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BioInform s Funding Update: Some Recent NIH Awards in Bioinformatics: Jun 16, 2003


Phenotype Microarrays for Drug Toxicity Screening. Start date: May 2003. Expires: April 2004. Principal investigator: Barry Bochner. Institution: Biolog. NIH Institute: NCI.

Project to use Biolog’s Phenotype Microarrays to build a prototype database of metabolic profiles for well-studied drugs in human liver and hematopoietic cell lines that can be used to screen small molecules for toxicity potential. The project will eventually lead to a predictive database that will include cell lines representing more tissues and organs.


Discovering New Human DNA Repair Genes by Bioinformatics. Start date: May 2003. Expires: April 2005. Principal investigator: Ashok Bhagwat. Institution: Wayne State University. NIH Institute: NCI.

Project to use homology-based methods to search for potential human DNA glycosylases and develop improved sequence profiles of glycosylase families for improved threading analysis of the human proteome. The project will also use non-homology-based methods including identification of catalytic centers and an associative search for DNA glycosylases in other known DNA-modifying enzymes.


Computational and Statistical Models for Human Pedigrees. Start date: May 2003. Expires: April 2008. Principal investigator: Goncalo Abecasis. Institution: University of Michigan at Ann Arbor. NIH Institute: NHGRI.

Project to build computational tools and methods for improved pedigree analysis to enable geneticists to analyze thousands of SNP markers and larger family datasets. Specific aims include further improvements in the estimation of haplotypes in pedigrees, superior detection and modeling of genotype error, and a comprehensive simulation framework for evaluating linkage findings in situations where multiple phenotypes are considered.


Sun Microsystems Sun Fire 6800 Server Supercomputer. Start date: June 2003. Expires: June 2004. Principal investigator: Judith Stenger. Institution: Duke University. NIH Institute: NCRR.

Provides funds to purchase a Sun Microsystems SunFire 6800 with 24 750-MHz processors, 72 GB of memory, and 3 terabytes of disk storage for the Center for Human Genetics at Duke University Medical Center for the bioinformatics analysis of clinical and genotypic data.


Discovery of Protein Sequence Structure Function Relationships. Start date: June 2003. Expires: May 2005. Principal Investigator: Vasant Honavar. Institution: Iowa State University of Science and Technology. NIH Institute: NIGMS.

Supports the development of a computational platform for investigating protein sequence-structure-function relationships. A suite of algorithms and data representations for assigning protein sequences to structural or functional families will be developed. Further developments include software to assemble data sets from multiple heterogeneous protein data repositories; computational tools for eliciting sequence and structural correlates of functionally important parts of proteins and characterizing; computational tools for predicting protein-protein interactions; and a set of software modules for analysis of protein structure and function.


Georgia State University Biomedical Computing Center. Start date: June 2003. Expires: May 2006. Principal investigator: Robert Harrison. Institution: Georgia State University. NIH Institute: NIGMS.

Supports a multidisciplinary program for research and education in bioinformatics and biomolecular computing at Georgia State University.


Systemic analysis of molecular networks. Start date: June 2003. Expires: May 2007. Principal investigator: Illya Mazo. Institution: Ariadne Genomics. NIH Institute: NIGMS.

Proposal to develop a set of algorithms for the analysis of cellular pathways, gene regulation, and protein interaction maps. The project will combine statistical approaches and a database of cell signaling networks compiled for the research, and will study correlation profiles and network motifs. Network information will be combined with gene expression and sequence data to build models aimed at the prediction of new regulatory links.


A Resource for Biomedical Ontologies and Knowledge Bases. Start date: June 2003. Expires: May 2007. Principal investigator: Mark Musen. Institution Stanford University. NIH Institute: NLM.

Supports further development of Protege-2000, a workbench that allows users to edit and apply controlled terminologies, ontologies, and knowledge bases to a wide range of information management problems in biomedical informatics.


Statistical and Computational Studies of Microarray Data. Start date: June 2003. Expires: May 2008. Principal investigator: Peter Park. Institution: Children’s Hospital (Boston). NIH Institute: NIGMS.

Supports the development of a statistical framework in order to understand the relationship between genotypic and phenotypic data. New computational techniques based on partial least squares will be developed.


BMI Bioinformatics Training Grant. Start date: July 2003. Expires: June 2008. Expected total amount: Principal investigator: Patricia Babbitt. Institution: University of California, San Francisco. NIH Institute: NIGMS.

Funds a predoctoral training program in bioinformatics and computational biology at UCSF.


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A new study finds that women tend to participate less at scientific meetings but that some changes can lead to increased involvement, the Guardian reports.

Right Whales' Decline

A research study plans to use genetic analysis to gain insight into population decline among North American right whales, according to CBC.

Science Papers Tie Rare Mutations to Short Stature, Immunodeficiency; Present Single-Cell Transcriptomics Map

In Science this week: pair of mutations in one gene uncovered in brothers with short stature and immunodeficiency, and more.