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NIH Grants in Bioinformatics Awarded June — May 2006

Software for large-scale analysis of heterozygous insertions and deletions. Start date: July 1, 2006. Expires: Dec. 31, 2006. Amount: $ 99,270. Principal investigator: Peter Richterich. Institution: CodonCode. NIH institute: NHGRI.
SBIR funds development of software modules for the automated analysis of heterozygous insertions and deletions in large-scale resequencing projects. While several useful software tools for the analysis of heterozygous point mutations are available, “no satisfactory tools for automatic detection and analysis of heterozygote indels currently exist,” according to the grantees. CodonCode has developed several algorithms for detecting and analyzing heterozygous indels in DNA sequence chromatograms, and the goal of this proposal is to adapt these tools for large-scale resequencing projects.

Algorithms to investigate transcriptional networks. Start date: July 1, 2006. Expires: June 30, 2008. Amount: $ 189,086. Principal investigator: Sridhar Hannenhalli. Institution: University of Pennsylvania. NIH institute: NIGMS.
Funds development of an EM approach to simultaneously detect transcription factor binding motifs and their interacting partners from genome-wide chromatin immunoprecipitation experiments. This method will be applied to genome-wide yeast ChlP-chip data and to genome-wide CREB binding data in rat. The investigators will also develop graph-theoretic approaches to detect transcriptional modules, and develop a Gibbs sampling approach to detect dense sub-graphs in a multi-partite graph as a means to identify modules and apply this to detect modules driving tissue-specificity in human.

Bayesian Mixture Modeling of Functional Genomics Data. Start date: July 1, 2006. Expires: June 30, 2010. Amount: $ 345,000. Principal investigator: Mario Medvedovic. Institution: University of Cincinnati. NIH institute: NHGRI.
Funds development of a mathematical framework and corresponding computational tools for identifying statistically significant patterns in functional genomics data. “Currently used computational tools for cluster analysis are inadequate with respect to assessing the statistical significance of clustering results, clustering data across different studies and biological systems, and integrating additional data types in the analysis,” the investigators note in the grant abstract. The grantees propose to extend the mathematical framework of Bayesian infinite mixtures and to develop related computational tools.

MolProbity Service and Related 3D-Analysis Resources. Start date: July 1, 2006. Expires: June 30, 2010. Amount: $ 264,159. Principal investigator: David Richardson. Institution: Duke University. NIH institute: NIGMS.
Proposal to extend and improve the MolProbity Web service for analyzing, validating, and improving 3D macromolecular structures. According to the grant abstract, the investigators intend to enhance the “basic capabilities, user-friendliness, generality, robustness, maintainability, and extensibility” of MolProbity and its suite of supporting software.  

Integrated Protein Surface Annotation Suite. Start date: Aug 1, 2006. Expires: Jan. 31, 2007. Amount: $ 100,000. Principal investigator: Maxim Totrov. Institution: Molsoft. NIH institute: NIGMS.
SBIR supports development of an integrated protein surface analysis and graphics tool that will allow users to apply several binding site prediction methods and visualize the results. The investigators will implement two novel protein surface analysis algorithms in the software suite: a previously developed protein-protein interface prediction method to detect small-molecule binding sites; and a surface structural motif detection and visualization method.

SBEVSL ­— Structural Biology Extensible Visualization Scripting Language. Start date: Aug. 1, 2006. Expires: July 31, 2009. Amount: $ 216,750. Principal investigator: Herbert Bernstein. Institution: Dowling College. NIH institute: NIGMS.
Supports development of a new extensible scripting language for molecular graphics, as used in structural biology. The language will combine the “expressive power of the widely used scripting language created by Roger Sayle for RasMol with the general object-oriented extensibility of the Python scripting of PyMOL,” according to the grant abstract. Existing open source molecular graphics programs, including RasMol, Jmol, and PyMol will be adapted to accept scripts written in the new scripting language. The SBEVSL project will extract all the concepts used in the command languages of major molecular graphics programs and gather them in one master ontology.

Experimental Standards and Computational Platform for HTP Proteomics. Start date: Aug. 1, 2006. Expires: July 31, 2009. $ 517,978. Principal investigator: Eugene Kolker. Institution: Biatech Institute. NIH institute: NIGMS.
Proposal to improve high-throughput proteomics analysis through experimental standards as well as a “flexible, transparent, and statistically sound computational platform.” The computational platform will include new statistical models and software tools for high-throughput proteomics.

Knowledge-based Gene Expression Analysis for Biomedical and Cancer Research. Start date: Aug. 1, 2006. Amount: $ 546,432. Expires: June 30, 2011. Principal investigator: Jill Mesirov. Institution: Massachusetts Institute of Technology. NIH institute: NCI.
Funds development of Gene Set Enrichment Analysis (GSEA), a method for interpreting gene expression data that focuses on groups of genes that share common biological function, chromosomal location, or regulation rather than on single genes. The grant also supports further enhancements for the Molecular Signatures Database (MSigDB), which contains around 1,300 annotated gene sets to be used with GSEA.

Statistics in Microbiology, Infectious Diseases & Bioinformatics. Start date: Aug. 1, 2006. Expires: June 30, 2011. Amount: $ 69,470. Principal investigator: Kathryn Chaloner. Institution: University of Iowa. NIH institute: NIGMS.
Funds a program that will train biostatisticians in interdisciplinary scientific research that includes training in statistics, microbiology, and in bioinformatics.

Predicting Protein Structure with Guided Conformation Space Search. Start date: August 1, 2006. Expires: July 31, 2011. Amount: $ 238,087. Principal investigator: Oliver Brock. Institution: University of Massachusetts, Amherst. NIH institute: NIGMS.
Funds development of a computational framework for protein structure prediction that takes a novel approach to conformation space search that combines methods from robotics and machine learning with techniques from molecular biology.the method usees target-specific information to effectively guide conformation space search towards biologically relevant regions.

A computer aided chromosome imaging technique for cancer diagnosis. Start date: July 14, 2006. Expires: May 31, 2011. Amount: $ 333,554. Principal investigator: Hong Liu. Institution: University of Oklahoma, Norman. NIH institute: NCI.

Funds development of a computer-aided chromosome imaging technique based on a high-speed microscopic imaging system using a time-delay-integration technique. The project includes development of a computer-aided diagnosis scheme that includes detecting analyzable metaphase chromosome cells, segmenting overlapped chromosomes, identifying and classifying distorted chromosomes associated with cancer cells, and predicting the cancer prognosis.

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The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.