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
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
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
PLOS Computational Biology: published May 31, 2012 | https://doi.org/10.1371/journal.pcbi.1002499
Crossing Over…Markov Meets Mendel
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
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
PLOS Computational Biology: published May 31, 2012 | https://doi.org/10.1371/journal.pcbi.1002516
Exploring Massive, Genome Scale Datasets with the GenometriCorr Package
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
PLOS Computational Biology: published May 31, 2012 | https://doi.org/10.1371/journal.pcbi.1002532
Quality of Computationally Inferred Gene Ontology Annotations
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
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
PLOS Computational Biology: published May 31, 2012 | https://doi.org/10.1371/journal.pcbi.1002540
Structure and Age Jointly Influence Rates of Protein Evolution
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
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
PLOS Computational Biology: published May 24, 2012 | https://doi.org/10.1371/journal.pcbi.1002515
Optimality of Human Contour Integration
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
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
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
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
PLOS Computational Biology: published May 24, 2012 | https://doi.org/10.1371/journal.pcbi.1002530
A Spatial Model of Mosquito Host-Seeking Behavior
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
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
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
PLOS Computational Biology: published May 17, 2012 | https://doi.org/10.1371/journal.pcbi.1002511
Mechanical Stress Inference for Two Dimensional Cell Arrays
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
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
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
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
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
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
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
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
PLOS Computational Biology: published May 10, 2012 | https://doi.org/10.1371/journal.pcbi.1002498
Virus Capsid Dissolution Studied by Microsecond Molecular Dynamics Simulations
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
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
PLOS Computational Biology: published May 10, 2012 | https://doi.org/10.1371/journal.pcbi.1002506
Modeling HIV-1 Drug Resistance as Episodic Directional Selection
PLOS Computational Biology: published May 10, 2012 | https://doi.org/10.1371/journal.pcbi.1002507
Dynamic Prestress in a Globular Protein
PLOS Computational Biology: published May 10, 2012 | https://doi.org/10.1371/journal.pcbi.1002509
Challenges and New Approaches to Proving the Existence of Muscle Synergies of Neural Origin
PLOS Computational Biology: published May 3, 2012 | https://doi.org/10.1371/journal.pcbi.1002434
Adhesion Failures Determine the Pattern of Choroidal Neovascularization in the Eye: A Computer Simulation Study
PLOS Computational Biology: published May 3, 2012 | https://doi.org/10.1371/journal.pcbi.1002440
Homeostatic Scaling of Excitability in Recurrent Neural Networks
PLOS Computational Biology: published May 3, 2012 | https://doi.org/10.1371/journal.pcbi.1002494
Modeling Meiotic Chromosomes Indicates a Size Dependent Contribution of Telomere Clustering and Chromosome Rigidity to Homologue Juxtaposition
PLOS Computational Biology: published May 3, 2012 | https://doi.org/10.1371/journal.pcbi.1002496