May 2012

Fluorescently stained wholemount of mouse small intestine. A single confocal optical section at the base of the crypts is stained to show nuclei (blue), F-actin (red), and intestinal stem cells (green). Actin-rich smooth muscle fibres forming the muscular mucosae appear as a meshwork around the crypt bases. Lgr5 positive stem cells labelled with green fluorescent protein are found only in the crypt bases. See Dunn, et al. (10.1371/journal.pcbi.1002515).

Image Credit: Paul Appleton, College of Life Sciences, University of Dundee.

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 Computational Biology: published May 31, 2012 | https://doi.org/10.1371/journal.pcbi.1002535

Education Articles

Simulation of Molecular Data under Diverse Evolutionary Scenarios

Miguel Arenas

PLOS Computational Biology: published May 31, 2012 | https://doi.org/10.1371/journal.pcbi.1002495

Accessible High-Throughput Virtual Screening Molecular Docking Software for Students and Educators

Reed B. Jacob, Tim Andersen, Owen M. McDougal

PLOS Computational Biology: published May 31, 2012 | https://doi.org/10.1371/journal.pcbi.1002499

Crossing Over…Markov Meets Mendel

Saad Mneimneh

PLOS Computational Biology: published May 17, 2012 | https://doi.org/10.1371/journal.pcbi.1002462

Research Articles

Termination of Ca²⁺ Release for Clustered IP₃R Channels

Sten Rüdiger, Peter Jung, Jian-Wei Shuai

PLOS Computational Biology: published May 31, 2012 | https://doi.org/10.1371/journal.pcbi.1002485

Entrainment of the Mammalian Cell Cycle by the Circadian Clock: Modeling Two Coupled Cellular Rhythms

Claude Gérard, Albert Goldbeter

PLOS Computational Biology: published May 31, 2012 | https://doi.org/10.1371/journal.pcbi.1002516

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 Computational Biology: published May 31, 2012 | https://doi.org/10.1371/journal.pcbi.1002529

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 Computational Biology: published May 31, 2012 | https://doi.org/10.1371/journal.pcbi.1002532

Quality of Computationally Inferred Gene Ontology Annotations

Nives Škunca, Adrian Altenhoff, Christophe Dessimoz

PLOS Computational Biology: published May 31, 2012 | https://doi.org/10.1371/journal.pcbi.1002533

Thermodynamic Basis for the Emergence of Genomes during Prebiotic Evolution

Hyung-June Woo, Ravi Vijaya Satya, Jaques Reifman

PLOS Computational Biology: published May 31, 2012 | https://doi.org/10.1371/journal.pcbi.1002534

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 Computational Biology: published May 31, 2012 | https://doi.org/10.1371/journal.pcbi.1002540

Structure and Age Jointly Influence Rates of Protein Evolution

Macarena Toll-Riera, David Bostick, M. Mar Albà, Joshua B. Plotkin

PLOS Computational Biology: published May 31, 2012 | https://doi.org/10.1371/journal.pcbi.1002542

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 Computational Biology: published May 24, 2012 | https://doi.org/10.1371/journal.pcbi.1002513

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 Computational Biology: published May 24, 2012 | https://doi.org/10.1371/journal.pcbi.1002515

Optimality of Human Contour Integration

Udo A. Ernst, Sunita Mandon, Nadja Schinkel–Bielefeld, Simon D. Neitzel, Andreas K. Kreiter, Klaus R. Pawelzik

PLOS Computational Biology: published May 24, 2012 | https://doi.org/10.1371/journal.pcbi.1002520

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 Computational Biology: published May 24, 2012 | https://doi.org/10.1371/journal.pcbi.1002523

Identification of Molecular Pathologies Sufficient to Cause Neuropathic Excitability in Primary Somatosensory Afferents Using Dynamical Systems Theory

Young-Ah Rho, Steven A. Prescott

PLOS Computational Biology: published May 24, 2012 | https://doi.org/10.1371/journal.pcbi.1002524

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 Computational Biology: published May 24, 2012 | https://doi.org/10.1371/journal.pcbi.1002525

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 Computational Biology: published May 24, 2012 | https://doi.org/10.1371/journal.pcbi.1002530

A Spatial Model of Mosquito Host-Seeking Behavior

Bree Cummins, Ricardo Cortez, Ivo M. Foppa, Justin Walbeck, James M. Hyman

PLOS Computational Biology: published May 17, 2012 | https://doi.org/10.1371/journal.pcbi.1002500

Insights into the Fold Organization of TIM Barrel from Interaction Energy Based Structure Networks

M. S. Vijayabaskar, Saraswathi Vishveshwara

PLOS Computational Biology: published May 17, 2012 | https://doi.org/10.1371/journal.pcbi.1002505

Optimal Control of Saccades by Spatial-Temporal Activity Patterns in the Monkey Superior Colliculus

H. H. L. M. Goossens, A. J. van Opstal

PLOS Computational Biology: published May 17, 2012 | https://doi.org/10.1371/journal.pcbi.1002508

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 Computational Biology: published May 17, 2012 | https://doi.org/10.1371/journal.pcbi.1002511

Mechanical Stress Inference for Two Dimensional Cell Arrays

Kevin K. Chiou, Lars Hufnagel, Boris I. Shraiman

PLOS Computational Biology: published May 17, 2012 | https://doi.org/10.1371/journal.pcbi.1002512

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 Computational Biology: published May 17, 2012 | https://doi.org/10.1371/journal.pcbi.1002514

Proteome Sampling by the HLA Class I Antigen Processing Pathway

Ilka Hoof, Debbie van Baarle, William H. Hildebrand, Can Keşmir

PLOS Computational Biology: published May 17, 2012 | https://doi.org/10.1371/journal.pcbi.1002517

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 Computational Biology: published May 17, 2012 | https://doi.org/10.1371/journal.pcbi.1002518

The Layer-Oriented Approach to Declarative Languages for Biological Modeling

Ivan Raikov, Erik De Schutter

PLOS Computational Biology: published May 17, 2012 | https://doi.org/10.1371/journal.pcbi.1002521

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 Computational Biology: published May 17, 2012 | https://doi.org/10.1371/journal.pcbi.1002522

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 Computational Biology: published May 17, 2012 | https://doi.org/10.1371/journal.pcbi.1002526

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 Computational Biology: published May 10, 2012 | https://doi.org/10.1371/journal.pcbi.1002490

Intermittent Motion in Desert Locusts: Behavioural Complexity in Simple Environments

Sepideh Bazazi, Frederic Bartumeus, Joseph J. Hale, Iain D. Couzin

PLOS Computational Biology: published May 10, 2012 | https://doi.org/10.1371/journal.pcbi.1002498

Virus Capsid Dissolution Studied by Microsecond Molecular Dynamics Simulations

Daniel S. D. Larsson, Lars Liljas, David van der Spoel

PLOS Computational Biology: published May 10, 2012 | https://doi.org/10.1371/journal.pcbi.1002502

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 Computational Biology: published May 10, 2012 | https://doi.org/10.1371/journal.pcbi.1002503

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 Computational Biology: published May 10, 2012 | https://doi.org/10.1371/journal.pcbi.1002506

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 Computational Biology: published May 3, 2012 | https://doi.org/10.1371/journal.pcbi.1002496

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Stem cells in small intestinal crypts

Message from ISCB

Education Articles

Research Articles