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ORCIDPLoS Computational Biology, Volume 8
Volume 8, Number 1, January 2012
- Rosemary Dickin, Chris James Hall, Laura K. Taylor
, Andrew M. Collings, Ruth Nussinov, Philip E. Bourne:
A Review of 2011 for PLoS Computational Biology.
- Ioannis Vlachos, Ad Aertsen, Arvind Kumar:
Beyond Statistical Significance: Implications of Network Structure on Neuronal Activity.
- William Stafford Noble, Michael J. MacCoss:
Computational and Statistical Analysis of Protein Mass Spectrometry Data.
- Justin Hsia, William J. Holtz, Daniel C. Huang, Murat Arcak, Michel M. Maharbiz:
A Feedback Quenched Oscillator Produces Turing Patterning with One Diffuser. - Yotam Luz, Maoz Shamir:
Balancing Feed-Forward Excitation and Inhibition via Hebbian Inhibitory Synaptic Plasticity. - Patrick D. McMullen, Erin Z. Aprison, Peter B. Winter, Luis A. Nunes Amaral, Richard I. Morimoto, Ilya Ruvinsky:
Macro-level Modeling of the Response of C. elegans Reproduction to Chronic Heat Stress. - Xinan Yang, Kelly Regan, Yong Huang, Qingbei Zhang, Jianrong Li, Tanguy Y. Seiwert, Ezra E. W. Cohen, H. Rosie Xing, Yves A. Lussier:
Single Sample Expression-Anchored Mechanisms Predict Survival in Head and Neck Cancer. - Caterina A. M. La Porta, Stefano Zapperi, James P. Sethna:
Senescent Cells in Growing Tumors: Population Dynamics and Cancer Stem Cells. - Justin R. Chumbley, Guillaume Flandin, Dominik R. Bach, Jean Daunizeau, Ernst Fehr, Raymond J. Dolan, Karl J. Friston:
Learning and Generalization under Ambiguity: An fMRI Study. - J. Naudé, J. T. Paz, Hugues Berry, Bruno Delord:
A Theory of Rate Coding Control by Intrinsic Plasticity Effects. - Fiona Achcar, Eduard J. Kerkhoven, Barbara M. Bakker, Michael P. Barrett, Rainer Breitling:
Dynamic Modelling under Uncertainty: The Case of Trypanosoma brucei Energy Metabolism. - Michael N. Economo, John A. White:
Membrane Properties and the Balance between Excitation and Inhibition Control Gamma-Frequency Oscillations Arising from Feedback Inhibition. - Max von Kleist, Philipp Metzner, Roland Marquet, Christof Schütte:
HIV-1 Polymerase Inhibition by Nucleoside Analogs: Cellular- and Kinetic Parameters of Efficacy, Susceptibility and Resistance Selection. - Navneet Rai, Rajat Anand, Krishna Ramkumar, Varun Sreenivasan, Sugat Dabholkar, Kareenhalli V. Venkatesh, Mukund Thattai:
Prediction by Promoter Logic in Bacterial Quorum Sensing. - Michael Seifert, André Gohr, Marc Strickert, Ivo Grosse:
Parsimonious Higher-Order Hidden Markov Models for Improved Array-CGH Analysis with Applications to Arabidopsis thaliana. - Artturi Koivuniemi, Timo Vuorela, Petri T. Kovanen, Ilpo Vattulainen, Marja T. Hyvönen:
Lipid Exchange Mechanism of the Cholesteryl Ester Transfer Protein Clarified by Atomistic and Coarse-grained Simulations. - Felix A. Krüger, John P. Overington:
Global Analysis of Small Molecule Binding to Related Protein Targets. - Pablo Gainza, Kyle E. Roberts, Bruce Randall Donald:
Protein Design Using Continuous Rotamers. - Eyal Akiva, Gilgi Friedlander, Zohar Itzhaki, Hanah Margalit:
A Dynamic View of Domain-Motif Interactions. - Kyung Hyuk Kim, Herbert M. Sauro:
Adjusting Phenotypes by Noise Control. - Juilee Thakar, Ashutosh K. Pathak, Lisa Murphy, Réka Albert, Isabella M. Cattadori:
Network Model of Immune Responses Reveals Key Effectors to Single and Co-infection Dynamics by a Respiratory Bacterium and a Gastrointestinal Helminth. - Ken Takiyama, Masato Okada:
Maximization of Learning Speed in the Motor Cortex Due to Neuronal Redundancy. - Iain H. Moal, Paul A. Bates:
Kinetic Rate Constant Prediction Supports the Conformational Selection Mechanism of Protein Binding. - Weihong Zhang, Debabani Ganguly, Jianhan Chen:
Residual Structures, Conformational Fluctuations, and Electrostatic Interactions in the Synergistic Folding of Two Intrinsically Disordered Proteins. - Shuoguo Wang, Lakshmi Chandrasekaran, Fernando R. Fernandez, John A. White, Carmen C. Canavier:
Short Conduction Delays Cause Inhibition Rather than Excitation to Favor Synchrony in Hybrid Neuronal Networks of the Entorhinal Cortex. - (Withdrawn) Multi-scale Inference of Interaction Rules in Animal Groups Using Bayesian Model Selection.
- Christian Meisel, Alexander Storch, Susanne Hallmeyer-Elgner, Ed Bullmore, Thilo Gross:
Failure of Adaptive Self-Organized Criticality during Epileptic Seizure Attacks. - Karl J. Friston, Tamara Shiner, Thomas H. B. FitzGerald, Joseph M. Galea, Rick A. Adams, Harriet R. Brown, Raymond J. Dolan, Rosalyn J. Moran, Klaas Enno Stephan, Sven Bestmann:
Dopamine, Affordance and Active Inference. - João A. N. Filipe, Richard C. Cobb, Ross K. Meentemeyer, Christopher A. Lee, Yana S. Valachovic, Alex R. Cook, David M. Rizzo, Christopher A. Gilligan:
Landscape Epidemiology and Control of Pathogens with Cryptic and Long-Distance Dispersal: Sudden Oak Death in Northern Californian Forests. - Benjamin Pfeuty, Jean-François Bodart, Ralf Blossey, Marc Lefranc:
A Dynamical Model of Oocyte Maturation Unveils Precisely Orchestrated Meiotic Decisions. - Nicoló Fusi, Oliver Stegle, Neil D. Lawrence:
Joint Modelling of Confounding Factors and Prominent Genetic Regulators Provides Increased Accuracy in Genetical Genomics Studies. - Bart Baddeley, Paul Graham, Philip Husbands, Andrew Philippides:
A Model of Ant Route Navigation Driven by Scene Familiarity. - Yu-Kang Cheng, Rameen Beroukhim, Ross L. Levine, Ingo K. Mellinghoff, Eric C. Holland, Franziska Michor:
A Mathematical Methodology for Determining the Temporal Order of Pathway Alterations Arising during Gliomagenesis. - Bambang S. Adiwijaya, Tara L. Kieffer, Joshua Henshaw, Karen Eisenhauer, Holly Kimko, John J. Alam, Robert S. Kauffman, Varun Garg:
A Viral Dynamic Model for Treatment Regimens with Direct-acting Antivirals for Chronic Hepatitis C Infection.
Volume 8, Number 2, February 2012
- Purvesh Khatri, Marina Sirota, Atul J. Butte:
Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges. - Marjet Elemans, Nafisa-Katrin Seich al Basatena, Becca Asquith:
The Efficiency of the Human CD8+ T Cell Response: How Should We Quantify It, What Determines It, and Does It Matter?
- Jing-yu Yu, Nan Zheng, Gerta Mane, Kyoung Ah Min, Juan P. Hinestroza, Huaning Zhu, Kathleen A. Stringer, Gus R. Rosania:
A Cell-based Computational Modeling Approach for Developing Site-Directed Molecular Probes. - Vered Kunik, Bjoern Peters, Yanay Ofran:
Structural Consensus among Antibodies Defines the Antigen Binding Site. - Trine Krogh-Madsen, Geoffrey W. Abbott, David J. Christini:
Effects of Electrical and Structural Remodeling on Atrial Fibrillation Maintenance: A Simulation Study. - Santiago Treviño III, Yudong Sun, Tim F. Cooper, Kevin E. Bassler:
Robust Detection of Hierarchical Communities from Escherichia coli Gene Expression Data. - Cai Chen, David Frankhouser, Ralf Bundschuh:
Comparison of Insertional RNA Editing in Myxomycetes. - Yukikazu Hidaka, Cheol E. Han, Steven L. Wolf, Carolee J. Winstein, Nicolas Schweighofer:
Use It and Improve It or Lose It: Interactions between Arm Function and Use in Humans Post-stroke. - António Roldão, Maria Candida M. Mellado, J. C. Lima, Manuel J. T. Carrondo, Paula M. Alves, Rui Oliveira:
On the Effect of Thermodynamic Equilibrium on the Assembly Efficiency of Complex Multi-Layered Virus-Like Particles (VLP): the Case of Rotavirus VLP. - Giulio Quarta, Ken Sin, Tamar Schlick:
Dynamic Energy Landscapes of Riboswitches Help Interpret Conformational Rearrangements and Function. - Shingo Iwami, Hiroshi Haeno, Franziska Michor:
A Race between Tumor Immunoescape and Genome Maintenance Selects for Optimum Levels of (epi)genetic Instability. - Yael Baran, Eran Halperin:
Joint Analysis of Multiple Metagenomic Samples. - Denis Menshykau, Conradin Kraemer, Dagmar Iber:
Branch Mode Selection during Early Lung Development. - K. Sriram, Maria Rodriguez-Fernandez, Francis J. Doyle III:
Modeling Cortisol Dynamics in the Neuro-endocrine Axis Distinguishes Normal, Depression, and Post-traumatic Stress Disorder (PTSD) in Humans. - Markus Hartenfeller, Heiko Zettl, Miriam Walter, Matthias Rupp, Felix Reisen, Ewgenij Proschak, Sascha Weggen, Holger Stark, Gisbert Schneider:
DOGS: Reaction-Driven de novo Design of Bioactive Compounds. - Johannes Rüter, Nicolas Marcille, Henning Sprekeler, Wulfram Gerstner, Michael H. Herzog:
Paradoxical Evidence Integration in Rapid Decision Processes. - Paul D. Thomas, Valerie Wood, Christopher J. Mungall, Suzanna E. Lewis, Judith A. Blake:
On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report. - Vincent Mirabet, Fabrice Besnard, Teva Vernoux, Arezki Boudaoud:
Noise and Robustness in Phyllotaxis. - Priyanka Prakash, Abdallah Sayyed-Ahmad, Alemayehu A. Gorfe:
The Role of Conserved Waters in Conformational Transitions of Q61H K-ras. - Daichi Shigemizu, Zhenjun Hu, Jui-Hung Hung, Chia-Ling Huang, Yajie Wang, Charles DeLisi:
Using Functional Signatures to Identify Repositioned Drugs for Breast, Myelogenous Leukemia and Prostate Cancer. - Christoph Börgers, Giovanni Talei Franzesi, Fiona E. N. LeBeau, Edward S. Boyden, Nancy Kopell:
Minimal Size of Cell Assemblies Coordinated by Gamma Oscillations. - Theo Arts, Joost Lumens, Wilco Kroon, Tammo Delhaas:
Control of Whole Heart Geometry by Intramyocardial Mechano-Feedback: A Model Study. - Iraj Hosseini, Feilim Mac Gabhann:
Multi-Scale Modeling of HIV Infection in vitro and APOBEC3G-Based Anti-Retroviral Therapy. - Rodrigo Freire Oliveira, Myungsook Kim, Kim T. Blackwell:
Subcellular Location of PKA Controls Striatal Plasticity: Stochastic Simulations in Spiny Dendrites. - Camille Morvan, Laurence T. Maloney:
Human Visual Search Does Not Maximize the Post-Saccadic Probability of Identifying Targets. - Yu Wu, Yao Lu, Weiqiang Chen, Jianping Fu, Rong Fan:
In silico Experimentation of Glioma Microenvironment Development and Anti-tumor Therapy. - István Miklós, Zoltán Zádori:
Positive Evolutionary Selection of an HD Motif on Alzheimer Precursor Protein Orthologues Suggests a Functional Role. - Pranidhi Sood, Robert J. Johnston Jr., Edo Kussell:
Stochastic De-repression of Rhodopsins in Single Photoreceptors of the Fly Retina. - Steven John Lade, Thilo Gross:
Early Warning Signals for Critical Transitions: A Generalized Modeling Approach. - Ali R. Zomorrodi, Costas D. Maranas:
OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities. - Nadav Rappoport, Michal Linial:
Viral Proteins Acquired from a Host Converge to Simplified Domain Architectures. - Ekaterina Kotelnikova, Maria A. Shkrob, Mikhail A. Pyatnitskiy, Alessandra Ferlini, Nikolai Daraselia:
Novel Approach to Meta-Analysis of Microarray Datasets Reveals Muscle Remodeling-related Drug Targets and Biomarkers in Duchenne Muscular Dystrophy. - Kaustubh Supekar, Vinod Menon:
Developmental Maturation of Dynamic Causal Control Signals in Higher-Order Cognition: A Neurocognitive Network Model. - Xueyang Feng, You Xu, Yixin Chen, Yinjie J. Tang:
Integrating Flux Balance Analysis into Kinetic Models to Decipher the Dynamic Metabolism of Shewanella oneidensis MR-1.
Volume 8, Number 3, March 2012
- Anthony C. Fletcher, Philip E. Bourne:
Ten Simple Rules for Starting a Company. - Shoshana J. Wodak, Daniel Mietchen, Andrew M. Collings, Robert B. Russell, Philip E. Bourne:
Topic Pages: PLoS Computational Biology Meets Wikipedia.
- Marc S. Sherman, Barak A. Cohen:
Thermodynamic State Ensemble Models of cis-Regulation.
- Gustavo Deco, Etienne Hugues:
Neural Network Mechanisms Underlying Stimulus Driven Variability Reduction. - Tyler J. Glembo, Daniel W. Farrell, Z. Nevin Gerek, M. F. Thorpe, S. Banu Ozkan:
Collective Dynamics Differentiates Functional Divergence in Protein Evolution. - Yu-Yao Tseng, Suzanne M. Hunt, Christian Heintzen, Susan K. Crosthwaite, Jean-Marc Schwartz:
Comprehensive Modelling of the Neurospora Circadian Clock and Its Temperature Compensation. - Spiro P. Pantazatos, Ardesheer Talati, Paul Pavlidis, Joy Hirsch:
Decoding Unattended Fearful Faces with Whole-Brain Correlations: An Approach to Identify Condition-Dependent Large-Scale Functional Connectivity. - Jesse A. Gillis, Paul Pavlidis:
"Guilt by Association" Is the Exception Rather Than the Rule in Gene Networks. - Rémi Lehe, Oskar Hallatschek, Luca Peliti:
The Rate of Beneficial Mutations Surfing on the Wave of a Range Expansion. - Graciano Dieck Kattas, Xiaoke Xu, Michael Small:
Dynamical Modeling of Collective Behavior from Pigeon Flight Data: Flock Cohesion and Dispersion. - James Trousdale, Yu Hu, Eric Shea-Brown, Kresimir Josic:
Impact of Network Structure and Cellular Response on Spike Time Correlations. - Ana Duarte, E. Scholtens, Franz J. Weissing:
Implications of Behavioral Architecture for the Evolution of Self-Organized Division of Labor. - Christian Keck, Cristina Savin, Jörg Lücke:
Feedforward Inhibition and Synaptic Scaling - Two Sides of the Same Coin? - Giulia Morra, Raffaello Potestio, Cristian Micheletti, Giorgio Colombo:
Corresponding Functional Dynamics across the Hsp90 Chaperone Family: Insights from a Multiscale Analysis of MD Simulations. - Kevin M. Aquino, Mark M. Schira, Peter A. Robinson, Peter M. Drysdale, Michael Breakspear:
Hemodynamic Traveling Waves in Human Visual Cortex. - Frederik Graw, Roland R. Regoes:
Influence of the Fibroblastic Reticular Network on Cell-Cell Interactions in Lymphoid Organs. - Demian Battaglia, Annette Witt, Fred Wolf, Theo Geisel:
Dynamic Effective Connectivity of Inter-Areal Brain Circuits. - Mehdi Moussaïd, Elsa G. Guillot, Mathieu Moreau, Jérôme Fehrenbach, Olivier Chabiron, Samuel Lemercier, Julien Pettré, Cécile Appert-Rolland, Pierre Degond, Guy Theraulaz:
Traffic Instabilities in Self-Organized Pedestrian Crowds. - Meghan K. Driscoll, Colin McCann, Rael Kopace, Tess Homan, John T. Fourkas, Carole Parent, Wolfgang Losert:
Cell Shape Dynamics: From Waves to Migration. - Jacob D. Durrant, James Andrew McCammon:
AutoClickChem: Click Chemistry in Silico. - Siu-Fai Chow, Stuart D. Wick, Hermann Riecke:
Neurogenesis Drives Stimulus Decorrelation in a Model of the Olfactory Bulb. - Mark G. F. Sun, Martin Sikora, Michael Costanzo, Charles Boone, Philip M. Kim:
Network Evolution: Rewiring and Signatures of Conservation in Signaling. - Alexander R. Macalalad, Michael C. Zody, Patrick Charlebois, Niall J. Lennon, Ruchi M. Newman, Christine M. Malboeuf, Elizabeth M. Ryan, Christian L. Boutwell, Karen A. Power, Doug E. Brackney, Kendra N. Pesko, Joshua Z. Levin, Gregory D. Ebel, Todd M. Allen, Bruce W. Birren, Matthew R. Henn:
Highly Sensitive and Specific Detection of Rare Variants in Mixed Viral Populations from Massively Parallel Sequence Data. - Elif Nihal Korkmaz, Ruth Nussinov, Türkan Haliloglu:
Conformational Control of the Binding of the Transactivation Domain of the MLL Protein and c-Myb to the KIX Domain of CREB. - Leonard Kaczmarek:
Gradients and Modulation of K+ Channels Optimize Temporal Accuracy in Networks of Auditory Neurons. - Ying-Ying Jiang, De-Xin Kong, Tao Qin, Xiao Li, Gustavo Caetano-Anollés, Hong-yu Zhang:
The Impact of Oxygen on Metabolic Evolution: A Chemoinformatic Investigation. - Martin Lindén, Pierre Sens, Rob Phillips:
Entropic Tension in Crowded Membranes. - Hideaki Shimazaki, Shun-ichi Amari, Emery N. Brown, Sonja Grün:
State-Space Analysis of Time-Varying Higher-Order Spike Correlation for Multiple Neural Spike Train Data. - Cyril F. Reboul, Grischa R. Meyer, Benjamin T. Porebski, Natalie A. Borg, Ashley M. Buckle:
Epitope Flexibility and Dynamic Footprint Revealed by Molecular Dynamics of a pMHC-TCR Complex. - Quentin J. M. Huys, Neir Eshel, Elizabeth J. P. O'Nions, Luke Sheridan, Peter Dayan, Jonathan P. Roiser:
Bonsai Trees in Your Head: How the Pavlovian System Sculpts Goal-Directed Choices by Pruning Decision Trees. - Gabriel E. Leventhal, Roger D. Kouyos, Tanja Stadler, Viktor von Wyl, Sabine Yerly, Jürg Böni, Cristina Cellerai, Thomas Klimkait, Huldrych F. Günthard, Sebastian Bonhoeffer:
Inferring Epidemic Contact Structure from Phylogenetic Trees. - Carlos J. Melián, David Alonso, Stefano Allesina, Richard S. Condit, Rampal S. Etienne:
Does Sex Speed Up Evolutionary Rate and Increase Biodiversity? - Iain G. Johnston, Bernadett Gaal, Ricardo Pires das Neves, Tariq Enver, Francisco J. Iborra, Nick S. Jones:
Mitochondrial Variability as a Source of Extrinsic Cellular Noise. - Marc Hafner, Heinz Koeppl, Didier Gonze:
Effect of Network Architecture on Synchronization and Entrainment Properties of the Circadian Oscillations in the Suprachiasmatic Nucleus. - Travis J. A. Craddock, Jack A. Tuszynski, Stuart R. Hameroff:
Cytoskeletal Signaling: Is Memory Encoded in Microtubule Lattices by CaMKII Phosphorylation? - Sang O. K. Song, Justin Hogg, Zhi-Yong Peng, Robert S. Parker, John A. Kellum, Gilles Clermont:
Ensemble Models of Neutrophil Trafficking in Severe Sepsis. - David M. Richards, Antje M. Hempel, Klas Flärdh, Mark J. Buttner, Martin Howard:
Mechanistic Basis of Branch-Site Selection in Filamentous Bacteria. - Ken T. D. Eames, Natasha L. Tilston, Ellen Brooks-Pollock, W. John Edmunds:
Measured Dynamic Social Contact Patterns Explain the Spread of H1N1v Influenza. - Xiaodong Pang, Huan-Xiang Zhou:
A Common Model for Cytokine Receptor Activation: Combined Scissor-Like Rotation and Self-Rotation of Receptor Dimer Induced by Class I Cytokine. - Stefano Mostarda, David Gfeller, Francesco Rao:
Beyond the Binding Site: The Role of the β2 - β3 Loop and Extra-Domain Structures in PDZ Domains. - András Lörincz, Zsolt Palotai, Gábor Szirtes:
Efficient Sparse Coding in Early Sensory Processing: Lessons from Signal Recovery. - Kendra S. Burbank, Gabriel Kreiman:
Depression-Biased Reverse Plasticity Rule Is Required for Stable Learning at Top-Down Connections. - Mathieu Lemay, Enno de Lange, Jan P. Kucera:
Uncovering the Dynamics of Cardiac Systems Using Stochastic Pacing and Frequency Domain Analyses. - Dimitrios V. Vavoulis, Volko A. Straub, John A. D. Aston, Jianfeng Feng:
A Self-Organizing State-Space-Model Approach for Parameter Estimation in Hodgkin-Huxley-Type Models of Single Neurons. - Athanasius F. M. Marée, Verônica A. Grieneisen, Leah Edelstein-Keshet:
How Cells Integrate Complex Stimuli: The Effect of Feedback from Phosphoinositides and Cell Shape on Cell Polarization and Motility. - Nicholas Furnham, Ian Sillitoe, Gemma L. Holliday, Alison L. Cuff, Roman A. Laskowski, Christine A. Orengo, Janet M. Thornton:
Exploring the Evolution of Novel Enzyme Functions within Structurally Defined Protein Superfamilies.