Works in PLoS Computational Biology, 2013, Vol 9, Issue 10

Results: 59

Lipid Receptor S1P1 Activation Scheme Concluded from Microsecond All-Atom Molecular Dynamics Simulations.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003261

By:

Yuan, Shuguang;
Wu, Rongliang;
Latek, Dorota;
Trzaskowski, Bartosz;
Filipek, Slawomir

Publication type:

Article

Deciding Not to Decide: Computational and Neural Evidence for Hidden Behavior in Sequential Choice.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003309

By:

Gluth, Sebastian;
Rieskamp, Jörg;
Büchel, Christian

Publication type:

Article

Natural, Persistent Oscillations in a Spatial Multi-Strain Disease System with Application to Dengue.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003308

By:

Lourenço, José;
Recker, Mario

Publication type:

Article

Swimming in Light: A Large-Scale Computational Analysis of the Metabolism of Dinoroseobacter shibae.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003224

By:

Rex, Rene;
Bill, Nelli;
Schmidt-Hohagen, Kerstin;
Schomburg, Dietmar

Publication type:

Article

Synaptic Scaling Enables Dynamically Distinct Short- and Long-Term Memory Formation.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003307

By:

Tetzlaff, Christian;
Kolodziejski, Christoph;
Timme, Marc;
Tsodyks, Misha;
Wörgötter, Florentin

Publication type:

Article

Thermal Adaptation of Conformational Dynamics in Ribonuclease H.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003218

By:

Stafford, Kate A.;
Robustelli, Paul;
Palmer, III, Arthur G.

Publication type:

Article

APBioNet—Transforming Bioinformatics in the Asia-Pacific Region.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003317

By:

Khan, Asif M.;
Tan, Tin Wee;
Schönbach, Christian;
Ranganathan, Shoba

Publication type:

Article

Conformational Changes in Talin on Binding to Anionic Phospholipid Membranes Facilitate Signaling by Integrin Transmembrane Helices.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003316

By:

Kalli, Antreas C.;
Campbell, Iain D.;
Sansom, Mark S. P.

Publication type:

Article

Dynamic Rendering of the Heterogeneous Cell Response to Anticancer Treatments.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003293

By:

Falcetta, Francesca;
Lupi, Monica;
Colombo, Valentina;
Ubezio, Paolo

Publication type:

Article

Explain Bioinformatics to Your Grandmother!

Published in:

PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003305

By:

Bernard, Virginie;
Michaut, Magali

Publication type:

Article

A Genome-Scale Integration and Analysis of Lactococcus lactis Translation Data.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003240

By:

Racle, Julien;
Picard, Flora;
Girbal, Laurence;
Cocaign-Bousquet, Muriel;
Hatzimanikatis, Vassily

Publication type:

Article

Emergence of Metastable State Dynamics in Interconnected Cortical Networks with Propagation Delays.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003304

By:

Kutchko, Katrina M.;
Fröhlich, Flavio

Publication type:

Article

The Molecular Mechanism of Ion-Dependent Gating in Secondary Transporters.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003296

By:

Zhao, Chunfeng;
Noskov, Sergei Yu.

Publication type:

Article

Reconstructing the Genomic Content of Microbiome Taxa through Shotgun Metagenomic Deconvolution.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003292

By:

Carr, Rogan;
Shen-Orr, Shai S.;
Borenstein, Elhanan

Publication type:

Article

A Comprehensive Survey of Small-Molecule Binding Pockets in Proteins.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003302

By:

Gao, Mu;
Skolnick, Jeffrey

Publication type:

Article

A Complex-Valued Firing-Rate Model That Approximates the Dynamics of Spiking Networks.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003301

By:

Schaffer, Evan S.;
Ostojic, Srdjan;
Abbott, L. F.

Publication type:

Article

Unraveling Adaptation in Eukaryotic Pathways: Lessons from Protocells.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003300

By:

De Palo, Giovanna;
Endres, Robert G.

Publication type:

Article

An Evolution-Based Approach to De Novo Protein Design and Case Study on Mycobacterium tuberculosis.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003298

By:

Mitra, Pralay;
Shultis, David;
Brender, Jeffrey R.;
Czajka, Jeff;
Marsh, David;
Gray, Felicia;
Cierpicki, Tomasz;
Zhang, Yang

Publication type:

Article

A Brain-Machine Interface for Control of Medically-Induced Coma.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003284

By:

Shanechi, Maryam M.;
Chemali, Jessica J.;
Liberman, Max;
Solt, Ken;
Brown, Emery N.

Publication type:

Article

The Convallis Rule for Unsupervised Learning in Cortical Networks.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003272

By:

Yger, Pierre;
Harris, Kenneth D.

Publication type:

Article

On the Role of Aggregation Prone Regions in Protein Evolution, Stability, and Enzymatic Catalysis: Insights from Diverse Analyses.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003291

By:

Buck, Patrick M.;
Kumar, Sandeep;
Singh, Satish K.

Publication type:

Article

Model of Fission Yeast Cell Shape Driven by Membrane-Bound Growth Factors and the Cytoskeleton.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003287

By:

Drake, Tyler;
Vavylonis, Dimitrios

Publication type:

Article

Integrative Modelling of the Influence of MAPK Network on Cancer Cell Fate Decision.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003286

By:

Grieco, Luca;
Calzone, Laurence;
Bernard-Pierrot, Isabelle;
Radvanyi, François;
Kahn-Perlès, Brigitte;
Thieffry, Denis

Publication type:

Article

Ten Simple Rules for Reproducible Computational Research.

Published in:

2013

By:

Sandve, Geir Kjetil;
Nekrutenko, Anton;
Taylor, James;
Hovig, Eivind

Publication type:

Editorial

Reverse-Engineering Post-Transcriptional Regulation of Gap Genes in Drosophila melanogaster.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003281

By:

Becker, Kolja;
Balsa-Canto, Eva;
Cicin-Sain, Damjan;
Hoermann, Astrid;
Janssens, Hilde;
Banga, Julio R.;
Jaeger, Johannes

Publication type:

Article

Comprehensive Repertoire of Foldable Regions within Whole Genomes.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003280

By:

Faure, Guilhem;
Callebaut, Isabelle

Publication type:

Article

Machines vs. Ensembles: Effective MAPK Signaling through Heterogeneous Sets of Protein Complexes.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003278

By:

Suderman, Ryan;
Deeds, Eric J.

Publication type:

Article

Exploring Protein-Peptide Binding Specificity through Computational Peptide Screening.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003277

By:

Bhattacherjee, Arnab;
Wallin, Stefan

Publication type:

Article

Molecular Mechanical Differences between Isoforms of Contractile Actin in the Presence of Isoforms of Smooth Muscle Tropomyosin.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003273

By:

Hilbert, Lennart;
Bates, Genevieve;
Roman, Horia N.;
Blumenthal, Jenna L.;
Zitouni, Nedjma B.;
Sobieszek, Apolinary;
Mackey, Michael C.;
Lauzon, Anne-Marie

Publication type:

Article

Novel Methods for Analysing Bacterial Tracks Reveal Persistence in Rhodobacter sphaeroides.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003276

By:

Rosser, Gabriel;
Fletcher, Alexander G.;
Wilkinson, David A.;
de Beyer, Jennifer A.;
Yates, Christian A.;
Armitage, Judith P.;
Maini, Philip K.;
Baker, Ruth E.

Publication type:

Article

Keeping up with the Joneses: Interpersonal Prediction Errors and the Correlation of Behavior in a Tandem Sequential Choice Task.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003275

By:

Lohrenz, Terry;
Bhatt, Meghana;
Apple, Nathan;
Montague, P. Read

Publication type:

Article

Prediction of the P. falciparum Target Space Relevant to Malaria Drug Discovery.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003257

By:

Spitzmüller, Andreas;
Mestres, Jordi

Publication type:

Article

Reassessing Google Flu Trends Data for Detection of Seasonal and Pandemic Influenza: A Comparative Epidemiological Study at Three Geographic Scales.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003256

By:

Olson, Donald R.;
Konty, Kevin J.;
Paladini, Marc;
Viboud, Cecile;
Simonsen, Lone

Publication type:

Article

CAPE: An R Package for Combined Analysis of Pleiotropy and Epistasis.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003270

By:

Tyler, Anna L.;
Lu, Wei;
Hendrick, Justin J.;
Philip, Vivek M.;
Carter, Gregory W.

Publication type:

Article

Dynamic Change of Global and Local Information Processing in Propofol-Induced Loss and Recovery of Consciousness.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003271

By:

Monti, Martin M.;
Lutkenhoff, Evan S.;
Rubinov, Mikail;
Boveroux, Pierre;
Vanhaudenhuyse, Audrey;
Gosseries, Olivia;
Bruno, Marie-Aurélie;
Noirhomme, Quentin;
Boly, Mélanie;
Laureys, Steven

Publication type:

Article

Inferring Evolutionary Histories of Pathway Regulation from Transcriptional Profiling Data.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003255

By:

Schraiber, Joshua G.;
Mostovoy, Yulia;
Hsu, Tiffany Y.;
Brem, Rachel B.

Publication type:

Article

A Network Approach to Analyzing Highly Recombinant Malaria Parasite Genes.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003268

By:

Larremore, Daniel B.;
Clauset, Aaron;
Buckee, Caroline O.

Publication type:

Article

Analysis of Initial Cell Spreading Using Mechanistic Contact Formulations for a Deformable Cell Model.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003267

By:

Odenthal, Tim;
Smeets, Bart;
Van Liedekerke, Paul;
Tijskens, Engelbert;
Van Oosterwyck, Hans;
Ramon, Herman

Publication type:

Article

Properties of MHC Class I Presented Peptides That Enhance Immunogenicity.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003266

By:

Calis, Jorg J. A.;
Maybeno, Matt;
Greenbaum, Jason A.;
Weiskopf, Daniela;
De Silva, Aruna D.;
Sette, Alessandro;
Keşmir, Can;
Peters, Bjoern

Publication type:

Article

Attention-Dependent Modulation of Cortical Taste Circuits Revealed by Granger Causality with Signal-Dependent Noise.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003265

By:

Luo, Qiang;
Ge, Tian;
Grabenhorst, Fabian;
Feng, Jianfeng;
Rolls, Edmund T.

Publication type:

Article

Virus Encoded MHC-Like Decoys Diversify the Inhibitory KIR Repertoire.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003264

By:

Carrillo-Bustamante, Paola;
Keşmir, Can;
de Boer, Rob J.

Publication type:

Article

Balanced Excitatory and Inhibitory Synaptic Currents Promote Efficient Coding and Metabolic Efficiency.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003263

By:

Sengupta, Biswa;
Laughlin, Simon B.;
Niven, Jeremy E.

Publication type:

Article

How Can PLOS Computational Biology Help the Biological Sciences?

Published in:

PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003262

By:

Nussinov, Ruth

Publication type:

Article

Target Prediction for an Open Access Set of Compounds Active against Mycobacterium tuberculosis.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003253

By:

Martínez-Jiménez, Francisco;
Papadatos, George;
Yang, Lun;
Wallace, Iain M.;
Kumar, Vinod;
Pieper, Ursula;
Sali, Andrej;
Brown, James R.;
Overington, John P.;
Marti-Renom, Marc A.

Publication type:

Article

A Dendritic Mechanism for Decoding Traveling Waves: Principles and Applications to Motor Cortex.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003260

By:

Heitmann, Stewart;
Boonstra, Tjeerd;
Breakspear, Michael

Publication type:

Article

A Simple Rule for Dendritic Spine and Axonal Bouton Formation Can Account for Cortical Reorganization after Focal Retinal Lesions.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003259

By:

Butz, Markus;
van Ooyen, Arjen

Publication type:

Article

Integrated Module and Gene-Specific Regulatory Inference Implicates Upstream Signaling Networks.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003252

By:

Roy, Sushmita;
Lagree, Stephen;
Hou, Zhonggang;
Thomson, James A.;
Stewart, Ron;
Gasch, Audrey P.

Publication type:

Article

The Lazy Visual Word Form Area: Computational Insights into Location-Sensitivity.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003250

By:

Hannagan, Thomas;
Grainger, Jonathan

Publication type:

Article

Feature Selection Methods for Identifying Genetic Determinants of Host Species in RNA Viruses.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003254

By:

Aguas, Ricardo;
Ferguson, Neil M.

Publication type:

Article

A Horizontal Alignment Tool for Numerical Trend Discovery in Sequence Data: Application to Protein Hydropathy.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003247

By:

Hadzipasic, Omar;
Wrabl, James O.;
Hilser, Vincent J.

Publication type:

Article