander Mensi, Olivier Hagens, Richard Naud, Christof Koch, Wulfram Gerstner. Automated High-Throughput Characterization of Single Neurons by Means of Simplified Spiking Models
0 -- 0Steven N. Steinway, Matthew B. Biggs, Thomas P. Loughran Jr., Jason A. Papin, Reka Albert. Inference of Network Dynamics and Metabolic Interactions in the Gut Microbiome
0 -- 0Daniel Lobo, Michael Levin. Inferring Regulatory Networks from Experimental Morphological Phenotypes: A Computational Method Reverse-Engineers Planarian Regeneration
0 -- 0Cordelia Ziraldo, Alexey Solovyev, Ana Allegretti, Shilpa Krishnan, M. Kristi Henzel, Gwendolyn A. Sowa, David Brienza, Gary An, Qi Mi, Yoram Vodovotz. A Computational, Tissue-Realistic Model of Pressure Ulcer Formation in Individuals with Spinal Cord Injury
0 -- 0Christiana N. Fogg, Diane E. Kovats. Computational Biology: Moving into the Future One Click at a Time
0 -- 0Christiana N. Fogg, Diane E. Kovats. ISMB/ECCB Rebooted: 2015 Brings Major Update to the Meeting Program
0 -- 0Florent Meyniel, Daniel Schlunegger, Stanislas Dehaene. The Sense of Confidence during Probabilistic Learning: A Normative Account
0 -- 0Ruian Ke, Claude Loverdo, Hangfei Qi, Ren Sun, James O. Lloyd-Smith. Rational Design and Adaptive Management of Combination Therapies for Hepatitis C Virus Infection
0 -- 0Kai Ueltzhöffer, Diana J. N. Armbruster-Genç, Christian J. Fiebach. Stochastic Dynamics Underlying Cognitive Stability and Flexibility
0 -- 0Uri Obolski, Gideon Y. Stein, Lilach Hadany. Antibiotic Restriction Might Facilitate the Emergence of Multi-drug Resistance
0 -- 0Catalina A. Vallejos, John C. Marioni, Sylvia Richardson. BASiCS: Bayesian Analysis of Single-Cell Sequencing Data
0 -- 0Duccio Malinverni, Simone Marsili, Alessandro Barducci, Paolo De Los Rios. Large-Scale Conformational Transitions and Dimerization Are Encoded in the Amino-Acid Sequences of Hsp70 Chaperones
0 -- 0Boris P. Hejblum, Jason Skinner, Rodolphe Thiébaut. Time-Course Gene Set Analysis for Longitudinal Gene Expression Data
0 -- 0Jeffrey W. Brown, Esther Bullitt, Sira Sriswasdi, Sandra Harper, David W. Speicher, C. James McKnight. The Physiological Molecular Shape of Spectrin: A Compact Supercoil Resembling a Chinese Finger Trap
0 -- 0Felipe Merino, Benjamin Bouvier, Vlad Cojocaru. Cooperative DNA Recognition Modulated by an Interplay between Protein-Protein Interactions and DNA-Mediated Allostery
0 -- 0Sadra Sadeh, Claudia Clopath, Stefan Rotter. Emergence of Functional Specificity in Balanced Networks with Synaptic Plasticity
0 -- 0Ingmar Kanitscheider, Ruben Coen Cagli, Adam Kohn, Alexandre Pouget. Measuring Fisher Information Accurately in Correlated Neural Populations
0 -- 0Gabriele Micali, Gerardo Aquino, David M. Richards, Robert G. Endres. Accurate Encoding and Decoding by Single Cells: Amplitude Versus Frequency Modulation
0 -- 0Christiana N. Fogg, Diane E. Kovats. 2015 ISCB Overton Prize Awarded to Curtis Huttenhower
0 -- 0João Sacramento, Andreas Wichert, Mark C. W. van Rossum. Energy Efficient Sparse Connectivity from Imbalanced Synaptic Plasticity Rules
0 -- 0Federico Abascal, Iakes Ezkurdia, Juan Rodriguez-Rivas, Jose Manuel Rodriguez, Angela del Pozo, Jesús Vázquez, Alfonso Valencia, Michael L. Tress. Alternatively Spliced Homologous Exons Have Ancient Origins and Are Highly Expressed at the Protein Level
0 -- 0Richard F. Murray, Khushbu Patel, Alan Yee. Posterior Probability Matching and Human Perceptual Decision Making
0 -- 0Philip E. Bourne, Steven E. Brenner, Michael B. Eisen. ‡ Computational Biology: A Decade of Appreciation and Innovation
0 -- 0Michael A. Andrews, Chris T. Bauch. Disease Interventions Can Interfere with One Another through Disease-Behaviour Interactions
0 -- 0Giulia Palermo, Inga Bauer, Pablo Campomanes, Andrea Cavalli, Andrea Armirotti, Stefania Girotto, Ursula Rothlisberger, Marco de Vivo. Keys to Lipid Selection in Fatty Acid Amide Hydrolase Catalysis: Structural Flexibility, Gating Residues and Multiple Binding Pockets

Volume 11, Issue 5

0 -- 0Julia C. Engelmann, Thomas Amann, Birgitta Ott-Rötzer, Margit Nützel, Yvonne Reinders, Jörg Reinders, Wolfgang E. Thasler, Theresa Kristl, Andreas Teufel, Christian G. Huber, Peter J. Oefner, Rainer Spang, Claus Hellerbrand. Causal Modeling of Cancer-Stromal Communication Identifies PAPPA as a Novel Stroma-Secreted Factor Activating NFκB Signaling in Hepatocellular Carcinoma
0 -- 0Wiktor Mlynarski. The Opponent Channel Population Code of Sound Location Is an Efficient Representation of Natural Binaural Sounds
0 -- 0Gaëlle Letort, Antonio Z. Politi, Hajer Ennomani, Manuel Théry, Francois Nedelec, Laurent Blanchoin. Geometrical and Mechanical Properties Control Actin Filament Organization
0 -- 0David W. P. Dolan, Anze Zupanic, Glyn Nelson, Philip Hall, Satomi Miwa, Thomas B. L. Kirkwood, Daryl P. Shanley. Integrated Stochastic Model of DNA Damage Repair by Non-homologous End Joining and p53/p21- Mediated Early Senescence Signalling
0 -- 0Gary K. Chen, Eric C. Chi, John M. O. Ranola, Kenneth Lange. Convex Clustering: An Attractive Alternative to Hierarchical Clustering
0 -- 0Christopher A. Lavender, Robert J. Gorelick, Kevin M. Weeks. Structure-Based Alignment and Consensus Secondary Structures for Three HIV-Related RNA Genomes
0 -- 0Thomas P. Prescott, Moritz Lang, Antonis Papachristodoulou. Quantification of Interactions between Dynamic Cellular Network Functionalities by Cascaded Layering
0 -- 0Tao Chen, Hue Sun Chan. Native Contact Density and Nonnative Hydrophobic Effects in the Folding of Bacterial Immunity Proteins
0 -- 0Zhi Yang Tam, Jan Gruber, Barry Halliwell, Rudiyanto Gunawan. Context-Dependent Role of Mitochondrial Fusion-Fission in Clonal Expansion of mtDNA Mutations
0 -- 0Jacopo Grilli, György Barabás, Stefano Allesina. Metapopulation Persistence in Random Fragmented Landscapes
0 -- 0Kiana Toufighi, Jae-Seong Yang, Nuno Miguel Luis, Salvador Aznar Benitah, Ben Lehner, Luis Serrano, Christina Kiel. Dissecting the Calcium-Induced Differentiation of Human Primary Keratinocytes Stem Cells by Integrative and Structural Network Analyses
0 -- 0Torsten Neher, Sen Cheng, Laurenz Wiskott. Memory Storage Fidelity in the Hippocampal Circuit: The Role of Subregions and Input Statistics
0 -- 0Kit Curtius, William D. Hazelton, Jihyoun Jeon, E. Georg Luebeck. A Multiscale Model Evaluates Screening for Neoplasia in Barrett's Esophagus
0 -- 0Wanling Song, Harsha Bajaj, Chady Nasrallah, Hualiang Jiang, Mathias Winterhalter, Jacques-Philippe Colletier, Yechun Xu. Providencia stuartii Porins at Atomic Level
0 -- 0Sebastien Naze, Christophe Bernard, Viktor K. Jirsa. Computational Modeling of Seizure Dynamics Using Coupled Neuronal Networks: Factors Shaping Epileptiform Activity
0 -- 0Matt Ravenhall, Nives Skunca, Florent Lassalle, Christophe Dessimoz. Inferring Horizontal Gene Transfer
0 -- 0Fabio Vandin, Alexandra Papoutsaki, Benjamin J. Raphael, Eli Upfal. Accurate Computation of Survival Statistics in Genome-Wide Studies
0 -- 0Thibaud Taillefumier, Ned S. Wingreen. Optimal Census by Quorum Sensing
0 -- 0Simon Farmer. Comment on "Broadband Criticality of Human Brain Network Synchronization" by Kitzbichler MG, Smith ML, Christensen SR, Bullmore E (2009) PLoS Comput Biol 5: e1000314
0 -- 0Yaroslav I. Molkov, Bartholomew J. Bacak, Adolfo E. Talpalar, Ilya A. Rybak. Mechanisms of Left-Right Coordination in Mammalian Locomotor Pattern Generation Circuits: A Mathematical Modeling View
0 -- 0Daniel Keller, Norbert Babai, Olexiy Kochubey, Yunyun Han, Henry Markram, Felix Schürmann, Ralf Schneggenburger. 2+ Channels around Docked Vesicles Explains Release Control by Multiple Channels at a CNS Synapse
0 -- 0Gianluca Ascolani, Annalisa Occhipinti, Pietro Liò. Modelling Circulating Tumour Cells for Personalised Survival Prediction in Metastatic Breast Cancer
0 -- 0Zachary D. Kurtz, Christian L. Müller, Emily R. Miraldi, Dan R. Littman, Martin J. Blaser, Richard A. Bonneau. Sparse and Compositionally Robust Inference of Microbial Ecological Networks
0 -- 0Matthew H. Ung, Frederick S. Varn, Shaoke Lou, Chao Cheng. Regulators Associated with Clinical Outcomes Revealed by DNA Methylation Data in Breast Cancer
0 -- 0Erik van Dijk, Arlo Hoogeveen, Sanne Abeln. The Hydrophobic Temperature Dependence of Amino Acids Directly Calculated from Protein Structures
0 -- 0Augustin Luna, Geoffrey B. McFadden, Mirit I. Aladjem, Kurt W. Kohn. Predicted Role of NAD Utilization in the Control of Circadian Rhythms during DNA Damage Response
0 -- 0Sepideh Babaei, Ahmed Mahfouz, Marc Hulsman, Boudewijn P. F. Lelieveldt, Jeroen de Ridder, Marcel J. T. Reinders. Hi-C Chromatin Interaction Networks Predict Co-expression in the Mouse Cortex
0 -- 0Wilfredo Blanco, Catia M. Pereira, Vinicius R. Cota, Annie C. Souza, César Rennó-Costa, Sharlene Santos, Gabriella Dias, Ana M. G. Guerreiro, Adriano B. L. Tort, Adrião D. Neto, Sidarta Ribeiro. Synaptic Homeostasis and Restructuring across the Sleep-Wake Cycle
0 -- 0Emma Pierson, Daphne Koller, Alexis Battle, Sara Mostafavi. Sharing and Specificity of Co-expression Networks across 35 Human Tissues
0 -- 0Cengiz Günay, Fred H. Sieling, Logesh Dharmar, Wei-Hsiang Lin, Verena Wolfram, Richard Marley, Richard A. Baines, Astrid A. Prinz. Drosophila Motoneuron
0 -- 0Christopher A. Lavender, Ronny Lorenz, Ge Zhang, Rita Tamayo, Ivo L. Hofacker, Kevin M. Weeks. Model-Free RNA Sequence and Structure Alignment Informed by SHAPE Probing Reveals a Conserved Alternate Secondary Structure for 16S rRNA
0 -- 0T. Scott Chen, Donald Petrey, José Ignacio Garzón, Barry Honig. Predicting Peptide-Mediated Interactions on a Genome-Wide Scale
0 -- 0Mookyung Cheon, Carol K. Hall, Iksoo Chang. 17-42 Peptides from Disordered Oligomers to U-Shape Protofilaments via Multiple Kinetic Pathways
0 -- 0Stepan Tymoshenko, Rebecca D. Oppenheim, Rasmus Agren, Jens Nielsen, Dominique Soldati-Favre, Vassily Hatzimanikatis. Toxoplasma gondii through Combined Computational and Experimental Analysis
0 -- 0Manu Setty, Christina S. Leslie. SeqGL Identifies Context-Dependent Binding Signals in Genome-Wide Regulatory Element Maps
0 -- 0Victor Garcia, Kirsten Richter, Frederik Graw, Annette Oxenius, Roland R. Regoes. Estimating the In Vivo Killing Efficacy of Cytotoxic T Lymphocytes across Different Peptide-MHC Complex Densities
0 -- 0Manfred G. Kitzbichler, Edward T. Bullmore. Power Law Scaling in Human and Empty Room MEG Recordings
0 -- 0Jonathan R. Karr, Alex H. Williams, Jeremy D. Zucker, Andreas Raue, Bernhard Steiert, Jens Timmer, Clemens Kreutz, Simon Wilkinson, Brandon A. Allgood, Brian M. Bot, Bruce R. Hoff, Michael R. Kellen, Markus W. Covert, Gustavo A. Stolovitzky, Pablo Meyer. Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models
0 -- 0Bader Al-Anzi, Patrick Arpp, Sherif Gerges, Christopher Ormerod, Noah Olsman, Kai Zinn. Experimental and Computational Analysis of a Large Protein Network That Controls Fat Storage Reveals the Design Principles of a Signaling Network
0 -- 0Isamu Okada, Hitoshi Yamamoto, Fujio Toriumi, Tatsuya Sasaki. The Effect of Incentives and Meta-incentives on the Evolution of Cooperation
0 -- 0Christoph W. Korn, Dominik R. Bach. Maintaining Homeostasis by Decision-Making
0 -- 0Alon Diament, Tamir Tuller. Improving 3D Genome Reconstructions Using Orthologous and Functional Constraints
0 -- 0Miho S. Kitazawa, Koichi Fujimoto. A Dynamical Phyllotaxis Model to Determine Floral Organ Number
0 -- 0Emily A. Cooper, Anthony M. Norcia. Predicting Cortical Dark/Bright Asymmetries from Natural Image Statistics and Early Visual Transforms
0 -- 0Ed Reznik, Chris Sander. Extensive Decoupling of Metabolic Genes in Cancer
0 -- 0Kyle S. Hickmann, Geoffrey Fairchild, Reid Priedhorsky, Nicholas Generous, James M. Hyman, Alina Deshpande, Sara Y. Del Valle. Forecasting the 2013-2014 Influenza Season Using Wikipedia
0 -- 0Michael J. Hull, Stephen R. Soffe, David J. Willshaw, Alan Roberts. Modelling the Effects of Electrical Coupling between Unmyelinated Axons of Brainstem Neurons Controlling Rhythmic Activity

Volume 11, Issue 4

0 -- 0Rodrigo Cilla, Vinodh Mechery, Beatriz Hernandez de Madrid, Steven Del Signore, Iván Dotú, Victor Hatini. Segmentation and Tracking of Adherens Junctions in 3D for the Analysis of Epithelial Tissue Morphogenesis
0 -- 0Bernhard Knapp, Rémi Bardenet, Miguel O. Bernabeu, Rafel Bordas, Maria Bruna, Ben Calderhead, Jonathan Cooper, Alexander G. Fletcher, Derek Groen, Bram Kuijper, Joanna Lewis, Greg J. McInerny, Timo Minssen, James M. Osborne, Verena Paulitschke, Joe Pitt-Francis, Jelena Todoric, Christian A. Yates, David Gavaghan, Charlotte M. Deane. Ten Simple Rules for a Successful Cross-Disciplinary Collaboration
0 -- 0Teresa K. Attwood, Erik Bongcam-Rudloff, Michelle E. Brazas, Manuel Corpas, Pascale Gaudet, Fran Lewitter, Nicola J. Mulder, Patricia M. Palagi, Maria Victoria Schneider, Celia W. G. van Gelder. GOBLET: The Global Organisation for Bioinformatics Learning, Education and Training
0 -- 0Xiliang Zheng, Jin Wang. The Universal Statistical Distributions of the Affinity, Equilibrium Constants, Kinetics and Specificity in Biomolecular Recognition
0 -- 0Debabani Ganguly, Jianhan Chen. Modulation of the Disordered Conformational Ensembles of the p53 Transactivation Domain by Cancer-Associated Mutations
0 -- 0Daniel Bendor. The Role of Inhibition in a Computational Model of an Auditory Cortical Neuron during the Encoding of Temporal Information
0 -- 0Tae J. Lee, Jeffrey V. Wong, Sena Bae, Anna Jisu Lee, Allison J. Lopatkin, Fan Yuan, Lingchong You. A Power-Law Dependence of Bacterial Invasion on Mammalian Host Receptors
0 -- 0Holly M. Bik, Alistair D. M. Dove, Miriam C. Goldstein, Rebecca R. Helm, Rick MacPherson, Kim Martini, Alexandria Warneke, Craig McClain. Ten Simple Rules for Effective Online Outreach
0 -- 0Paul Egan, Jeffrey Moore, Christian Schunn, Jonathan Cagan, Philip LeDuc. Emergent Systems Energy Laws for Predicting Myosin Ensemble Processivity
0 -- 0Simon Sponberg, Thomas L. Daniel, Adrienne L. Fairhall. Dual Dimensionality Reduction Reveals Independent Encoding of Motor Features in a Muscle Synergy for Insect Flight Control
0 -- 0Nils A. Berglund, Thomas J. Piggot, Damien Jefferies, Richard B. Sessions, Peter J. Bond, Syma Khalid. coli: A Molecular Dynamics Study
0 -- 0Christiaan A. de Leeuw, Joris M. Mooij, Tom Heskes, Danielle Posthuma. MAGMA: Generalized Gene-Set Analysis of GWAS Data
0 -- 0Daifeng Wang, Koon-Kiu Yan, Cristina Sisu, Chao Cheng, Joel S. Rozowsky, William Meyerson, Mark B. Gerstein. Loregic: A Method to Characterize the Cooperative Logic of Regulatory Factors
0 -- 0Jyotika Bahuguna, Ad Aertsen, Arvind Kumar. Existence and Control of Go/No-Go Decision Transition Threshold in the Striatum
0 -- 0Ross S. Williamson, Maneesh Sahani, Jonathan W. Pillow. The Equivalence of Information-Theoretic and Likelihood-Based Methods for Neural Dimensionality Reduction
0 -- 0Nathan F. Lepora, Giovanni Pezzulo. Embodied Choice: How Action Influences Perceptual Decision Making
0 -- 0Ayala Matzner, Izhar Bar-Gad. Quantifying Spike Train Oscillations: Biases, Distortions and Solutions
0 -- 0Iddo Friedberg, Mark N. Wass, Sean D. Mooney, Predrag Radivojac. Ten Simple Rules for a Community Computational Challenge
0 -- 0Adam J. Kucharski, W. John Edmunds. Characterizing the Transmission Potential of Zoonotic Infections from Minor Outbreaks
0 -- 0Joon-Young Moon, UnCheol Lee, Stefanie Blain-Moraes, George A. Mashour. General Relationship of Global Topology, Local Dynamics, and Directionality in Large-Scale Brain Networks
0 -- 0Stuart Aitken, Shigeyuki Magi, Ahmad M. N. Alhendi, Masayoshi Itoh, Hideya Kawaji, Timo Lassmann, Carsten O. Daub, Erik Arner, Piero Carninci, Alistair R. R. Forrest, Yoshihide Hayashizaki, Levon M. Khachigian, Mariko Okada-Hatakeyama, Colin A. Semple. Transcriptional Dynamics Reveal Critical Roles for Non-coding RNAs in the Immediate-Early Response
0 -- 0Ka Wai Lin, Angela Liao, Amina A. Qutub. Simulation Predicts IGFBP2-HIF1α Interaction Drives Glioblastoma Growth
0 -- 0Manoj Gambhir, Thomas A. Clark, Simon Cauchemez, Sara Y. Tartof, David L. Swerdlow, Neil M. Ferguson. A Change in Vaccine Efficacy and Duration of Protection Explains Recent Rises in Pertussis Incidence in the United States
0 -- 0Katja N. Rybakova, Frank J. Bruggeman, Aleksandra Tomaszewska, Martijn J. Moné, Carsten Carlberg, Hans V. Westerhoff. Multiplex Eukaryotic Transcription (In)activation: Timing, Bursting and Cycling of a Ratchet Clock Mechanism
0 -- 0Giulia Menconi, Andrea Bedini, Roberto Barale, Isabella Sbrana. Saccharomyces cerevisiae
0 -- 0Ickwon Choi, Amy W. Chung, Todd J. Suscovich, Supachai Rerks-Ngarm, Punnee Pitisuttithum, Sorachai Nitayaphan, Jaranit Kaewkungwal, Robert J. O'Connell, Donald Francis, Merlin L. Robb, Nelson Michael, Jerome H. Kim, Galit Alter, Margaret E. Ackerman, Chris Bailey-Kellogg. Machine Learning Methods Enable Predictive Modeling of Antibody Feature: Function Relationships in RV144 Vaccinees
0 -- 0Noa Slater, Yoram Louzoun, Loren Gragert, Martin Maiers, Ansu Chatterjee, Mark Albrecht. Power Laws for Heavy-Tailed Distributions: Modeling Allele and Haplotype Diversity for the National Marrow Donor Program
0 -- 0Jian Tian, Jaie C. Woodard, Anna Whitney, Eugene I. Shakhnovich. Thermal Stabilization of Dihydrofolate Reductase Using Monte Carlo Unfolding Simulations and Its Functional Consequences
0 -- 0Kai Olav Ellefsen, Jean-Baptiste Mouret, Jeff Clune. Neural Modularity Helps Organisms Evolve to Learn New Skills without Forgetting Old Skills
0 -- 0William F. Flynn, Max W. Chang, Zhiqiang Tan, Glenn Oliveira, Jinyun Yuan, Jason F. Okulicz, Bruce E. Torbett, Ronald M. Levy. Deep Sequencing of Protease Inhibitor Resistant HIV Patient Isolates Reveals Patterns of Correlated Mutations in Gag and Protease
0 -- 0Sébastien Giguère, François Laviolette, Mario Marchand, Denise Tremblay, Sylvain Moineau, Xinxia Liang, Éric Biron, Jacques Corbeil. Machine Learning Assisted Design of Highly Active Peptides for Drug Discovery
0 -- 0Fernando R. Fernandez, Paola Malerba, John A. White. Non-linear Membrane Properties in Entorhinal Cortical Stellate Cells Reduce Modulation of Input-Output Responses by Voltage Fluctuations
0 -- 0Naoki Hiratani, Tomoki Fukai. Mixed Signal Learning by Spike Correlation Propagation in Feedback Inhibitory Circuits
0 -- 0Tor D. Wager, Jian Kang, Timothy D. Johnson, Thomas E. Nichols, Ajay B. Satpute, Lisa Feldman Barrett. A Bayesian Model of Category-Specific Emotional Brain Responses
0 -- 0Stefan Flasche, Olivier Le Polain de Waroux, Katherine L. O'Brien, W. John Edmunds. The Serotype Distribution among Healthy Carriers before Vaccination Is Essential for Predicting the Impact of Pneumococcal Conjugate Vaccine on Invasive Disease
0 -- 0Timo R. Maarleveld, Meike T. Wortel, Brett G. Olivier, Bas Teusink, Frank J. Bruggeman. Interplay between Constraints, Objectives, and Optimality for Genome-Scale Stoichiometric Models
0 -- 0Mei Zhan, Matthew M. Crane, Eugeni V. Entchev, Antonio Caballero, Diana Andrea Fernandes de Abreu, QueeLim Ch'ng, Hang Lu. Caenorhabditis elegans
0 -- 0Thomas W. Spiesser, Clemens Kühn, Marcus Krantz, Edda Klipp. CLB2 mRNA Can Constitute a Growth Rate Dependent Daughter Sizer
0 -- 0Kevin Thurley, Daniel Gerecht, Elfriede Friedmann, Thomas Höfer. Three-Dimensional Gradients of Cytokine Signaling between T Cells
0 -- 0Juliane Siebourg-Polster, Daria Mudrak, Mario Emmenlauer, Pauli Rämö, Christoph Dehio, Urs Greber, Holger Fröhlich, Niko Beerenwinkel. NEMix: Single-cell Nested Effects Models for Probabilistic Pathway Stimulation
0 -- 0Hannah R. Meredith, Allison J. Lopatkin, Deverick J. Anderson, Lingchong You. Bacterial Temporal Dynamics Enable Optimal Design of Antibiotic Treatment
0 -- 0Anne-Laure Boulesteix. Ten Simple Rules for Reducing Overoptimistic Reporting in Methodological Computational Research
0 -- 0Willemijn Groenendaal, Francis A. Ortega, Armen R. Kherlopian, Andrew C. Zygmunt, Trine Krogh-Madsen, David J. Christini. Cell-Specific Cardiac Electrophysiology Models
0 -- 0Albertas Janulevicius, Mark van Loosdrecht, Cristian Picioreanu. Short-Range Guiding Can Result in the Formation of Circular Aggregates in Myxobacteria Populations
0 -- 0Nancy K. Drew, Mackenzie A. Eagleson, Danny B. Baldo Jr., Kevin Kit Parker, Anna Grosberg. Metrics for Assessing Cytoskeletal Orientational Correlations and Consistency
0 -- 0Fabio Pardi, Celine Scornavacca. Reconstructible Phylogenetic Networks: Do Not Distinguish the Indistinguishable
0 -- 0Daniel K. Wells, Yishan Chuang, Louis M. Knapp, Dirk Brockmann, William L. Kath, Joshua N. Leonard. Spatial and Functional Heterogeneities Shape Collective Behavior of Tumor-Immune Networks
0 -- 0Susan Dina Ghiassian, Jörg Menche, Albert-László Barabási. A DIseAse MOdule Detection (DIAMOnD) Algorithm Derived from a Systematic Analysis of Connectivity Patterns of Disease Proteins in the Human Interactome
0 -- 0Romain Brette. What Is the Most Realistic Single-Compartment Model of Spike Initiation?
0 -- 0Jorge G. T. Zañudo, Réka Albert. Cell Fate Reprogramming by Control of Intracellular Network Dynamics
0 -- 0Noorain Khan, Narendar Kolimi, Thenmalarchelvi Rathinavelan. Twisting Right to Left: A...A Mismatch in a CAG Trinucleotide Repeat Overexpansion Provokes Left-Handed Z-DNA Conformation
0 -- 0Melanie I. Stefan, Johanna L. Gutlerner, Richard T. Born, Michael Springer. The Quantitative Methods Boot Camp: Teaching Quantitative Thinking and Computing Skills to Graduate Students in the Life Sciences
0 -- 0Andy Phaiboun, Yiming Zhang, Boryung Park, Minsu Kim. Survival Kinetics of Starving Bacteria Is Biphasic and Density-Dependent
0 -- 0Lorenza Alice D'Alessandro, Regina Samaga, Tim Maiwald, Seong-Hwan Rho, Sandra Bonefas, Andreas Raue, Nao Iwamoto, Alexandra Kienast, Katharina Waldow, Rene Meyer, Marcel Schilling, Jens Timmer, Steffen Klamt, Ursula Klingmüller. Disentangling the Complexity of HGF Signaling by Combining Qualitative and Quantitative Modeling
0 -- 0Pedro Saa, Lars K. Nielsen. A General Framework for Thermodynamically Consistent Parameterization and Efficient Sampling of Enzymatic Reactions
0 -- 0Ethan S. Sokol, Sandhya Sanduja, Dexter X. Jin, Daniel H. Miller, Robert A. Mathis, Piyush B. Gupta. Perturbation-Expression Analysis Identifies RUNX1 as a Regulator of Human Mammary Stem Cell Differentiation
0 -- 0Cody J. Weinberger, James A. Evans, Stefano Allesina. Ten Simple (Empirical) Rules for Writing Science
0 -- 0Juan Palacios-Moreno, Lauren Foltz, Ailan Guo, Matthew P. Stokes, Emily D. Kuehn, Lynn George, Michael Comb, Mark L. Grimes. Neuroblastoma Tyrosine Kinase Signaling Networks Involve FYN and LYN in Endosomes and Lipid Rafts
0 -- 0Michael D. O'Connell, Gregory T. Reeves. Drosophila Embryo May Extend the Dynamic Range of the Dorsal Gradient
0 -- 0Tom Lindström, Michael J. Tildesley, Colleen Webb. A Bayesian Ensemble Approach for Epidemiological Projections
0 -- 0Tomás Trnka, Stanislav Kozmon, Igor Tvaroska, Jaroslav Koca. Stepwise Catalytic Mechanism via Short-Lived Intermediate Inferred from Combined QM/MM MERP and PES Calculations on Retaining Glycosyltransferase ppGalNAcT2
0 -- 0Changwang Zhang, Shi Zhou, Elisabetta Groppelli, Pierre Pellegrino, Ian Williams, Persephone Borrow, Benjamin M. Chain, Clare Jolly. Hybrid Spreading Mechanisms and T Cell Activation Shape the Dynamics of HIV-1 Infection
0 -- 0Federica Lombardi, Kalyan Golla, Darren J. Fitzpatrick, Fergal P. Casey, Niamh Moran, Denis C. Shields. Discovering Anti-platelet Drug Combinations with an Integrated Model of Activator-Inhibitor Relationships, Activator-Activator Synergies and Inhibitor-Inhibitor Synergies
0 -- 0Richard J. Roberts. Ten Simple Rules to Win a Nobel Prize
0 -- 0Peter Klimek, Alexandra Kautzky-Willer, Anna Chmiel, Irmgard Schiller-Frühwirth, Stefan Thurner. Quantification of Diabetes Comorbidity Risks across Life Using Nation-Wide Big Claims Data
0 -- 0Gabriel R. A. Margarido, David Heckerman. ConPADE: Genome Assembly Ploidy Estimation from Next-Generation Sequencing Data
0 -- 0Nik J. Cunniffe, Richard O. J. H. Stutt, R. Erik DeSimone, Tim R. Gottwald, Christopher A. Gilligan. Optimising and Communicating Options for the Control of Invasive Plant Disease When There Is Epidemiological Uncertainty

Volume 11, Issue 3

0 -- 0Matteo Mainetti, Giorgio A. Ascoli. A Neural Mechanism for Background Information-Gated Learning Based on Axonal-Dendritic Overlaps
0 -- 0Jaldert O. Rombouts, Sander M. Bohte, Pieter R. Roelfsema. How Attention Can Create Synaptic Tags for the Learning of Working Memories in Sequential Tasks
0 -- 0Woochul Nam, Bogdan I. Epureanu. Highly Loaded Behavior of Kinesins Increases the Robustness of Transport Under High Resisting Loads
0 -- 0Antreas C. Kalli, Mark S. P. Sansom, Reinhart A. F. Reithmeier. +-Uracil Symporter in Lipid Bilayers Reveal a Closed State and a Selective Interaction with Cardiolipin
0 -- 0Davide Provasi, Mustafa Burak Boz, Jennifer M. Johnston, Marta Filizola. Preferred Supramolecular Organization and Dimer Interfaces of Opioid Receptors from Simulated Self-Association
0 -- 0Francisco Martínez-Jiménez, Marc A. Martí-Renom. Ligand-Target Prediction by Structural Network Biology Using nAnnoLyze
0 -- 0João Couto, Daniele Linaro, E. De Schutter, Michele Giugliano. In Vitro
0 -- 0Nicolas Guex, Isaac Crespo, Sylvian Bron, Assia Ifticene-Treboux, Eveline Faes-van't Hull, Solange Kharoubi, Robin Liechti, Patricia Werffeli, Mark Ibberson, Francois Majo, Michäel Nicolas, Julien Laurent, Abhishek Garg, Khalil Zaman, Hans-Anton Lehr, Brian J. Stevenson, Curzio Rüegg, George Coukos, Jean-François Delaloye, Ioannis Xenarios, Marie-Agnes Doucey. Angiogenic Activity of Breast Cancer Patients' Monocytes Reverted by Combined Use of Systems Modeling and Experimental Approaches
0 -- 0Alejandro Torres-Sánchez, Jesús Gómez-Gardeñes, Fernando Falo. An Integrative Approach for Modeling and Simulation of Heterocyst Pattern Formation in Cyanobacteria Filaments
0 -- 0Vesna Memisevic, Nela Zavaljevski, Seesandra V. Rajagopala, Keehwan Kwon, Rembert Pieper, David DeShazer, Jaques Reifman, Anders Wallqvist. Burkholderia mallei Infectivity Mechanisms
0 -- 0Jérémie Sibille, Khanh Dao Duc, David Holcman, Nathalie Rouach. The Neuroglial Potassium Cycle during Neurotransmission: Role of Kir4.1 Channels
0 -- 0Loes C. J. van Dam, Marc O. Ernst. Mapping Shape to Visuomotor Mapping: Learning and Generalisation of Sensorimotor Behaviour Based on Contextual Information
0 -- 0Feng Fu, Martin A. Nowak, Sebastian Bonhoeffer. Spatial Heterogeneity in Drug Concentrations Can Facilitate the Emergence of Resistance to Cancer Therapy
0 -- 0Davide Albanese, Carlotta De Filippo, Duccio Cavalieri, Claudio Donati. Explaining Diversity in Metagenomic Datasets by Phylogenetic-Based Feature Weighting
0 -- 0Adrien Wohrer, Christian K. Machens. On the Number of Neurons and Time Scale of Integration Underlying the Formation of Percepts in the Brain
0 -- 0Matthew Hartfield, Samuel Alizon. Within-Host Stochastic Emergence Dynamics of Immune-Escape Mutants
0 -- 0Jan Poleszczuk, Philip Hahnfeldt, Heiko Enderling. Evolution and Phenotypic Selection of Cancer Stem Cells
0 -- 0Giles W. Story, Ivo Vlaev, Peter Dayan, Ben Seymour, Ara Darzi, Raymond J. Dolan. Anticipation and Choice Heuristics in the Dynamic Consumption of Pain Relief
0 -- 0Adrian M. Haith, David M. Huberdeau, John W. Krakauer. Hedging Your Bets: Intermediate Movements as Optimal Behavior in the Context of an Incomplete Decision
0 -- 0Jérôme R. D. Soiné, Christoph A. Brand, Jonathan Stricker, Patrick W. Oakes, Margaret L. Gardel, Ulrich S. Schwarz. Model-based Traction Force Microscopy Reveals Differential Tension in Cellular Actin Bundles
0 -- 0Adam Sol Shai, Costas A. Anastassiou, Matthew E. Larkum, Christof Koch. Physiology of Layer 5 Pyramidal Neurons in Mouse Primary Visual Cortex: Coincidence Detection through Bursting
0 -- 0Tomás Helikar, Christine E. Cutucache, Lauren M. Dahlquist, Tyler A. Herek, Joshua J. Larson, Jim A. Rogers. Integrating Interactive Computational Modeling in Biology Curricula
0 -- 0Oren E. Livne, Lide Han, Gorka Alkorta-Aranburu, William Wentworth-Sheilds, Mark Abney, Carole Ober, Dan L. Nicolae. PRIMAL: Fast and Accurate Pedigree-based Imputation from Sequence Data in a Founder Population
0 -- 0Marco D. Visser, Sean M. McMahon, Cory Merow, Philip M. Dixon, Sydne Record, Eelke Jongejans. Speeding Up Ecological and Evolutionary Computations in R; Essentials of High Performance Computing for Biologists
0 -- 0Eugenio Valdano, Chiara Poletto, Armando Giovannini, Diana Palma, Lara Savini, Vittoria Colizza. Predicting Epidemic Risk from Past Temporal Contact Data
0 -- 0Christopher M. DeBoever, Emanuela M. Ghia, Peter J. Shepard, Laura Rassenti, Christian L. Barrett, Kristen Jepsen, Catriona H. M. Jamieson, Dennis Carson, Thomas J. Kipps, Kelly A. Frazer. SF3B1-mutated Cancers
0 -- 0Minseung Kim, Violeta Zorraquino, Ilias Tagkopoulos. Microbial Forensics: Predicting Phenotypic Characteristics and Environmental Conditions from Large-Scale Gene Expression Profiles
0 -- 0Christopher R. S. Banerji, Simone Severini, Carlos Caldas, Andrew E. Teschendorff. Intra-Tumour Signalling Entropy Determines Clinical Outcome in Breast and Lung Cancer
0 -- 0David Lovell, Vera Pawlowsky-Glahn, Juan José Egozcue, Samuel Marguerat, Jürg Bähler. Proportionality: A Valid Alternative to Correlation for Relative Data
0 -- 0Maxim Volgushev, Vladimir Ilin, Ian H. Stevenson. In Vitro Experiments
0 -- 0Fiete Haack, Heiko Lemcke, Roland Ewald, Tareck Rharass, Adelinde M. Uhrmacher. Spatio-temporal Model of Endogenous ROS and Raft-Dependent WNT/Beta-Catenin Signaling Driving Cell Fate Commitment in Human Neural Progenitor Cells
0 -- 0Thomas Obadia, Romain Silhol, Lulla Opatowski, Laura Temime, Judith Legrand, Anne C. M. Thiébaut, Jean-Louis Herrmann, Eric Fleury, Didier Guillemot, Pierre-Yves Boëlle. Staphylococcus aureus in Hospitals
0 -- 0James A. Geraets, Eric C. Dykeman, Peter G. Stockley, Neil A. Ranson, Reidun Twarock. Asymmetric Genome Organization in an RNA Virus Revealed via Graph-Theoretical Analysis of Tomographic Data
0 -- 0Yu-Chen Lo, Silvia Senese, Chien-Ming Li, Qiyang Hu, Yong Huang, Robert Damoiseaux, Jorge Z. Torres. Large-Scale Chemical Similarity Networks for Target Profiling of Compounds Identified in Cell-Based Chemical Screens
0 -- 0Deborah A. Weighill, Daniel A. Jacobson. 3-way Networks: Application of Hypergraphs for Modelling Increased Complexity in Comparative Genomics
0 -- 0Omar Al Hammal, David Alonso, Rampal S. Etienne, Stephen J. Cornell. When Can Species Abundance Data Reveal Non-neutrality?
0 -- 0Tamar Friedlander, Avraham E. Mayo, Tsvi Tlusty, Uri Alon. Evolution of Bow-Tie Architectures in Biology
0 -- 0Lucas A. Defelipe, Esteban Lanzarotti, Diego F. Gauto, Marcelo A. Marti, Adrian Gustavo Turjanski. Protein Topology Determines Cysteine Oxidation Fate: The Case of Sulfenyl Amide Formation among Protein Families
0 -- 0Marc D. Ryser, Evan R. Myers, Rick Durrett. HPV Clearance and the Neglected Role of Stochasticity
0 -- 0Cheng Lv, Xiaoguang Li, Fangting Li, Tiejun Li. Energy Landscape Reveals That the Budding Yeast Cell Cycle Is a Robust and Adaptive Multi-stage Process
0 -- 0Vassilios Christopoulos, James Bonaiuto, Richard A. Andersen. A Biologically Plausible Computational Theory for Value Integration and Action Selection in Decisions with Competing Alternatives
0 -- 0Alan L. Hutchison, Mark Maienschein-Cline, Andrew H. Chiang, S. M. Ali Tabei, Herman Gudjonson, Neil Bahroos, Ravi Allada, Aaron R. Dinner. Improved Statistical Methods Enable Greater Sensitivity in Rhythm Detection for Genome-Wide Data
0 -- 0Fan Yang, Evangelia Petsalaki, Thomas Rolland, David E. Hill, Marc Vidal, Frederick P. Roth. Protein Domain-Level Landscape of Cancer-Type-Specific Somatic Mutations
0 -- 0Dimitri Yatsenko, Kresimir Josic, Alexander S. Ecker, Emmanouil Froudarakis, R. James Cotton, Andreas S. Tolias. Improved Estimation and Interpretation of Correlations in Neural Circuits
0 -- 0Alistair M. Senior, Michael A. Charleston, Mathieu Lihoreau, Jérôme Buhl, David Raubenheimer, Stephen J. Simpson. Evolving Nutritional Strategies in the Presence of Competition: A Geometric Agent-Based Model
0 -- 0Kristen Fortney, Joshua Griesman, Max Kotlyar, Chiara Pastrello, Marc Angeli, Ming-Sound Tsao, Igor Jurisica. Prioritizing Therapeutics for Lung Cancer: An Integrative Meta-analysis of Cancer Gene Signatures and Chemogenomic Data
0 -- 0Luca Giuggioli, Thomas J. McKetterick, Marc Holderied. Delayed Response and Biosonar Perception Explain Movement Coordination in Trawling Bats
0 -- 0Miriam C. Klein-Flügge, Steven W. Kennerley, Ana C. Saraiva, Will D. Penny, Sven Bestmann. Behavioral Modeling of Human Choices Reveals Dissociable Effects of Physical Effort and Temporal Delay on Reward Devaluation
0 -- 0Amanda Miguel, Jen Hsin, Tianyun Liu, Grace W. Tang, Russ B. Altman, Kerwyn Casey Huang. Variations in the Binding Pocket of an Inhibitor of the Bacterial Division Protein FtsZ across Genotypes and Species
0 -- 0Bruno B. Averbeck. Theory of Choice in Bandit, Information Sampling and Foraging Tasks
0 -- 0Carson C. Chow, Kelsey K. Finn, Geoffery B. Storchan, Xinping Lu, Xiaoyan Sheng, S. Stoney Simons Jr.. Kinetically-Defined Component Actions in Gene Repression

Volume 11, Issue 2

0 -- 0Johannes Eckstein, Nikolaus Berndt, Hermann-Georg Holzhütter. Computer Simulations Suggest a Key Role of Membranous Nanodomains in Biliary Lipid Secretion
0 -- 0Renaud Jolivet, Jay S. Coggan, Igor Allaman, Pierre J. Magistretti. Multi-timescale Modeling of Activity-Dependent Metabolic Coupling in the Neuron-Glia-Vasculature Ensemble
0 -- 0David G. García Münzer, Margaritis Kostoglou, Michael C. Georgiadis, Efstratios N. Pistikopoulos, Athanasios Mantalaris. Cyclin and DNA Distributed Cell Cycle Model for GS-NS0 Cells
0 -- 0Elisa M. Tartaglia, Nicolas Brunel, Gianluigi Mongillo. Modulation of Network Excitability by Persistent Activity: How Working Memory Affects the Response to Incoming Stimuli
0 -- 0Kasper Jensen, Yueqiong Ni, Gianni Panagiotou, Irene Kouskoumvekaki. Developing a Molecular Roadmap of Drug-Food Interactions
0 -- 0Benjamin J. Binder, Joanna F. Sundstrom, Jennifer M. Gardner, Vladimir Jiranek, Stephen G. Oliver. Quantifying Two-Dimensional Filamentous and Invasive Growth Spatial Patterns in Yeast Colonies
0 -- 0Benjamin Allen, Christine Sample, Yulia Dementieva, Ruben C. Medeiros, Christopher Paoletti, Martin A. Nowak. The Molecular Clock of Neutral Evolution Can Be Accelerated or Slowed by Asymmetric Spatial Structure
0 -- 0Renaud Bastien, Stéphane Douady, Bruno Moulia. A Unified Model of Shoot Tropism in Plants: Photo-, Gravi- and Propio-ception
0 -- 0Claude Gérard, John J. Tyson, Damien Coudreuse, Béla Novák. Cell Cycle Control by a Minimal Cdk Network
0 -- 0Aidan Budd, Manuel Corpas, Michelle D. Brazas, Jonathan C. Fuller, Jeremy Goecks, Nicola J. Mulder, Magali Michaut, B. F. Francis Ouellette, Aleksandra Pawlik, Niklas Blomberg. A Quick Guide for Building a Successful Bioinformatics Community
0 -- 0Mei Yan Lee, Scott L. Diamond. A Human Platelet Calcium Calculator Trained by Pairwise Agonist Scanning
0 -- 0David K. Johnson, John Karanicolas. Selectivity by Small-Molecule Inhibitors of Protein Interactions Can Be Driven by Protein Surface Fluctuations
0 -- 0Laura R. González-Ramírez, Omar J. Ahmed, Sydney S. Cash, C. Eugene Wayne, Mark A. Kramer. A Biologically Constrained, Mathematical Model of Cortical Wave Propagation Preceding Seizure Termination
0 -- 0Jagannath Swaminathan, Alexander A. Boulgakov, Edward M. Marcotte. A Theoretical Justification for Single Molecule Peptide Sequencing
0 -- 0Martina Kutmon, Martijn P. van Iersel, Anwesha Bohler, Thomas Kelder, Nuno Nunes, Alexander R. Pico, Chris T. A. Evelo. PathVisio 3: An Extendable Pathway Analysis Toolbox
0 -- 0Andrew J. K. Conlan, Ellen Brooks-Pollock, Trevelyan J. McKinley, Andrew P. Mitchell, Gareth J. Jones, Martin Vordermeier, James L. N. Wood. Potential Benefits of Cattle Vaccination as a Supplementary Control for Bovine Tuberculosis
0 -- 0Philip E. Bourne. Confronting the Ethical Challenges of Big Data in Public Health
0 -- 0Edward J. Banigan, Tajie H. Harris, David A. Christian, Christopher A. Hunter, Andrea J. Liu. + T Cell Migration in the Lymph Node in the Absence of Inflammation Revealed by Quantitative Migration Analysis
0 -- 0Daniel M. Keenan, Amy W. Quinkert, Donald W. Pfaff. Stochastic Modeling of Mouse Motor Activity under Deep Brain Stimulation: The Extraction of Arousal Information
0 -- 0Hinrich Arnoldt, Shuwen Chang, Sven Jahnke, Birk Urmersbach, Holger Taschenberger, Marc Timme. When Less Is More: Non-monotonic Spike Sequence Processing in Neurons
0 -- 0Christian Meisel, Andreas Klaus, Christian Kuehn, Dietmar Plenz. Critical Slowing Down Governs the Transition to Neuron Spiking
0 -- 0Daniel Malagarriga, Alessandro E. P. Villa, Jordi García-Ojalvo, Antonio J. Pons Rivero. Mesoscopic Segregation of Excitation and Inhibition in a Brain Network Model
0 -- 0Guangyou Duan, Dirk Walther. The Roles of Post-translational Modifications in the Context of Protein Interaction Networks
0 -- 0Ishutesh Jain, Mandar M. Inamdar, Ranjith Padinhateeri. Statistical Mechanics Provides Novel Insights into Microtubule Stability and Mechanism of Shrinkage
0 -- 0Ignacia Echeverria, Garegin A. Papoian. DNA Exit Ramps Are Revealed in the Binding Landscapes Obtained from Simulations in Helical Coordinates
0 -- 0Hanna Julienne, Benjamin Audit, Alain Arneodo. Embryonic Stem Cell Specific "Master" Replication Origins at the Heart of the Loss of Pluripotency
0 -- 0Eric Bonnet, Laurence Calzone, Tom Michoel. Integrative Multi-omics Module Network Inference with Lemon-Tree
0 -- 0Yoonji Lee, Sun Choi, Changbong Hyeon. 2A Adenosine Receptor
0 -- 0J. Harry Caufield, Marco Abreu, Christopher Wimble, Peter Uetz. Protein Complexes in Bacteria
0 -- 0Vladimir Potapov, Jenifer B. Kaplan, Amy E. Keating. Data-Driven Prediction and Design of bZIP Coiled-Coil Interactions
0 -- 0Thomas Lengauer, Ruth Nussinov. How to Write a Presubmission Inquiry
0 -- 0Yonatan Schweitzer, Michael M. Kozlov. Membrane-Mediated Interaction between Strongly Anisotropic Protein Scaffolds
0 -- 0Julien Jorda, Yu Liu, Thomas A. Bobik, Todd O. Yeates. Exploring Bacterial Organelle Interactomes: A Model of the Protein-Protein Interaction Network in the Pdu Microcompartment
0 -- 0Paul Thatcher Edlefsen, Morgane Rolland, Tomer Hertz, Sodsai Tovanabutra, Andrew J. Gartland, Allan C. deCamp, Craig A. Magaret, Hasan Ahmed, Raphael Gottardo, Michal Juraska, Connor McCoy, Brendan B. Larsen, Eric Sanders-Buell, Chris Carrico, Sergey Menis, Meera Bose, Miguel A. Arroyo, Robert J. O'Connell, Sorachai Nitayaphan, Punnee Pitisuttithum, Jaranit Kaewkungwal, Supachai Rerks-Ngarm, Merlin L. Robb, Tatsiana Kirys, Ivelin Georgiev, Peter D. Kwong, Konrad Scheffler, Sergei L. Kosakovsky Pond, Jonathan M. Carlson, Nelson Michael, William R. Schief, James I. Mullins, Jerome Kim, Peter B. Gilbert. : Comprehensive Sieve Analysis of Breakthrough HIV-1 Sequences in the RV144 Vaccine Efficacy Trial
0 -- 0Thomas C. Erren, Tracy E. Slanger, J. Valérie Groß, Philip E. Bourne, Paul Cullen. Ten Simple Rules for Lifelong Learning, According to Hamming
0 -- 0Adrián Ponce-Alvarez, Gustavo Deco, Patric Hagmann, Gian Luca Romani, Dante Mantini, Maurizio Corbetta. Resting-State Temporal Synchronization Networks Emerge from Connectivity Topology and Heterogeneity
0 -- 0Bence Ferdinandy, Enys Mones, Tamás Vicsek, Viktor Müller. HIV Competition Dynamics over Sexual Networks: First Comer Advantage Conserves Founder Effects
0 -- 0Jorge M. Pacheco, Vítor V. Vasconcelos, Francisco C. Santos, Brian Skyrms. Co-evolutionary Dynamics of Collective Action with Signaling for a Quorum
0 -- 0Ying Li, Guang Li, Benjamin Görling, Burkhard Luy, Jiulin Du, Jun Yan. Integrative Analysis of Circadian Transcriptome and Metabolic Network Reveals the Role of De Novo Purine Synthesis in Circadian Control of Cell Cycle
0 -- 0Saheed Imam, Daniel R. Noguera, Timothy J. Donohue. An Integrated Approach to Reconstructing Genome-Scale Transcriptional Regulatory Networks
0 -- 0Xavier Didelot, Daniel J. Wilson. ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes
0 -- 0Tiberiu Tesileanu, Lucy J. Colwell, Stanislas Leibler. Protein Sectors: Statistical Coupling Analysis versus Conservation
0 -- 0Effy Vayena, Marcel Salathé, Lawrence C. Madoff, John S. Brownstein. Ethical Challenges of Big Data in Public Health
0 -- 0Renske M. A. Vroomans, Paulien Hogeweg, Kirsten H. W. J. ten Tusscher. Segment-Specific Adhesion as a Driver of Convergent Extension
0 -- 0Benjamin Dunn, Maria Mørreaunet, Yasser Roudi. Correlations and Functional Connections in a Population of Grid Cells
0 -- 0Eric Lowet, Mark Roberts, Avgis Hadjipapas, Alina Peter, Jan van der Eerden, Peter De Weerd. Input-Dependent Frequency Modulation of Cortical Gamma Oscillations Shapes Spatial Synchronization and Enables Phase Coding

Volume 11, Issue 12

0 -- 0Lavisha Jindal, Eldon Emberly. In Vitro ParA-ParB System
0 -- 0Shyam Kumar Sudhakar, Benjamin Torben-Nielsen, Erik De Schutter. Cerebellar Nuclear Neurons Use Time and Rate Coding to Transmit Purkinje Neuron Pauses
0 -- 0Adam James Waite, Caroline Cannistra, Wenying Shou. Defectors Can Create Conditions That Rescue Cooperation
0 -- 0Alex Pavlides, S. John Hogan, Rafal Bogacz. Computational Models Describing Possible Mechanisms for Generation of Excessive Beta Oscillations in Parkinson's Disease
0 -- 0Shree Hari Gautam, Thanh T. Hoang, Kylie McClanahan, Stephen K. Grady, Woodrow L. Shew. Maximizing Sensory Dynamic Range by Tuning the Cortical State to Criticality
0 -- 0Matthew Ruffalo, Mehmet Koyutürk, Roded Sharan. Network-Based Integration of Disparate Omic Data To Identify "Silent Players" in Cancer
0 -- 0Taina T. Immonen, Jessica M. Conway, Ethan O. Romero-Severson, Alan S. Perelson, Thomas Leitner. Recombination Enhances HIV-1 Envelope Diversity by Facilitating the Survival of Latent Genomic Fragments in the Plasma Virus Population
0 -- 0Christoph Hartmann, Andreea Lazar, Bernhard Nessler, Jochen Triesch. Where's the Noise? Key Features of Spontaneous Activity and Neural Variability Arise through Learning in a Deterministic Network
0 -- 0Marcelo Gomes Mattar, Michael W. Cole, Sharon L. Thompson-Schill, Danielle S. Bassett. A Functional Cartography of Cognitive Systems
0 -- 0Ankit N. Khambhati, Kathryn A. Davis, Brian S. Oommen, Stephanie H. Chen, Timothy H. Lucas, Brian Litt, Danielle S. Bassett. Dynamic Network Drivers of Seizure Generation, Propagation and Termination in Human Neocortical Epilepsy
0 -- 0Henrik Ronellenfitsch, Jana Lasser, Douglas C. Daly, Eleni Katifori. Topological Phenotypes Constitute a New Dimension in the Phenotypic Space of Leaf Venation Networks
0 -- 0Istvan Bartha, Antonio Rausell, Paul J. Mclaren, Pejman Mohammadi, Manuel Tardaguila, Nimisha Chaturvedi, Jacques Fellay, Amalio Telenti. The Characteristics of Heterozygous Protein Truncating Variants in the Human Genome
0 -- 0Zhichao Miao, Eric Westhof. A Large-Scale Assessment of Nucleic Acids Binding Site Prediction Programs
0 -- 0Soma Ghosh, Nagasuma R. Chandra, Saraswathi Vishveshwara. Mechanism of Iron-Dependent Repressor (IdeR) Activation and DNA Binding: A Molecular Dynamics and Protein Structure Network Study
0 -- 0Zev N. Kronenberg, Edward J. Osborne, Kelsey R. Cone, Brett J. Kennedy, Eric T. Domyan, Michael D. Shapiro, Nels C. Elde, Mark Yandell. Wham: Identifying Structural Variants of Biological Consequence
0 -- 0Matthew Hall, Mark E. J. Woolhouse, Andrew Rambaut. Epidemic Reconstruction in a Phylogenetics Framework: Transmission Trees as Partitions of the Node Set
0 -- 0Michael Fauth, Florentin Wörgötter, Christian Tetzlaff. Formation and Maintenance of Robust Long-Term Information Storage in the Presence of Synaptic Turnover
0 -- 0Costas Mitsopoulos, Amanda C. Schierz, Paul Workman, Bissan Al-Lazikani. Distinctive Behaviors of Druggable Proteins in Cellular Networks
0 -- 0Elodie Laine, Alessandra Carbone. Local Geometry and Evolutionary Conservation of Protein Surfaces Reveal the Multiple Recognition Patches in Protein-Protein Interactions
0 -- 0Thomas Buder, Andreas Deutsch, Barbara Klink, Anja Voss-Böhme. Model-Based Evaluation of Spontaneous Tumor Regression in Pilocytic Astrocytoma
0 -- 0James Kaminski, Molly K. Gibson, Eric A. Franzosa, Nicola Segata, Gautam Dantas, Curtis Huttenhower. High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED
0 -- 0Alan Veliz-Cuba, Andrew J. Hirning, Adam A. Atanas, Faiza Hussain, Flavia Vancia, Kresimir Josic, Matthew R. Bennett. Sources of Variability in a Synthetic Gene Oscillator
0 -- 0Theo Arts, Robert S. Reneman, James B. Bassingthwaighte, Ger J. van der Vusse. Modeling Fatty Acid Transfer from Artery to Cardiomyocyte
0 -- 0S. S. Soumya, Animesh Gupta, Andrea Cugno, Luca Deseri, Kaushik Dayal, Dibyendu Das, Shamik Sen, Mandar M. Inamdar. Coherent Motion of Monolayer Sheets under Confinement and Its Pathological Implications
0 -- 0Wolfram Möbius, Andrew W. Murray, David R. Nelson. How Obstacles Perturb Population Fronts and Alter Their Genetic Structure
0 -- 0Alice E. Milne, James R. Bell, William D. Hutchison, Frank van den Bosch, Paul D. Mitchell, David Crowder, Stephen Parnell, Andrew P. Whitmore. Bt Crops: A Billion Dollar Game of Strategy
0 -- 0Andreas Carlson, L. Mahadevan. Elastohydrodynamics and Kinetics of Protein Patterning in the Immunological Synapse
0 -- 0Pradeep Anand Ravindranath, Stefano Forli, David S. Goodsell, Arthur J. Olson, Michel F. Sanner. AutoDockFR: Advances in Protein-Ligand Docking with Explicitly Specified Binding Site Flexibility
0 -- 0Michela Riz, Morten Gram Pedersen. Mathematical Modeling of Interacting Glucose-Sensing Mechanisms and Electrical Activity Underlying Glucagon-Like Peptide 1 Secretion
0 -- 0Brian Odegaard, David R. Wozny, Ladan Shams. Biases in Visual, Auditory, and Audiovisual Perception of Space
0 -- 0Richard Moore, Hsu Kiang Ooi, Taek Kang, Leonidas Bleris, Lan Ma. MiR-192-Mediated Positive Feedback Loop Controls the Robustness of Stress-Induced p53 Oscillations in Breast Cancer Cells
0 -- 0Sunpeng Wang, Patricia Hottz, Mauro Schechter, Libin Rong. Modeling the Slow CD4+ T Cell Decline in HIV-Infected Individuals
0 -- 0Stephan Eismann, Robert G. Endres. Protein Connectivity in Chemotaxis Receptor Complexes
0 -- 0Piotr J. Kamola, Yuko Nakano, Tomoko Takahashi, Paul A. Wilson, Kumiko Ui-Tei. The siRNA Non-seed Region and Its Target Sequences Are Auxiliary Determinants of Off-Target Effects
0 -- 0Wei Zhang 0032, Jae-Woong Chang, Lilong Lin, Kay Minn, Baolin Wu, Jeremy Chien, Jeongsik Yong, Hui Zheng, Rui Kuang. Network-Based Isoform Quantification with RNA-Seq Data for Cancer Transcriptome Analysis
0 -- 0Tatjana Braun, Julia Koehler Leman, Oliver F. Lange. Combining Evolutionary Information and an Iterative Sampling Strategy for Accurate Protein Structure Prediction
0 -- 0Maximilian Puelma Touzel, Fred Wolf. Complete Firing-Rate Response of Neurons with Complex Intrinsic Dynamics
0 -- 0Alberto Mazzoni, Henrik Lindén, Hermann Cuntz, Anders Lansner, Stefano Panzeri, Gaute T. Einevoll. Computing the Local Field Potential (LFP) from Integrate-and-Fire Network Models
0 -- 0Sridevi Nagaraja, Jaques Reifman, Alexander Y. Mitrophanov. Computational Identification of Mechanistic Factors That Determine the Timing and Intensity of the Inflammatory Response
0 -- 0Dominik R. Bach. Anxiety-Like Behavioural Inhibition Is Normative under Environmental Threat-Reward Correlations
0 -- 0Fabiana A. Caetano, Brennan S. Dirk, Joshua H. K. Tam, P. Craig Cavanagh, Maria Goiko, Stephen S. G. Ferguson, Stephen H. Pasternak, Jimmy D. Dikeakos, John R. de Bruyn, Bryan Heit. MIiSR: Molecular Interactions in Super-Resolution Imaging Enables the Analysis of Protein Interactions, Dynamics and Formation of Multi-protein Structures
0 -- 0Jochen Kursawe, Pavel A. Brodskiy, Jeremiah J. Zartman, Ruth E. Baker, Alexander G. Fletcher. Capabilities and Limitations of Tissue Size Control through Passive Mechanical Forces
0 -- 0Mathieu Golos, Viktor K. Jirsa, Emmanuel Daucé. Multistability in Large Scale Models of Brain Activity
0 -- 0Akli Ben Imeddourene, Ahmad Elbahnsi, Marc Gueroult, Christophe Oguey, Nicolas Foloppe, Brigitte Hartmann. Simulations Meet Experiment to Reveal New Insights into DNA Intrinsic Mechanics
0 -- 0Kevin Lloyd, Peter Dayan. Tamping Ramping: Algorithmic, Implementational, and Computational Explanations of Phasic Dopamine Signals in the Accumbens
0 -- 0Gregory R. Johnson, Jieyue Li, Aabid Shariff, Gustavo K. Rohde, Robert F. Murphy. Automated Learning of Subcellular Variation among Punctate Protein Patterns and a Generative Model of Their Relation to Microtubules
0 -- 0Kendra S. Burbank. Mirrored STDP Implements Autoencoder Learning in a Network of Spiking Neurons
0 -- 0Ivar L. Thorson, Jean Liénard, Stephen V. David. The Essential Complexity of Auditory Receptive Fields
0 -- 0Thomas E. Akam, Rui Costa, Peter Dayan. Simple Plans or Sophisticated Habits? State, Transition and Learning Interactions in the Two-Step Task
0 -- 0Dan Wilson, Jeff Moehlis. Clustered Desynchronization from High-Frequency Deep Brain Stimulation
0 -- 0Takuya Isomura, Kiyoshi Kotani, Yasuhiko Jimbo. Cultured Cortical Neurons Can Perform Blind Source Separation According to the Free-Energy Principle
0 -- 0Brenda N. Vo, Christopher C. Drovandi, Anthony N. Pettitt, Graeme J. Pettet. Melanoma Cell Colony Expansion Parameters Revealed by Approximate Bayesian Computation
0 -- 0Ossnat Bar-Shira, Ronnie Maor, Gal Chechik. Gene Expression Switching of Receptor Subunits in Human Brain Development
0 -- 0Liang Wang, Jie Zheng, Akiko Maehara, Chun Yang, Kristen Billiar, Zheyang Wu, Richard G. Bach, David Muccigrosso, Gary S. Mintz, Dalin Tang. Morphological and Stress Vulnerability Indices for Human Coronary Plaques and Their Correlations with Cap Thickness and Lipid Percent: An IVUS-Based Fluid-Structure Interaction Multi-patient Study
0 -- 0Naoyuki Ohta, Kana Waki, Atsushi Mochizuki, Yutaka Satou. A Boolean Function for Neural Induction Reveals a Critical Role of Direct Intercellular Interactions in Patterning the Ectoderm of the Ascidian Embryo
0 -- 0Gil Ariel, Amir Ayali. Locust Collective Motion and Its Modeling
0 -- 0R. Gonzalo Parra, Rocío Espada, Nina Verstraete, Diego U. Ferreiro. Structural and Energetic Characterization of the Ankyrin Repeat Protein Family
0 -- 0Varsha D. Badal, Petras J. Kundrotas, Ilya A. Vakser. Text Mining for Protein Docking
0 -- 0Jienian Yang, Maksim V. Plikus, Natalia L. Komarova. The Role of Symmetric Stem Cell Divisions in Tissue Homeostasis
0 -- 0Frances Hutchings, Cheol E. Han, Simon S. Keller, Bernd Weber, Peter Neal Taylor, Marcus Kaiser. Predicting Surgery Targets in Temporal Lobe Epilepsy through Structural Connectome Based Simulations
0 -- 0Shiqiu Liu, Adam S. Smith, Yuting Gu, Jie Tan, C. Karen Liu, Greg Turk. Computer Simulations Imply Forelimb-Dominated Underwater Flight in Plesiosaurs

Volume 11, Issue 11

0 -- 0David Bednar, Koen Beerens, Eva Sebestova, Jaroslav Bendl, Sagar Khare, Radka Chaloupkova, Zbynek Prokop, Jan Brezovsky, David Baker, Jirí Damborský. FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants
0 -- 0Jia Li, Marie-Anne Poursat, Damien Drubay, Arnaud Motz, Zohra Saci, Antonin Morillon, Stefan Michiels, Daniel Gautheret. A Dual Model for Prioritizing Cancer Mutations in the Non-coding Genome Based on Germline and Somatic Events
0 -- 0Guido Gigante, Gustavo Deco, Shimon Marom, Paolo Del Giudice. Network Events on Multiple Space and Time Scales in Cultured Neural Networks and in a Stochastic Rate Model
0 -- 0Stephen Nayfach, Patrick H. Bradley, Stacia K. Wyman, Timothy J. Laurent, Alexander G. Williams, Jonathan A. Eisen, Katherine S. Pollard, Thomas J. Sharpton. Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes
0 -- 0Peter Neri. The Elementary Operations of Human Vision Are Not Reducible to Template-Matching
0 -- 0Max Hinne, Ronald J. Janssen, Tom Heskes, Marcel A. J. van Gerven. Bayesian Estimation of Conditional Independence Graphs Improves Functional Connectivity Estimates
0 -- 0Laura Hindersin, Arne Traulsen. Most Undirected Random Graphs Are Amplifiers of Selection for Birth-Death Dynamics, but Suppressors of Selection for Death-Birth Dynamics
0 -- 0Joanne L. Dunster, Francoise Mazet, Michael J. Fry, Jonathan M. Gibbins, Marcus J. Tindall. Regulation of Early Steps of GPVI Signal Transduction by Phosphatases: A Systems Biology Approach
0 -- 0Florian Raudies, Michael E. Hasselmo. Differences in Visual-Spatial Input May Underlie Different Compression Properties of Firing Fields for Grid Cell Modules in Medial Entorhinal Cortex
0 -- 0Alberto Romagnoni, Jérôme Ribot, Daniel Bennequin, Jonathan Touboul. Parsimony, Exhaustivity and Balanced Detection in Neocortex
0 -- 0Sam Walcott, Neil M. Kad. Direct Measurements of Local Coupling between Myosin Molecules Are Consistent with a Model of Muscle Activation
0 -- 0Won-Min Song, Bin Zhang. Multiscale Embedded Gene Co-expression Network Analysis
0 -- 0Marina Martinez-Garcia, Andrea Insabato, Mario Pannunzi, Jose L. Pardo-Vazquez, Carlos Acuña, Gustavo Deco. The Encoding of Decision Difficulty and Movement Time in the Primate Premotor Cortex
0 -- 0Anna Rubinski, Noam E. Ziv. Remodeling and Tenacity of Inhibitory Synapses: Relationships with Network Activity and Neighboring Excitatory Synapses
0 -- 0Jonathan W. Armond, Edward F. Harry, Andrew D. McAinsh, Nigel J. Burroughs. Inferring the Forces Controlling Metaphase Kinetochore Oscillations by Reverse Engineering System Dynamics
0 -- 0M. Senthil Kumar, Joshua B. Plotkin, Sridhar Hannenhalli. Regulated CRISPR Modules Exploit a Dual Defense Strategy of Restriction and Abortive Infection in a Model of Prokaryote-Phage Coevolution
0 -- 0Olivier J. N. Bertrand, Jens Peter Lindemann, Martin Egelhaaf. A Bio-inspired Collision Avoidance Model Based on Spatial Information Derived from Motion Detectors Leads to Common Routes
0 -- 0Jonathan Cannon, Nancy Kopell, Timothy J. Gardner, Jeffrey E. Markowitz. Neural Sequence Generation Using Spatiotemporal Patterns of Inhibition
0 -- 0Joseph G. Makin, Benjamin K. Dichter, Philip N. Sabes. Learning to Estimate Dynamical State with Probabilistic Population Codes
0 -- 0David Kappel, Stefan Habenschuss, Robert A. Legenstein, Wolfgang Maass. Network Plasticity as Bayesian Inference
0 -- 0Kimberly Glass, Michelle Girvan. Finding New Order in Biological Functions from the Network Structure of Gene Annotations
0 -- 0Max S. Y. Lau, Glenn Marion, George Streftaris, Gavin J. Gibson. A Systematic Bayesian Integration of Epidemiological and Genetic Data
0 -- 0Pablo Cordero, Rhiju Das. Rich RNA Structure Landscapes Revealed by Mutate-and-Map Analysis
0 -- 0Etienne Baratchart, Sébastien Benzekry, Andreas Bikfalvi, Thierry Colin, Lindsay S. Cooley, Raphäel Pineau, Emeline J. Ribot, Olivier Saut, Wilfried Souleyreau. Computational Modelling of Metastasis Development in Renal Cell Carcinoma
0 -- 0Silvia Lovera, Maria Morando, Encarna Pucheta-Martinez, Jorge L. Martinez-Torrecuadrada, Giorgio Saladino, Francesco L. Gervasio. Towards a Molecular Understanding of the Link between Imatinib Resistance and Kinase Conformational Dynamics
0 -- 0Minzhe Guo, Hui Wang, S. Steven Potter, Jeffrey A. Whitsett, Yan Xu. SINCERA: A Pipeline for Single-Cell RNA-Seq Profiling Analysis
0 -- 0Mark A. Walker, Tobias Kohl, Stephan E. Lehnart, Joseph L. Greenstein, W. J. Lederer, Raimond L. Winslow. On the Adjacency Matrix of RyR2 Cluster Structures
0 -- 0Dmitry Svetlichnyy, Hana Imrichová, Mark Fiers, Zeynep Kalender Atak, Stein Aerts. cis-Regulatory Mutations Using Transcription Factor Specific Random Forest Models
0 -- 0Emile R. Chimusa, Mamana Mbiyavanga, Velaphi Masilela, Judit Kumuthini. "Broadband" Bioinformatics Skills Transfer with the Knowledge Transfer Programme (KTP): Educational Model for Upliftment and Sustainable Development
0 -- 0Peter Jedlicka, Lubica Benuskova, Wickliffe C. Abraham. In Vivo
0 -- 0Samuel J. Gershman. A Unifying Probabilistic View of Associative Learning
0 -- 0Jing Zhou, Camilo Aponte-Santamaría, Sebastian Sturm, Jakob Tómas Bullerjahn, Agnieszka Bronowska, Frauke Gräter. Mechanism of Focal Adhesion Kinase Mechanosensing
0 -- 0Gaurav Dwivedi, Margaret A. Gran, Pritha Bagchi, Melissa L. Kemp. Dynamic Redox Regulation of IL-4 Signaling
0 -- 0Shuyi Ma, Kyle J. Minch, Tige R. Rustad, Samuel Hobbs, Suk-Lin Zhou, David R. Sherman, Nathan D. Price. Mycobacterium tuberculosis
0 -- 0Tri Hieu Nim, Le Luo, Jacob K. White, Marie-Véronique Clément, Lisa Tucker-Kellogg. Non-canonical Activation of Akt in Serum-Stimulated Fibroblasts, Revealed by Comparative Modeling of Pathway Dynamics
0 -- 0Jordi Fonollosa, Emre Neftci, Mikhail Rabinovich. Learning of Chunking Sequences in Cognition and Behavior
0 -- 0Peter C. St John, Francis J. Doyle III. Quantifying Stochastic Noise in Cultured Circadian Reporter Cells
0 -- 0Masato S. Abe, Masakazu Shimada. Lévy Walks Suboptimal under Predation Risk
0 -- 0Hisashi Ohtsuki, Yoh Iwasa, Martin A. Nowak. Reputation Effects in Public and Private Interactions
0 -- 0James Rankin, Elyse Sussman, John Rinzel. Neuromechanistic Model of Auditory Bistability
0 -- 0Tian Hong, Kazuhide Watanabe, Catherine Ha Ta, Alvaro Villarreal-Ponce, Qing Nie, Xing Dai. An Ovol2-Zeb1 Mutual Inhibitory Circuit Governs Bidirectional and Multi-step Transition between Epithelial and Mesenchymal States
0 -- 0Maciej Jan Ejsmond, Jacek Radwan. Red Queen Processes Drive Positive Selection on Major Histocompatibility Complex (MHC) Genes
0 -- 0Kristin J. Adolfsen, Mark P. Brynildsen. Escherichia coli
0 -- 0Makoto Ito, Kenji Doya. Parallel Representation of Value-Based and Finite State-Based Strategies in the Ventral and Dorsal Striatum
0 -- 0Mikhail Shugay, Dmitriy V. Bagaev, Maria A. Turchaninova, Dmitriy A. Bolotin, Olga V. Britanova, Ekaterina V. Putintseva, Mikhail V. Pogorelyy, Vadim I. Nazarov, Ivan V. Zvyagin, Vitalina I. Kirgizova, Kirill I. Kirgizov, Elena V. Skorobogatova, Dmitriy M. Chudakov. VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires
0 -- 0Manuel Schottdorf, Wolfgang Keil, David Coppola, Leonard E. White, Fred Wolf. Random Wiring, Ganglion Cell Mosaics, and the Functional Architecture of the Visual Cortex
0 -- 0Zhongyang Zhang, Ke Hao. SAAS-CNV: A Joint Segmentation Approach on Aggregated and Allele Specific Signals for the Identification of Somatic Copy Number Alterations with Next-Generation Sequencing Data
0 -- 0Satohiro Tajima, Toru Yanagawa, Naotaka Fujii, Taro Toyoizumi. Untangling Brain-Wide Dynamics in Consciousness by Cross-Embedding
0 -- 0David P. A. Cohen, Loredana Martignetti, Sylvie Robine, Emmanuel Barillot, Andrei Yu. Zinovyev, Laurence Calzone. Mathematical Modelling of Molecular Pathways Enabling Tumour Cell Invasion and Migration
0 -- 0Goker Erdogan, Ilker Yildirim, Robert A. Jacobs. From Sensory Signals to Modality-Independent Conceptual Representations: A Probabilistic Language of Thought Approach
0 -- 0Chen Zhao, Aleksander S. Popel. Computational Model of MicroRNA Control of HIF-VEGF Pathway: Insights into the Pathophysiology of Ischemic Vascular Disease and Cancer
0 -- 0Gabriel Madirolas, Gonzalo G. de Polavieja. Improving Collective Estimations Using Resistance to Social Influence
0 -- 0Andrea Maesani, Pavan Ramdya, Steeve Cruchet, Kyle Gustafson, Richard Benton, Dario Floreano. Drosophila Locomotor Patterns
0 -- 0Lin-tai Da, Chao E, Baogen Duan, Chuanbiao Zhang, Xin Zhou, Jin Yu. A Jump-from-Cavity Pyrophosphate Ion Release Assisted by a Key Lysine Residue in T7 RNA Polymerase Transcription Elongation
0 -- 0Daniel Yakubovich, Shai Berlin, Uri Kahanovitch, Moran Rubinstein, Isabella Farhy-Tselnicker, Boaz Styr, Tal Keren-Raifman, Carmen W. Dessauer, Nathan Dascal. A Quantitative Model of the GIRK1/2 Channel Reveals That Its Basal and Evoked Activities Are Controlled by Unequal Stoichiometry of Gα and Gβγ
0 -- 0Alejandro Ochoa, John D. Storey, Manuel Llinás, Mona Singh. E-Value: Stratified Statistics for Protein Domain Prediction
0 -- 0Miriam Grace, Marc-Thorsten Hütt. Dictyostelium discoideum
0 -- 0Benjamin D. Heavner, Nathan D. Price. Comparative Analysis of Yeast Metabolic Network Models Highlights Progress, Opportunities for Metabolic Reconstruction
0 -- 0Robert P. Jenkins, Anja Hanisch, Cristian Soza-Ried, Erik Sahai, Julian Lewis. Stochastic Regulation of her1/7 Gene Expression Is the Source of Noise in the Zebrafish Somite Clock Counteracted by Notch Signalling
0 -- 0Donatien F. Chedom, Pablo R. Murcia, Chris D. Greenman. Inferring the Clonal Structure of Viral Populations from Time Series Sequencing
0 -- 0Sandeep Choubey, Jané Kondev, Alvaro Sanchez. Deciphering Transcriptional Dynamics In Vivo by Counting Nascent RNA Molecules
0 -- 0Alex Davies, Matthieu Louis, Barbara Webb. Drosophila Larva Chemotaxis

Volume 11, Issue 10

0 -- 0Xiongwu Wu, Bernard R. Brooks. A Virtual Mixture Approach to the Study of Multistate Equilibrium: Application to Constant pH Simulation in Explicit Water
0 -- 0Sedeer el-Showk, Hanna Help-Rinta-Rahko, Tiina Blomster, Riccardo Siligato, Athanasius F. M. Marée, Ari Pekka Mähönen, Verônica A. Grieneisen. Parsimonious Model of Vascular Patterning Links Transverse Hormone Fluxes to Lateral Root Initiation: Auxin Leads the Way, while Cytokinin Levels Out
0 -- 0Tiffany Kee, Pavel Sanda, Nitin Gupta, Mark Stopfer, Maxim Bazhenov. Feed-Forward versus Feedback Inhibition in a Basic Olfactory Circuit
0 -- 0Simon D. Angus, Jonathan Newton. Emergence of Shared Intentionality Is Coupled to the Advance of Cumulative Culture
0 -- 0Sean L. Seyler, Avishek Kumar, M. F. Thorpe, Oliver Beckstein. Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways
0 -- 0Xin Zeng, Bo Li 0015, Rene Welch, Constanza Rojo, Ye Zheng, Colin N. Dewey, Sündüz Keles. Perm-seq: Mapping Protein-DNA Interactions in Segmental Duplication and Highly Repetitive Regions of Genomes with Prior-Enhanced Read Mapping
0 -- 0Stanislav Nagy, Marc Goessling, Yali Amit, David Biron. A Generative Statistical Algorithm for Automatic Detection of Complex Postures
0 -- 0Lane W. Votapka, Rommie E. Amaro. Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning
0 -- 0Toni Kazic. Ten Simple Rules for Experiments' Provenance
0 -- 0Sivan Leviyang, Vitaly V. Ganusov. Broad CTL Response in Early HIV Infection Drives Multiple Concurrent CTL Escapes
0 -- 0Jan Karbowski. Cortical Composition Hierarchy Driven by Spine Proportion Economical Maximization or Wire Volume Minimization
0 -- 0Graeme Mitchison. The Shape of an Auxin Pulse, and What It Tells Us about the Transport Mechanism
0 -- 0Alexander D. Malkin, Robert P. Sheehan, Shibin Mathew, William J. Federspiel, Heinz Redl, Gilles Clermont. A Neutrophil Phenotype Model for Extracorporeal Treatment of Sepsis
0 -- 0Serge Dmitrieff, François Nédélec. Membrane Mechanics of Endocytosis in Cells with Turgor
0 -- 0William K. Michener. Ten Simple Rules for Creating a Good Data Management Plan
0 -- 0David M. Shaw, Thomas C. Erren. Ten Simple Rules for Protecting Research Integrity
0 -- 0Amarda Shehu, Ruth Nussinov. Computational Methods for Exploration and Analysis of Macromolecular Structure and Dynamics
0 -- 0Laurence Aitchison, Dan Bang, Bahador Bahrami, Peter E. Latham. Doubly Bayesian Analysis of Confidence in Perceptual Decision-Making
0 -- 0Orit Adato, Noga Ninyo, Uri Gophna, Sagi Snir. Detecting Horizontal Gene Transfer between Closely Related Taxa
0 -- 0Niraj Kumar, Abhyudai Singh, Rahul V. Kulkarni. Transcriptional Bursting in Gene Expression: Analytical Results for General Stochastic Models
0 -- 0Radhakrishna Bettadapura, Muhibur Rasheed, Antje Vollrath, Chandrajit Bajaj. fit: Polar Fast Fourier Matched Alignment of Atomistic Structures with 3D Electron Microscopy Maps
0 -- 0Dario Cuevas Rivera, Sebastian Bitzer, Stefan J. Kiebel. Modelling Odor Decoding in the Antennal Lobe by Combining Sequential Firing Rate Models with Bayesian Inference
0 -- 0Seren Soner, Pemra Ozbek, Jose Ignacio Garzon, Nir Ben-Tal, Turkan Haliloglu. DynaFace: Discrimination between Obligatory and Non-obligatory Protein-Protein Interactions Based on the Complex's Dynamics
0 -- 0Robin van der Lee, Qian Feng, Martijn A. Langereis, Rob ter Horst, Radek Szklarczyk, Mihai G. Netea, Arno C. Andeweg, Frank J. M. van Kuppeveld, Martijn A. Huynen. Integrative Genomics-Based Discovery of Novel Regulators of the Innate Antiviral Response
0 -- 0Juan A. Delgado-SanMartin, Jennifer I. Hare, Alessandro P. S. de Moura, James W. T. Yates. Oxygen-Driven Tumour Growth Model: A Pathology-Relevant Mathematical Approach
0 -- 0Priyanka Prakash, Abdallah Sayyed-Ahmad, Alemayehu A. Gorfe. pMD-Membrane: A Method for Ligand Binding Site Identification in Membrane-Bound Proteins
0 -- 0Daniel A. Keedy, James S. Fraser, Henry van den Bedem. Exposing Hidden Alternative Backbone Conformations in X-ray Crystallography Using qFit
0 -- 0Jason D. Wittenbach, Kristofer E. Bouchard, Michael S. Brainard, Dezhe Z. Jin. An Adapting Auditory-motor Feedback Loop Can Contribute to Generating Vocal Repetition
0 -- 0Bruce S. Gardiner, Kelvin K. L. Wong, Grand R. Joldes, Addison J. Rich, Chin Wee Tan, Antony W. Burgess, David W. Smith. Discrete Element Framework for Modelling Extracellular Matrix, Deformable Cells and Subcellular Components
0 -- 0Kushagra Singhal, Jocelyne Vreede, Alireza Mashaghi, Sander J. Tans, Peter G. Bolhuis. The Trigger Factor Chaperone Encapsulates and Stabilizes Partial Folds of Substrate Proteins
0 -- 0Michael A. DeJesus, Chaitra Ambadipudi, Richard Baker, Christopher M. Sassetti, Thomas R. Ioerger. TRANSIT - A Software Tool for Himar1 TnSeq Analysis
0 -- 0Pablo Szekely, Yael Korem, Uri Moran, Avi E. Mayo, Uri Alon. The Mass-Longevity Triangle: Pareto Optimality and the Geometry of Life-History Trait Space
0 -- 0Alexandra Jacunski, Scott J. Dixon, Nicholas P. Tatonetti. Connectivity Homology Enables Inter-Species Network Models of Synthetic Lethality
0 -- 0Joel Z. Leibo, Qianli Liao, Fabio Anselmi, Tomaso A. Poggio. The Invariance Hypothesis Implies Domain-Specific Regions in Visual Cortex
0 -- 0Mingming Chen, Daqing Guo, Min Li, Tao Ma, Shengdun Wu, Jingling Ma, Yan Cui, Yang Xia, Peng Xu, Dezhong Yao. Critical Roles of the Direct GABAergic Pallido-cortical Pathway in Controlling Absence Seizures
0 -- 0Armin Meier, Johannes Söding. Automatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling
0 -- 0Manuel Wahle, Willy Wriggers. Multi-scale Visualization of Molecular Architecture Using Real-Time Ambient Occlusion in Sculptor
0 -- 0Richard de Grijs. Ten Simple Rules for Establishing International Research Collaborations
0 -- 0Eduard Porta-Pardo, Luz Garcia-Alonso, Thomas Hrabe, Joaquín Dopazo, Adam Godzik. A Pan-Cancer Catalogue of Cancer Driver Protein Interaction Interfaces
0 -- 0Ioana Niculescu, Johannes Textor, Rob J. De Boer. Crawling and Gliding: A Computational Model for Shape-Driven Cell Migration
0 -- 0Tristan Aumentado-Armstrong, Michael G. Metzen, Michael K. J. Sproule, Maurice J. Chacron. Electrosensory Midbrain Neurons Display Feature Invariant Responses to Natural Communication Stimuli
0 -- 0Jeffrey R. Brender, Yang Zhang. Predicting the Effect of Mutations on Protein-Protein Binding Interactions through Structure-Based Interface Profiles
0 -- 0Anja Winter, Ralf Schmid, Richard Bayliss. Structural Insights into Separase Architecture and Substrate Recognition through Computational Modelling of Caspase-Like and Death Domains
0 -- 0Mauricio Santillana, André T. Nguyen, Mark Dredze, Michael J. Paul, Elaine O. Nsoesie, John S. Brownstein. Combining Search, Social Media, and Traditional Data Sources to Improve Influenza Surveillance
0 -- 0Yuri Pritykin, Dario Ghersi, Mona Singh. Genome-Wide Detection and Analysis of Multifunctional Genes
0 -- 0Matteo Tiberti, Elena Papaleo, Tone Bengtsen, Wouter Boomsma, Kresten Lindorff-Larsen. ENCORE: Software for Quantitative Ensemble Comparison
0 -- 0Philipp S. Orekhov, Daniel Klose, Armen Y. Mulkidjanian, Konstantin V. Shaitan, Martin Engelhard, Johann P. Klare, Heinz-Jürgen Steinhoff. Natronomonas pharaonis
0 -- 0Raya Ahmed, Liset Westera, Julia Drylewicz, Marjet Elemans, Yan Zhang, Elizabeth Kelly, Rajko Reljic, Kiki Tesselaar, Rob J. De Boer, Derek C. Macallan, José A. M. Borghans, Becca Asquith. Reconciling Estimates of Cell Proliferation from Stable Isotope Labeling Experiments
0 -- 0Rong Shen, Wei Han, Giacomo Fiorin, Shahidul M. Islam, Klaus Schulten, Benoît Roux. Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments
0 -- 0Mark P. Simmons. Ten Simple Rules for Writing a Reply Paper
0 -- 0Dimitrije Markovic, Jan Gläscher, Peter Bossaerts, John P. O'Doherty, Stefan J. Kiebel. Modeling the Evolution of Beliefs Using an Attentional Focus Mechanism
0 -- 0Àngel Gómez-Sicilia, Mateusz Sikora, Marek Cieplak, Mariano Carrión-Vázquez. An Exploration of the Universe of Polyglutamine Structures
0 -- 0Don-On Daniel Mak, King-Ho Cheung, Patrick Toglia, J. Kevin Foskett, Ghanim Ullah. 3 Receptor Gating by Familial Alzheimer's Disease-Causing Mutants in Presenilins
0 -- 0Paul C. Bressloff, Samuel R. Carroll. Laminar Neural Field Model of Laterally Propagating Waves of Orientation Selectivity
0 -- 0Zhaoping Li, Li Zhe. Primary Visual Cortex as a Saliency Map: A Parameter-Free Prediction and Its Test by Behavioral Data
0 -- 0Andreas Henschel, Muhammad Zohaib Anwar, Vimitha Manohar. Comprehensive Meta-analysis of Ontology Annotated 16S rRNA Profiles Identifies Beta Diversity Clusters of Environmental Bacterial Communities
0 -- 0Michael Chevalier, Ophelia Venturelli, Hana El-Samad. The Impact of Different Sources of Fluctuations on Mutual Information in Biochemical Networks
0 -- 0Pengcheng Zhou, Shawn D. Burton, Adam C. Snyder, Matthew A. Smith, Nathaniel N. Urban, Robert E. Kass. Establishing a Statistical Link between Network Oscillations and Neural Synchrony
0 -- 0Chris M. Stone, Nakul Chitnis. Trypanosomiasis brucei gambiense Transmission and Control
0 -- 0Christian L. Vestergaard, Mathieu Génois. Temporal Gillespie Algorithm: Fast Simulation of Contagion Processes on Time-Varying Networks
0 -- 0Predrag Kukic, Arvind Kannan, Maurits J. J. Dijkstra, Sanne Abeln, Carlo Camilloni, Michele Vendruscolo. Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations
0 -- 0Noushin Niknafs, Violeta Beleva Guthrie, Daniel Q. Naiman, Rachel Karchin. SubClonal Hierarchy Inference from Somatic Mutations: Automatic Reconstruction of Cancer Evolutionary Trees from Multi-region Next Generation Sequencing
0 -- 0Omer Ziv, Assaf Zaritsky, Yakey Yaffe, Naresh Mutukula, Reuven Edri, Yechiel Elkabetz. Quantitative Live Imaging of Human Embryonic Stem Cell Derived Neural Rosettes Reveals Structure-Function Dynamics Coupled to Cortical Development
0 -- 0Dieter Vanderelst, Marc W. Holderied, Herbert Peremans. Sensorimotor Model of Obstacle Avoidance in Echolocating Bats
0 -- 0Daniel Soudry, Suraj Keshri, Patrick Stinson, Min-hwan Oh, Garud Iyengar, Liam Paninski. Efficient "Shotgun" Inference of Neural Connectivity from Highly Sub-sampled Activity Data
0 -- 0Tobias Brosch, Heiko Neumann, Pieter R. Roelfsema. Reinforcement Learning of Linking and Tracing Contours in Recurrent Neural Networks
0 -- 0Christian Rössert, Paul Dean, John Porrill. At the Edge of Chaos: How Cerebellar Granular Layer Network Dynamics Can Provide the Basis for Temporal Filters
0 -- 0Farras Abdelnour, Susanne G. Mueller, Ashish Raj. Relating Cortical Atrophy in Temporal Lobe Epilepsy with Graph Diffusion-Based Network Models
0 -- 0Hsin-Hung Li, Marisa Carrasco, David J. Heeger. Deconstructing Interocular Suppression: Attention and Divisive Normalization
0 -- 0Simone Rizzetto, Corrado Priami, Attila Csikász-Nagy. Qualitative and Quantitative Protein Complex Prediction Through Proteome-Wide Simulations
0 -- 0Claire Colas, Christof Grewer, Nicholas James Otte, Armanda Gameiro, Thomas Albers, Kurnvir Singh, Helen Shere, Massimiliano Bonomi, Jeff Holst, Avner Schlessinger. Ligand Discovery for the Alanine-Serine-Cysteine Transporter (ASCT2, SLC1A5) from Homology Modeling and Virtual Screening
0 -- 0Santhosh Kannan Venkatesan, Kusumika Saha, Azmat Sohail, Walter Sandtner, Michael Freissmuth, Gerhard F. Ecker, Harald H. Sitte, Thomas Stockner. Refinement of the Central Steps of Substrate Transport by the Aspartate Transporter GltPh: Elucidating the Role of the Na2 Sodium Binding Site
0 -- 0Hyuntae Na, Robert L. Jernigan, Guang Song. Bridging between NMA and Elastic Network Models: Preserving All-Atom Accuracy in Coarse-Grained Models
0 -- 0Matthias S. Keil. Dendritic Pooling of Noisy Threshold Processes Can Explain Many Properties of a Collision-Sensitive Visual Neuron
0 -- 0Roland G. Huber, Hao Fan, Peter J. Bond. The Structural Basis for Activation and Inhibition of ZAP-70 Kinase Domain
0 -- 0Nidhi Tyagi, Edward J. Farnell, Colin M. Fitzsimmons, Stephanie Ryan, Edridah M. Tukahebwa, Rick M. Maizels, David W. Dunne, Janet M. Thornton, Nicholas Furnham. Comparisons of Allergenic and Metazoan Parasite Proteins: Allergy the Price of Immunity
0 -- 0Min-Cheol Kim, Jordan Whisler, Yaron R. Silberberg, Roger D. Kamm, H. Harry Asada. Cell Invasion Dynamics into a Three Dimensional Extracellular Matrix Fibre Network
0 -- 0Francisco G. Vital-Lopez, Jaques Reifman, Anders Wallqvist. Pseudomonas aeruginosa Predicted via Genome-Scale Kinetic Models of Bacterial Metabolism
0 -- 0Meekyum Olivia Kim, Patrick G. Blachly, James Andrew McCammon. Conformational Dynamics and Binding Free Energies of Inhibitors of BACE-1: From the Perspective of Protonation Equilibria
0 -- 0David Bruce Borenstein, Peter Ringel, Marek Basler, Ned S. Wingreen. Established Microbial Colonies Can Survive Type VI Secretion Assault
0 -- 0Hirenkumar K. Makadia, James S. Schwaber, Rajanikanth Vadigepalli. Intracellular Information Processing through Encoding and Decoding of Dynamic Signaling Features
0 -- 0Benfeard Williams II, Marino Convertino, Jhuma Das, Nikolay V. Dokholyan. ApoE4-specific Misfolded Intermediate Identified by Molecular Dynamics Simulations
0 -- 0Peter K. Koo, Matthew Weitzman, Chandran R. Sabanaygam, Kenneth L. van Golen, Simon G. J. Mochrie. In Vivo Biochemistry
0 -- 0Ian Krajbich, Todd A. Hare, Björn Bartling, Yosuke Morishima, Ernst Fehr. A Common Mechanism Underlying Food Choice and Social Decisions
0 -- 0Marinka Zitnik, Edward A. Nam, Christopher Dinh, Adam Kuspa, Gad Shaulsky, Blaz Zupan. Gene Prioritization by Compressive Data Fusion and Chaining
0 -- 0Jeewoen Shin, Thomas MacCarthy. Antagonistic Coevolution Drives Whack-a-Mole Sensitivity in Gene Regulatory Networks

Volume 11, Issue 1

0 -- 0Massimo Lai, Denis Brun, Stuart J. Edelstein, Nicolas Le Novère. Modulation of Calmodulin Lobes by Different Targets: An Allosteric Model with Hemiconcerted Conformational Transitions
0 -- 0Jamie T. Griffin. The Interaction between Seasonality and Pulsed Interventions against Malaria in Their Effects on the Reproduction Number
0 -- 0Peter D. Karp, Bonnie Berger, Diane E. Kovats, Thomas Lengauer, Michal Linial, Pardis Sabeti, Winston Hide, Burkhard Rost. ISCB Ebola Award for Important Future Research on the Computational Biology of Ebola Virus
0 -- 0Martin Rückl, Ian Parker, Jonathan S. Marchant, Chamakuri Nagaiah, Friedrich W. Johenning, Sten Rüdiger. 3R Cluster Model
0 -- 0Emilie Montastier, Nathalie Villa-Vialaneix, Sylvie Caspar-Bauguil, Petr Hlavaty, Eva Tvrzicka, Ignacio Gonzalez, Wim H. M. Saris, Dominique Langin, Marie Kunesova, Nathalie Viguerie. System Model Network for Adipose Tissue Signatures Related to Weight Changes in Response to Calorie Restriction and Subsequent Weight Maintenance
0 -- 0Alboukadel Kassambara, Thierry Rème, Michel Jourdan, Thierry Fest, Dirk Hose, Karin Tarte, Bernard Klein. GenomicScape: An Easy-to-Use Web Tool for Gene Expression Data Analysis. Application to Investigate the Molecular Events in the Differentiation of B Cells into Plasma Cells
0 -- 0Erick A. Perez Alday, Michael A. Colman, Philip Langley, Timothy D. Butters, Jonathan Higham, Antony J. Workman, Jules C. Hancox, Henggui Zhang. A New Algorithm to Diagnose Atrial Ectopic Origin from Multi Lead ECG Systems - Insights from 3D Virtual Human Atria and Torso
0 -- 0Davod Alizadehrad, Timothy Krüger, Markus Engstler, Holger Stark. Trypanosoma brucei and Its Motility
0 -- 0Eberhard O. Voit, Harald A. Martens, Stig W. Omholt. 150 Years of the Mass Action Law
0 -- 0Regina S. Salvat, Andrew S. Parker, Yoonjoo Choi, Chris Bailey-Kellogg, Karl E. Griswold. Mapping the Pareto Optimal Design Space for a Functionally Deimmunized Biotherapeutic Candidate
0 -- 0Lu Chen, Lei Du-Cuny, Sylvestor Moses, Sabrina Dumas, Zuohe Song, Abdol Hossein Rezaeian, Hui-Kuan Lin, Emmanuelle J. Meuillet, Shuxing Zhang. Novel Inhibitors Induce Large Conformational Changes of GAB1 Pleckstrin Homology Domain and Kill Breast Cancer Cells
0 -- 0Ioannis Andrianakis, Ian R. Vernon, Nicky McCreesh, Trevelyan J. McKinley, Jeremy E. Oakley, Rebecca N. Nsubuga, Michael Goldstein, Richard G. White. Bayesian History Matching of Complex Infectious Disease Models Using Emulation: A Tutorial and a Case Study on HIV in Uganda
0 -- 0Benjamin Simmonds, Maurice J. Chacron. Activation of Parallel Fiber Feedback by Spatially Diffuse Stimuli Reduces Signal and Noise Correlations via Independent Mechanisms in a Cerebellum-Like Structure
0 -- 0Eduard Porta-Pardo, Adam Godzik. Analysis of Individual Protein Regions Provides Novel Insights on Cancer Pharmacogenomics
0 -- 0Ueli Rutishauser, Jean-Jacques E. Slotine, Rodney J. Douglas. Computation in Dynamically Bounded Asymmetric Systems
0 -- 0Ruth Nussinov. Advancements and Challenges in Computational Biology
0 -- 0Nigel Stepp, Dietmar Plenz, Narayan Srinivasa. Synaptic Plasticity Enables Adaptive Self-Tuning Critical Networks
0 -- 0Andrei N. Lupas, Hongbo Zhu, Mateusz Korycinski. The Thalidomide-Binding Domain of Cereblon Defines the CULT Domain Family and Is a New Member of the β-Tent Fold
0 -- 0Michael Fauth, Florentin Wörgötter, Christian Tetzlaff. The Formation of Multi-synaptic Connections by the Interaction of Synaptic and Structural Plasticity and Their Functional Consequences
0 -- 0Thomas Sakoparnig, Patrick Fried, Niko Beerenwinkel. Identification of Constrained Cancer Driver Genes Based on Mutation Timing
0 -- 0Diana Stefan, Corinne Pinel, Stéphane Pinhal, Eugenio Cinquemani, Johannes Geiselmann, Hidde de Jong. Inference of Quantitative Models of Bacterial Promoters from Time-Series Reporter Gene Data
0 -- 0Daeyong Jin, Hyunju Lee. A Computational Approach to Identifying Gene-microRNA Modules in Cancer
0 -- 0Aidan Budd, Holger Dinkel, Manuel Corpas, Jonathan C. Fuller, Laura Rubinat, Damien P. Devos, Pierre H. Khoueiry, Konrad U. Förstner, Fotis Georgatos, Francis Rowland, Malvika Sharan, Janos X. Binder, Tom Grace, Karyn Traphagen, Adam Gristwood, Natasha T. Wood. Ten Simple Rules for Organizing an Unconference
0 -- 0Helen L. Ramsden, Gülsen Sürmeli, Steven G. McDonagh, Matthew F. Nolan. Laminar and Dorsoventral Molecular Organization of the Medial Entorhinal Cortex Revealed by Large-scale Anatomical Analysis of Gene Expression
0 -- 0Andreas Wilke, Jared Bischof, Travis Harrison, Tom Brettin, Mark D'Souza, Wolfgang Gerlach, Hunter Matthews, Tobias Paczian, Jared Wilkening, Elizabeth M. Glass, Narayan Desai, Folker Meyer. A RESTful API for Accessing Microbial Community Data for MG-RAST
0 -- 0Sadra Sadeh, Stefan Rotter. Orientation Selectivity in Inhibition-Dominated Networks of Spiking Neurons: Effect of Single Neuron Properties and Network Dynamics
0 -- 0Frédéric Boudon, Jérôme Chopard, Olivier Ali, Benjamin Gilles, Olivier Hamant, Arezki Boudaoud, Jan Traas, Christophe Godin. A Computational Framework for 3D Mechanical Modeling of Plant Morphogenesis with Cellular Resolution
0 -- 0Loic Matthey, Paul M. Bays, Peter Dayan. A Probabilistic Palimpsest Model of Visual Short-term Memory
0 -- 0Elizabeth N. Davison, Kimberly J. Schlesinger, Danielle S. Bassett, Mary-Ellen Lynall, Michael B. Miller, Scott T. Grafton, Jean M. Carlson. Brain Network Adaptability across Task States
0 -- 0J. Matthew Mahoney, Jaclyn Taroni, Viktor Martyanov, Tammara A. Wood, Casey S. Greene, Patricia A. Pioli, Monique E. Hinchcliff, Michael L. Whitfield. Systems Level Analysis of Systemic Sclerosis Shows a Network of Immune and Profibrotic Pathways Connected with Genetic Polymorphisms
0 -- 0Raimon Sabate, Frederic Rousseau, Joost Schymkowitz, Salvador Ventura. What Makes a Protein Sequence a Prion?
0 -- 0Markus Niklasson, Alexandra Ahlner, Cecilia Andresen, Joseph A. Marsh, Patrik Lundström. Fast and Accurate Resonance Assignment of Small-to-Large Proteins by Combining Automated and Manual Approaches