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BioInform s Funding Update: NSF Awards in Bioinformatics through January 25, 2003


Nonlinear Analysis Approach to Protein Structure/Dynamics. Start date: January 1, 2003. Expires: December 31, 2005. Expected total amount: $374,308. Principal investigator: Joseph Zbilut. Sponsor: Rush-Presbyterian St. Luke’s Medical Center.

This project treats the amino acid code as a “signal” in order to determine hydrophobicity singularities using recurrence analysis, a method derived from nonlinear dynamics that obviates mathematical assumptions. Project goals include the development of a preliminary taxonomy of hydrophobic singularities, a catalogue of their protein context, and an evaluation of their correlation with physico-chemical properties.


The Gramene Community Curation Network. Start date: Jan. 15, 2003. Expires: Dec. 31, 2005. Expected total amount: $271,097. Principal investigator: Lincoln Stein. Sponsor: Cold Spring Harbor Laboratory.

Project goal is to develop a network of community-based curators for the Gramene comparative mapping database for rice and other cereals ( The project will support workshops through which curators will develop standard operating procedures, data entry resources, and curricula and other training materials.


Comprehensive Database Resource on Protein Localization. Start date: Feb. 1, 2003. Expires: Jan. 31, 2005. Expected total amount: $499,407. Principal investigator: Christopher Larsen. Sponsor: Cognia.

This SBIR Phase II project proposes to develop a database and software to enable analysis of protein trafficking and localization. During Phase I, the awardees identified proteins involved in trafficking and diseases related to mislocalization, built a relational database, and developed curation software. During Phase II, the investigators will populate the database from the journal literature.


A Computational Environment for Prokaryotic Genome Projects. Start date: Feb. 1, 2003. Expires: Jan. 31, 2008. Expected total amount: $587,990. Principal investigator: Sun Kim. Sponsor: Indiana University.

This project aims to develop a reconfigurable computational environment for prokaryotic genome projects, comprising four major components: toolkits for string matching and clustering; an ordering procedure for sets of assembled sequence; a platform for comparative alignment and annotation; and an exploratory sequence analysis environment.


Computational Statistics For Phylogenetic Trees. Start date: Sept. 1, 2003. Expires: Aug. 31, 2007. Expected total amount: $737,913. Principal Investigator: Susan Holmes. Sponsor: Stanford University.

This project aims to provide ways of averaging, building confidence regions, running Monte Carlo algorithms, and doing regression and testing models for rooted binary trees for applications in phylogenetic analysis.

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The Scan

Myotonic Dystrophy Repeat Detected in Family Genome Sequencing Analysis

While sequencing individuals from a multi-generation family, researchers identified a myotonic dystrophy type 2-related short tandem repeat in the European Journal of Human Genetics.

TB Resistance Insights Gleaned From Genome Sequence, Antimicrobial Response Assays

Researchers in PLOS Biology explore M. tuberculosis resistance with a combination of sequencing and assays looking at the minimum inhibitory concentrations of 13 drugs.

Mendelian Disease Genes Prioritized Using Tissue-Specific Expression Clues

Mendelian gene candidates could be flagged for further functional analyses based on tissue-specific transcriptome and proteome profiles, a new Journal of Human Genetics paper says.

Single-Cell Sequencing Points to Embryo Mosaicism

Mosaicism may affect preimplantation genetic tests for aneuploidy, a single-cell sequencing-based analysis of almost three dozen embryos in PLOS Genetics finds.