Journal: PLoS Computational Biology

Volume 12, Issue 6

0 -- 0Olof Leimar, Sasha R. X. Dall, Peter Hammerstein, John M. McNamara. Genes as Cues of Relatedness and Social Evolution in Heterogeneous Environments
0 -- 0Xiao Fu, J. Scott Gens, James A. Glazier, Stephen A. Burns, Thomas J. Gast. Progression of Diabetic Capillary Occlusion: A Model
0 -- 0Tobias Sikosek, Heinrich Krobath, Hue Sun Chan. Theoretical Insights into the Biophysics of Protein Bi-stability and Evolutionary Switches
0 -- 0Johanni Brea, Alexisz Tamás Gaál, Robert Urbanczik, Walter Senn. Prospective Coding by Spiking Neurons
0 -- 0Da-Cang Huang, Jin Feng Wang, Ji-Xia Huang, Daniel Z. Sui, Hong-Yan Zhang, Mao-Gui Hu, Cheng-Dong Xu. Towards Identifying and Reducing the Bias of Disease Information Extracted from Search Engine Data
0 -- 0Gudrun Schappacher-Tilp, Timothy Leonard, Gertrud Desch, Walter Herzog. Computing Average Passive Forces in Sarcomeres in Length-Ramp Simulations
0 -- 0Anthony Szedlak, Nicholas Smith, Li Liu, Giovanni Paternostro, Carlo Piermarocchi. Evolutionary and Topological Properties of Genes and Community Structures in Human Gene Regulatory Networks
0 -- 0Ingo Titze, Tobias Riede, Ted Mau. Predicting Achievable Fundamental Frequency Ranges in Vocalization Across Species
0 -- 0David Noren, Byron Long, Raquel Norel, Kahn Rrhissorrakrai, Kenneth R. Hess, Chenyue W. Hu, Alex Bisberg, André Schultz, Erik Engquist, Li Liu, Xihui Lin, Gregory M. Chen, Honglei Xie, Geoffrey A. M. Hunter, Paul C. Boutros, Oleg Stepanov, DREAM 9 AML-OPC Consortium, Thea Norman, Stephen H. Friend, Gustavo Stolovitzky, Steven M. Kornblau, Amina A. Qutub. A Crowdsourcing Approach to Developing and Assessing Prediction Algorithms for AML Prognosis
0 -- 0Rossana Mastrandrea, Alain Barrat. How to Estimate Epidemic Risk from Incomplete Contact Diaries Data?
0 -- 0Yu Toyoshima, Terumasa Tokunaga, Osamu Hirose, Manami Kanamori, Takayuki Teramoto, Moon Sun Jang, Sayuri Kuge, Takeshi Ishihara, Ryo Yoshida, Yuichi Iino. Accurate Automatic Detection of Densely Distributed Cell Nuclei in 3D Space
0 -- 0Daniel H. Huson, Sina Beier, Isabell Flade, Anna Górska, Mohamed El-Hadidi, Suparna Mitra, Hans-Joachim Ruscheweyh, Rewati Tappu. MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data
0 -- 0Elisa Boari de Lima, Wagner Meira Júnior, Raquel Cardoso de Melo Minardi. Isofunctional Protein Subfamily Detection Using Data Integration and Spectral Clustering
0 -- 0Rebeca Campos-Sánchez, Marzia A. Cremona, Alessia Pini, Francesca Chiaromonte, Kateryna D. Makova. Integration and Fixation Preferences of Human and Mouse Endogenous Retroviruses Uncovered with Functional Data Analysis
0 -- 0Samuel Hertig, Naomi R. Latorraca, Ron O. Dror. Revealing Atomic-Level Mechanisms of Protein Allostery with Molecular Dynamics Simulations
0 -- 0Ren Hua Chung, Wei-Yun Tsai, Chen-Yu Kang, Po-Ju Yao, Hui-Ju Tsai, Chia-Hsiang Chen. FamPipe: An Automatic Analysis Pipeline for Analyzing Sequencing Data in Families for Disease Studies
0 -- 0Stojan Jovanovic, Stefan Rotter. Interplay between Graph Topology and Correlations of Third Order in Spiking Neuronal Networks
0 -- 0Asa Thibodeau, Eladio J. Márquez, Oscar Luo, Yijun Ruan, Francesca Menghi, Dong-Guk Shin, Michael L. Stitzel, Paola Vera-Licona, Duygu Ucar. QuIN: A Web Server for Querying and Visualizing Chromatin Interaction Networks
0 -- 0Zhuo Wang, Andrew T. Sornborger, Louis Tao. Graded, Dynamically Routable Information Processing with Synfire-Gated Synfire Chains
0 -- 0Margaritis Voliotis, Philipp Thomas, Ramon Grima, Clive G. Bowsher. Stochastic Simulation of Biomolecular Networks in Dynamic Environments
0 -- 0Pintu Patra, Kimberley Kissoon, Isabel Cornejo, Heidi B. Kaplan, Oleg A. Igoshin. Colony Expansion of Socially Motile Myxococcus xanthus Cells Is Driven by Growth, Motility, and Exopolysaccharide Production
0 -- 0Daniel L. Parton, Patrick B. Grinaway, Sonya M. Hanson, Kyle Beauchamp, John D. Chodera. Ensembler: Enabling High-Throughput Molecular Simulations at the Superfamily Scale
0 -- 0Bastian Schiffthaler, Myrto Kostadima, NGS Trainer Consortium, Nicolas Delhomme, Gabriella Rustici. Training in High-Throughput Sequencing: Common Guidelines to Enable Material Sharing, Dissemination, and Reusability
0 -- 0Jérôme Wong-Ng, Anna Melbinger, Antonio Celani, Massimo Vergassola. The Role of Adaptation in Bacterial Speed Races
0 -- 0Danilo Bzdok, Gaël Varoquaux, Olivier Grisel, Michael Eickenberg, Cyril Poupon, Bertrand Thirion. Formal Models of the Network Co-occurrence Underlying Mental Operations
0 -- 0Frank J. Poelwijk, Vinod Krishna, Rama Ranganathan. The Context-Dependence of Mutations: A Linkage of Formalisms
0 -- 0Dario Corrada, Anatoly A. Soshilov, Michael S. Denison, Laura Bonati. Deciphering Dimerization Modes of PAS Domains: Computational and Experimental Analyses of the AhR: ARNT Complex Reveal New Insights Into the Mechanisms of AhR Transformation
0 -- 0Julio M. Belmonte, Maciej H. Swat, James A. Glazier. Filopodial-Tension Model of Convergent-Extension of Tissues
0 -- 0K. Aurelia Ball, Jeffrey R. Johnson, Mary K. Lewinski, John Guatelli, Erik Verschueren, Nevan J. Krogan, Matthew P. Jacobson. Non-degradative Ubiquitination of Protein Kinases
0 -- 0Kumari Sonal Choudhary, Neha Rohatgi, Skarphedinn Halldorsson, Eirikur Briem, Thorarinn Gudjonsson, Steinn Gudmundsson, Ottar Rolfsson. EGFR Signal-Network Reconstruction Demonstrates Metabolic Crosstalk in EMT
0 -- 0Michelle D. Brazas, B. F. Francis Ouellette. Continuing Education Workshops in Bioinformatics Positively Impact Research and Careers
0 -- 0Zhihui Wang, Romica Kerketta, Yao-Li Chuang, Prashant Dogra, Joseph D. Butner, Terisse A. Brocato, Armin Day, Rong Xu, Haifa Shen, Eman Simbawa, A. S. Al-Fhaid, S. R. Mahmoud, Steven A. Curley, Mauro Ferrari, Eugene J. Koay, Vittorio Cristini. Theory and Experimental Validation of a Spatio-temporal Model of Chemotherapy Transport to Enhance Tumor Cell Kill
0 -- 0Andra Waagmeester, Martina Kutmon, Anders Riutta, Ryan Miller, Egon L. Willighagen, Chris T. A. Evelo, Alexander R. Pico. Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources
0 -- 0Jin Liu 0005, Ruth Nussinov. Allostery: An Overview of Its History, Concepts, Methods, and Applications
0 -- 0Patrick Gemmell, Jotun Hein, Aris Katzourakis. Phylogenetic Analysis Reveals That ERVs "Die Young" but HERV-H Is Unusually Conserved
0 -- 0Robert E. Kass, Brian S. Caffo, Marie Davidian, Xiao-Li Meng, Bin Yu 0001, Nancy Reid. Ten Simple Rules for Effective Statistical Practice
0 -- 0Carlo Albert, Sören Vogel, Roman Ashauer. Computationally Efficient Implementation of a Novel Algorithm for the General Unified Threshold Model of Survival (GUTS)
0 -- 0Oliver W. Layton, Brett R. Fajen. Competitive Dynamics in MSTd: A Mechanism for Robust Heading Perception Based on Optic Flow
0 -- 0X. Jessie Jeng, Z. John Daye, Wenbin Lu, Jung-Ying Tzeng. Rare Variants Association Analysis in Large-Scale Sequencing Studies at the Single Locus Level
0 -- 0Olivier Rivoire, Kimberly A. Reynolds, Rama Ranganathan. Evolution-Based Functional Decomposition of Proteins
0 -- 0Dominik Thalmeier, Marvin Uhlmann, Hilbert J. Kappen, Raoul-Martin Memmesheimer. Learning Universal Computations with Spikes
0 -- 0Gentian Buzi, Mustafa Khammash. Implementation Considerations, Not Topological Differences, Are the Main Determinants of Noise Suppression Properties in Feedback and Incoherent Feedforward Circuits
0 -- 0Rupamanjari Majumder, Wanchana Jangsangthong, Iolanda Feola, Dirk L. Ypey, Daniël A. Pijnappels, Alexander V. Panfilov. A Mathematical Model of Neonatal Rat Atrial Monolayers with Constitutively Active Acetylcholine-Mediated K+ Current
0 -- 0Raquel Bromberg, Nick V. Grishin, Zbyszek Otwinowski. Phylogeny Reconstruction with Alignment-Free Method That Corrects for Horizontal Gene Transfer
0 -- 0Hui Liu, Gene E. Robinson, Eric Jakobsson. Conservation in Mammals of Genes Associated with Aggression-Related Behavioral Phenotypes in Honey Bees
0 -- 0David A. Lee, Sayoni Das, Natalie L. Dawson, Dragana Dobrijevic, John Ward, Christine A. Orengo. Novel Computational Protocols for Functionally Classifying and Characterising Serine Beta-Lactamases
0 -- 0Edward J. O'Brien, Jose Utrilla, Bernhard O. Palsson. Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments
0 -- 0Karin Lundengård, Gunnar Cedersund, Sebastian Sten, Felix Leong, Alexander Smedberg, Fredrik Elinder, Maria Engström. Mechanistic Mathematical Modeling Tests Hypotheses of the Neurovascular Coupling in fMRI
0 -- 0George A. Tsianos, Lisa N. MacFadden. Validated Predictions of Metabolic Energy Consumption for Submaximal Effort Movement
0 -- 0Henok Mengistu, Joost Huizinga, Jean-Baptiste Mouret, Jeff Clune. The Evolutionary Origins of Hierarchy
0 -- 0Adam Spiro, Ehud Y. Shapiro. Accuracy of Answers to Cell Lineage Questions Depends on Single-Cell Genomics Data Quality and Quantity
0 -- 0Sebastian Germerodt, Katrin Bohl, Anja Lück, Samay Pande, Anja Schröter, Christoph Kaleta, Stefan Schuster, Christian Kost. Pervasive Selection for Cooperative Cross-Feeding in Bacterial Communities
0 -- 0Ján Antolík, Sonja B. Hofer, James A. Bednar, Thomas D. Mrsic-Flogel. Model Constrained by Visual Hierarchy Improves Prediction of Neural Responses to Natural Scenes
0 -- 0Stefano Palminteri, Emma J. Kilford, Giorgio Coricelli, Sarah-Jayne Blakemore. The Computational Development of Reinforcement Learning during Adolescence
0 -- 0John D. O'Brien, Zamin Iqbal, Jason Wendler, Lucas Amenga-Etego. Inferring Strain Mixture within Clinical Plasmodium falciparum Isolates from Genomic Sequence Data
0 -- 0Thomas Eggert, Farrel R. Robinson, Andreas Straube. Modeling Inter-trial Variability of Saccade Trajectories: Effects of Lesions of the Oculomotor Part of the Fastigial Nucleus
0 -- 0Pierre Enel, Emmanuel Procyk, René Quilodran, Peter Ford Dominey. Reservoir Computing Properties of Neural Dynamics in Prefrontal Cortex
0 -- 0Aditya V. S. Ponnaluri, Luigi E. Perotti, Michael Liu, Zhilin Qu, James N. Weiss, Daniel B. Ennis, William S. Klug, Alan Garfinkel. Electrophysiology of Heart Failure Using a Rabbit Model: From the Failing Myocyte to Ventricular Fibrillation
0 -- 0Balázs Brankovics, Hao Zhang, Anne D. van Diepeningen, Theo A. J. van der Lee, Cees Waalwijk, G. Sybren de Hoog. GRAbB: Selective Assembly of Genomic Regions, a New Niche for Genomic Research
0 -- 0Chao Huang, Andrey Resnik, Tansu Celikel, Bernhard Englitz. Adaptive Spike Threshold Enables Robust and Temporally Precise Neuronal Encoding
0 -- 0Arun Chandramohan, Srinath Krishnamurthy, Andreas Larsson, Paer Nordlund, Anna Jansson, Ganesh S. Anand. Predicting Allosteric Effects from Orthosteric Binding in Hsp90-Ligand Interactions: Implications for Fragment-Based Drug Design
0 -- 0Go Ashida, Jutta Kretzberg, Daniel J. Tollin. Roles for Coincidence Detection in Coding Amplitude-Modulated Sounds
0 -- 0Berk Ekmekci, Charles E. McAnany, Cameron Mura. An Introduction to Programming for Bioscientists: A Python-Based Primer
0 -- 0Christiana N. Fogg, Diane E. Kovats. Program Bytes: Satellite Meetings, SIGs, and AKEs at ISMB 2016
0 -- 0Ana-Maria Florescu, Pierre Therizols, Angelo Rosa. Large Scale Chromosome Folding Is Stable against Local Changes in Chromatin Structure
0 -- 0Matteo Mori, Terence Hwa, Olivier C. Martin, Andrea De Martino, Enzo Marinari. Constrained Allocation Flux Balance Analysis