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Recent NIH Awards in Bioinformatics: May 2005

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Bioinformatics Standards for Flow Cytometry. Start date: May 1, 2005. Expires: Feb. 28, 2009. Amount: $218,700. Principal investigator: Ryan Brinkman. Institution: British Columbia Cancer Research Center. NIH institute: NIBIB.

Proposal to implement a standardized approach to capturing, analyzing, and disseminating flow cytometry data by building and extending existing open source software tools. Initial work will focus on developing community-based guidelines for recording and reporting the details of flow cytometry experiments. Platform-independent software implementations of this standard will be created to facilitate data exchange between both software components and collaborative groups. Statistical tools with reference implementations will also be developed.


BioMolecular Networks in Antibiotic Resistance Evolution. Start date: June 1, 2005. Expires: April 30, 2009. Amount: $140,921. Principal investigator: Ryan Gill. Institution: University of Colorado at Boulder. NIH institute: NIAID.

Using network theory, the grantees hypothesize that resistance mutations in genes with a large number biological interactions will impose a higher cost than mutations in genes with a small number of biological interactions. A major objective of this study is to develop several genomics/bioinformatics tools that will allow the researchers to test this hypothesis.


Bioinformatic and Computational Biology Training Program. Start date: July 1, 2005. Expires: June 30, 2010. Amount: $134,876. Principal investigator: Thomas Kepler. Institution: Duke University. NIH institute: NIGMS.

Funds development of a training program for PhD students in bioinformatics, genome technology, and computational biology. The program builds upon a solid foundation in statistics and computer science, while providing direct integration into experimental biology laboratories, clinical research programs, and "the culture of the life sciences."


HIV-1 Envelope Phenotype/Genotype Database Resources. Start date: May 1, 2005. Expires: April 30, 2007. Amount: $417,557. Principal investigator: Colombe Chappey. Institution: ViroLogic. NIH institute: NIAID.

SBIR grant supports the creation and population of an HIV-1 envelope database comprised of data derived from genotypic and phenotypic assays recently developed at ViroLogic to characterize and evaluate entry inhibitors and vaccines. Within the database, each envelope genotype will be associated with phenotypic data comprised of co-receptor tropism, entry inhibitor susceptibility, and/or neutralizing antibody sensitivity. The project will also develop computational methods to efficiently compile HIV-1 envelope genotypes, standardize envelope genotype reporting, and correlate genetic determinants with phenotype.


Recognizing Protein Folds with Discriminative Learning. Start date: May 1, 2005. Expires: April 30, 2010. Amount: $303,213. Principal investigator: Christina Leslie. Institution: Columbia University. NIH institute: NIGMS

Proposal to develop computational methods and tools for recognizing protein folds. The first aim involves building and delivering a web-based, discriminative fold-recognition software engine. According to the grantees, "This type of algorithm has been described and repeatedly validated in the scientific literature over the past five years, but no easy-to-use software tools yet exist to bring this technology to the end user." The second aim improves upon existing fold-recognition algorithms by exploiting the inherently multiclass nature of the problem. Previous approaches have treated each fold class independently, thereby sacrificing statistical power, according to the researchers.


Networks from Toxicogenomics Gene Expression Data. Start date: May 10, 2005. Expires: Oct. 31, 2005. Amount: $98,648. Principal investigator: Tatiana Nikolskaya. Institution: GeneGo. NIH institute: NIEHS.

Phase I SBIR funds development of an approach for identifying and analyzing functional networks and modules implicated in toxicity in human and experimental models. GeneGo will use its MetaCore data-mining suite to analyze publicly available toxicogenomics microarray expression data and reconstruct signaling, regulatory, and metabolic networks specifically implicated in different types of hepatotoxicity in rat. The networks will be adjusted to reflect the difference in protein-protein interactions between human and rat and analyzed using multiple network comparison algorithms within MetaCore. The resulting "signature networks" characteristic for specific toxicities will be tested in genome-wide microarray experiments in collaboration with the University of Wisconsin.


Toward Rapid Rigorous Calculations of Binding Affinities. Start date: Sept. 23, 2005. Expires: NA. Amount: $49,928. Principal investigator: Frederick Ytreberg. Institution: University of Pittsburgh. NIH institute: NIGMS.

Supports the development of rapid, rigorous calculations of binding affinities with the long-term goal of providing techniques suitable for virtual screening of compounds for drug design. According to the grantees, "Existing rigorous methods for binding affinity calculations require long simulation and thus are not feasible for virtual screening." The proposed methods will calculate equilibrium binding affinities from non-equilibrium computer simulations for a range of molecular and protein systems.


Computational Suite for RNA-Targeted Drug Design. Start date: May 1, 2005. Expires: April 30, 2006. Amount: $230,220. Principal investigator: Erin Duffy. Institution: Rib-X Pharmaceuticals. NIH institute: NIGMS.

Project aims to extend and validate computational methods and protocols for treating accurately the interactions among RNA, ions, and ligands. The project will develop a computational approach to identify ion-binding sites and preferences in RNA model systems, explore nucleic acid flexibility in simulating RNA systems, and identify an energy scoring function for explaining and predicting the binding of small molecules to RNA systems.


Information Integration of Heterogeneous Data Sources. Start date: March 15, 2005. Expires: Feb. 28, 2007. Amount: $260,661. Principal investigator: Mansur Kabuka. Institution: Infotech Soft. NIH institute: NCRR.

Funds development of an information integration architecture and associated tools to support rapid integration of data and knowledge from distributed heterogeneous data sources for biomedical research. The proposed architecture includes new generalized integration algorithms and tools for the generation of mediators to capture the functional behavior of data sources, semantic representation of data sources to support automated generation of integration agents, and optimization of integrated data queries.


System to Predict Novel Genetic Disease Associations. Start date: May 3, 2005. Expires: Oct. 31, 2005. Amount: $99,757. Principal investigator: Martin Reese. Institution: Omicia. NIH institute: NHGRI.

SBIR grant supports development of a genetics-based informatics infrastructure that can be used to predict the functional outcome of gene mutations and their relationship to human disease by integrating diverse knowledge bases. The technology will mine classification systems for large numbers of genes and create statistical associations as well as integrate ontologies to allow for reliable inferences about functions of genes and their relation to disease phenotypes. The predictive capabilities of the technology are expected to assign functions to orphan genes and genetic markers for which very little functional information is available.

Filed under

The Scan

For Better Odds

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Booster Decision Expected

The New York Times reports the US Food and Drug Administration is expected to authorize a booster dose of the Pfizer-BioNTech SARS-CoV-2 vaccine this week for individuals over 65 or at high risk.

Snipping HIV Out

The Philadelphia Inquirer reports Temple University researchers are to test a gene-editing approach for treating HIV.

PLOS Papers on Cancer Risk Scores, Typhoid Fever in Colombia, Streptococcus Protection

In PLOS this week: application of cancer polygenic risk scores across ancestries, genetic diversity of typhoid fever-causing Salmonella, and more.