Table of Contents: March 2013

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


New Methods Section in PLOS Computational Biology

Thomas Lengauer, Ruth Nussinov

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  5. Principal Component Analysis Characterizes Shared Pathogenetics from Genome-Wide Association Studies
  6. Identification of Allelic Imbalance with a Statistical Model for Subtle Genomic Mosaicism
  7. VASP-E: Specificity Annotation with a Volumetric Analysis of Electrostatic Isopotentials
  8. Unbiased Functional Clustering of Gene Variants with a Phenotypic-Linkage Network
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  21. Enhanced Methods for Local Ancestry Assignment in Sequenced Admixed Individuals
  22. Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible
  23. Exact Hybrid Particle/Population Simulation of Rule-Based Models of Biochemical Systems
  24. MRFalign: Protein Homology Detection through Alignment of Markov Random Fields
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  32. Novel Methods for Analysing Bacterial Tracks Reveal Persistence in Rhodobacter sphaeroides
  33. A Horizontal Alignment Tool for Numerical Trend Discovery in Sequence Data: Application to Protein Hydropathy
  34. Analyzing and Synthesizing Phylogenies Using Tree Alignment Graphs
  35. Detecting and Removing Inconsistencies between Experimental Data and Signaling Network Topologies Using Integer Linear Programming on Interaction Graphs
  36. A Self-Directed Method for Cell-Type Identification and Separation of Gene Expression Microarrays
  37. Consistent Estimation of Gibbs Energy Using Component Contributions
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