Works in PLoS Computational Biology, 2011, Vol 7, Issue 10

Results: 69

Automatic Morphological Subtyping Reveals New Roles of Caspases in Mitochondrial Dynamics.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002212

By:

Peng, Jyh-Ying;
Lin, Chung-Chih;
Chen, Yen-Jen;
Kao, Lung-Sen;
Liu, Young-Chau;
Chou, Chung-Chien;
Huang, Yi-Hung;
Chang, Fang-Rong;
Wu, Yang-Chang;
Tsai, Yuh-Show;
Hsu, Chun-Nan

Publication type:

Article

Estimating the Relevance of World Disturbances to Explain Savings, Interference and Long-Term Motor Adaptation Effects.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002210

By:

Berniker, Max;
Kording, Konrad P.

Publication type:

Article

Evolution of Networks for Body Plan Patterning; Interplay of Modularity, Robustness and Evolvability.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002208

By:

Ten Tusscher, Kirsten H.;
Hogeweg, Paulien

Publication type:

Article

B Cell Activation Triggered by the Formation of the Small Receptor Cluster: A Computational Study.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002197

By:

Hat, Beata;
Kazmierczak, Bogdan;
Lipniacki, Tomasz

Publication type:

Article

Local Orientation and the Evolution of Foraging: Changes in Decision Making Can Eliminate Evolutionary Trade-offs.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002186

By:

van der Post, Daniel J.;
Semmann, Dirk

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Article

Three People Can Synchronize as Coupled Oscillators during Sports Activities.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002181

By:

Yokoyama, Keiko;
Yamamoto, Yuji

Publication type:

Article

Computational Modeling of Allosteric Communication Reveals Organizing Principles of Mutation-Induced Signaling in ABL and EGFR Kinases.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002179

By:

Dixit, Anshuman;
Verkhivker, Gennady M.

Publication type:

Article

Synchronous Chaos and Broad Band Gamma Rhythm in a Minimal Multi-Layer Model of Primary Visual Cortex.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002176

By:

Battaglia, Demian;
Hansel, David

Publication type:

Article

Using Structure to Explore the Sequence Alignment Space of Remote Homologs.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002175

By:

Kuziemko, Andrew;
Honig, Barry;
Petrey, Donald

Publication type:

Article

High-Precision, In Vitro Validation of the Sequestration Mechanism for Generating Ultrasensitive Dose-Response Curves in Regulatory Networks.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002171

By:

Ricci, Francesco;
Valleé-Bélisle, Alexis;
Plaxco, Kevin W.

Publication type:

Article

Identification of a Novel Class of Farnesylation Targets by Structure-Based Modeling of Binding Specificity.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002170

By:

London, Nir;
Lamphear, Corissa L.;
Hougland, James L.;
Fierke, Carol A.;
Schueler-Furman, Ora

Publication type:

Article

Formation of Regulatory Modules by Local Sequence Duplication.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002167

By:

Nourmohammad, Armita;
Lässig, Michael

Publication type:

Article

Hydrophobicity and Charge Shape Cellular Metabolite Concentrations.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002166

By:

Bar-Even, Arren;
Noor, Elad;
Flamholz, Avi;
Buescher, Joerg M.;
Milo, Ron

Publication type:

Article

Model Cortical Association Fields Account for the Time Course and Dependence on Target Complexity of Human Contour Perception.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002162

By:

Gintautas, Vadas;
Ham, Michael I.;
Kunsberg, Benjamin;
Barr, Shawn;
Brumby, Steven P.;
Rasmussen, Craig;
George, John S.;
Nemenman, Ilya;
Bettencourt, Luís M. A.;
Kenyon, Garret T.

Publication type:

Article

Coexistence of Lateral and Co-Tuned Inhibitory Configurations in Cortical Networks.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002161

By:

Levy, Robert B.;
Reyes, Alex D.

Publication type:

Article

A Multi-cell, Multi-scale Model of Vertebrate Segmentation and Somite Formation.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002155

By:

Hester, Susan D.;
Belmonte, Julio M.;
Gens, J. Scott;
Clendenon, Sherry G.;
Glazier, James A.

Publication type:

Article

Change in Allosteric Network Affects Binding Affinities of PDZ Domains: Analysis through Perturbation Response Scanning.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002154

By:

Gerek, Z. Nevin;
Ozkan, S. Banu

Publication type:

Article

Conflicting Biomedical Assumptions for Mathematical Modeling: The Case of Cancer Metastasis.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002132

By:

Divoli, Anna;
Mendonça, Eneida A.;
Evans, James A.;
Rzhetsky, Andrey

Publication type:

Article

Coupled Information Diffusion-Pest Dynamics Models Predict Delayed Benefits of Farmer Cooperation in Pest Management Programs.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002222

By:

Rebaudo, François;
Dangles, Olivier

Publication type:

Article

Bacteria Modulate the CD8+ T Cell Epitope Repertoire of Host Cytosol-Exposed Proteins to Manipulate the Host Immune Response.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002220

By:

Maman, Yaakov;
Nir-Paz, Ran;
Louzoun, Yoram

Publication type:

Article

Thousands of Rab GTPases for the Cell Biologist.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002217

By:

Diekmann, Yoan;
Seixas, Elsa;
Gouw, Marc;
Tavares-Cadete, Filipe;
Seabra, Miguel C.;
Pereira-Leal, José B.

Publication type:

Article

Modelling Reveals Kinetic Advantages of Co-Transcriptional Splicing.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002215

By:

Aitken, Stuart;
Alexander, Ross D.;
Beggs, Jean D.

Publication type:

Article

Chemical Basis of Metabolic Network Organization.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002214

By:

Zhu, Qiang;
Qin, Tao;
Jiang, Ying-Ying;
Ji, Cong;
Kong, De-Xin;
Ma, Bin-Guang;
Zhang, Hong-Yu

Publication type:

Article

Number and Size Distribution of Colorectal Adenomas under the Multistage Clonal Expansion Model of Cancer.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002213

By:

Dewanji, Anup;
Jeon, Jihyoun;
Meza, Rafael;
Luebeck, E. Georg

Publication type:

Article

Computation of Steady-State Probability Distributions in Stochastic Models of Cellular Networks.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002209

By:

Hallen, Mark;
Li, Bochong;
Tanouchi, Yu;
Tan, Cheemeng;
West, Mike;
You, Lingchong

Publication type:

Article

Brain Rhythms Reveal a Hierarchical Network Organization.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002207

By:

Steinke, G. Karl;
Galán, Roberto F.

Publication type:

Article

The Dynamics of Supply and Demand in mRNA Translation.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002203

By:

Brackley, Chris A.;
Romano, M. Carmen;
Thiel, Marco

Publication type:

Article

Assessing Vaccination Sentiments with Online Social Media: Implications for Infectious Disease Dynamics and Control.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002199

By:

Salathé, Marcel;
Khandelwal, Shashank

Publication type:

Article

Ligand-Induced Modulation of the Free-Energy Landscape of G Protein-Coupled Receptors Explored by Adaptive Biasing Techniques.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002193

By:

Provasi, Davide;
Artacho, Marta Camacho;
Negri, Ana;
Mobarec, Juan Carlos;
Filizola, Marta

Publication type:

Article

Quantifying Intramolecular Binding in Multivalent Interactions: A Structure-Based Synergistic Study on Grb2-Sos1 Complex.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002192

By:

Sethi, Anurag;
Goldstein, Byron;
Gnanakaran, S.

Publication type:

Article

Identification of Potent EGFR Inhibitors from TCM Database@Taiwan.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002189

By:

Yang, Shun-Chieh;
Chang, Su-Sen;
Chen, Hsin-Yi;
Chen, Calvin Yu-Chian

Publication type:

Article

Neural Computation via Neural Geometry: A Place Code for Inter-whisker Timing in the Barrel Cortex?

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002188

By:

Wilson, Stuart P.;
Bednar, James A.;
Prescott, Tony J.;
Mitchinson, Ben

Publication type:

Article

Heat Shock Partially Dissociates the Overlapping Modules of the Yeast Protein-Protein Interaction Network: A Systems Level Model of Adaptation.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002187

By:

Mihalik, Ágoston;
Csermely, Peter

Publication type:

Article

Transmission Selects for HIV-1 Strains of Intermediate Virulence: A Modelling Approach.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002185

By:

Shirreff, George;
Pellis, Lorenzo;
Laeyendecker, Oliver;
Fraser, Christophe

Publication type:

Article

Evidence for Composite Cost Functions in Arm Movement Planning: An Inverse Optimal Control Approach.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002183

By:

Berret, Bastien;
Chiovetto, Enrico;
Nori, Francesco;
Pozzo, Thierry

Publication type:

Article

Barriers to Diffusion in Dendrites and Estimation of Calcium Spread Following Synaptic Inputs.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002182

By:

Biess, Armin;
Korkotian, Eduard;
Holcman, David

Publication type:

Article

Large-Scale Conformational Changes of Trypanosoma cruzi Proline Racemase Predicted by Accelerated Molecular Dynamics Simulation.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002178

By:

de Oliveira, Cé sar Augusto F.;
Grant, Barry J.;
Zhou, Michelle;
McCammon, J. Andrew

Publication type:

Article

Inversion of the Balance between Hydrophobic and Hydrogen Bonding Interactions in Protein Folding and Aggregation.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002169

By:

Fitzpatrick, Anthony W.;
Knowles, Tuomas P. J.;
Waudby, Christopher A.;
Vendruscolo, Michele;
Dobson, Christopher M.

Publication type:

Article

A Peptide Filtering Relation Quantifies MHC Class I Peptide Optimization.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002144

By:

Dalchau, Neil;
Phillips, Andrew;
Goldstein, Leonard D.;
Howarth, Mark;
Cardelli, Luca;
Emmott, Cardelli;
Elliott, Tim;
Werner, Joern M.

Publication type:

Article

The Effects of Dominance on Leadership and Energetic Gain: A Dynamic Game between Pairs of Social Foragers.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002252

By:

Rands, Sean A.

Publication type:

Article

Representation of Dynamical Stimuli in Populations of Threshold Neurons.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002239

By:

Tchumatchenko, Tatjana;
Wolf, Fred

Publication type:

Article

Decoding Complex Chemical Mixtures with a Physical Model of a Sensor Array.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002224

By:

Tsitron, Julia;
Ault, Addison D.;
Broach, James R.;
Morozov, Alexandre V.

Publication type:

Article

A Neurodynamic Account of Spontaneous Behaviour.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002221

By:

Namikawa, Jun;
Nishimoto, Ryunosuke;
Tani, Jun

Publication type:

Article

Transmembrane Helix Dynamics of Bacterial Chemoreceptors Supports a Piston Model of Signalling.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002204

By:

Hall, Benjamin A.;
Armitage, Judith P.;
Sansom, Mark S. P.

Publication type:

Article

NHE Inhibition Does Not Improve Na<sup>+</sup> or Ca<sup>2+</sup> Overload During Reperfusion: Using Modeling to Illuminate the Mechanisms Underlying a Therapeutic Failure.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002241

By:

Roberts, Byron N.;
Christini, David J.

Publication type:

Article

Most Random Gene Expression Signatures Are Significantly Associated with Breast Cancer Outcome.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002240

By:

Venet, David;
Dumont, Jacques E.;
Detours, Vincent

Publication type:

Article

Accelerated Profile HMM Searches.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002195

By:

Eddy, Sean R.

Publication type:

Article

Ensemble-Based Computational Approach Discriminates Functional Activity of p53 Cancer and Rescue Mutants.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002238

By:

Demir, Özlem;
Baronio, Roberta;
Salehi, Faezeh;
Wassman, Christopher D.;
Hall, Linda;
Hatfield, G. Wesley;
Chamberlin, Richard;
Kaiser, Peter;
Lathrop, Richard H.;
Amaro, Rommie E.

Publication type:

Article

Explaining Observed Infection and Antibody Age-Profiles in Populations with Urogenital Schistosomiasis.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002237

By:

Mitchell, Kate M.;
Mutapi, Francisca;
Savill, Nicholas J.;
Woolhouse, Mark E. J.

Publication type:

Article

Integrated Information Increases with Fitness in the Evolution of Animats.

Published in:

PLoS Computational Biology, 2011, v. 7, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002236

By:

Edlund, Jeffrey A.;
Chaumont, Nicolas;
Hintze, Arend;
Koch, Christof;
Tononi, Giulio;
Adami, Christoph

Publication type:

Article