The yellow bundle in the foreground represents a coarse-grained, computer-generated conformation of human Chromosome 19. The structure was obtained by using steered molecular dynamics simulations to enforce a comprehensive set of knowledge-based constraints. Specifically, the simulations were used to promote the spatial proximity of hundreds of gene pairs that are known to be significantly co-regulated. Conformations were obtained with LAMMPS and visualized by VMD. See Di Stefano, et al.
Image Credit: Marco Di Stefano, Angelo Rosa, Cristian Micheletti
Editorial
New Methods Section in PLOS Computational Biology
PLOS Computational Biology: published March 7, 2013 | https://doi.org/10.1371/journal.pcbi.1002972
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Viral Phylodynamics
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Evolving Digital Ecological Networks
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Combined Model of Intrinsic and Extrinsic Variability for Computational Network Design with Application to Synthetic Biology
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The Fidelity of Dynamic Signaling by Noisy Biomolecular Networks
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Explaining the Determinants of First Phase HIV Decay Dynamics through the Effects of Stage-dependent Drug Action
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Automated Analysis of a Diverse Synapse Population
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Sustained Firing of Model Central Auditory Neurons Yields a Discriminative Spectro-temporal Representation for Natural Sounds
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Stability and Responsiveness in a Self-Organized Living Architecture
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A Circadian Clock-Regulated Toggle Switch Explains AtGRP7 and AtGRP8 Oscillations in Arabidopsis thaliana
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A Model of Binocular Rivalry and Cross-orientation Suppression
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The Fate of Cooperation during Range Expansions
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Outlier Responses Reflect Sensitivity to Statistical Structure in the Human Brain
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Transcriptome Profiling of Giardia intestinalis Using Strand-specific RNA-Seq
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Systems Model of T Cell Receptor Proximal Signaling Reveals Emergent Ultrasensitivity
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Origin and Evolution of Protein Fold Designs Inferred from Phylogenomic Analysis of CATH Domain Structures in Proteomes
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Sparse Distributed Representation of Odors in a Large-scale Olfactory Bulb Circuit
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Colocalization of Coregulated Genes: A Steered Molecular Dynamics Study of Human Chromosome 19
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A Discriminative Approach for Unsupervised Clustering of DNA Sequence Motifs
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Multi-scale Inference of Interaction Rules in Animal Groups Using Bayesian Model Selection
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Stimulus-dependent Maximum Entropy Models of Neural Population Codes
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Differential Expression Analysis for Pathways
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