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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

Editorials

New Methods Section in PLOS Computational Biology

Thomas Lengauer, Ruth Nussinov

Related Articles

  1. A Future Vision for PLOS Computational Biology
  2. Consistent Estimation of Gibbs Energy Using Component Contributions
  3. A Self-Directed Method for Cell-Type Identification and Separation of Gene Expression Microarrays
  4. Detecting and Removing Inconsistencies between Experimental Data and Signaling Network Topologies Using Integer Linear Programming on Interaction Graphs
  5. Analyzing and Synthesizing Phylogenies Using Tree Alignment Graphs
  6. A Horizontal Alignment Tool for Numerical Trend Discovery in Sequence Data: Application to Protein Hydropathy
  7. Novel Methods for Analysing Bacterial Tracks Reveal Persistence in Rhodobacter sphaeroides
  8. A Tunable Coarse-Grained Model for Ligand-Receptor Interaction
  9. Inferring the Source of Transmission with Phylogenetic Data
  10. Fast Reconstruction of Compact Context-Specific Metabolic Network Models
  11. Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data
  12. Universal Count Correction for High-Throughput Sequencing
  13. Probabilistic Approach to Predicting Substrate Specificity of Methyltransferases
  14. MRFalign: Protein Homology Detection through Alignment of Markov Random Fields
  15. HapTree: A Novel Bayesian Framework for Single Individual Polyplotyping Using NGS Data
  16. Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible
  17. Exact Hybrid Particle/Population Simulation of Rule-Based Models of Biochemical Systems
  18. Phylogenetic Quantification of Intra-tumour Heterogeneity
  19. Enhanced Methods for Local Ancestry Assignment in Sequenced Admixed Individuals
  20. Fast Protein Loop Sampling and Structure Prediction Using Distance-Guided Sequential Chain-Growth Monte Carlo Method
  21. Determining Effects of Non-synonymous SNPs on Protein-Protein Interactions using Supervised and Semi-supervised Learning
  22. High-Resolution Modeling of Transmembrane Helical Protein Structures from Distant Homologues
  23. Historical Pedigree Reconstruction from Extant Populations Using PArtitioning of RElatives (PREPARE)
  24. A Digital Framework to Build, Visualize and Analyze a Gene Expression Atlas with Cellular Resolution in Zebrafish Early Embryogenesis
  25. Optimal Sampling Strategies for Detecting Zoonotic Disease Epidemics
  26. A Scalable Computational Framework for Establishing Long-Term Behavior of Stochastic Reaction Networks
  27. ODE Constrained Mixture Modelling: A Method for Unraveling Subpopulation Structures and Dynamics
  28. Algorithms to Model Single Gene, Single Chromosome, and Whole Genome Copy Number Changes Jointly in Tumor Phylogenetics
  29. A Scalable and Accurate Targeted Gene Assembly Tool (SAT-Assembler) for Next-Generation Sequencing Data
  30. Defining the Estimated Core Genome of Bacterial Populations Using a Bayesian Decision Model
  31. Identification of Allelic Imbalance with a Statistical Model for Subtle Genomic Mosaicism
  32. VASP-E: Specificity Annotation with a Volumetric Analysis of Electrostatic Isopotentials
  33. Unbiased Functional Clustering of Gene Variants with a Phenotypic-Linkage Network
  34. Principal Component Analysis Characterizes Shared Pathogenetics from Genome-Wide Association Studies
  35. Characterizing Protein Interactions Employing a Genome-Wide siRNA Cellular Phenotyping Screen
  36. Improved Contact Predictions Using the Recognition of Protein Like Contact Patterns
  37. Protein-Protein Docking with Dynamic Residue Protonation States
  38. How to Write a Presubmission Inquiry

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Erik M. Volz, Katia Koelle, Trevor Bedford

Evolving Digital Ecological Networks

Miguel A. Fortuna, Luis Zaman, Aaron P. Wagner, Charles Ofria

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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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