Th1 and Th2 lymphocytes are thought to be counter-regulatory. A network model of genes that regulate Th1 and Th2 cells was constructed by automated mining of 18 million abstracts in Medline. Analysis of the dynamics of this model using in silico knock-outs suggested a synergistic, rather than a counter-regulatory, relationship between Th1 and Th2 cells. This was supported by analysis of public gene expression microarray data from different inflammatory diseases. Network modeling using public data may be generally applicable to understand complex regulatory networks in health and disease. (See Pedicini et al., doi:10.1371/journal.pcbi.1001032.)
Image Credit: Filippo Castiglione
Research Articles
Widespread Compensatory Evolution Conserves DNA-Encoded Nucleosome Organization in Yeast
PLOS Computational Biology: published December 23, 2010 | https://doi.org/10.1371/journal.pcbi.1001039
Phase-Locked Signals Elucidate Circuit Architecture of an Oscillatory Pathway
PLOS Computational Biology: published December 23, 2010 | https://doi.org/10.1371/journal.pcbi.1001040
Determinants of Heterogeneity, Excitation and Conduction in the Sinoatrial Node: A Model Study
PLOS Computational Biology: published December 23, 2010 | https://doi.org/10.1371/journal.pcbi.1001041
The Evolutionary Analysis of Emerging Low Frequency HIV-1 CXCR4 Using Variants through Time—An Ultra-Deep Approach
PLOS Computational Biology: published December 16, 2010 | https://doi.org/10.1371/journal.pcbi.1001022
How Noisy Adaptation of Neurons Shapes Interspike Interval Histograms and Correlations
PLOS Computational Biology: published December 16, 2010 | https://doi.org/10.1371/journal.pcbi.1001026
Kinetics of Rhodopsin Deactivation and Its Role in Regulating Recovery and Reproducibility of Rod Photoresponse
PLOS Computational Biology: published December 16, 2010 | https://doi.org/10.1371/journal.pcbi.1001031
Combining Network Modeling and Gene Expression Microarray Analysis to Explore the Dynamics of Th1 and Th2 Cell Regulation
PLOS Computational Biology: published December 16, 2010 | https://doi.org/10.1371/journal.pcbi.1001032
Rhythmic Dynamics and Synchronization via Dimensionality Reduction: Application to Human Gait
PLOS Computational Biology: published December 16, 2010 | https://doi.org/10.1371/journal.pcbi.1001033
Mapping Dynamic Histone Acetylation Patterns to Gene Expression in Nanog-Depleted Murine Embryonic Stem Cells
PLOS Computational Biology: published December 16, 2010 | https://doi.org/10.1371/journal.pcbi.1001034
Mathematical Model of a Cell Size Checkpoint
PLOS Computational Biology: published December 16, 2010 | https://doi.org/10.1371/journal.pcbi.1001036
Modeling the Evolution of Regulatory Elements by Simultaneous Detection and Alignment with Phylogenetic Pair HMMs
PLOS Computational Biology: published December 16, 2010 | https://doi.org/10.1371/journal.pcbi.1001037
Encoding of Spatio-Temporal Input Characteristics by a CA1 Pyramidal Neuron Model
PLOS Computational Biology: published December 16, 2010 | https://doi.org/10.1371/journal.pcbi.1001038
Sequence-Based Prediction for Vaccine Strain Selection and Identification of Antigenic Variability in Foot-and-Mouth Disease Virus
PLOS Computational Biology: published December 9, 2010 | https://doi.org/10.1371/journal.pcbi.1001027
A Scalable Approach for Discovering Conserved Active Subnetworks across Species
PLOS Computational Biology: published December 9, 2010 | https://doi.org/10.1371/journal.pcbi.1001028
Cholera- and Anthrax-Like Toxins Are among Several New ADP-Ribosyltransferases
PLOS Computational Biology: published December 9, 2010 | https://doi.org/10.1371/journal.pcbi.1001029
Spatial Pattern Switching Enables Cyclic Evolution in Spatial Epidemics
PLOS Computational Biology: published December 9, 2010 | https://doi.org/10.1371/journal.pcbi.1001030
Incremental Mutual Information: A New Method for Characterizing the Strength and Dynamics of Connections in Neuronal Circuits
PLOS Computational Biology: published December 9, 2010 | https://doi.org/10.1371/journal.pcbi.1001035
Self-Organized Criticality in Developing Neuronal Networks
PLOS Computational Biology: published December 2, 2010 | https://doi.org/10.1371/journal.pcbi.1001013
Gene Expression Network Reconstruction by Convex Feature Selection when Incorporating Genetic Perturbations
PLOS Computational Biology: published December 2, 2010 | https://doi.org/10.1371/journal.pcbi.1001014
Modeling Conformational Ensembles of Slow Functional Motions in Pin1-WW
PLOS Computational Biology: published December 2, 2010 | https://doi.org/10.1371/journal.pcbi.1001015
Axial and Radial Forces of Cross-Bridges Depend on Lattice Spacing
PLOS Computational Biology: published December 2, 2010 | https://doi.org/10.1371/journal.pcbi.1001018
Modeling Mechanisms of In Vivo Variability in Methotrexate Accumulation and Folate Pathway Inhibition in Acute Lymphoblastic Leukemia Cells
PLOS Computational Biology: published December 2, 2010 | https://doi.org/10.1371/journal.pcbi.1001019
Assessing Computational Methods of Cis-Regulatory Module Prediction
PLOS Computational Biology: published December 2, 2010 | https://doi.org/10.1371/journal.pcbi.1001020
Little Italy: An Agent-Based Approach to the Estimation of Contact Patterns- Fitting Predicted Matrices to Serological Data
PLOS Computational Biology: published December 2, 2010 | https://doi.org/10.1371/journal.pcbi.1001021
Gambling in the Visual Periphery: A Conjoint-Measurement Analysis of Human Ability to Judge Visual Uncertainty
PLOS Computational Biology: published December 2, 2010 | https://doi.org/10.1371/journal.pcbi.1001023
A Systems Model for Immune Cell Interactions Unravels the Mechanism of Inflammation in Human Skin
PLOS Computational Biology: published December 2, 2010 | https://doi.org/10.1371/journal.pcbi.1001024
Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++
PLOS Computational Biology: published December 2, 2010 | https://doi.org/10.1371/journal.pcbi.1001025
Structure Learning in Human Sequential Decision-Making
PLOS Computational Biology: published December 2, 2010 | https://doi.org/10.1371/journal.pcbi.1001003
A Minimal Model of Metabolism-Based Chemotaxis
PLOS Computational Biology: published December 2, 2010 | https://doi.org/10.1371/journal.pcbi.1001004