Journal: PLoS Computational Biology

Volume 9, Issue 9

0 -- 0James J. Lee, Justin Huang, Christopher G. England, Lacey R. McNally, Hermann B. Frieboes. In Vivo Response to Gemcitabine in Pancreatic Cancer
0 -- 0Hassan Masum, Aarthi Rao, Benjamin M. Good, Matthew H. Todd, Aled M. Edwards, Leslie Chan, Barry A. Bunin, Andrew I. Su, Zakir Thomas, Philip E. Bourne. Ten Simple Rules for Cultivating Open Science and Collaborative R&D
0 -- 0Dipak Barua, William S. Hlavacek. Modeling the Effect of APC Truncation on Destruction Complex Function in Colorectal Cancer Cells
0 -- 0Audrey Salles, Cyrille Billaudeau, Arnauld Sergé, Anne-Marie Bernard, Marie-Claire Phélipot, Nicolas Bertaux, Mathieu Fallet, Pierre Grenot, Didier Marguet, Hai-Tao He, Yannick Hamon. Barcoding T Cell Calcium Response Diversity with Methods for Automated and Accurate Analysis of Cell Signals (MAAACS)
0 -- 0Sulyman Barkho, Levi C. T. Pierce, Maria L. McGlone, Sheng Li, Virgil L. Woods Jr., Ross C. Walker, Joseph A. Adams, Patricia A. Jennings. Distal Loop Flexibility of a Regulatory Domain Modulates Dynamics and Activity of C-Terminal Src Kinase (Csk)
0 -- 0Tristan Ursell, Rosanna Man Wah Chau, Susanne Wisen, Devaki Bhaya, Kerwyn Casey Huang. Motility Enhancement through Surface Modification Is Sufficient for Cyanobacterial Community Organization during Phototaxis
0 -- 0John C. Williams, Jianjin Xu, Zhongju Lu, Aleksandra Klimas, Xuxin Chen, Christina M. Ambrosi, Ira S. Cohen, Emilia Entcheva. Computational Optogenetics: Empirically-Derived Voltage- and Light-Sensitive Channelrhodopsin-2 Model
0 -- 0Izzet B. Yildiz, Katharina von Kriegstein, Stefan J. Kiebel. From Birdsong to Human Speech Recognition: Bayesian Inference on a Hierarchy of Nonlinear Dynamical Systems
0 -- 0Geoff Macintyre, Magali Michaut, Thomas Abeel. The Regional Student Group Program of the ISCB Student Council: Stories from the Road
0 -- 0Yun M. Zhao, Anthony R. French. Mechanistic Model of Natural Killer Cell Proliferative Response to IL-15 Receptor Stimulation
0 -- 0Jianhui Song, Sheung Chun Ng, Peter Tompa, Kevin A. W. Lee, Hue Sun Chan. Polycation-π Interactions Are a Driving Force for Molecular Recognition by an Intrinsically Disordered Oncoprotein Family
0 -- 0Jing Chen, Zhen Hu, Mukta Phatak, John Reichard, Johannes M. Freudenberg, Siva Sivaganesan, Mario Medvedovic. Genome-Wide Signatures of Transcription Factor Activity: Connecting Transcription Factors, Disease, and Small Molecules
0 -- 0Laurence T. Hunt, Mark William Woolrich, Matthew F. S. Rushworth, Timothy Edward John Behrens. Trial-Type Dependent Frames of Reference for Value Comparison
0 -- 0Kobi Snitz, Adi Yablonka, Tali Weiss, Idan Frumin, Rehan M. Khan, Noam Sobel. Predicting Odor Perceptual Similarity from Odor Structure
0 -- 0Ben Mitchinson, Tony J. Prescott. Whisker Movements Reveal Spatial Attention: A Unified Computational Model of Active Sensing Control in the Rat
0 -- 0Vishal N. Patel, Giridharan Gokulrangan, Salim A. Chowdhury, YanWen Chen, Andrew E. Sloan, Mehmet Koyutürk, Jill S. Barnholtz-Sloan, Mark R. Chance. Network Signatures of Survival in Glioblastoma Multiforme
0 -- 0Giuseppe Maccari, Mariagrazia Di Luca, Riccardo Nifosí, Francesco Cardarelli, Giovanni Signore, Claudia Boccardi, Angelo Bifone. Antimicrobial Peptides Design by Evolutionary Multiobjective Optimization
0 -- 0Jing Tang, Leena Karhinen, Tao Xu, Agnieszka Szwajda, Bhagwan Yadav, Krister Wennerberg, Tero Aittokallio. Target Inhibition Networks: Predicting Selective Combinations of Druggable Targets to Block Cancer Survival Pathways
0 -- 0Danielle S. Bassett, Nicholas F. Wymbs, M. Puck Rombach, Mason A. Porter, Peter J. Mucha, Scott T. Grafton. Task-Based Core-Periphery Organization of Human Brain Dynamics
0 -- 0William Pontius, Michael W. Sneddon, Thierry Emonet. Adaptation Dynamics in Densely Clustered Chemoreceptors
0 -- 0Jorge F. Mejías, Gary Marsat, Kieran Bol, Leonard Maler, André Longtin. Learning Contrast-Invariant Cancellation of Redundant Signals in Neural Systems
0 -- 0Emek Demir, Özgün Babur, Igor Rodchenkov, Bülent Arman Aksoy, Ken I. Fukuda, Benjamin E. Gross, Selçuk Onur Sümer, Gary D. Bader, Chris Sander. Using Biological Pathway Data with Paxtools
0 -- 0Julia Lasserre, Ho-Ryun Chung, Martin Vingron. Finding Associations among Histone Modifications Using Sparse Partial Correlation Networks
0 -- 0Andrew J. K. Phillips, B. D. Fulcher, Peter A. Robinson, E. B. Klerman. Mammalian Rest/Activity Patterns Explained by Physiologically Based Modeling
0 -- 0Noa Liscovitch, Gal Chechik. Specialization of Gene Expression during Mouse Brain Development
0 -- 0Stephen A. Smith, Joseph W. Brown, Cody E. Hinchliff. Analyzing and Synthesizing Phylogenies Using Tree Alignment Graphs
0 -- 0Kartik Subramanian, Mark R. Paul, John J. Tyson. Caulobacter crescentus
0 -- 0Anthony Mathelier, Wyeth W. Wasserman. The Next Generation of Transcription Factor Binding Site Prediction
0 -- 0Linhui Hao, Qiuling He, Zhishi Wang, Mark Craven, Michael A. Newton, Paul Ahlquist. Limited Agreement of Independent RNAi Screens for Virus-Required Host Genes Owes More to False-Negative than False-Positive Factors
0 -- 0Martin D. Vesper, Bert L. de Groot. Collective Dynamics Underlying Allosteric Transitions in Hemoglobin
0 -- 0Dilek Eren, Burak Alakent. Frequency Response of a Protein to Local Conformational Perturbations
0 -- 0Eddy J. Bautista, Joseph Zinski, Steven M. Szczepanek, Erik L. Johnson, Edan R. Tulman, Wei-Mei Ching, Steven J. Geary, Ranjan Srivastava. Mycoplasma gallisepticum
0 -- 0Ioannis N. Melas, Regina Samaga, Leonidas G. Alexopoulos, Steffen Klamt. Detecting and Removing Inconsistencies between Experimental Data and Signaling Network Topologies Using Integer Linear Programming on Interaction Graphs
0 -- 0Rudi Agius, Mieczyslaw Torchala, Iain H. Moal, Juan Fernández-Recio, Paul A. Bates. Characterizing Changes in the Rate of Protein-Protein Dissociation upon Interface Mutation Using Hotspot Energy and Organization
0 -- 0Johnatan Aljadeff, Ronen Segev, Michael J. Berry II, Tatyana O. Sharpee. Spike Triggered Covariance in Strongly Correlated Gaussian Stimuli
0 -- 0Javier Garcia-Bernardo, Mary J. Dunlop. Escherichia coli Multiple Antibiotic Resistance Network from Interlinked Positive and Negative Feedback Loops
0 -- 0Julián Candia, Ryan Maunu, Meghan K. Driscoll, Angélique Biancotto, Pradeep Dagur, J. Philip McCoy Jr., H. Nida Sen, Lai Wei, Amos Maritan, Kan Cao, Robert B. Nussenblatt, Jayanth R. Banavar, Wolfgang Losert. From Cellular Characteristics to Disease Diagnosis: Uncovering Phenotypes with Supercells
0 -- 0Alex Bateman, Janet Kelso, Daniel Mietchen, Geoff Macintyre, Tomás Di Domenico, Thomas Abeel, Darren W. Logan, Predrag Radivojac, Burkhard Rost. ISCB Computational Biology Wikipedia Competition

Volume 9, Issue 8

0 -- 0Casey Diekman, Mino D. C. Belle, Robert P. Irwin, Charles N. Allen, Hugh D. Piggins, Daniel B. Forger. Causes and Consequences of Hyperexcitation in Central Clock Neurons
0 -- 0Chunhe Li, Jin Wang. Quantifying Cell Fate Decisions for Differentiation and Reprogramming of a Human Stem Cell Network: Landscape and Biological Paths
0 -- 0Jung H. Lee, Miles A. Whittington, Nancy J. Kopell. Top-Down Beta Rhythms Support Selective Attention via Interlaminar Interaction: A Model
0 -- 0Lendert Gelens, Lydia Hill, Alexandra Vandervelde, Jan Danckaert, Remy Loris. E. coli
0 -- 0Volodymyr Babin, Dongli Wang, Robert B. Rose, Celeste Sagui. Binding Polymorphism in the DNA Bound State of the Pdx1 Homeodomain
0 -- 0Kathrin Poos, Jan Smida, Michaela Nathrath, Doris Maugg, Daniel Baumhoer, Eberhard Korsching. How MicroRNA and Transcription Factor Co-regulatory Networks Affect Osteosarcoma Cell Proliferation
0 -- 0Mengchen Zhu, Christopher J. Rozell. Visual Nonclassical Receptive Field Effects Emerge from Sparse Coding in a Dynamical System
0 -- 0Andrew M. Hein, Scott A. McKinley. Sensory Information and Encounter Rates of Interacting Species
0 -- 0András Szilágyi, István Zachar, Eörs Szathmáry. Gause's Principle and the Effect of Resource Partitioning on the Dynamical Coexistence of Replicating Templates
0 -- 0Duncan J. MacGregor, Gareth Leng. Spike Triggered Hormone Secretion in Vasopressin Cells; a Model Investigation of Mechanism and Heterogeneous Population Function
0 -- 0Guillermo Rodrigo, Thomas E. Landrain, Eszter Majer, José-Antonio Daròs, Alfonso Jaramillo. Full Design Automation of Multi-State RNA Devices to Program Gene Expression Using Energy-Based Optimization
0 -- 0Simona Cocco, Rémi Monasson, Martin Weigt. From Principal Component to Direct Coupling Analysis of Coevolution in Proteins: Low-Eigenvalue Modes are Needed for Structure Prediction
0 -- 0Joel Zylberberg, Michael Robert DeWeese. Sparse Coding Models Can Exhibit Decreasing Sparseness while Learning Sparse Codes for Natural Images
0 -- 0Carlo Baldassi, Alireza Alemi-Neissi, Marino Pagan, James J. DiCarlo, Riccardo Zecchina, Davide Zoccolan. Shape Similarity, Better than Semantic Membership, Accounts for the Structure of Visual Object Representations in a Population of Monkey Inferotemporal Neurons
0 -- 0Yves Dehouck, Alexander S. Mikhailov. Effective Harmonic Potentials: Insights into the Internal Cooperativity and Sequence-Specificity of Protein Dynamics
0 -- 0Simona Mariani, Daniele Dell'Orco, Angelo Felline, Francesco Raimondi, Francesca Fanelli. Network and Atomistic Simulations Unveil the Structural Determinants of Mutations Linked to Retinal Diseases
0 -- 0Christoph Bauermeister, Tilo Schwalger, David F. Russell, Alexander B. Neiman, Benjamin Lindner. Characteristic Effects of Stochastic Oscillatory Forcing on Neural Firing: Analytical Theory and Comparison to Paddlefish Electroreceptor Data
0 -- 0Bruno M. C. Martins, Peter S. Swain. Ultrasensitivity in Phosphorylation-Dephosphorylation Cycles with Little Substrate
0 -- 0Evgeniy A. Ozonov, Erik van Nimwegen. Nucleosome Free Regions in Yeast Promoters Result from Competitive Binding of Transcription Factors That Interact with Chromatin Modifiers
0 -- 0Harish Shankaran, Yi Zhang, Yunbing Tan, Haluk Resat. Model-Based Analysis of HER Activation in Cells Co-Expressing EGFR, HER2 and HER3
0 -- 0Frédéric Crevecoeur, Stephen H. Scott. Priors Engaged in Long-Latency Responses to Mechanical Perturbations Suggest a Rapid Update in State Estimation
0 -- 0Michael Graupner, Reinoud Maex, Boris S. Gutkin. Endogenous Cholinergic Inputs and Local Circuit Mechanisms Govern the Phasic Mesolimbic Dopamine Response to Nicotine
0 -- 0Ilaria Cataudella, Kim Sneppen, Kenn Gerdes, Namiko Mitarai. Conditional Cooperativity of Toxin - Antitoxin Regulation Can Mediate Bistability between Growth and Dormancy
0 -- 0Pablo Szekely, Hila Sheftel, Avi E. Mayo, Uri Alon. Evolutionary Tradeoffs between Economy and Effectiveness in Biological Homeostasis Systems
0 -- 0Frederic Zubler, Andreas Hauri, Sabina Pfister, Roman Bauer, John C. Anderson, Adrian M. Whatley, Rodney J. Douglas. Simulating Cortical Development as a Self Constructing Process: A Novel Multi-Scale Approach Combining Molecular and Physical Aspects
0 -- 0Chiara Poletto, Sandro Meloni, Vittoria Colizza, Yamir Moreno, Alessandro Vespignani. Host Mobility Drives Pathogen Competition in Spatially Structured Populations
0 -- 0Niko Beerenwinkel, Hesam Montazeri, Heike Schuhmacher, Patrick Knupfer, Viktor von Wyl, Hansjakob Furrer, Manuel Battegay, Bernard Hirschel, Matthias Cavassini, Pietro Vernazza, Enos Bernasconi, Sabine Yerly, Jürg Böni, Thomas Klimkait, Cristina Cellerai, Huldrych F. Günthard. The Individualized Genetic Barrier Predicts Treatment Response in a Large Cohort of HIV-1 Infected Patients
0 -- 0Eric T. C. Wong, Dokyun Na, Jörg Gsponer. On the Importance of Polar Interactions for Complexes Containing Intrinsically Disordered Proteins
0 -- 0Michael F. Lawrence, Wolfgang Huber, Hervé Pagès, Patrick Aboyoun, Marc Carlson, Robert Gentleman, Martin T. Morgan, Vincent J. Carey. Software for Computing and Annotating Genomic Ranges
0 -- 0Karen van Eunen, Sereh M. J. Simons, Albert Gerding, Aycha Bleeker, Gijs den Besten, Catharina M. L. Touw, Sander M. Houten, Bert K. Groen, Klaas Krab, Dirk-Jan Reijngoud, Barbara M. Bakker. Biochemical Competition Makes Fatty-Acid β-Oxidation Vulnerable to Substrate Overload
0 -- 0Jose Teles, Cristina Pina, Patrik Edén, Mattias Ohlsson, Tariq Enver, Carsten Peterson. Transcriptional Regulation of Lineage Commitment - A Stochastic Model of Cell Fate Decisions
0 -- 0Ed Reznik, Pankaj Mehta, Daniel Segrè. Flux Imbalance Analysis and the Sensitivity of Cellular Growth to Changes in Metabolite Pools
0 -- 0Ohad Manor, Eran Segal. Predicting Disease Risk Using Bootstrap Ranking and Classification Algorithms
0 -- 0Christian A. Tiemann, Joep Vanlier, Maaike H. Oosterveer, Albert K. Groen, Peter A. J. Hilbers, Natal A. W. van Riel. Parameter Trajectory Analysis to Identify Treatment Effects of Pharmacological Interventions
0 -- 0Angelo Pavesi, Gkikas Magiorkinis, David G. Karlin. Deltaretroviruses
0 -- 0Neta S. Zuckerman, Yair Noam, Andrea J. Goldsmith, Peter P. Lee. A Self-Directed Method for Cell-Type Identification and Separation of Gene Expression Microarrays
0 -- 0Matan Sorek, Nathalie Q. Balaban, Yonatan Loewenstein. Stochasticity, Bistability and the Wisdom of Crowds: A Model for Associative Learning in Genetic Regulatory Networks
0 -- 0Jordi Heijman, Antonio Zaza, Daniel M. Johnson, Yoram Rudy, Ralf L. M. Peeters, Paul G. A. Volders, Ronald L. Westra. Determinants of Beat-to-Beat Variability of Repolarization Duration in the Canine Ventricular Myocyte: A Computational Analysis
0 -- 0Christiana N. Fogg, Diane E. Kovats. International Society for Computational Biology Welcomes Its Newest Class of Fellows
0 -- 0Chun Wu, Joan-Emma Shea. Structural Similarities and Differences between Amyloidogenic and Non-Amyloidogenic Islet Amyloid Polypeptide (IAPP) Sequences and Implications for the Dual Physiological and Pathological Activities of These Peptides

Volume 9, Issue 7

0 -- 0Marco Pautasso. Ten Simple Rules for Writing a Literature Review
0 -- 0Denis Bucher, Yuan-Hao Hsu, Varnavas D. Mouchlis, Edward A. Dennis, James Andrew McCammon. 2 into a Phospholipid Bilayer via Coarse-Grained and Atomistic Molecular Dynamics Simulations
0 -- 0Michael J. Lawson, Brian Drawert, Mustafa Khammash, Linda Petzold, Tau-Mu Yi. Spatial Stochastic Dynamics Enable Robust Cell Polarization
0 -- 0Idan Menashe, Pascal Grange, Eric C. Larsen, Sharmila Banerjee-Basu, Partha P. Mitra. Co-expression Profiling of Autism Genes in the Mouse Brain
0 -- 0Archana Bajpai, Anna Feoktistova, Jun-Song Chen, Dannel McCollum, Masamitsu Sato, Rafael Edgardo Carazo-Salas, Kathleen L. Gould, Attila Csikasz-Nagy. Dynamics of SIN Asymmetry Establishment
0 -- 0Shuzhao Li, Youngja Park, Sai Duraisingham, Frederick H. Strobel, Nooruddin Khan, Quinlyn A. Soltow, Dean P. Jones, Bali Pulendran. Predicting Network Activity from High Throughput Metabolomics
0 -- 0James C. Robertson, Nate C. Hurley, Marcello Tortorici, Giuseppe Ciossani, Maria Teresa Borrello, Nadeem A. Vellore, A. Ganesan, Andrea Mattevi, Riccardo Baron. Expanding the Druggable Space of the LSD1/CoREST Epigenetic Target: New Potential Binding Regions for Drug-Like Molecules, Peptides, Protein Partners, and Chromatin
0 -- 0David P. Reichert, Peggy Seriès, Amos J. Storkey. Charles Bonnet Syndrome: Evidence for a Generative Model in the Cortex?
0 -- 0Pinkesh K. Patel, Orian Shirihai, Kerwyn Casey Huang. Optimal Dynamics for Quality Control in Spatially Distributed Mitochondrial Networks
0 -- 0Joshua T. Schiffer, Dave A. Swan, Daniel Stone, Keith R. Jerome. Predictors of Hepatitis B Cure Using Gene Therapy to Deliver DNA Cleavage Enzymes: A Mathematical Modeling Approach
0 -- 0Changji Shi, Chuan-Hsiang Huang, Peter N. Devreotes, Pablo A. Iglesias. Interaction of Motility, Directional Sensing, and Polarity Modules Recreates the Behaviors of Chemotaxing Cells
0 -- 0Szymon Leski, Henrik Lindén, Tom Tetzlaff, Klas H. Pettersen, Gaute T. Einevoll. Frequency Dependence of Signal Power and Spatial Reach of the Local Field Potential
0 -- 0Umadevi Paila, Brad A. Chapman, Rory Kirchner, Aaron R. Quinlan. GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations
0 -- 0Kai-Cheng Hsu, Wen-Chi Cheng, Yen-Fu Chen, Wen-Ching Wang, Jinn-Moon Yang. Pathway-based Screening Strategy for Multitarget Inhibitors of Diverse Proteins in Metabolic Pathways
0 -- 0Xiujuan Wang, Bram Thijssen, Haiyuan Yu. Target Essentiality and Centrality Characterize Drug Side Effects
0 -- 0Xiangfei Song, Yefei Wang, Zhiyu Shu, Jingbo Hong, Tong Li, Lishan Yao. Bacillus subtilis YtvA LOV Domain by a Computer Aided Rational Design Method
0 -- 0Kathryn Miller-Jensen, Ron Skupsky, Priya S. Shah, Adam P. Arkin, David V. Schaffer. Genetic Selection for Context-Dependent Stochastic Phenotypes: Sp1 and TATA Mutations Increase Phenotypic Noise in HIV-1 Gene Expression
0 -- 0Felipe Gerhard, Tilman Kispersky, Gabrielle J. Gutierrez, Eve Marder, Mark A. Kramer, Uri T. Eden. Successful Reconstruction of a Physiological Circuit with Known Connectivity from Spiking Activity Alone
0 -- 0Iren Bains, Hisse M. van Santen, Benedict Seddon, Andrew J. Yates. Models of Self-Peptide Sampling by Developing T Cells Identify Candidate Mechanisms of Thymic Selection
0 -- 0Andrew Cron, Cécile Gouttefangeas, Jacob Frelinger, Lin Lin, Satwinder K. Singh, Cedrik M. Britten, Marij J. P. Welters, Sjoerd H. van der Burg, Mike West, Cliburn Chan. Hierarchical Modeling for Rare Event Detection and Cell Subset Alignment across Flow Cytometry Samples
0 -- 0Petter Holme. Epidemiologically Optimal Static Networks from Temporal Network Data
0 -- 0Jincheng Wu, Emmanuel S. Tzanakakis. Distinct Allelic Patterns of Nanog Expression Impart Embryonic Stem Cell Population Heterogeneity
0 -- 0Elad Noor, Hulda S. Haraldsdóttir, Ron Milo, Ronan M. T. Fleming. Consistent Estimation of Gibbs Energy Using Component Contributions
0 -- 0Alex Roxin, Stefano Fusi. Efficient Partitioning of Memory Systems and Its Importance for Memory Consolidation
0 -- 0Swagatam Mukhopadhyay, Anirvan M. Sengupta. The Role of Multiple Marks in Epigenetic Silencing and the Emergence of a Stable Bivalent Chromatin State
0 -- 0Robert C. Wilson, Matthew R. Nassar, Joshua I. Gold. A Mixture of Delta-Rules Approximation to Bayesian Inference in Change-Point Problems
0 -- 0Natalia Pietrosemoli, Rita Pancsa, Peter Tompa. Structural Disorder Provides Increased Adaptability for Vesicle Trafficking Pathways
0 -- 0Chao Cheng, Matthew Ung, Gavin D. Grant, Michael L. Whitfield. Transcription Factor Binding Profiles Reveal Cyclic Expression of Human Protein-coding Genes and Non-coding RNAs
0 -- 0James M. McFarland, Yuwei Cui, Daniel A. Butts. Inferring Nonlinear Neuronal Computation Based on Physiologically Plausible Inputs
0 -- 0Nikhil J. Joshi, Giulio Tononi, Christof Koch. The Minimal Complexity of Adapting Agents Increases with Fitness
0 -- 0Justin Ritz, Joshua S. Martin, Alain Laederach. Evolutionary Evidence for Alternative Structure in RNA Sequence Co-variation
0 -- 0Nadine Veith, Anna Feldman-Salit, Vlad Cojocaru, Stefan Henrich, Ursula Kummer, Rebecca C. Wade. Organism-Adapted Specificity of the Allosteric Regulation of Pyruvate Kinase in Lactic Acid Bacteria
0 -- 0Ashutosh Malhotra, Erfan Younesi, Harsha Gurulingappa, Martin Hofmann-Apitius. 'HypothesisFinder: ' A Strategy for the Detection of Speculative Statements in Scientific Text
0 -- 0Burcu Aykaç Fas, Yusuf Tutar, Türkan Haliloglu. Dynamic Fluctuations Provide the Basis of a Conformational Switch Mechanism in Apo Cyclic AMP Receptor Protein
0 -- 0Jonathan M. Dreyfuss, Jeremy D. Zucker, Heather M. Hood, Linda R. Ocasio, Matthew S. Sachs, James E. Galagan. Neurospora crassa Using FARM
0 -- 0Joshua I. Glaser, Bradley M. Zamft, Adam H. Marblestone, Jeffrey R. Moffitt, Keith Tyo, Edward S. Boyden III, George M. Church, Konrad P. Körding. Statistical Analysis of Molecular Signal Recording
0 -- 0Biswa Sengupta, Martin B. Stemmler, Karl J. Friston. Information and Efficiency in the Nervous System - A Synthesis
0 -- 0Hadas Zur, Tamir Tuller. New Universal Rules of Eukaryotic Translation Initiation Fidelity
0 -- 0Iaroslav Ispolatov, Anne Müsch. A Model for the Self-Organization of Vesicular Flux and Protein Distributions in the Golgi Apparatus
0 -- 0Eleanor R. Brush, David C. Krakauer, Jessica C. Flack. A Family of Algorithms for Computing Consensus about Node State from Network Data
0 -- 0Deeptak Verma, Donald J. Jacobs, Dennis R. Livesay. Variations within Class-A β-Lactamase Physiochemical Properties Reflect Evolutionary and Environmental Patterns, but not Antibiotic Specificity
0 -- 0Adrian Schneider, Michael F. Seidl, Berend Snel. Shared Protein Complex Subunits Contribute to Explaining Disrupted Co-occurrence
0 -- 0Drazen Petrov, Christian Margreitter, Melanie Grandits, Chris Oostenbrink, Bojan Zagrovic. A Systematic Framework for Molecular Dynamics Simulations of Protein Post-Translational Modifications
0 -- 0Jaeyun Sung, Pan Jun Kim, Shuyi Ma, Cory C. Funk, Andrew T. Magis, Yuliang Wang, Leroy Hood, Donald Geman, Nathan D. Price. Multi-study Integration of Brain Cancer Transcriptomes Reveals Organ-Level Molecular Signatures
0 -- 0Eduardo Serrano, Thomas Nowotny, Rafael Levi, Brian H. Smith, Ramón Huerta. Gain Control Network Conditions in Early Sensory Coding
0 -- 0Gibin G. Powathil, Douglas J. A. Adamson, Mark A. J. Chaplain. Towards Predicting the Response of a Solid Tumour to Chemotherapy and Radiotherapy Treatments: Clinical Insights from a Computational Model
0 -- 0C. J. Zopf, Katie Quinn, Joshua Zeidman, Narendra Maheshri. Cell-Cycle Dependence of Transcription Dominates Noise in Gene Expression
0 -- 0Katherine Kay, Ian M. Hastings. Improving Pharmacokinetic-Pharmacodynamic Modeling to Investigate Anti-Infective Chemotherapy with Application to the Current Generation of Antimalarial Drugs

Volume 9, Issue 6

0 -- 0Drew H. Bryant, Mark Moll, Paul W. Finn, Lydia E. Kavraki. Combinatorial Clustering of Residue Position Subsets Predicts Inhibitor Affinity across the Human Kinome
0 -- 0Melanie I. Stefan, Nicolas Le Novère. Cooperative Binding
0 -- 0Rui Zhao, Franziska Michor. Patterns of Proliferative Activity in the Colonic Crypt Determine Crypt Stability and Rates of Somatic Evolution
0 -- 0Amneet Pal Singh Bhalla, Boyce E. Griffith, Neelesh A. Patankar. A Forced Damped Oscillation Framework for Undulatory Swimming Provides New Insights into How Propulsion Arises in Active and Passive Swimming
0 -- 0Diane M. Longo, Jangir Selimkhanov, Jeffrey D. Kearns, Jeff Hasty, Alexander Hoffmann, Lev S. Tsimring. κB Signaling Module
0 -- 0Hannah C. Slater, Manoj Gambhir, Paul E. Parham, Edwin Michael. Modelling Co-Infection with Malaria and Lymphatic Filariasis
0 -- 0Gabriel E. Hoffman, Benjamin A. Logsdon, Jason G. Mezey. PUMA: A Unified Framework for Penalized Multiple Regression Analysis of GWAS Data
0 -- 0Louisa Wood, Philipp Gebhardt. Bioinformatics Goes to School - New Avenues for Teaching Contemporary Biology
0 -- 0Louis-François Handfield, Yolanda T. Chong, Jibril Simmons, Brenda J. Andrews, Alan M. Moses. Unsupervised Clustering of Subcellular Protein Expression Patterns in High-Throughput Microscopy Images Reveals Protein Complexes and Functional Relationships between Proteins
0 -- 0Balázs Könnyü, S. Kashif Sadiq, Tamás Turányi, Rita Hírmondó, Barbara Müller, Hans-Georg Kräusslich, Peter V. Coveney, Viktor Müller. Gag-Pol Processing during HIV-1 Virion Maturation: A Systems Biology Approach
0 -- 0Joshua L. Payne, Andreas Wagner. Constraint and Contingency in Multifunctional Gene Regulatory Circuits
0 -- 0William R. Harcombe, Nigel F. Delaney, Nicholas Leiby, Niels Klitgord, Christopher J. Marx. The Ability of Flux Balance Analysis to Predict Evolution of Central Metabolism Scales with the Initial Distance to the Optimum
0 -- 0Oleg V. Kim, Zhiliang Xu, Elliot D. Rosen, Mark S. Alber. Fibrin Networks Regulate Protein Transport during Thrombus Development
0 -- 0Annalisa Nuccitelli, C. Daniela Rinaudo, Barbara Brogioni, Roberta Cozzi, Mario Ferrer-Navarro, Daniel Yero, John L. Telford, Guido Grandi, Xavier Daura, Martin Zacharias, Domenico Maione. Streptococcus
0 -- 0Nicholas Ketz, Srinimisha G. Morkonda, Randall C. O'Reilly. Theta Coordinated Error-Driven Learning in the Hippocampus
0 -- 0Christian P. Koch, Anna Maria Perna, Max Pillong, Nickolay K. Todoroff, Paul Wrede, Gerd Folkers, Jan A. Hiss, Gisbert Schneider. Scrutinizing MHC-I Binding Peptides and Their Limits of Variation
0 -- 0Koichi Fujimoto, Satoshi Sawai. A Design Principle of Group-level Decision Making in Cell Populations
0 -- 0Jörg Bornschein, Marc Henniges, Jörg Lücke. Are V1 Simple Cells Optimized for Visual Occlusions? A Comparative Study
0 -- 0Ritwik K. Niyogi, KongFatt Wong-Lin. Dynamic Excitatory and Inhibitory Gain Modulation Can Produce Flexible, Robust and Optimal Decision-making
0 -- 0Lyudmyla Dorosh, Olesya A. Kharenko, Nandhakishore Rajagopalan, Michele C. Loewen, Maria Stepanova. Molecular Mechanisms in the Activation of Abscisic Acid Receptor PYR1
0 -- 0Yan Zhang, Hye Kyong Kweon, Christian Shively, Anuj Kumar, Philip C. Andrews. Towards Systematic Discovery of Signaling Networks in Budding Yeast Filamentous Growth Stress Response Using Interventional Phosphorylation Data
0 -- 0David R. Riley, Karsten B. Sieber, Kelly M. Robinson, James Robert White, Ashwinkumar Ganesan, Syrus Nourbakhsh, Julie C. Dunning Hotopp. Bacteria-Human Somatic Cell Lateral Gene Transfer Is Enriched in Cancer Samples
0 -- 0Kristian Ovaska, Filomena Matarese, Korbinian Grote, Iryna Charapitsa, Alejandra Cervera, Chengyu Liu, George Reid, Martin Seifert, Hendrik G. Stunnenberg, Sampsa Hautaniemi. ATAD3B to Poor Survival in Breast Cancer
0 -- 0Katy Robinson, Nick Fyson, Ted Cohen, Christophe Fraser, Caroline Colijn. How the Dynamics and Structure of Sexual Contact Networks Shape Pathogen Phylogenies
0 -- 0S. G. Raju, Annika F. Barber, David N. LeBard, Michael L. Klein, Vincenzo Carnevale. Exploring Volatile General Anesthetic Binding to a Closed Membrane-Bound Bacterial Voltage-Gated Sodium Channel via Computation
0 -- 0Christiana N. Fogg, Diane E. Kovats. International Society for Computational Biology Honors David Eisenberg with 2013 Accomplishment by a Senior Scientist Award
0 -- 0Meagan C. Small, Pedro Lopes, Rodrigo B. Andrade, Alexander D. MacKerell Jr. Impact of Ribosomal Modification on the Binding of the Antibiotic Telithromycin Using a Combined Grand Canonical Monte Carlo/Molecular Dynamics Simulation Approach
0 -- 0Nanye Long, Samuel P. Dickson, Jessica M. Maia, Hee Shin Kim, Qianqian Zhu, Andrew S. Allen. Leveraging Prior Information to Detect Causal Variants via Multi-Variant Regression
0 -- 0Richard A. Morton, Jonathan R. Stone, Rama S. Singh. Mate Choice and the Origin of Menopause
0 -- 0Henning Knoop, Marianne Gründel, Yvonne Zilliges, Robert Lehmann, Sabrina Hoffmann, Wolfgang Lockau, Ralf Steuer. Flux Balance Analysis of Cyanobacterial Metabolism: The Metabolic Network of Synechocystis sp. PCC 6803
0 -- 0Antonio G. Zippo, Riccardo Storchi, Sara Nencini, Giancarlo Caramenti, Maurizio Valente, Gabriele Eliseo M. Biella. Neuronal Functional Connection Graphs among Multiple Areas of the Rat Somatosensory System during Spontaneous and Evoked Activities
0 -- 0Elzbieta Petelenz-Kurdziel, Clemens Kühn, Bodil Nordlander, Dagmara Klein, Kuk-Ki Hong, Therese Jacobson, Peter Dahl, Jörg Schaber, Jens Nielsen, Stefan Hohmann, Edda Klipp. Quantitative Analysis of Glycerol Accumulation, Glycolysis and Growth under Hyper Osmotic Stress
0 -- 0Mateus Joffily, Giorgio Coricelli. Emotional Valence and the Free-Energy Principle

Volume 9, Issue 5

0 -- 0Ginestra Bianconi, Kun Zhao, Irene A. Chen, Martin A. Nowak. Selection for Replicases in Protocells
0 -- 0Jonathan L. Robinson, Mark P. Brynildsen. Escherichia coli
0 -- 0David W. Eyre, Madeleine L. Cule, David Griffiths, Derrick W. Crook, Tim E. A. Peto, A. Sarah Walker, Daniel J. Wilson. Clostridium difficile Transmission
0 -- 0Peng Jiang, Mona Singh, Hilary A. Coller. Computational Assessment of the Cooperativity between RNA Binding Proteins and MicroRNAs in Transcript Decay
0 -- 0Michiel van Boven, Wilhelmina L. M. Ruijs, Jacco Wallinga, Philip D. O'Neill, Susan Hahné. Estimation of Vaccine Efficacy and Critical Vaccination Coverage in Partially Observed Outbreaks
0 -- 0Xiaodong Cai, Juan-Andrés Bazerque, Georgios B. Giannakis. Inference of Gene Regulatory Networks with Sparse Structural Equation Models Exploiting Genetic Perturbations
0 -- 0Jeffrey E. Markowitz, Elizabeth Ivie, Laura Kligler, Timothy J. Gardner. Long-range Order in Canary Song
0 -- 0Richard A. White, Jørgen V. Bjørnholt, Donna D. Baird, Tore Midtvedt, Jennifer R. Harris, Marcello Pagano, Winston Hide, Knut Rudi, Birgitte Moen, Nina Iszatt, Shyamal D. Peddada, Merete Eggesbø. Novel Developmental Analyses Identify Longitudinal Patterns of Early Gut Microbiota that Affect Infant Growth
0 -- 0Hang Zhang, Nathaniel D. Daw, Laurence T. Maloney. Testing Whether Humans Have an Accurate Model of Their Own Motor Uncertainty in a Speeded Reaching Task
0 -- 0Alessio Franci, Guillaume Drion, Vincent Seutin, Rodolphe Sepulchre. A Balance Equation Determines a Switch in Neuronal Excitability
0 -- 0Janusz M. Bujnicki, Jerzy Tiuryn. Bioinformatics and Computational Biology in Poland
0 -- 0Yunlang Li, Tamar Schlick. "Gate-keeper" Residues and Active-Site Rearrangements in DNA Polymerase μ Help Discriminate Non-cognate Nucleotides
0 -- 0Jonathan J. Hunt, Peter Dayan, Geoffrey J. Goodhill. Sparse Coding Can Predict Primary Visual Cortex Receptive Field Changes Induced by Abnormal Visual Input
0 -- 0Po-Wei Chen, Luís L. Fonseca, Yusuf A. Hannun, Eberhard O. Voit. Coordination of Rapid Sphingolipid Responses to Heat Stress in Yeast
0 -- 0Alexey Solovyev, Qi Mi, Yi-Ting Tzen, David Brienza, Yoram Vodovotz. Hybrid Equation/Agent-Based Model of Ischemia-Induced Hyperemia and Pressure Ulcer Formation Predicts Greater Propensity to Ulcerate in Subjects with Spinal Cord Injury
0 -- 0Wei Huang, Joohyun Kim, Shantenu Jha, Fareed Aboul-Ela. The Impact of a Ligand Binding on Strand Migration in the SAM-I Riboswitch
0 -- 0Fanny Gascuel, Marc Choisy, Jean-Marc Duplantier, Florence Débarre, Carine Brouat. Host Resistance, Population Structure and the Long-Term Persistence of Bubonic Plague: Contributions of a Modelling Approach in the Malagasy Focus
0 -- 0Ayako Watanabe, Daisuke Hoshino, Naohiko Koshikawa, Motoharu Seiki, Takashi Suzuki, Kazuhisa Ichikawa. Critical Role of Transient Activity of MT1-MMP for ECM Degradation in Invadopodia
0 -- 0Kendrick N. Kay, Jonathan Winawer, Ariel Rokem, Aviv Mezer, Brian A. Wandell. A Two-Stage Cascade Model of BOLD Responses in Human Visual Cortex
0 -- 0Anurag Sethi, Jianhui Tian, Cynthia A. Derdeyn, Bette T. Korber, S. Gnanakaran. A Mechanistic Understanding of Allosteric Immune Escape Pathways in the HIV-1 Envelope Glycoprotein
0 -- 0Szymon Stoma, Alexandre Donzé, François Bertaux, Oded Maler, Grégory Batt. STL-based Analysis of TRAIL-induced Apoptosis Challenges the Notion of Type I/Type II Cell Line Classification
0 -- 0Adam S. LaPrad, Kenneth R. Lutchen, Béla Suki. A Mechanical Design Principle for Tissue Structure and Function in the Airway Tree
0 -- 0James G. Dyke, Iain S. Weaver. The Emergence of Environmental Homeostasis in Complex Ecosystems
0 -- 0Christoph A. Haselwandter, Rob Phillips. Connection between Oligomeric State and Gating Characteristics of Mechanosensitive Ion Channels
0 -- 0Erhan Bilal, Janusz Dutkowski, Justin Guinney, In Sock Jang, Benjamin A. Logsdon, Gaurav Pandey, Benjamin A. Sauerwine, Yishai Shimoni, Hans Kristian Moen Vollan, Brigham H. Mecham, Oscar M. Rueda, Jorg Tost, Christina Curtis, Mariano J. Alvarez, Vessela N. Kristensen, Samuel Aparicio, Anne-Lise Børresen-Dale, Carlos Caldas, Andrea Califano, Stephen H. Friend, Trey Ideker, Eric E. Schadt, Gustavo A. Stolovitzky, Adam A. Margolin. Improving Breast Cancer Survival Analysis through Competition-Based Multidimensional Modeling
0 -- 0Mark D. M. Leiserson, Dima Blokh, Roded Sharan, Benjamin J. Raphael. Simultaneous Identification of Multiple Driver Pathways in Cancer
0 -- 0Lawrence E. Hunter. Rocky Mountain Conference on Bioinformatics Celebrates 10 Years
0 -- 0Seth Blumberg, James O. Lloyd-Smith. 0 and Transmission Heterogeneity from the Size Distribution of Stuttering Chains
0 -- 0Wei-Hua Chen, Xing-Ming Zhao, Vera van Noort, Peer Bork. Human Monogenic Disease Genes Have Frequently Functionally Redundant Paralogs
0 -- 0Can Guven, Erin Rericha, Edward Ott, Wolfgang Losert. Modeling and Measuring Signal Relay in Noisy Directed Migration of Cell Groups
0 -- 0HaiPeng Li, Thomas Wiehe. Coalescent Tree Imbalance and a Simple Test for Selective Sweeps Based on Microsatellite Variation
0 -- 0Alexandra M. Schnoes, David C. Ream, Alexander W. Thorman, Patricia C. Babbitt, Iddo Friedberg. Biases in the Experimental Annotations of Protein Function and Their Effect on Our Understanding of Protein Function Space
0 -- 0Pete Riley, Michal Ben-Nun, Richard Armenta, Jon A. Linker, Angela A. Eick, Jose L. Sanchez, Dylan George, David P. Bacon, Steven Riley. Multiple Estimates of Transmissibility for the 2009 Influenza Pandemic Based on Influenza-like-Illness Data from Small US Military Populations
0 -- 0Vincent Vagenende, Alvin X. Han, Han B. Pek, Bernard L. W. Loo. Quantifying the Molecular Origins of Opposite Solvent Effects on Protein-Protein Interactions
0 -- 0Tobias Linder, Bert L. de Groot, Anna Stary-Weinzinger. Probing the Energy Landscape of Activation Gating of the Bacterial Potassium Channel KcsA
0 -- 0Rafael A. Barrio, José Roberto Romero-Arias, Marco A. Noguez, Eugenio Azpeitia, Elizabeth Ortiz-Gutiérrez, Valeria Hernández-Hernández, Yuriria Cortes-Poza, Elena R. Alvarez-Buylla. Arabidopsis thaliana Root as a Study System
0 -- 0Gouri Shankar Pandey, Chen Yanover, Tom E. Howard, Zuben E. Sauna. F8 Gene and MHC-II Variants as Risk Factors for the Development of Inhibitory Anti-Factor VIII Antibodies during the Treatment of Hemophilia A: A Computational Assessment
0 -- 0Julian Garrec, Ivano Tavernelli, Ursula Rothlisberger. Two Misfolding Routes for the Prion Protein around pH 4.5
0 -- 0Yunpeng Wang, Jon Olav Vik, Stig W. Omholt, Arne B. Gjuvsland. Effect of Regulatory Architecture on Broad versus Narrow Sense Heritability
0 -- 0Margaret E. Johnson, Gerhard Hummer. Interface-Resolved Network of Protein-Protein Interactions

Volume 9, Issue 4

0 -- 0Juergen Dukart, Ferath Kherif, Karsten Mueller, Stanislaw Adaszewski, Matthias L. Schroeter, Richard S. J. Frackowiak, Bogdan Draganski. Generative FDG-PET and MRI Model of Aging and Disease Progression in Alzheimer's Disease
0 -- 0K. Bretonnel Cohen, Lawrence E. Hunter. Chapter 16: Text Mining for Translational Bioinformatics
0 -- 0Emily V. Chambers, Wendy A. Bickmore, Colin A. Semple. Divergence of Mammalian Higher Order Chromatin Structure Is Associated with Developmental Loci
0 -- 0Yana Bromberg. Chapter 15: Disease Gene Prioritization
0 -- 0Kyriakos Kentzoglanakis, Diana García López, Sam P. Brown, Richard A. Goldstein. The Evolution of Collective Restraint: Policing and Obedience among Non-conjugative Plasmids
0 -- 0Matthew R. Nassar, Joshua I. Gold. A Healthy Fear of the Unknown: Perspectives on the Interpretation of Parameter Fits from Computational Models in Neuroscience
0 -- 0yassmine chebaro, Ismail Amal, Natacha Rochel, Cécile Rochette-Egly, Roland H. Stote, Annick Dejaegere. Phosphorylation of the Retinoic Acid Receptor Alpha Induces a Mechanical Allosteric Regulation and Changes in Internal Dynamics
0 -- 0Yosef Y. Kuttner, Tal Nagar, Stanislav Engel. 2+
0 -- 0Bernhard Nessler, Michael Pfeiffer, Lars Buesing, Wolfgang Maass. Bayesian Computation Emerges in Generic Cortical Microcircuits through Spike-Timing-Dependent Plasticity
0 -- 0Andrei Yu. Zinovyev, Inna Kuperstein, Emmanuel Barillot, Wolf-Dietrich Heyer. Synthetic Lethality between Gene Defects Affecting a Single Non-essential Molecular Pathway with Reversible Steps
0 -- 0Joseph L. Baker, Nicolas Biais, Florence Tama. Steered Molecular Dynamics Simulations of a Type IV Pilus Probe Initial Stages of a Force-Induced Conformational Transition
0 -- 0Daniel L. Parton, Alex Tek, Marc Baaden, Mark S. P. Sansom. Formation of Raft-Like Assemblies within Clusters of Influenza Hemagglutinin Observed by MD Simulations
0 -- 0Jordan R. Willis, Bryan S. Briney, Samuel L. DeLuca, James E. Crowe Jr., Jens Meiler. Human Germline Antibody Gene Segments Encode Polyspecific Antibodies
0 -- 0Domenico Campolo, Ferdinan Widjaja, Hong Xu, Wei Tech Ang, Etienne Burdet. Analysis of Accuracy in Pointing with Redundant Hand-held Tools: A Geometric Approach to the Uncontrolled Manifold Method
0 -- 0Juho Rousu, Daniel D. Agranoff, Olugbemiro Sodeinde, John Shawe-Taylor, Delmiro Fernandez-Reyes. Biomarker Discovery by Sparse Canonical Correlation Analysis of Complex Clinical Phenotypes of Tuberculosis and Malaria
0 -- 0Dominic Standage, Hongzhi You, Da-Hui Wang, Michael C. Dorris. Trading Speed and Accuracy by Coding Time: A Coupled-circuit Cortical Model
0 -- 0Adria Carbo, Raquel Hontecillas, Barbara Kronsteiner, Monica Viladomiu, Mireia Pedragosa, Pinyi Lu, Casandra W. Philipson, Stefan Hoops, Madhav V. Marathe, Stephen Eubank, Keith R. Bisset, Katherine V. Wendelsdorf, Abdul Jarrah, Yongguo Mei, Josep Bassaganya-Riera. Systems Modeling of Molecular Mechanisms Controlling Cytokine-driven CD4+ T Cell Differentiation and Phenotype Plasticity
0 -- 0Annabelle Ballesta, Jonathan Lopez, Nikolay Popgeorgiev, Philippe Gonzalo, Marie Doumic, Germain Gillet. Data-Driven Modeling of Src Control on the Mitochondrial Pathway of Apoptosis: Implication for Anticancer Therapy Optimization
0 -- 0Fuhai Li, Zheng Yin, Guangxu Jin, Hong Zhao, Stephen T. C. Wong. Chapter 17: Bioimage Informatics for Systems Pharmacology
0 -- 0Stefano Lonardi, Denisa Duma, Matthew Alpert, Francesca Cordero, Marco Beccuti, Prasanna R. Bhat, Yonghui Wu, Gianfranco Ciardo, Burair Alsaihati, Yaqin Ma, Steve Wanamaker, Josh Resnik, Serdar Bozdag, Ming-Cheng Luo, Timothy J. Close. Combinatorial Pooling Enables Selective Sequencing of the Barley Gene Space
0 -- 0Masayo Inoue, Kunihiko Kaneko. Cooperative Adaptive Responses in Gene Regulatory Networks with Many Degrees of Freedom
0 -- 0Henrik Failmezger, Benjamin Jaegle, Andrea Schrader, Martin Hülskamp, Achim Tresch. Semi-automated 3D Leaf Reconstruction and Analysis of Trichome Patterning from Light Microscopic Images
0 -- 0Anne-Sophie Coquel, Jean-Pascal Jacob, Maël Primet, Alice Demarez, Mariella Dimiccoli, Thomas Julou, Lionel Moisan, Ariel B. Lindner, Hugues Berry. Escherichia coli Is Governed by Diffusion and Nucleoid Macromolecular Crowding Effect
0 -- 0Lin-tai Da, Fátima Pardo Avila, Dong Wang, Xuhui Huang. A Two-State Model for the Dynamics of the Pyrophosphate Ion Release in Bacterial RNA Polymerase
0 -- 0Matthias Schultze-Kraft, Markus Diesmann, Sonja Grün, Moritz Helias. Noise Suppression and Surplus Synchrony by Coincidence Detection
0 -- 0Joseph E. Goose, Mark S. P. Sansom. Reduced Lateral Mobility of Lipids and Proteins in Crowded Membranes
0 -- 0Julian E. Fuchs, Susanne von Grafenstein, Roland G. Huber, Michael A. Margreiter, Gudrun M. Spitzer, Hannes G. Wallnoefer, Klaus R. Liedl. Cleavage Entropy as Quantitative Measure of Protease Specificity
0 -- 0Purushottam D. Dixit, Sergei Maslov. Evolutionary Capacitance and Control of Protein Stability in Protein-Protein Interaction Networks
0 -- 0Recep Colak, Taehyung Kim, Magali Michaut, Mark G. F. Sun, Manuel Irimia, Jeremy Bellay, Chad L. Myers, Benjamin J. Blencowe, Philip M. Kim. Distinct Types of Disorder in the Human Proteome: Functional Implications for Alternative Splicing
0 -- 0Nicole Kleinstreuer, David Dix, Michael Rountree, Nancy Baker, Nisha Sipes, David Reif, Richard Spencer, Thomas Knudsen. A Computational Model Predicting Disruption of Blood Vessel Development
0 -- 0Geoffrey L. Johnston, David L. Smith, David A. Fidock. Plasmodium falciparum Infection and Transmission
0 -- 0Hans B. Sieburg, Giulio Cattarossi, Christa E. Müller-Sieburg. Lifespan Differences in Hematopoietic Stem Cells are Due to Imperfect Repair and Unstable Mean-Reversion
0 -- 0Nicolas Frémaux, Henning Sprekeler, Wulfram Gerstner. Reinforcement Learning Using a Continuous Time Actor-Critic Framework with Spiking Neurons
0 -- 0Gabriela V. Cohen Freue, Anna Meredith, Derek Smith, Axel Bergman, Mayu Sasaki, Karen K. Y. Lam, Zsuzsanna Hollander, Nina Opushneva, Mandeep Takhar, David Lin, Janet Wilson-McManus, Robert Balshaw, Paul A. Keown, Christoph H. Borchers, Bruce McManus, Raymond T. Ng, W. Robert McMaster. Computational Biomarker Pipeline from Discovery to Clinical Implementation: Plasma Proteomic Biomarkers for Cardiac Transplantation
0 -- 0Lauren M. Bragg, Glenn Stone, Margaret K. Butler, Philip Hugenholtz, Gene W. Tyson. Shining a Light on Dark Sequencing: Characterising Errors in Ion Torrent PGM Data
0 -- 0Joseph G. Makin, Matthew R. Fellows, Philip N. Sabes. Learning Multisensory Integration and Coordinate Transformation via Density Estimation
0 -- 0Xiaobo Wan, Yue Ma, Christopher L. McClendon, Lily Jun-shen Huang, Niu Huang. Ab Initio Modeling and Experimental Assessment of Janus Kinase 2 (JAK2) Kinase-Pseudokinase Complex Structure
0 -- 0Adam Ponzi, Jeffery R. Wickens. Optimal Balance of the Striatal Medium Spiny Neuron Network
0 -- 0Javad Golji, Mohammad R. K. Mofrad. The Interaction of Vinculin with Actin
0 -- 0Marie Devaine, Florian Waszak, Pascal Mamassian. Dual Process for Intentional and Reactive Decisions

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

Volume 9, Issue 2

0 -- 0Thomas Stockner, Therese R. Montgomery, Oliver Kudlacek, Rene Weissensteiner, Gerhard F. Ecker, Michael Freissmuth, Harald H. Sitte. Mutational Analysis of the High-Affinity Zinc Binding Site Validates a Refined Human Dopamine Transporter Homology Model
0 -- 0Shaiyan Keshvari, Ronald Van den Berg, Wei Ji Ma. No Evidence for an Item Limit in Change Detection
0 -- 0Kieran Alden, Mark Read, Jonathan Timmis, Paul S. Andrews, Henrique Veiga-Fernandes, Mark Coles. Spartan: A Comprehensive Tool for Understanding Uncertainty in Simulations of Biological Systems
0 -- 0Tanya Gurieva, Martin C. J. Bootsma, Marc J. M. Bonten. Staphylococcus aureus
0 -- 0Andraz Stozer, Marko Gosak, Jurij Dolensek, Matjaz Perc, Marko Marhl, Marjan Slak Rupnik, Dean Korosak. Functional Connectivity in Islets of Langerhans from Mouse Pancreas Tissue Slices
0 -- 0Charlotte Prévost, Daniel McNamee, Ryan K. Jessup, Peter Bossaerts, John P. O'Doherty. Evidence for Model-based Computations in the Human Amygdala during Pavlovian Conditioning
0 -- 0Kolbjørn Tunstrøm, Yael Katz, Christos C. Ioannou, Cristián Huepe, Matthew J. Lutz, Iain D. Couzin. Collective States, Multistability and Transitional Behavior in Schooling Fish
0 -- 0Min-Cheol Kim, Devin M. Neal, Roger D. Kamm, H. Harry Asada. Dynamic Modeling of Cell Migration and Spreading Behaviors on Fibronectin Coated Planar Substrates and Micropatterned Geometries
0 -- 0Lizhe Zhu, Peter G. Bolhuis, Jocelyne Vreede. The HAMP Signal Relay Domain Adopts Multiple Conformational States through Collective Piston and Tilt Motions
0 -- 0Hamish Cunningham, Valentin Tablan, Angus Roberts, Kalina Bontcheva. Getting More Out of Biomedical Documents with GATE's Full Lifecycle Open Source Text Analytics
0 -- 0Davide Reato, Fernando Gasca, Abhishek Datta, Marom Bikson, Lisa Marshall, Lucas C. Parra. Transcranial Electrical Stimulation Accelerates Human Sleep Homeostasis
0 -- 0Michael Thomas, Dylan Jayatilaka, Ben Corry. An Entropic Mechanism of Generating Selective Ion Binding in Macromolecules
0 -- 0Paul Michael Loriaux, Glenn Tesler, Alexander Hoffmann. Characterizing the Relationship between Steady State and Response Using Analytical Expressions for the Steady States of Mass Action Models
0 -- 0Paul Michael Loriaux, Alexander Hoffmann. A Protein Turnover Signaling Motif Controls the Stimulus-Sensitivity of Stress Response Pathways
0 -- 0Shanshan Cheng, Charles L. Brooks III. Viral Capsid Proteins Are Segregated in Structural Fold Space
0 -- 0Alexander T. Dilthey, Stephen Leslie, Loukas Moutsianas, Judong Shen, Charles Cox, Matthew R. Nelson, Gil McVean. Multi-Population Classical HLA Type Imputation
0 -- 0Andrea Censi, Andrew D. Straw, Rosalyn W. Sayaman, Richard M. Murray, Michael H. Dickinson. Drosophila
0 -- 0Carsten Magnus. Virus Neutralisation: New Insights from Kinetic Neutralisation Curves
0 -- 0Shao-Shan Carol Huang, David C. Clarke, Sara J. C. Gosline, Adam Labadorf, Candace R. Chouinard, William Gordon, Douglas A. Lauffenburger, Ernest Fraenkel. Linking Proteomic and Transcriptional Data through the Interactome and Epigenome Reveals a Map of Oncogene-induced Signaling
0 -- 0David Managadze, Alexander E. Lobkovsky, Yuri I. Wolf, Svetlana A. Shabalina, Igor B. Rogozin, Eugene V. Koonin. The Vast, Conserved Mammalian lincRNome
0 -- 0Zhe Zhang, Yueli Zheng, Margo Petukh, Anthony Pegg, Yoshihiko Ikeguchi, Emil Alexov. Enhancing Human Spermine Synthase Activity by Engineered Mutations
0 -- 0Benjamin M. Althouse, Oscar Patterson-Lomba, Georg M. Goerg, Laurent Hébert-Dufresne. The Timing and Targeting of Treatment in Influenza Pandemics Influences the Emergence of Resistance in Structured Populations
0 -- 0Claudia Clopath, Nicolas Brunel. Optimal Properties of Analog Perceptrons with Excitatory Weights
0 -- 0Gerard J. P. van Westen, Alwin Hendriks, Jörg K. Wegner, Adriaan P. IJzerman, Herman W. T. van Vlijmen, Andreas Bender. Significantly Improved HIV Inhibitor Efficacy Prediction Employing Proteochemometric Models Generated From Antivirogram Data
0 -- 0Robert R. Kerr, Anthony N. Burkitt, Doreen A. Thomas, Matthieu Gilson, David B. Grayden. Delay Selection by Spike-Timing-Dependent Plasticity in Recurrent Networks of Spiking Neurons Receiving Oscillatory Inputs
0 -- 0Ryo Kanada, Takeshi Kuwata, Hiroo Kenzaki, Shoji Takada. Structure-based Molecular Simulations Reveal the Enhancement of Biased Brownian Motions in Single-headed Kinesin
0 -- 0Ying Li, Guang Li, Haifang Wang, Jiulin Du, Jun Yan. Analysis of a Gene Regulatory Cascade Mediating Circadian Rhythm in Zebrafish
0 -- 0David C. Sterratt, Daniel Lyngholm, David J. Willshaw, Ian D. Thompson. Standard Anatomical and Visual Space for the Mouse Retina: Computational Reconstruction and Transformation of Flattened Retinae with the Retistruct Package
0 -- 0Philip E. Bourne. Let's Make Those Book Chapters Open Too!
0 -- 0Wei-Yi Cheng, Tai-Hsien Ou Yang, Dimitris Anastassiou. Biomolecular Events in Cancer Revealed by Attractor Metagenes
0 -- 0Romain Daniel Cazé, Mark D. Humphries, Boris S. Gutkin. Passive Dendrites Enable Single Neurons to Compute Linearly Non-separable Functions
0 -- 0Roberto Latorre, Rafael Levi, Pablo Varona. Transformation of Context-dependent Sensory Dynamics into Motor Behavior
0 -- 0Eduardo J. Izquierdo, Randall D. Beer. C. elegans Klinotaxis
0 -- 0Jimin Song, Mona Singh. From Hub Proteins to Hub Modules: The Relationship Between Essentiality and Centrality in the Yeast Interactome at Different Scales of Organization
0 -- 0Falk Lieder, Jean Daunizeau, Marta I. Garrido, Karl J. Friston, Klaas E. Stephan. Modelling Trial-by-Trial Changes in the Mismatch Negativity
0 -- 0Cherrie H. T. Kong, Derek R. Laver, Mark B. Cannell. Extraction of Sub-microscopic Ca Fluxes from Blurred and Noisy Fluorescent Indicator Images with a Detailed Model Fitting Approach
0 -- 0Baktash Babadi, L. F. Abbott. Pairwise Analysis Can Account for Network Structures Arising from Spike-Timing Dependent Plasticity

Volume 9, Issue 12

0 -- 0Sébastien Béhuret, Charlotte Deleuze, Leonel Gómez, Yves Frégnac, Thierry Bal. Cortically-Controlled Population Stochastic Facilitation as a Plausible Substrate for Guiding Sensory Transfer across the Thalamic Gateway
0 -- 0Geir Halnes, Ivar Østby, Klas H. Pettersen, Stig W. Omholt, Gaute T. Einevoll. Electrodiffusive Model for Astrocytic and Neuronal Ion Concentration Dynamics
0 -- 0Fran Lewitter. Moving Education Forward, Again!
0 -- 0Ambuj Kumar, Rituraj Purohit. Use of Long Term Molecular Dynamics Simulation in Predicting Cancer Associated SNPs
0 -- 0Adam Mahdi, Jacob Sturdy, Johnny T. Ottesen, Mette S. Olufsen. Modeling the Afferent Dynamics of the Baroreflex Control System
0 -- 0Kristina D. Simmons, Jason S. Prentice, Gasper Tkacik, Jan Homann, Heather K. Yee, Stephanie E. Palmer, Philip C. Nelson, Vijay Balasubramanian. Transformation of Stimulus Correlations by the Retina
0 -- 0Xiaoqiang Sun, Jiguang Bao, Kyle C. Nelson, King Chuen Li, George Kulik, Xiaobo Zhou. Systems Modeling of Anti-apoptotic Pathways in Prostate Cancer: Psychological Stress Triggers a Synergism Pattern Switch in Drug Combination Therapy
0 -- 0Christel Kamp, Mathieu Moslonka-Lefebvre, Samuel Alizon. Epidemic Spread on Weighted Networks
0 -- 0Adrien Nicolaï, Patrice Delarue, Patrick Senet. Decipher the Mechanisms of Protein Conformational Changes Induced by Nucleotide Binding through Free-Energy Landscape Analysis: ATP Binding to Hsp70
0 -- 0Nevena Todorova, Adam J. Makarucha, Nicholas D. M. Hine, Arash A. Mostofi, Irene Yarovsky. Dimensionality of Carbon Nanomaterials Determines the Binding and Dynamics of Amyloidogenic Peptides: Multiscale Theoretical Simulations
0 -- 0Aaron M. Bornstein, Nathaniel D. Daw. Cortical and Hippocampal Correlates of Deliberation during Model-Based Decisions for Rewards in Humans
0 -- 0Artemis Koukounari, Christl A. Donnelly, Irini Moustaki, Edridah M. Tukahebwa, Narcis B. Kabatereine, Shona Wilson, Joanne P. Webster, André M. Deelder, Birgitte J. Vennervald, Govert J. van Dam. A Latent Markov Modelling Approach to the Evaluation of Circulating Cathodic Antigen Strips for Schistosomiasis Diagnosis Pre- and Post-Praziquantel Treatment in Uganda
0 -- 0Sylvie Estrela, Sam P. Brown. Metabolic and Demographic Feedbacks Shape the Emergent Spatial Structure and Function of Microbial Communities
0 -- 0Alexander M. Walter, Paulo S. Pinheiro, Matthijs Verhage, Jakob B. Sørensen. 2+-Dependent Properties of Neurosecretion
0 -- 0Anne Lopes, Sophie Sacquin-Mora, Viktoriya Dimitrova, Elodie Laine, Yann Ponty, Alessandra Carbone. Protein-Protein Interactions in a Crowded Environment: An Analysis via Cross-Docking Simulations and Evolutionary Information
0 -- 0Patrick G. Blachly, César Augusto F. de Oliveira, Sarah L. Williams, James Andrew McCammon. Utilizing a Dynamical Description of IspH to Aid in the Development of Novel Antimicrobial Drugs
0 -- 0Amir Dezfouli, Bernard W. Balleine. Actions, Action Sequences and Habits: Evidence That Goal-Directed and Habitual Action Control Are Hierarchically Organized
0 -- 0Srinivasan Sivanandan, Athi N. Naganathan. A Disorder-Induced Domino-Like Destabilization Mechanism Governs the Folding and Functional Dynamics of the Repeat Protein IκBα
0 -- 0Kieran O'Neill, Nima Aghaeepour, Josef Spidlen, Ryan R. Brinkman. Flow Cytometry Bioinformatics
0 -- 0Tjaart A. P. de Beer, Roman A. Laskowski, Sarah L. Parks, Botond Sipos, Nick Goldman, Janet M. Thornton. Amino Acid Changes in Disease-Associated Variants Differ Radically from Variants Observed in the 1000 Genomes Project Dataset
0 -- 0Masaki Sasai, Yudai Kawabata, Koh Makishi, Kazuhito Itoh, Tomoki P. Terada. Time Scales in Epigenetic Dynamics and Phenotypic Heterogeneity of Embryonic Stem Cells
0 -- 0Evan J. Molinelli, Anil Korkut, Weiqing Wang, Martin L. Miller, Nicholas P. Gauthier, Xiaohong Jing, Poorvi Kaushik, Qin He, Gordon Mills, David B. Solit, Christine A. Pratilas, Martin Weigt, Alfredo Braunstein, Andrea Pagnani, Riccardo Zecchina, Chris Sander. Perturbation Biology: Inferring Signaling Networks in Cellular Systems
0 -- 0Regina Joice, Vagheesh Narasimhan, Jacqui Montgomery, Amar Bir Sidhu, Keunyoung Oh, Evan Meyer, Willythssa Pierre-Louis, Karl Seydel, Danny Milner, Kim Williamson, Roger Wiegand, Daouda Ndiaye, Johanna Daily, Dyann Wirth, Terrie Taylor, Curtis Huttenhower, Matthias Marti. Inferring Developmental Stage Composition from Gene Expression in Human Malaria
0 -- 0Matthias Jeschke, Stephan Baumgärtner, Stefan Legewie. Determinants of Cell-to-Cell Variability in Protein Kinase Signaling
0 -- 0Michela Candotti, Alberto Pérez, Carles Ferrer-Costa, Manuel Rueda, Tim Meyer, Josep Lluis Gelpí, Modesto Orozco. Exploring Early Stages of the Chemical Unfolding of Proteins at the Proteome Scale
0 -- 0Roger Guimerà, Marta Sales-Pardo. A Network Inference Method for Large-Scale Unsupervised Identification of Novel Drug-Drug Interactions
0 -- 0Teresa Szczepinska, Wataru Iwasaki, Thomas Abeel. The Spirit of Competition: To Win or Not To Win
0 -- 0T. Alex Perkins, Thomas W. Scott, Arnaud Le Menach, David L. Smith. Heterogeneity, Mixing, and the Spatial Scales of Mosquito-Borne Pathogen Transmission
0 -- 0Sriram Chandrasekaran, Nathan D. Price. Metabolic Constraint-Based Refinement of Transcriptional Regulatory Networks
0 -- 0Will D. Penny, Peter Zeidman, Neil Burgess. Forward and Backward Inference in Spatial Cognition
0 -- 0Joanne A. Fox, B. F. Francis Ouellette. Education in Computational Biology Today and Tomorrow
0 -- 0Ayse Ozlem Aykut, Ali Rana Atilgan, Canan Atilgan. Designing Molecular Dynamics Simulations to Shift Populations of the Conformational States of Calmodulin
0 -- 0Ben Klünder, Tina Freisinger, Roland Wedlich-Söldner, Erwin Frey. GDI-Mediated Cell Polarization in Yeast Provides Precise Spatial and Temporal Control of Cdc42 Signaling
0 -- 0Chieh-Chun Chen, Shu Xiao, Dan Xie, Xiaoyi Cao, Chun-Xiao Song, Ting Wang, Chuan He, Sheng Zhong. Understanding Variation in Transcription Factor Binding by Modeling Transcription Factor Genome-Epigenome Interactions
0 -- 0Antoine Neuraz, Laurent Chouchana, Georgia Malamut, Christine Le Beller, Denis Roche, Philippe Beaune, Patrice Degoulet, Anita Burgun, Marie-Anne Loriot, Paul Avillach. Phenome-Wide Association Studies on a Quantitative Trait: Application to TPMT Enzyme Activity and Thiopurine Therapy in Pharmacogenomics
0 -- 0Bin Wu, Julián García, Christoph Hauert, Arne Traulsen. Extrapolating Weak Selection in Evolutionary Games
0 -- 0Richard R. Stein, Vanni Bucci, Nora C. Toussaint, Charlie G. Buffie, Gunnar Rätsch, Eric G. Pamer, Chris Sander, João B. Xavier. Ecological Modeling from Time-Series Inference: Insight into Dynamics and Stability of Intestinal Microbiota
0 -- 0Max Sajitz-Hermstein, Zoran Nikoloski. Structural Control of Metabolic Flux
0 -- 0Shouneng Peng, Jingze Tan, Sile Hu, Hang Zhou, Jing Guo, Li Jin, Kun Tang. Detecting Genetic Association of Common Human Facial Morphological Variation Using High Density 3D Image Registration
0 -- 0Erik M. Volz, Simon D. W. Frost. Inferring the Source of Transmission with Phylogenetic Data
0 -- 0Eduard J. Kerkhoven, Fiona Achcar, Vincent P. Alibu, Richard J. Burchmore, Ian H. Gilbert, Maciej Trybilo, Nicole N. Driessen, David Gilbert, Rainer Breitling, Barbara M. Bakker, Michael P. Barrett. Trypanosoma brucei
0 -- 0Sara El-Metwally, Taher Hamza, Magdi Zakaria, Mohamed Helmy. Next-Generation Sequence Assembly: Four Stages of Data Processing and Computational Challenges
0 -- 0Mike Bonny, Elisabeth Fischer-Friedrich, Martin Loose, Petra Schwille, Karsten Kruse. Membrane Binding of MinE Allows for a Comprehensive Description of Min-Protein Pattern Formation
0 -- 0Romain Brette. Sharpness of Spike Initiation in Neurons Explained by Compartmentalization

Volume 9, Issue 11

0 -- 0Lennart Martens. About Dice, Bouldering, and Team Empowerment: Running the CompOmics Group at VIB and Ghent University, Belgium
0 -- 0Jeroen de Ridder, Yana Bromberg, Magali Michaut, Venkata P. Satagopam, Manuel Corpas, Geoff Macintyre, Theodore Alexandrov. The Young PI Buzz: Learning from the Organizers of the Junior Principal Investigator Meeting at ISMB-ECCB 2013
0 -- 0Peter Man-Un Ung, Andrea D. Thompson, Lyra Chang, Jason E. Gestwicki, Heather A. Carlson. E. coli Hsp70/DnaK
0 -- 0Theodore Alexandrov, Philip E. Bourne. Learning How to Run a Lab: Interviews with Principal Investigators
0 -- 0Murat Çetinbas, Eugene I. Shakhnovich. Catalysis of Protein Folding by Chaperones Accelerates Evolutionary Dynamics in Adapting Cell Populations
0 -- 0Guido Polles, Giuliana Indelicato, Raffaello Potestio, Paolo Cermelli, Reidun Twarock, Cristian Micheletti. Mechanical and Assembly Units of Viral Capsids Identified via Quasi-Rigid Domain Decomposition
0 -- 0Christophe Micheyl, Paul R. Schrater, Andrew J. Oxenham. Auditory Frequency and Intensity Discrimination Explained Using a Cortical Population Rate Code
0 -- 0Hannah Edwards, Sanne Abeln, Charlotte M. Deane. Exploring Fold Space Preferences of New-born and Ancient Protein Superfamilies
0 -- 0Xiaoxia Wang, Sarada Panchanathan, Gerardo Chowell. A Data-Driven Mathematical Model of CA-MRSA Transmission among Age Groups: Evaluating the Effect of Control Interventions
0 -- 0Stefan Habenschuss, Zeno Jonke, Wolfgang Maass. Stochastic Computations in Cortical Microcircuit Models
0 -- 0Olga Vitek. Leading a Statistical Bioinformatics Lab: It's All About Finding Balance
0 -- 0Davi R. Ortega, Guoya Mo, Kwangwoon Lee, Hongjun Zhou, Jérôme Baudry, Frederick W. Dahlquist, Igor B. Zhulin. Conformational Coupling between Receptor and Kinase Binding Sites through a Conserved Salt Bridge in a Signaling Complex Scaffold Protein
0 -- 0Avinash Kumar Shanmugam, Geoff Macintyre, Magali Michaut, Thomas Abeel. Ten Simple Rules for Starting a Regional Student Group
0 -- 0Janez Konc, Milan Hodoscek, Mitja Ogrizek, Joanna Trykowska Konc, Dusanka Janezic. Structure-Based Function Prediction of Uncharacterized Protein Using Binding Sites Comparison
0 -- 0Jakob J. Metzger, Stephan Eule. Distribution of the Fittest Individuals and the Rate of Muller's Ratchet in a Model with Overlapping Generations
0 -- 0Shayoni Ray, Daniel Yuan, Nimit Dhulekar, Basak Oztan, Bülent Yener, Melinda Larsen. Cell-Based Multi-Parametric Model of Cleft Progression during Submandibular Salivary Gland Branching Morphogenesis
0 -- 0Noa Chapal-Ilani, Yosef E. Maruvka, Adam Spiro, Yitzhak Reizel, Rivka Adar, Liran I. Shlush, Ehud Y. Shapiro. Comparing Algorithms That Reconstruct Cell Lineage Trees Utilizing Information on Microsatellite Mutations
0 -- 0Lucas Theis, Andrè Maia Chagas, Daniel Arnstein, Cornelius Schwarz, Matthias Bethge. Beyond GLMs: A Generative Mixture Modeling Approach to Neural System Identification
0 -- 0Miranda D. Stobbe, Tarun Mishra, Geoff Macintyre. Breaking the Ice and Forging Links: The Importance of Socializing in Research
0 -- 0Rotem Ben-Hamo, Sol Efroni. MicroRNA-Gene Association As a Prognostic Biomarker in Cancer Exposes Disease Mechanisms
0 -- 0Oliwia M. Szklarczyk, Nélido González-Segredo, Philipp Kukura, Ariella Oppenheim, Daniel Choquet, Vahid Sandoghdar, Ari Helenius, Ivo F. Sbalzarini, Helge Ewers. Receptor Concentration and Diffusivity Control Multivalent Binding of Sv40 to Membrane Bilayers
0 -- 0Weronika Sikora-Wohlfeld, Marit Ackermann, Eleni G. Christodoulou, Singaravelu Kalaimathy, Andreas Beyer. Assessing Computational Methods for Transcription Factor Target Gene Identification Based on ChIP-seq Data
0 -- 0Alex Dickson, Charles L. Brooks III. E. coli
0 -- 0Varun B. Kothamachu, Elisenda Feliu, Carsten Wiuf, Luca Cardelli, Orkun S. Soyer. Phosphorelays Provide Tunable Signal Processing Capabilities for the Cell
0 -- 0Simon Mitchell, Pedro Mendes. A Computational Model of Liver Iron Metabolism
0 -- 0Noah Ollikainen, Tanja Kortemme. Computational Protein Design Quantifies Structural Constraints on Amino Acid Covariation
0 -- 0Martin Boerlin, Christian K. Machens, Sophie Denève. Predictive Coding of Dynamical Variables in Balanced Spiking Networks
0 -- 0Kejian Wang, Jiazhi Sun, Shufeng Zhou, Chunling Wan, Shengying Qin, Can Li, Lin He, Lun Yang. Prediction of Drug-Target Interactions for Drug Repositioning Only Based on Genomic Expression Similarity
0 -- 0Takeshi Hase, Samik Ghosh, Ryota Yamanaka, Hiroaki Kitano. Harnessing Diversity towards the Reconstructing of Large Scale Gene Regulatory Networks
0 -- 0Kazunari Mouri, Yasushi Sako. Optimality Conditions for Cell-Fate Heterogeneity That Maximize the Effects of Growth Factors in PC12 Cells
0 -- 0Luca Albergante, Jon Timmis, Lynette Beattie, Paul M. Kaye. Leishmania donovani Infection
0 -- 0Friedemann Zenke, Guillaume Hennequin, Wulfram Gerstner. Synaptic Plasticity in Neural Networks Needs Homeostasis with a Fast Rate Detector
0 -- 0Nickolay A. Khazanov, Heather A. Carlson. Exploring the Composition of Protein-Ligand Binding Sites on a Large Scale
0 -- 0Adam M. Sullivan, Xiaopeng Zhao, Yasuhiro Suzuki, Eri Ochiai, Stephen Crutcher, Michael A. Gilchrist. Toxoplasma gondii Cysts Based on Data-Driven Model Selection
0 -- 0Teresa Ruiz-Herrero, Javier Estrada, Raúl Guantes, David G. Miguez. A Tunable Coarse-Grained Model for Ligand-Receptor Interaction
0 -- 0Timothy Bailey, Pawel Krajewski, Istvan Ladunga, Céline Lefebvre, Qunhua Li, Tao Liu, Pedro Madrigal, Cenny Taslim, Jie Zhang. Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data
0 -- 0Natalie Berestovsky, Wanding Zhou, Deepak Nagrath, Luay Nakhleh. Modeling Integrated Cellular Machinery Using Hybrid Petri-Boolean Networks
0 -- 0Biyu J. He, John M. Zempel. Average Is Optimal: An Inverted-U Relationship between Trial-to-Trial Brain Activity and Behavioral Performance
0 -- 0Julian E. Fuchs, Susanne von Grafenstein, Roland G. Huber, Christian Kramer, Klaus R. Liedl. Substrate-Driven Mapping of the Degradome by Comparison of Sequence Logos
0 -- 0Denis Valle, James Clark. Improving the Modeling of Disease Data from the Government Surveillance System: A Case Study on Malaria in the Brazilian Amazon
0 -- 0Damon A. Clark, Raphael Benichou, Markus Meister, Rava Azeredo da Silveira. Dynamical Adaptation in Photoreceptors
0 -- 0Judith A. Blake. Ten Quick Tips for Using the Gene Ontology
0 -- 0Guido Scarabelli, Barry J. Grant. Mapping the Structural and Dynamical Features of Kinesin Motor Domains
0 -- 0Frank S. Heldt, Timo Frensing, Antje Pflugmacher, Robin Gröpler, Britta Peschel, Udo Reichl. Multiscale Modeling of Influenza A Virus Infection Supports the Development of Direct-Acting Antivirals
0 -- 0Antoine Frénoy, François Taddei, Dusan Misevic. Genetic Architecture Promotes the Evolution and Maintenance of Cooperation
0 -- 0Giles W. Story, Ivaylo Vlaev, Ben Seymour, Joel S. Winston, Ara Darzi, Raymond J. Dolan. Dread and the Disvalue of Future Pain
0 -- 0Debabani Ganguly, Weihong Zhang, Jianhan Chen. Electrostatically Accelerated Encounter and Folding for Facile Recognition of Intrinsically Disordered Proteins
0 -- 0Falk Lieder, Klaas E. Stephan, Jean Daunizeau, Marta I. Garrido, Karl J. Friston. A Neurocomputational Model of the Mismatch Negativity
0 -- 0Guillem Portella, Federica Battistini, Modesto Orozco. Understanding the Connection between Epigenetic DNA Methylation and Nucleosome Positioning from Computer Simulations
0 -- 0Erez Persi, David Horn. Systematic Analysis of Compositional Order of Proteins Reveals New Characteristics of Biological Functions and a Universal Correlate of Macroevolution
0 -- 0Ashwini Patil, Yutaro Kumagai, Kuo-ching Liang, Yutaka Suzuki, Kenta Nakai. Linking Transcriptional Changes over Time in Stimulated Dendritic Cells to Identify Gene Networks Activated during the Innate Immune Response
0 -- 0Ridvan Eksi, Hongdong Li, Rajasree Menon, Yuchen Wen, Gilbert S. Omenn, Matthias Kretzler, Yuanfang Guan. Systematically Differentiating Functions for Alternatively Spliced Isoforms through Integrating RNA-seq Data
0 -- 0Harald Kempf, Haralampos Hatzikirou, Marcus Bleicher, Michael Meyer-Hermann. In Silico Analysis of Cell Cycle Synchronisation Effects in Radiotherapy of Tumour Spheroids
0 -- 0Tobias Warnecke, Erin A. Becker, Marc T. Facciotti, Corey Nislow, Ben Lehner. Conserved Substitution Patterns around Nucleosome Footprints in Eukaryotes and Archaea Derive from Frequent Nucleosome Repositioning through Evolution
0 -- 0Peter Godfrey-Smith, Manolo Martínez. Communication and Common Interest

Volume 9, Issue 10

0 -- 0Ramakrishnan Iyer, Vilas Menon, Michael Buice, Christof Koch, Stefan Mihalas. The Influence of Synaptic Weight Distribution on Neuronal Population Dynamics
0 -- 0Maryam Modir Shanechi, Jessica J. Chemali, Max Liberman, Ken Solt, Emery N. Brown. A Brain-Machine Interface for Control of Medically-Induced Coma
0 -- 0Sven-Eric Schelhorn, Matthias Fischer, Laura Tolosi, Janine Altmüller, Peter Nürnberg, Herbert Pfister, Thomas Lengauer, Frank Berthold. Sensitive Detection of Viral Transcripts in Human Tumor Transcriptomes
0 -- 0Evan S. Schaffer, Srdjan Ostojic, L. F. Abbott. A Complex-Valued Firing-Rate Model That Approximates the Dynamics of Spiking Networks
0 -- 0Julien Racle, Flora Picard, Laurence Girbal, Muriel Cocaign-Bousquet, Vassily Hatzimanikatis. Lactococcus lactis Translation Data
0 -- 0Guilhem Faure, Isabelle Callebaut. Comprehensive Repertoire of Foldable Regions within Whole Genomes
0 -- 0Mu Gao, Jeffrey Skolnick. A Comprehensive Survey of Small-Molecule Binding Pockets in Proteins
0 -- 0Gabriel Rosser, Alexander G. Fletcher, David A. Wilkinson, Jennifer A. de Beyer, Christian A. Yates, Judith P. Armitage, Philip K. Maini, Ruth E. Baker. Rhodobacter sphaeroides
0 -- 0Yuri Pritykin, Mona Singh. Simple Topological Features Reflect Dynamics and Modularity in Protein Interaction Networks
0 -- 0Antreas C. Kalli, Iain D. Campbell, Mark S. P. Sansom. Conformational Changes in Talin on Binding to Anionic Phospholipid Membranes Facilitate Signaling by Integrin Transmembrane Helices
0 -- 0Daniel B. Larremore, Aaron Clauset, Caroline O. Buckee. A Network Approach to Analyzing Highly Recombinant Malaria Parasite Genes
0 -- 0Omar Hadzipasic, James O. Wrabl, Vincent J. Hilser. A Horizontal Alignment Tool for Numerical Trend Discovery in Sequence Data: Application to Protein Hydropathy
0 -- 0Terry Lohrenz, Meghana Bhatt, Nathan Apple, P. Read Montague. Keeping up with the Joneses: Interpersonal Prediction Errors and the Correlation of Behavior in a Tandem Sequential Choice Task
0 -- 0Tyler Drake, Dimitrios Vavylonis. Model of Fission Yeast Cell Shape Driven by Membrane-Bound Growth Factors and the Cytoskeleton
0 -- 0Kate A. Stafford, Paul Robustelli, Arthur G. Palmer III. Thermal Adaptation of Conformational Dynamics in Ribonuclease H
0 -- 0Thomas Hannagan, Jonathan Grainger. The Lazy Visual Word Form Area: Computational Insights into Location-Sensitivity
0 -- 0Ricardo Aguas, Neil M. Ferguson. Feature Selection Methods for Identifying Genetic Determinants of Host Species in RNA Viruses
0 -- 0Sushmita Roy, Stephen Lagree, Zhonggang Hou, James A. Thomson, Ron M. Stewart, Audrey P. Gasch. Integrated Module and Gene-Specific Regulatory Inference Implicates Upstream Signaling Networks
0 -- 0Giovanna De Palo, Robert G. Endres. Unraveling Adaptation in Eukaryotic Pathways: Lessons from Protocells
0 -- 0Asif M. Khan, Tin Wee Tan, Christian Schönbach, Shoba Ranganathan. APBioNet - Transforming Bioinformatics in the Asia-Pacific Region
0 -- 0Hanna Julienne, Azedine Zoufir, Benjamin Audit, Alain Arneodo. Human Genome Replication Proceeds through Four Chromatin States
0 -- 0Lennart Hilbert, Genevieve Bates, Horia N. Roman, Jenna L. Blumenthal, Nedjma B. Zitouni, Apolinary Sobieszek, Michael C. Mackey, Anne-Marie Lauzon. Molecular Mechanical Differences between Isoforms of Contractile Actin in the Presence of Isoforms of Smooth Muscle Tropomyosin
0 -- 0Shuguang Yuan, Rongliang Wu, Dorota Latek, Bartosz Trzaskowski, Slawomir Filipek. 1 Activation Scheme Concluded from Microsecond All-Atom Molecular Dynamics Simulations
0 -- 0Kolja Becker, Eva Balsa-Canto, Damjan Cicin-Sain, Astrid Hoermann, Hilde Janssens, Julio R. Banga, Johannes Jaeger. Drosophila melanogaster
0 -- 0Paola Carrillo-Bustamante, Can Kesmir, Rob J. De Boer. Virus Encoded MHC-Like Decoys Diversify the Inhibitory KIR Repertoire
0 -- 0Pralay Mitra, David Shultis, Jeffrey R. Brender, Jeff Czajka, David Marsh, Felicia Gray, Tomasz Cierpicki, Yang Zhang. Mycobacterium tuberculosis
0 -- 0Stewart Heitmann, Tjeerd W. Boonstra, Michael Breakspear. A Dendritic Mechanism for Decoding Traveling Waves: Principles and Applications to Motor Cortex
0 -- 0Geir Kjetil Sandve, Anton Nekrutenko, James Taylor, Eivind Hovig. Ten Simple Rules for Reproducible Computational Research
0 -- 0José Lourenço, Mario Recker. Natural, Persistent Oscillations in a Spatial Multi-Strain Disease System with Application to Dengue
0 -- 0Tim Odenthal, Bart Smeets, Paul Van Liedekerke, Engelbert Tijskens, Hans Van Oosterwyck, Herman Ramon. Analysis of Initial Cell Spreading Using Mechanistic Contact Formulations for a Deformable Cell Model
0 -- 0Dongjun Chung, Dan Park, Kevin Myers, Jeffrey Grass, Patricia Kiley, Robert Landick, Sündüz Keles. dPeak: High Resolution Identification of Transcription Factor Binding Sites from PET and SET ChIP-Seq Data
0 -- 0Biswa Sengupta, Simon B. Laughlin, Jeremy E. Niven. Balanced Excitatory and Inhibitory Synaptic Currents Promote Efficient Coding and Metabolic Efficiency
0 -- 0Joshua G. Schraiber, Yulia Mostovoy, Tiffany Y. Hsu, Rachel B. Brem. Inferring Evolutionary Histories of Pathway Regulation from Transcriptional Profiling Data
0 -- 0Fan Jin, Chen Yu, Luhua Lai, Zhirong Liu. Ligand Clouds around Protein Clouds: A Scenario of Ligand Binding with Intrinsically Disordered Proteins
0 -- 0Andreas Spitzmüller, Jordi Mestres. P. falciparum Target Space Relevant to Malaria Drug Discovery
0 -- 0Anna L. Tyler, Wei Lu, Justin J. Hendrick, Vivek M. Philip, Gregory W. Carter. CAPE: An R Package for Combined Analysis of Pleiotropy and Epistasis
0 -- 0Donald R. Olson, Kevin J. Konty, Marc Paladini, Cécile Viboud, Lone Simonsen. Reassessing Google Flu Trends Data for Detection of Seasonal and Pandemic Influenza: A Comparative Epidemiological Study at Three Geographic Scales
0 -- 0Katrina M. Kutchko, Flavio Fröhlich. Emergence of Metastable State Dynamics in Interconnected Cortical Networks with Propagation Delays
0 -- 0Pierre Yger, Kenneth D. Harris. The Convallis Rule for Unsupervised Learning in Cortical Networks
0 -- 0Luca Grieco, Laurence Calzone, Isabelle Bernard-Pierrot, François Radvanyi, Brigitte Kahn-Perlès, Denis Thieffry. Integrative Modelling of the Influence of MAPK Network on Cancer Cell Fate Decision
0 -- 0Jorg J. A. Calis, Matt Maybeno, Jason A. Greenbaum, Daniela Weiskopf, Aruna D. De Silva, Alessandro Sette, Can Kesmir, Björn Peters. Properties of MHC Class I Presented Peptides That Enhance Immunogenicity
0 -- 0Markus Butz, Arjen Van Ooyen. A Simple Rule for Dendritic Spine and Axonal Bouton Formation Can Account for Cortical Reorganization after Focal Retinal Lesions
0 -- 0Francisco Martínez-Jiménez, George Papadatos, Lun Yang, Iain M. Wallace, Vinod Kumar, Ursula Pieper, Andrej Sali, James R. Brown, John P. Overington, Marc A. Martí-Renom. Mycobacterium tuberculosis
0 -- 0Virginie Bernard, Magali Michaut. Explain Bioinformatics to Your Grandmother!
0 -- 0Qiang Luo, Tian Ge, Fabian Grabenhorst, Jianfeng Feng, Edmund T. Rolls. Attention-Dependent Modulation of Cortical Taste Circuits Revealed by Granger Causality with Signal-Dependent Noise
0 -- 0Rene Rex, Nelli Bill, Kerstin Schmidt-Hohagen, Dietmar Schomburg. Dinoroseobacter shibae
0 -- 0Kriti Puniyani, Eric P. Xing. GINI: From ISH Images to Gene Interaction Networks
0 -- 0Francesca Falcetta, Monica Lupi, Valentina Colombo, Paolo Ubezio. Dynamic Rendering of the Heterogeneous Cell Response to Anticancer Treatments
0 -- 0Ryan Suderman, Eric J. Deeds. Machines vs. Ensembles: Effective MAPK Signaling through Heterogeneous Sets of Protein Complexes
0 -- 0Christian Tetzlaff, Christoph Kolodziejski, Marc Timme, Misha Tsodyks, Florentin Wörgötter. Synaptic Scaling Enables Dynamically Distinct Short- and Long-Term Memory Formation
0 -- 0Farzad Farkhooi, Anja Froese, Eilif Muller, Randolf Menzel, Martin P. Nawrot. Cellular Adaptation Facilitates Sparse and Reliable Coding in Sensory Pathways
0 -- 0Patrick M. Buck, Sandeep Kumar, Satish K. Singh. On the Role of Aggregation Prone Regions in Protein Evolution, Stability, and Enzymatic Catalysis: Insights from Diverse Analyses
0 -- 0Ruth Nussinov. PLOS Computational Biology Help the Biological Sciences?
0 -- 0Sebastian Gluth, Jörg Rieskamp, Christian Büchel. Deciding Not to Decide: Computational and Neural Evidence for Hidden Behavior in Sequential Choice
0 -- 0Martin M. Monti, Evan S. Lutkenhoff, Mikail Rubinov, Pierre Boveroux, Audrey Vanhaudenhuyse, Olivia Gosseries, Marie-Aurélie Bruno, Quentin Noirhomme, Mélanie Boly, Steven Laureys. Dynamic Change of Global and Local Information Processing in Propofol-Induced Loss and Recovery of Consciousness
0 -- 0Rogan Carr, Shai S. Shen-Orr, Elhanan Borenstein. Reconstructing the Genomic Content of Microbiome Taxa through Shotgun Metagenomic Deconvolution
0 -- 0André Yoshiaki Kashiwabara, Ígor Bonadio, Vitor Onuchic, Felipe Amado, Rafael Mathias, Alan Mitchell Durham. ToPS: A Framework to Manipulate Probabilistic Models of Sequence Data
0 -- 0Chunfeng Zhao, Sergei Yu Noskov. The Molecular Mechanism of Ion-Dependent Gating in Secondary Transporters
0 -- 0Arnab Bhattacherjee, Stefan Wallin. Exploring Protein-Peptide Binding Specificity through Computational Peptide Screening

Volume 9, Issue 1

0 -- 0Stefan Wuchty, Dolores Arjona, Peter O. Bauer. Important miRs of Pathways in Different Tumor Types
0 -- 0Hang Yu, Klaus Schulten. Membrane Sculpting by F-BAR Domains Studied by Molecular Dynamics Simulations
0 -- 0Jing Dong, Jiazhang Qiu, Yu Zhang, Chongjian Lu, Xiaohan Dai, Jianfeng Wang, Hongen Li, Xin Wang, Wei Tan, Mingjing Luo, Xiaodi Niu, Xuming Deng. Oroxylin A Inhibits Hemolysis via Hindering the Self-Assembly of α-Hemolysin Heptameric Transmembrane Pore
0 -- 0Ming Hu, Ke Deng, Zhaohui S. Qin, Jesse Dixon, Siddarth Selvaraj, Jennifer Fang, Bing Ren, Jun S. Liu. Bayesian Inference of Spatial Organizations of Chromosomes
0 -- 0Gkikas Magiorkinis, Vana Sypsa, Emmanouil Magiorkinis, Dimitrios Paraskevis, Antigoni Katsoulidou, Robert Belshaw, Christophe Fraser, Oliver George Pybus, Angelos Hatzakis. Integrating Phylodynamics and Epidemiology to Estimate Transmission Diversity in Viral Epidemics
0 -- 0Nol Chindapol, Jaap A. Kaandorp, Carolina Cronemberger, Tali Mass, Amatzia Genin. Pocillopora verrucosa and the Influence of Hydrodynamics
0 -- 0Pengsheng Zheng, Christos Dimitrakakis, Jochen Triesch. Network Self-Organization Explains the Statistics and Dynamics of Synaptic Connection Strengths in Cortex
0 -- 0Mario Pujato, Thomas MacCarthy, András Fiser, Aviv Bergman. The Underlying Molecular and Network Level Mechanisms in the Evolution of Robustness in Gene Regulatory Networks
0 -- 0Thomas Lemmin, Cinque S. Soto, Graham Clinthorne, William F. DeGrado, Matteo Dal Peraro. E. coli PhoQ Histidine Kinase: Implications for Signal Transduction from Molecular Simulations
0 -- 0Cibele Vieira Falkenberg, Leslie M. Loew. Computational Analysis of Rho GTPase Cycling
0 -- 0Wyming Lee Pang, Amardeep Kaur, Alexander V. Ratushny, Aleksandar Cvetkovic, Sunil Kumar, Min Pan, Adam P. Arkin, John D. Aitchison, Michael W. W. Adams, Nitin S. Baliga. Metallochaperones Regulate Intracellular Copper Levels
0 -- 0Anatoly Rinberg, Adam L. Taylor, Eve Marder. The Effects of Temperature on the Stability of a Neuronal Oscillator
0 -- 0Jeroen de Ridder, Thomas Abeel, Magali Michaut, Venkata P. Satagopam, Nils Gehlenborg. Don't Wear Your New Shoes (Yet): Taking the Right Steps to Become a Successful Principal Investigator
0 -- 0Vladislav Volman, Maxim Bazhenov, Terrence J. Sejnowski. Divide and Conquer: Functional Segregation of Synaptic Inputs by Astrocytic Microdomains Could Alleviate Paroxysmal Activity Following Brain Trauma
0 -- 0Yohan Kim, Jonathan W. Yewdell, Alessandro Sette, Björn Peters. Positional Bias of MHC Class I Restricted T-Cell Epitopes in Viral Antigens Is Likely due to a Bias in Conservation
0 -- 0Luca Ciandrini, Ian Stansfield, M. Carmen Romano. Ribosome Traffic on mRNAs Maps to Gene Ontology: Genome-wide Quantification of Translation Initiation Rates and Polysome Size Regulation
0 -- 0Mathieu d'Acremont, Eleonora Fornari, Peter Bossaerts. Activity in Inferior Parietal and Medial Prefrontal Cortex Signals the Accumulation of Evidence in a Probability Learning Task
0 -- 0A. Ercument Cicek, Ilya Bederman, Leigh Henderson, Mitchell L. Drumm, Gultekin Özsoyoglu. ADEMA: An Algorithm to Determine Expected Metabolite Level Alterations Using Mutual Information
0 -- 0Satomi Matsuoka, Tatsuo Shibata, Masahiro Ueda. Asymmetric PTEN Distribution Regulated by Spatial Heterogeneity in Membrane-Binding State Transitions
0 -- 0Martin H. Schaefer, Tiago J. S. Lopes, Nancy Mah, Jason E. Shoemaker, Yukiko Matsuoka, Jean-Fred Fontaine, Caroline Louis-Jeune, Amie J. Eisfeld, Gabriele Neumann, Carol Perez-Iratxeta, Yoshihiro Kawaoka, Hiroaki Kitano, Miguel A. Andrade-Navarro. Adding Protein Context to the Human Protein-Protein Interaction Network to Reveal Meaningful Interactions
0 -- 0Yann Le Cunff, Annette Baudisch, Khashayar Pakdaman. How Evolving Heterogeneity Distributions of Resource Allocation Strategies Shape Mortality Patterns
0 -- 0Holly E. Gerhard, Felix A. Wichmann, Matthias Bethge. How Sensitive Is the Human Visual System to the Local Statistics of Natural Images?
0 -- 0Cédric Debès, Minglei Wang, Gustavo Caetano-Anollés, Frauke Gräter. Evolutionary Optimization of Protein Folding
0 -- 0Anne L. Wheeler, Cátia M. Teixeira, Afra H. Wang, Xuejian Xiong, Natasa Kovacevic, Jason P. Lerch, Anthony Randal McIntosh, John Parkinson, Paul W. Frankland. Identification of a Functional Connectome for Long-Term Fear Memory in Mice
0 -- 0Linan Xu, Naushaba Hasin, Manli Shen, Jianwei He, Youlin Xue, Xiaohong Zhou, Sarah Perrett, Youtao Song, Gary W. Jones. Using Steered Molecular Dynamics to Predict and Assess Hsp70 Substrate-Binding Domain Mutants that Alter Prion Propagation
0 -- 0Ruian Ke, Piers J. Ingram, Ken Haynes. An Integrative Model of Ion Regulation in Yeast
0 -- 0Chiara Pastrello, David Otasek, Kristen Fortney, Giuseppe Agapito, Mario Cannataro, Elize Shirdel, Igor Jurisica. Visual Data Mining of Biological Networks: One Size Does Not Fit All
0 -- 0Niklas Wilming, Simon Harst, Nico M. Schmidt, Peter König. Saccadic Momentum and Facilitation of Return Saccades Contribute to an Optimal Foraging Strategy
0 -- 0Fabian H. Sinz, Matthias Bethge. Temporal Adaptation Enhances Efficient Contrast Gain Control on Natural Images
0 -- 0Corentin M. Barbu, Andrew Hong, Jennifer M. Manne, Dylan S. Small, Javier E. Quintanilla Calderón, Karthik Sethuraman, Víctor Quispe-Machaca, Jenny Ancca-Juárez, Juan G. Cornejo del Carpio, Fernando S. Málaga Chavez, César Náquira, Michael Z. Levy. The Effects of City Streets on an Urban Disease Vector
0 -- 0Jeromos Vukov, Flávio L. Pinheiro, Francisco C. Santos, Jorge M. Pacheco. Reward from Punishment Does Not Emerge at All Costs
0 -- 0Graham Rockwell, Nicholas J. Guido, George M. Church. Redirector: Designing Cell Factories by Reconstructing the Metabolic Objective
0 -- 0Kristy Nowak-Lovato, Ludmil B. Alexandrov, Afsheen Banisadr, Amy L. Bauer, Alan R. Bishop, Anny Usheva, Fangping Mu, Elizabeth Hong-Geller, Kim Ø. Rasmussen, William S. Hlavacek, Boian S. Alexandrov. Binding of Nucleoid-Associated Protein Fis to DNA Is Regulated by DNA Breathing Dynamics
0 -- 0Sandra V. Bennun, Kevin J. Yarema, Michael J. Betenbaugh, Frederick J. Krambeck. Integration of the Transcriptome and Glycome for Identification of Glycan Cell Signatures
0 -- 0Giovanni Settanni, David Serquera, Piotr E. Marszalek, Emanuele Paci, Laura S. Itzhaki. Effects of Ligand Binding on the Mechanical Properties of Ankyrin Repeat Protein Gankyrin
0 -- 0Nives Skunca, Matko Bosnjak, Anita Krisko, Pance Panov, Saso Dzeroski, Tomislav Smuc, Fran Supek. Phyletic Profiling with Cliques of Orthologs Is Enhanced by Signatures of Paralogy Relationships
0 -- 0Sebastian Funk, Hiroshi Nishiura, Hans Heesterbeek, W. John Edmunds, Francesco Checchi. Identifying Transmission Cycles at the Human-Animal Interface: The Role of Animal Reservoirs in Maintaining Gambiense Human African Trypanosomiasis
0 -- 0Juliane Liepe, Sarah Filippi, Michal Komorowski, Michael P. H. Stumpf. Maximizing the Information Content of Experiments in Systems Biology
0 -- 0Karen E. Joyce, Satoru Hayasaka, Paul J. Laurienti. The Human Functional Brain Network Demonstrates Structural and Dynamical Resilience to Targeted Attack
0 -- 0Andrew H. Beck, Nicholas W. Knoblauch, Marco M. Hefti, Jennifer Kaplan, Stuart J. Schnitt, Aedín C. Culhane, Markus S. Schröder, Thomas Risch, John Quackenbush, Benjamin Haibe-Kains. Significance Analysis of Prognostic Signatures
0 -- 0Mikael Sunnåker, Alberto Giovanni Busetto, Elina Numminen, Jukka Corander, Matthieu Foll, Christophe Dessimoz. Approximate Bayesian Computation
0 -- 0Giovanni Lo Iacono, Frank van den Bosch, Chris A. Gilligan. Durable Resistance to Crop Pathogens: An Epidemiological Framework to Predict Risk under Uncertainty
0 -- 0Stefka Tyanova, Jürgen Cox, Jesper V. Olsen, Matthias Mann 0002, Dmitrij Frishman. Phosphorylation Variation during the Cell Cycle Scales with Structural Propensities of Proteins
0 -- 0George Forrest Young, Luca Scardovi, Andrea Cavagna, Irene Giardina, Naomi Ehrich Leonard. Starling Flock Networks Manage Uncertainty in Consensus at Low Cost
0 -- 0Michael A. Buice, Carson C. Chow. Dynamic Finite Size Effects in Spiking Neural Networks
0 -- 0Cornelis van de Kamp, Peter J. Gawthrop, Henrik Gollee, Ian D. Loram. Refractoriness in Sustained Visuo-Manual Control: Is the Refractory Duration Intrinsic or Does It Depend on External System Properties?
0 -- 0Omry Koren, Dan Knights, Antonio Gonzalez, Levi Waldron, Nicola Segata, Rob Knight, Curtis Huttenhower, Ruth E. Ley. A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets