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Volume 8(5);  May 2012
Education
Crossing Over…Markov Meets Mendel
Saad Mneimneh
PLoS Comput Biol. 2012 May; 8(5): e1002462. Published online 2012 May 17. doi: 10.1371/journal.pcbi.1002462
PMCID:
PMC3355070
Abstract Full Text PDF–397K
Simulation of Molecular Data under Diverse Evolutionary Scenarios
Miguel Arenas
PLoS Comput Biol. 2012 May; 8(5): e1002495. Published online 2012 May 31. doi: 10.1371/journal.pcbi.1002495
PMCID:
PMC3364941
Full Text PDF–345K
Accessible High-Throughput Virtual Screening Molecular Docking Software for Students and Educators
Reed B. Jacob, Tim Andersen, Owen M. McDougal
PLoS Comput Biol. 2012 May; 8(5): e1002499. Published online 2012 May 31. doi: 10.1371/journal.pcbi.1002499
PMCID:
PMC3364939
Abstract Full Text PDF–190K
Message from ISCB
International Society for Computational Biology Honours Gunnar von Heijne and Ziv Bar-Joseph with Top Bioinformatics/Computational Biology Awards for 2012
Justin Mullins, BJ. Morrison McKay
PLoS Comput Biol. 2012 May; 8(5): e1002535. Published online 2012 May 31. doi: 10.1371/journal.pcbi.1002535
PMCID:
PMC3364933
Full Text PDF–620K
Research Articles
Challenges and New Approaches to Proving the Existence of Muscle Synergies of Neural Origin
Jason J. Kutch, Francisco J. Valero-Cuevas
PLoS Comput Biol. 2012 May; 8(5): e1002434. Published online 2012 May 3. doi: 10.1371/journal.pcbi.1002434
PMCID:
PMC3342930
Abstract Full Text PDF–2.7M
Adhesion Failures Determine the Pattern of Choroidal Neovascularization in the Eye: A Computer Simulation Study
Abbas Shirinifard, James Alexander Glazier, Maciej Swat, J. Scott Gens, Fereydoon Family, Yi Jiang, Hans E. Grossniklaus
PLoS Comput Biol. 2012 May; 8(5): e1002440. Published online 2012 May 3. doi: 10.1371/journal.pcbi.1002440
PMCID:
PMC3342931
Abstract Full Text PDF–10M Supplementary Material
Termination of Ca2+ Release for Clustered IP3R Channels
Sten Rüdiger, Peter Jung, Jian-Wei Shuai
PLoS Comput Biol. 2012 May; 8(5): e1002485. Published online 2012 May 31. doi: 10.1371/journal.pcbi.1002485
PMCID:
PMC3364945
Abstract Full Text PDF–1.7M Supplementary Material
NIBBS-Search for Fast and Accurate Prediction of Phenotype-Biased Metabolic Systems
Matthew C. Schmidt, Andrea M. Rocha, Kanchana Padmanabhan, Yekaterina Shpanskaya, Jill Banfield, Kathleen Scott, James R. Mihelcic, Nagiza F. Samatova
PLoS Comput Biol. 2012 May; 8(5): e1002490. Published online 2012 May 10. doi: 10.1371/journal.pcbi.1002490
PMCID:
PMC3349732
Abstract Full Text PDF–771K Supplementary Material
Homeostatic Scaling of Excitability in Recurrent Neural Networks
Michiel W. H. Remme, Wytse J. Wadman
PLoS Comput Biol. 2012 May; 8(5): e1002494. Published online 2012 May 3. doi: 10.1371/journal.pcbi.1002494
PMCID:
PMC3342932
Abstract Full Text PDF–813K
Modeling Meiotic Chromosomes Indicates a Size Dependent Contribution of Telomere Clustering and Chromosome Rigidity to Homologue Juxtaposition
Christopher A. Penfold, Paul E. Brown, Neil D. Lawrence, Alastair S. H. Goldman
PLoS Comput Biol. 2012 May; 8(5): e1002496. Published online 2012 May 3. doi: 10.1371/journal.pcbi.1002496
PMCID:
PMC3342934
Abstract Full Text PDF–1.5M Supplementary Material
Intermittent Motion in Desert Locusts: Behavioural Complexity in Simple Environments
Sepideh Bazazi, Frederic Bartumeus, Joseph J. Hale, Iain D. Couzin
PLoS Comput Biol. 2012 May; 8(5): e1002498. Published online 2012 May 10. doi: 10.1371/journal.pcbi.1002498
PMCID:
PMC3349720
Abstract Full Text PDF–798K Supplementary Material
A Spatial Model of Mosquito Host-Seeking Behavior
Bree Cummins, Ricardo Cortez, Ivo M. Foppa, Justin Walbeck, James M. Hyman
PLoS Comput Biol. 2012 May; 8(5): e1002500. Published online 2012 May 17. doi: 10.1371/journal.pcbi.1002500
PMCID:
PMC3355069
Abstract Full Text PDF–872K
Virus Capsid Dissolution Studied by Microsecond Molecular Dynamics Simulations
Daniel S. D. Larsson, Lars Liljas, David van der Spoel
PLoS Comput Biol. 2012 May; 8(5): e1002502. Published online 2012 May 10. doi: 10.1371/journal.pcbi.1002502
PMCID:
PMC3349721
Abstract Full Text PDF–2.1M
Prediction of Drug-Target Interactions and Drug Repositioning via Network-Based Inference
Feixiong Cheng, Chuang Liu, Jing Jiang, Weiqiang Lu, Weihua Li, Guixia Liu, Weixing Zhou, Jin Huang, Yun Tang
PLoS Comput Biol. 2012 May; 8(5): e1002503. Published online 2012 May 10. doi: 10.1371/journal.pcbi.1002503
PMCID:
PMC3349722
Abstract Full Text PDF–1.5M Supplementary Material
Insights into the Fold Organization of TIM Barrel from Interaction Energy Based Structure Networks
M. S. Vijayabaskar, Saraswathi Vishveshwara
PLoS Comput Biol. 2012 May; 8(5): e1002505. Published online 2012 May 17. doi: 10.1371/journal.pcbi.1002505
PMCID:
PMC3355060
Abstract Full Text PDF–1.8M Supplementary Material
Filament Compliance Influences Cooperative Activation of Thin Filaments and the Dynamics of Force Production in Skeletal Muscle
Bertrand C. W. Tanner, Thomas L. Daniel, Michael Regnier
PLoS Comput Biol. 2012 May; 8(5): e1002506. Published online 2012 May 10. doi: 10.1371/journal.pcbi.1002506
PMCID:
PMC3349719
Abstract Full Text PDF–834K Supplementary Material
Modeling HIV-1 Drug Resistance as Episodic Directional Selection
Ben Murrell, Tulio de Oliveira, Chris Seebregts, Sergei L. Kosakovsky Pond, Konrad Scheffler, on behalf of the Southern African Treatment and Resistance Network (SATuRN) Consortium
PLoS Comput Biol. 2012 May; 8(5): e1002507. Published online 2012 May 10. doi: 10.1371/journal.pcbi.1002507
PMCID:
PMC3349733
Abstract Full Text PDF–223K Supplementary Material
Optimal Control of Saccades by Spatial-Temporal Activity Patterns in the Monkey Superior Colliculus
H. H. L. M. Goossens, A. J. van Opstal
PLoS Comput Biol. 2012 May; 8(5): e1002508. Published online 2012 May 17. doi: 10.1371/journal.pcbi.1002508
PMCID:
PMC3355059
Abstract Full Text PDF–3.4M Supplementary Material
Dynamic Prestress in a Globular Protein
Scott A. Edwards, Johannes Wagner, Frauke Gräter
PLoS Comput Biol. 2012 May; 8(5): e1002509. Published online 2012 May 10. doi: 10.1371/journal.pcbi.1002509
PMCID:
PMC3349725
Abstract Full Text PDF–1.1M Supplementary Material
Google Goes Cancer: Improving Outcome Prediction for Cancer Patients by Network-Based Ranking of Marker Genes
Christof Winter, Glen Kristiansen, Stephan Kersting, Janine Roy, Daniela Aust, Thomas Knösel, Petra Rümmele, Beatrix Jahnke, Vera Hentrich, Felix Rückert, Marco Niedergethmann, Wilko Weichert, Marcus Bahra, Hans J. Schlitt, Utz Settmacher, Helmut Friess, Markus Büchler, Hans-Detlev Saeger, Michael Schroeder, Christian Pilarsky, Robert Grützmann
PLoS Comput Biol. 2012 May; 8(5): e1002511. Published online 2012 May 17. doi: 10.1371/journal.pcbi.1002511
PMCID:
PMC3355064
Abstract Full Text PDF–548K Supplementary Material
Mechanical Stress Inference for Two Dimensional Cell Arrays
Kevin K. Chiou, Lars Hufnagel, Boris I. Shraiman
PLoS Comput Biol. 2012 May; 8(5): e1002512. Published online 2012 May 17. doi: 10.1371/journal.pcbi.1002512
PMCID:
PMC3355066
Abstract Full Text PDF–1.0M Supplementary Material
Measuring Granger Causality between Cortical Regions from Voxelwise fMRI BOLD Signals with LASSO
Wei Tang, Steven L. Bressler, Chad M. Sylvester, Gordon L. Shulman, Maurizio Corbetta
PLoS Comput Biol. 2012 May; 8(5): e1002513. Published online 2012 May 24. doi: 10.1371/journal.pcbi.1002513
PMCID:
PMC3359965
Abstract Full Text PDF–2.6M Supplementary Material
Resolving the Ortholog Conjecture: Orthologs Tend to Be Weakly, but Significantly, More Similar in Function than Paralogs
Adrian M. Altenhoff, Romain A. Studer, Marc Robinson-Rechavi, Christophe Dessimoz
PLoS Comput Biol. 2012 May; 8(5): e1002514. Published online 2012 May 17. doi: 10.1371/journal.pcbi.1002514
PMCID:
PMC3355068
Abstract Full Text PDF–700K Supplementary Material
A Two-Dimensional Model of the Colonic Crypt Accounting for the Role of the Basement Membrane and Pericryptal Fibroblast Sheath
Sara-Jane Dunn, Paul L. Appleton, Scott A. Nelson, Inke S. Näthke, David J. Gavaghan, James M. Osborne
PLoS Comput Biol. 2012 May; 8(5): e1002515. Published online 2012 May 24. doi: 10.1371/journal.pcbi.1002515
PMCID:
PMC3359972
Abstract Full Text PDF–3.4M Supplementary Material
Entrainment of the Mammalian Cell Cycle by the Circadian Clock: Modeling Two Coupled Cellular Rhythms
Claude Gérard, Albert Goldbeter
PLoS Comput Biol. 2012 May; 8(5): e1002516. Published online 2012 May 31. doi: 10.1371/journal.pcbi.1002516
PMCID:
PMC3364934
Abstract Full Text PDF–4.2M
Proteome Sampling by the HLA Class I Antigen Processing Pathway
Ilka Hoof, Debbie van Baarle, William H. Hildebrand, Can Keşmir
PLoS Comput Biol. 2012 May; 8(5): e1002517. Published online 2012 May 17. doi: 10.1371/journal.pcbi.1002517
PMCID:
PMC3355062
Abstract Full Text PDF–374K Supplementary Material
Reconstruction of Genome-Scale Active Metabolic Networks for 69 Human Cell Types and 16 Cancer Types Using INIT
Rasmus Agren, Sergio Bordel, Adil Mardinoglu, Natapol Pornputtapong, Intawat Nookaew, Jens Nielsen
PLoS Comput Biol. 2012 May; 8(5): e1002518. Published online 2012 May 17. doi: 10.1371/journal.pcbi.1002518
PMCID:
PMC3355067
Abstract Full Text PDF–472K Supplementary Material
Optimality of Human Contour Integration
Udo A. Ernst, Sunita Mandon, Nadja Schinkel–Bielefeld, Simon D. Neitzel, Andreas K. Kreiter, Klaus R. Pawelzik
PLoS Comput Biol. 2012 May; 8(5): e1002520. Published online 2012 May 24. doi: 10.1371/journal.pcbi.1002520
PMCID:
PMC3360074
Abstract Full Text PDF–962K
The Layer-Oriented Approach to Declarative Languages for Biological Modeling
Ivan Raikov, Erik De Schutter
PLoS Comput Biol. 2012 May; 8(5): e1002521. Published online 2012 May 17. doi: 10.1371/journal.pcbi.1002521
PMCID:
PMC3355071
Abstract Full Text PDF–922K Supplementary Material
Emergence of a Small-World Functional Network in Cultured Neurons
Julia H. Downes, Mark W. Hammond, Dimitris Xydas, Matthew C. Spencer, Victor M. Becerra, Kevin Warwick, Ben J. Whalley, Slawomir J. Nasuto
PLoS Comput Biol. 2012 May; 8(5): e1002522. Published online 2012 May 17. doi: 10.1371/journal.pcbi.1002522
PMCID:
PMC3355061
Abstract Full Text PDF–1.2M Supplementary Material
Conformational Spread in the Flagellar Motor Switch: A Model Study
Qi Ma, Dan V. Nicolau, Jr, Philip K. Maini, Richard M. Berry, Fan Bai
PLoS Comput Biol. 2012 May; 8(5): e1002523. Published online 2012 May 24. doi: 10.1371/journal.pcbi.1002523
PMCID:
PMC3359969
Abstract Full Text PDF–1.8M
Identification of Molecular Pathologies Sufficient to Cause Neuropathic Excitability in Primary Somatosensory Afferents Using Dynamical Systems Theory
Young-Ah Rho, Steven A. Prescott
PLoS Comput Biol. 2012 May; 8(5): e1002524. Published online 2012 May 24. doi: 10.1371/journal.pcbi.1002524
PMCID:
PMC3359967
Abstract Full Text PDF–2.1M Supplementary Material
Estimating the Fitness Cost of Escape from HLA Presentation in HIV-1 Protease and Reverse Transcriptase
Rafal Mostowy, Roger D. Kouyos, Ilka Hoof, Trevor Hinkley, Mojgan Haddad, Jeannette M. Whitcomb, Christos J. Petropoulos, Can Keşmir, Sebastian Bonhoeffer
PLoS Comput Biol. 2012 May; 8(5): e1002525. Published online 2012 May 24. doi: 10.1371/journal.pcbi.1002525
PMCID:
PMC3359966
Abstract Full Text PDF–665K Supplementary Material
Network Topologies and Dynamics Leading to Endotoxin Tolerance and Priming in Innate Immune Cells
Yan Fu, Trevor Glaros, Meng Zhu, Ping Wang, Zhanghan Wu, John J. Tyson, Liwu Li, Jianhua Xing
PLoS Comput Biol. 2012 May; 8(5): e1002526. Published online 2012 May 17. doi: 10.1371/journal.pcbi.1002526
PMCID:
PMC3355072
Abstract Full Text PDF–2.0M Supplementary Material
Exploring Massive, Genome Scale Datasets with the GenometriCorr Package
Alexander Favorov, Loris Mularoni, Leslie M. Cope, Yulia Medvedeva, Andrey A. Mironov, Vsevolod J. Makeev, Sarah J. Wheelan
PLoS Comput Biol. 2012 May; 8(5): e1002529. Published online 2012 May 31. doi: 10.1371/journal.pcbi.1002529
PMCID:
PMC3364938
Abstract Full Text PDF–2.1M
A Computational Investigation on the Connection between Dynamics Properties of Ribosomal Proteins and Ribosome Assembly
Brittany Burton, Michael T. Zimmermann, Robert L. Jernigan, Yongmei Wang
PLoS Comput Biol. 2012 May; 8(5): e1002530. Published online 2012 May 24. doi: 10.1371/journal.pcbi.1002530
PMCID:
PMC3359968
Abstract Full Text PDF–2.7M Supplementary Material
General Anesthetics Predicted to Block the GLIC Pore with Micromolar Affinity
David N. LeBard, Jérôme Hénin, Roderic G. Eckenhoff, Michael L. Klein, Grace Brannigan
PLoS Comput Biol. 2012 May; 8(5): e1002532. Published online 2012 May 31. doi: 10.1371/journal.pcbi.1002532
PMCID:
PMC3364936
Abstract Full Text PDF–270K Supplementary Material
Quality of Computationally Inferred Gene Ontology Annotations
Nives Škunca, Adrian Altenhoff, Christophe Dessimoz
PLoS Comput Biol. 2012 May; 8(5): e1002533. Published online 2012 May 31. doi: 10.1371/journal.pcbi.1002533
PMCID:
PMC3364937
Abstract Full Text PDF–3.8M Supplementary Material
Thermodynamic Basis for the Emergence of Genomes during Prebiotic Evolution
Hyung-June Woo, Ravi Vijaya Satya, Jaques Reifman
PLoS Comput Biol. 2012 May; 8(5): e1002534. Published online 2012 May 31. doi: 10.1371/journal.pcbi.1002534
PMCID:
PMC3364946
Abstract Full Text PDF–1.3M
The CanOE Strategy: Integrating Genomic and Metabolic Contexts across Multiple Prokaryote Genomes to Find Candidate Genes for Orphan Enzymes
Adam Alexander Thil Smith, Eugeni Belda, Alain Viari, Claudine Medigue, David Vallenet
PLoS Comput Biol. 2012 May; 8(5): e1002540. Published online 2012 May 31. doi: 10.1371/journal.pcbi.1002540
PMCID:
PMC3364942
Abstract Full Text PDF–1.1M Supplementary Material
Structure and Age Jointly Influence Rates of Protein Evolution
Macarena Toll-Riera, David Bostick, M. Mar Albà, Joshua B. Plotkin
PLoS Comput Biol. 2012 May; 8(5): e1002542. Published online 2012 May 31. doi: 10.1371/journal.pcbi.1002542
PMCID:
PMC3364943
Abstract Full Text PDF–364K Supplementary Material
Corrections
Correction: Automatic Filtering and Substantiation of Drug Safety Signals
Anna Bauer-Mehren, Erik M. van Mullingen, Paul Avillach, María del Carmen Carrascosa, Ricard Garcia-Serna, Janet Piñero, Bharat Singh, Pedro Lopes, José L. Oliveira, Gayo Diallo, Ernst Ahlberg Helgee, Scott Boyer, Jordi Mestres, Ferran Sanz, Jan A. Kors, Laura I. Furlong
PLoS Comput Biol. 2012 May; 8(5): 10.1371/annotation/695450aa-95a0-491d-804d-470cbfa861e8. Published online 2012 May 4. doi: 10.1371/annotation/695450aa-95a0-491d-804d-470cbfa861e8
Corrects:
PLoS Comput Biol. 2012 April; 8(4): e1002457.
PMCID:
PMC3344945
Correction Original Article
Correction: Differences in Cell Division Rates Drive the Evolution of Terminal Differentiation in Microbes
João F. Matias Rodrigues, Daniel J. Rankin, Valentina Rossetti, Andreas Wagner, Homayoun C. Bagheri
PLoS Comput Biol. 2012 May; 8(5): 10.1371/annotation/cea2d6e3-28ce-4284-84d1-08e9453e773e. Published online 2012 May 17. doi: 10.1371/annotation/cea2d6e3-28ce-4284-84d1-08e9453e773e
Corrects:
PLoS Comput Biol. 2012 April; 8(4): e1002468.
PMCID:
PMC3359375
Correction Original Article
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