Journal: PLoS Computational Biology

Volume 9, Issue 3

0 -- 0David Amar, Hershel Safer, Ron Shamir. Dissection of Regulatory Networks that Are Altered in Disease via Differential Co-expression
0 -- 0Wei Zhang 0032, Takayo Ota, Viji Shridhar, Jeremy Chien, Baolin Wu, Rui Kuang. Network-based Survival Analysis Reveals Subnetwork Signatures for Predicting Outcomes of Ovarian Cancer Treatment
0 -- 0Paul C. Whitford, Scott C. Blanchard, Jamie H. D. Cate, Karissa Y. Sanbonmatsu. Connecting the Kinetics and Energy Landscape of tRNA Translocation on the Ribosome
0 -- 0Néstor Sepúlveda, Laurence Petitjean, Olivier Cochet, Erwan Grasland-Mongrain, Pascal Silberzan, Vincent Hakim. Collective Cell Motion in an Epithelial Sheet Can Be Quantitatively Described by a Stochastic Interacting Particle Model
0 -- 0Marco Di Stefano, Angelo Rosa, Vincenzo Belcastro, Diego di Bernardo, Cristian Micheletti. Colocalization of Coregulated Genes: A Steered Molecular Dynamics Study of Human Chromosome 19
0 -- 0Tina Toni, Bruce Tidor. Combined Model of Intrinsic and Extrinsic Variability for Computational Network Design with Application to Synthetic Biology
0 -- 0Tomoki Kurikawa, Kunihiko Kaneko. Embedding Responses in Spontaneous Neural Activity Shaped through Sequential Learning
0 -- 0Dazhi Jiao, Yuzhen Ye, Haixu Tang. Probabilistic Inference of Biochemical Reactions in Microbial Communities from Metagenomic Sequences
0 -- 0Bóris Marin, William H. Barnett, Anca Doloc-Mihu, Ronald L. Calabrese, Gennady S. Cymbalyuk. High Prevalence of Multistability of Rest States and Bursting in a Database of a Model Neuron
0 -- 0Michael A. Carlin, Mounya Elhilali. Sustained Firing of Model Central Auditory Neurons Yields a Discriminative Spectro-temporal Representation for Natural Sounds
0 -- 0Zheng Chen, Weixiong Zhang. Integrative Analysis Using Module-Guided Random Forests Reveals Correlated Genetic Factors Related to Mouse Weight
0 -- 0Christopher P. Said, David J. Heeger. A Model of Binocular Rivalry and Cross-orientation Suppression
0 -- 0Douglas E. White, Melissa A. Kinney, Todd C. McDevitt, Melissa L. Kemp. Spatial Pattern Dynamics of 3D Stem Cell Loss of Pluripotency via Rules-Based Computational Modeling
0 -- 0Katarzyna Bozek, Thomas Lengauer, Saleta Sierra, Rolf Kaiser, Francisco S. Domingues. Analysis of Physicochemical and Structural Properties Determining HIV-1 Coreceptor Usage
0 -- 0Yuguo Yu, Thomas S. McTavish, Michael L. Hines, Gordon M. Shepherd, Cesare Valenti, Michele Migliore. Sparse Distributed Representation of Odors in a Large-scale Olfactory Bulb Circuit
0 -- 0Yuhan Chen, Shengjun Wang, Claus C. Hilgetag, Changsong Zhou. Trade-off between Multiple Constraints Enables Simultaneous Formation of Modules and Hubs in Neural Systems
0 -- 0Andrew M. Reynolds, Mathieu Lihoreau, Lars Chittka. A Simple Iterative Model Accurately Captures Complex Trapline Formation by Bumblebees Across Spatial Scales and Flower Arrangements
0 -- 0Philip Stegmaier, Alexander E. Kel, Edgar Wingender, Jürgen Borlak. A Discriminative Approach for Unsupervised Clustering of DNA Sequence Motifs
0 -- 0Silvio a Beccara, Tatjana Skrbic, Roberto Covino, Cristian Micheletti, Pietro Faccioli. Folding Pathways of a Knotted Protein with a Realistic Atomistic Force Field
0 -- 0Simon Garnier, Tucker Murphy, Matthew J. Lutz, Edward Hurme, Simon Leblanc, Iain D. Couzin. Stability and Responsiveness in a Self-Organized Living Architecture
0 -- 0Sergio Rossell, Martijn A. Huynen, Richard A. Notebaart. Inferring Metabolic States in Uncharacterized Environments Using Gene-Expression Measurements
0 -- 0Sunhwan Jo, Hui Sun Lee, Jeffrey Skolnick, Wonpil Im. Restricted N-glycan Conformational Space in the PDB and Its Implication in Glycan Structure Modeling
0 -- 0Zhixing Feng, Gang Fang, Jonas Korlach, Tyson Clark, Khai Luong, Xuegong Zhang, Wing Wong, Eric Schadt. Detecting DNA Modifications from SMRT Sequencing Data by Modeling Sequence Context Dependence of Polymerase Kinetic
0 -- 0Oscar Franzén, Jon Jerlström-Hultqvist, Elin Einarsson, Johan Ankarklev, Marcela Ferella, Björn Andersson, Staffan G. Svärd. Giardia intestinalis Using Strand-specific RNA-Seq
0 -- 0Ophir Shalem, Lucas Carey, Danny Zeevi, Eilon Sharon, Leeat Keren, Adina Weinberger, Orna Dahan, Yitzhak Pilpel, Eran Segal. Measurements of the Impact of 3′ End Sequences on Gene Expression Reveal Wide Range and Sequence Dependent Effects
0 -- 0Erik M. Volz, Katia Koelle, Trevor Bedford. Viral Phylodynamics
0 -- 0Marta I. Garrido, Maneesh Sahani, Raymond J. Dolan. Outlier Responses Reflect Sensitivity to Statistical Structure in the Human Brain
0 -- 0Frank H. Wallrapp, Alexander A. Voityuk, Victor Guallar. In-silico Assessment of Protein-Protein Electron Transfer. A Case Study: Cytochrome c Peroxidase - Cytochrome c
0 -- 0Jan Grau, Annett Wolf, Maik Reschke, Ulla Bonas, Stefan Posch, Jens Boch. Computational Predictions Provide Insights into the Biology of TAL Effector Target Sites
0 -- 0Kirill S. Korolev. The Fate of Cooperation during Range Expansions
0 -- 0Pouria Dasmeh, Adrian W. R. Serohijos, Kasper P. Kepp, Eugene I. Shakhnovich. Positively Selected Sites in Cetacean Myoglobins Contribute to Protein Stability
0 -- 0Syed Y. Abbas, Khaldoun C. Hamade, Ellen J. Yang, Scott Nawy, Robert G. Smith, Diana L. Pettit. Directional Summation in Non-direction Selective Retinal Ganglion Cells
0 -- 0Hyun-Jun Nam, Seong Kyu Han, James U. Bowie, Sanguk Kim. Rampant Exchange of the Structure and Function of Extramembrane Domains between Membrane and Water Soluble Proteins
0 -- 0Rasmus Agren, Liming Liu, Saeed Shoaie, Wanwipa Vongsangnak, Intawat Nookaew, Jens Nielsen. Penicillium chrysogenum
0 -- 0Miguel A. Fortuna, Luis Zaman, Aaron P. Wagner, Charles Ofria. Evolving Digital Ecological Networks
0 -- 0Gary R. Mirams, Christopher J. Arthurs, Miguel O. Bernabeu, Rafel Bordas, Jonathan Cooper, Alberto Corrias, Yohan Davit, Sara-Jane Dunn, Alexander G. Fletcher, Daniel G. Harvey, Megan E. Marsh, James M. Osborne, Pras Pathmanathan, Joe Pitt-Francis, James Southern, Nejib Zemzemi, David Gavaghan. Chaste: An Open Source C++ Library for Computational Physiology and Biology
0 -- 0Stefanie Hertel, Christian Brettschneider, Ilka M. Axmann. Revealing a Two-Loop Transcriptional Feedback Mechanism in the Cyanobacterial Circadian Clock
0 -- 0Chad R. Wells, Eili Y. Klein, Chris T. Bauch. Policy Resistance Undermines Superspreader Vaccination Strategies for Influenza
0 -- 0Viola Priesemann, Mario Valderrama, Michael Wibral, Michel Le Van Quyen. Neuronal Avalanches Differ from Wakefulness to Deep Sleep - Evidence from Intracranial Depth Recordings in Humans
0 -- 0BoHung Kim, Sarah L. Hawes, Fawad Gillani, Lane J. Wallace, Kim T. Blackwell. Signaling Pathways Involved in Striatal Synaptic Plasticity are Sensitive to Temporal Pattern and Exhibit Spatial Specificity
0 -- 0Nisha Rajagopal, Wei Xie, Yan Li, Uli Wagner, Wei Wang, John A. Stamatoyannopoulos, Jason Ernst, Manolis Kellis, Bing Ren. RFECS: A Random-Forest Based Algorithm for Enhancer Identification from Chromatin State
0 -- 0Hermann B. Frieboes, Bryan R. Smith, Yao-Li Chuang, Ken Ito, Allison M. Roettgers, Sanjiv S. Gambhir, Vittorio Cristini. An Integrated Computational/Experimental Model of Lymphoma Growth
0 -- 0Einat Granot-Atedgi, Gasper Tkacik, Ronen Segev, Elad Schneidman. Stimulus-dependent Maximum Entropy Models of Neural Population Codes
0 -- 0Libin Rong, Jérémie Guedj, Harel Dahari, Daniel J. Coffield Jr., Micha Levi, Patrick Smith, Alan S. Perelson. Analysis of Hepatitis C Virus Decline during Treatment with the Protease Inhibitor Danoprevir Using a Multiscale Model
0 -- 0Winston A. Haynes, Roger Higdon, Larissa Stanberry, Dwayne Collins, Eugene Kolker. Differential Expression Analysis for Pathways
0 -- 0R. Channing Moore, Tyler Lee, Frédéric E. Theunissen. Noise-invariant Neurons in the Avian Auditory Cortex: Hearing the Song in Noise
0 -- 0Jialiang Huang, Chaoqun Niu, Christopher D. Green, Lun Yang, Hongkang Mei, Jing-Dong J. Han. Systematic Prediction of Pharmacodynamic Drug-Drug Interactions through Protein-Protein-Interaction Network
0 -- 0Himadri Mukhopadhyay, Shaun-Paul Cordoba, Philip K. Maini, P. Anton van der Merwe, Omer Dushek. Systems Model of T Cell Receptor Proximal Signaling Reveals Emergent Ultrasensitivity
0 -- 0Andreas Handel, Justin Brown, David E. Stallknecht, Pejman Rohani. A Multi-scale Analysis of Influenza A Virus Fitness Trade-offs due to Temperature-dependent Virus Persistence
0 -- 0Jonathan Woodsmith, Atanas Kamburov, Ulrich Stelzl. Dual Coordination of Post Translational Modifications in Human Protein Networks
0 -- 0Brad Busse, Stephen Smith. Automated Analysis of a Diverse Synapse Population
0 -- 0Ron M. Stewart, Cynthia Alexander Rascón, Shulan Tian, Jeff Nie, Chris Barry, Li-Fang Chu, Hamisha Ardalani, Ryan J. Wagner, Mitchell D. Probasco, Jennifer M. Bolin, Ning Leng, Srikumar Sengupta, Michael Volkmer, Bianca Habermann, Elly M. Tanaka, James A. Thomson, Colin N. Dewey. Comparative RNA-seq Analysis in the Unsequenced Axolotl: The Oncogene Burst Highlights Early Gene Expression in the Blastema
0 -- 0Alane Izu, Ted Cohen, Victor DeGruttola. Bayesian Estimation of Mixture Models with Prespecified Elements to Compare Drug Resistance in Treatment-Naïve and Experienced Tuberculosis Cases
0 -- 0Simon Garnier, Maud Combe, Christian Jost, Guy Theraulaz. Do Ants Need to Estimate the Geometrical Properties of Trail Bifurcations to Find an Efficient Route? A Swarm Robotics Test Bed
0 -- 0Robert W. Mill, Tamás Bohm, Alexandra Bendixen, István Winkler, Susan L. Denham. Modelling the Emergence and Dynamics of Perceptual Organisation in Auditory Streaming
0 -- 0Thomas Lengauer, Ruth Nussinov. PLOS Computational Biology
0 -- 0Mehrdad Mehrbod, Mohammad R. K. Mofrad. Localized Lipid Packing of Transmembrane Domains Impedes Integrin Clustering
0 -- 0Syed Abbas Bukhari, Gustavo Caetano-Anollés. Origin and Evolution of Protein Fold Designs Inferred from Phylogenomic Analysis of CATH Domain Structures in Proteomes
0 -- 0David K. Johnson, John Karanicolas. Druggable Protein Interaction Sites Are More Predisposed to Surface Pocket Formation than the Rest of the Protein Surface
0 -- 0Alexander J. Stewart, Robert M. Seymour, Andrew Pomiankowski, Max Reuter. Under-Dominance Constrains the Evolution of Negative Autoregulation in Diploids
0 -- 0Christopher Y. Park, Aaron K. Wong, Casey S. Greene, Jessica Rowland, Yuanfang Guan, Lars Ailo Bongo, Rebecca D. Burdine, Olga G. Troyanskaya. Functional Knowledge Transfer for High-accuracy Prediction of Under-studied Biological Processes
0 -- 0Luis E. C. Rocha, Vincent D. Blondel. Bursts of Vertex Activation and Epidemics in Evolving Networks
0 -- 0Laura Matrajt, M. Elizabeth Halloran, Ira M. Longini Jr.. Optimal Vaccine Allocation for the Early Mitigation of Pandemic Influenza
0 -- 0Ekta Khurana, Yao Fu, Jieming Chen, Mark Gerstein. Interpretation of Genomic Variants Using a Unified Biological Network Approach
0 -- 0Richard P. Mann, Andrea Perna, Daniel Strömbom, Roman Garnett, James E. Herbert-Read, David J. T. Sumpter, Ashley J. W. Ward. Multi-scale Inference of Interaction Rules in Animal Groups Using Bayesian Model Selection
0 -- 0Anton Spanne, Henrik Jörntell. Processing of Multi-dimensional Sensorimotor Information in the Spinal and Cerebellar Neuronal Circuitry: A New Hypothesis
0 -- 0Christian G. Fink, Geoffrey G. Murphy, Michal Zochowski, Victoria Booth. A Dynamical Role for Acetylcholine in Synaptic Renormalization
0 -- 0Clive G. Bowsher, Margaritis Voliotis, Peter S. Swain. The Fidelity of Dynamic Signaling by Noisy Biomolecular Networks
0 -- 0James B. Gilmore, Anthony D. Kelleher, David A. Cooper, John M. Murray. Explaining the Determinants of First Phase HIV Decay Dynamics through the Effects of Stage-dependent Drug Action
0 -- 0Per Larsson, Peter M. Kasson. Lipid Tail Protrusion in Simulations Predicts Fusogenic Activity of Influenza Fusion Peptide Mutants and Conformational Models
0 -- 0Christoph Schmal, Peter Reimann, Dorothee Staiger. Arabidopsis thaliana
0 -- 0Munia Amin, Steven L. Porter, Orkun S. Soyer. Split Histidine Kinases Enable Ultrasensitivity and Bistability in Two-Component Signaling Networks
0 -- 0Timothy W. Secomb, Jonathan P. Alberding, Richard Hsu, Mark W. Dewhirst, Axel R. Pries. Angiogenesis: An Adaptive Dynamic Biological Patterning Problem