The three dimensional conformation of the genome in the cell nucleus influences important biological processes such as gene expression regulation. Recent studies have shown a strong correlation between chromatin interactions and gene co-expression. However, predicting gene co-expression from frequent long-range chromatin interactions remains challenging. We address this by characterizing the topology of the cortical chromatin interaction network using scale-aware topological measures. We demonstrate that based on these characterizations it is possible to accurately predict spatial co-expression between genes in the mouse cortex. Babaei et al.
Image Credit: Ms. Annelies te Selle
Perspective
Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models
PLOS Computational Biology: published May 28, 2015 | https://doi.org/10.1371/journal.pcbi.1004096
Topic Page
Inferring Horizontal Gene Transfer
PLOS Computational Biology: published May 28, 2015 | https://doi.org/10.1371/journal.pcbi.1004095
Research Articles
Maintaining Homeostasis by Decision-Making
PLOS Computational Biology: published May 29, 2015 | https://doi.org/10.1371/journal.pcbi.1004301
Predicted Role of NAD Utilization in the Control of Circadian Rhythms during DNA Damage Response
PLOS Computational Biology: published May 28, 2015 | https://doi.org/10.1371/journal.pcbi.1004144
Synaptic Homeostasis and Restructuring across the Sleep-Wake Cycle
PLOS Computational Biology: published May 28, 2015 | https://doi.org/10.1371/journal.pcbi.1004241
Integrated Stochastic Model of DNA Damage Repair by Non-homologous End Joining and p53/p21- Mediated Early Senescence Signalling
PLOS Computational Biology: published May 28, 2015 | https://doi.org/10.1371/journal.pcbi.1004246
Experimental and Computational Analysis of a Large Protein Network That Controls Fat Storage Reveals the Design Principles of a Signaling Network
PLOS Computational Biology: published May 28, 2015 | https://doi.org/10.1371/journal.pcbi.1004264
Predicting Cortical Dark/Bright Asymmetries from Natural Image Statistics and Early Visual Transforms
PLOS Computational Biology: published May 28, 2015 | https://doi.org/10.1371/journal.pcbi.1004268
Causal Modeling of Cancer-Stromal Communication Identifies PAPPA as a Novel Stroma-Secreted Factor Activating NFκB Signaling in Hepatocellular Carcinoma
PLOS Computational Biology: published May 28, 2015 | https://doi.org/10.1371/journal.pcbi.1004293
Geometrical and Mechanical Properties Control Actin Filament Organization
PLOS Computational Biology: published May 27, 2015 | https://doi.org/10.1371/journal.pcbi.1004245
Native Contact Density and Nonnative Hydrophobic Effects in the Folding of Bacterial Immunity Proteins
PLOS Computational Biology: published May 27, 2015 | https://doi.org/10.1371/journal.pcbi.1004260
SeqGL Identifies Context-Dependent Binding Signals in Genome-Wide Regulatory Element Maps
PLOS Computational Biology: published May 27, 2015 | https://doi.org/10.1371/journal.pcbi.1004271
Metabolic Needs and Capabilities of Toxoplasma gondii through Combined Computational and Experimental Analysis
PLOS Computational Biology: published May 22, 2015 | https://doi.org/10.1371/journal.pcbi.1004261
A Multiscale Model Evaluates Screening for Neoplasia in Barrett’s Esophagus
PLOS Computational Biology: published May 22, 2015 | https://doi.org/10.1371/journal.pcbi.1004272
The Hydrophobic Temperature Dependence of Amino Acids Directly Calculated from Protein Structures
PLOS Computational Biology: published May 22, 2015 | https://doi.org/10.1371/journal.pcbi.1004277
Improving 3D Genome Reconstructions Using Orthologous and Functional Constraints
PLOS Computational Biology: published May 22, 2015 | https://doi.org/10.1371/journal.pcbi.1004298
Context-Dependent Role of Mitochondrial Fusion-Fission in Clonal Expansion of mtDNA Mutations
PLOS Computational Biology: published May 21, 2015 | https://doi.org/10.1371/journal.pcbi.1004183
Regulators Associated with Clinical Outcomes Revealed by DNA Methylation Data in Breast Cancer
PLOS Computational Biology: published May 21, 2015 | https://doi.org/10.1371/journal.pcbi.1004269
The Opponent Channel Population Code of Sound Location Is an Efficient Representation of Natural Binaural Sounds
PLOS Computational Biology: published May 21, 2015 | https://doi.org/10.1371/journal.pcbi.1004294
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Model-Free RNA Sequence and Structure Alignment Informed by SHAPE Probing Reveals a Conserved Alternate Secondary Structure for 16S rRNA
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Structure-Based Alignment and Consensus Secondary Structures for Three HIV-Related RNA Genomes
PLOS Computational Biology: published May 20, 2015 | https://doi.org/10.1371/journal.pcbi.1004230
Metapopulation Persistence in Random Fragmented Landscapes
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Distal Spike Initiation Zone Location Estimation by Morphological Simulation of Ionic Current Filtering Demonstrated in a Novel Model of an Identified Drosophila Motoneuron
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Modelling Circulating Tumour Cells for Personalised Survival Prediction in Metastatic Breast Cancer
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The Effect of Incentives and Meta-incentives on the Evolution of Cooperation
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Forecasting the 2013–2014 Influenza Season Using Wikipedia
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Computational Modeling of Seizure Dynamics Using Coupled Neuronal Networks: Factors Shaping Epileptiform Activity
PLOS Computational Biology: published May 13, 2015 | https://doi.org/10.1371/journal.pcbi.1004209
Sharing and Specificity of Co-expression Networks across 35 Human Tissues
PLOS Computational Biology: published May 13, 2015 | https://doi.org/10.1371/journal.pcbi.1004220
Mechanisms of Left-Right Coordination in Mammalian Locomotor Pattern Generation Circuits: A Mathematical Modeling View
PLOS Computational Biology: published May 13, 2015 | https://doi.org/10.1371/journal.pcbi.1004270
Hi-C Chromatin Interaction Networks Predict Co-expression in the Mouse Cortex
PLOS Computational Biology: published May 12, 2015 | https://doi.org/10.1371/journal.pcbi.1004221
Convex Clustering: An Attractive Alternative to Hierarchical Clustering
PLOS Computational Biology: published May 12, 2015 | https://doi.org/10.1371/journal.pcbi.1004228
Optimal Census by Quorum Sensing
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Extensive Decoupling of Metabolic Genes in Cancer
PLOS Computational Biology: published May 11, 2015 | https://doi.org/10.1371/journal.pcbi.1004176
Modelling the Effects of Electrical Coupling between Unmyelinated Axons of Brainstem Neurons Controlling Rhythmic Activity
PLOS Computational Biology: published May 8, 2015 | https://doi.org/10.1371/journal.pcbi.1004240
Memory Storage Fidelity in the Hippocampal Circuit: The Role of Subregions and Input Statistics
PLOS Computational Biology: published May 8, 2015 | https://doi.org/10.1371/journal.pcbi.1004250
Understanding Voltage Gating of Providencia stuartii Porins at Atomic Level
PLOS Computational Biology: published May 8, 2015 | https://doi.org/10.1371/journal.pcbi.1004255
Structural Conversion of Aβ17–42 Peptides from Disordered Oligomers to U-Shape Protofilaments via Multiple Kinetic Pathways
PLOS Computational Biology: published May 8, 2015 | https://doi.org/10.1371/journal.pcbi.1004258
Accurate Computation of Survival Statistics in Genome-Wide Studies
PLOS Computational Biology: published May 7, 2015 | https://doi.org/10.1371/journal.pcbi.1004071
A Dynamical Phyllotaxis Model to Determine Floral Organ Number
PLOS Computational Biology: published May 7, 2015 | https://doi.org/10.1371/journal.pcbi.1004145
Sparse and Compositionally Robust Inference of Microbial Ecological Networks
PLOS Computational Biology: published May 7, 2015 | https://doi.org/10.1371/journal.pcbi.1004226
An Exclusion Zone for Ca2+ Channels around Docked Vesicles Explains Release Control by Multiple Channels at a CNS Synapse
PLOS Computational Biology: published May 7, 2015 | https://doi.org/10.1371/journal.pcbi.1004253
Dissecting the Calcium-Induced Differentiation of Human Primary Keratinocytes Stem Cells by Integrative and Structural Network Analyses
PLOS Computational Biology: published May 6, 2015 | https://doi.org/10.1371/journal.pcbi.1004256
Predicting Peptide-Mediated Interactions on a Genome-Wide Scale
PLOS Computational Biology: published May 4, 2015 | https://doi.org/10.1371/journal.pcbi.1004248
Estimating the In Vivo Killing Efficacy of Cytotoxic T Lymphocytes across Different Peptide-MHC Complex Densities
PLOS Computational Biology: published May 1, 2015 | https://doi.org/10.1371/journal.pcbi.1004178
Quantification of Interactions between Dynamic Cellular Network Functionalities by Cascaded Layering
PLOS Computational Biology: published May 1, 2015 | https://doi.org/10.1371/journal.pcbi.1004235
Formal Comments
Power Law Scaling in Human and Empty Room MEG Recordings
PLOS Computational Biology: published May 8, 2015 | https://doi.org/10.1371/journal.pcbi.1004175
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Comment on “Broadband Criticality of Human Brain Network Synchronization” by Kitzbichler MG, Smith ML, Christensen SR, Bullmore E (2009) PLoS Comput Biol 5: e1000314
PLOS Computational Biology: published May 7, 2015 | https://doi.org/10.1371/journal.pcbi.1004174