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BioInform s Funding Update: Some Recent NIH Awards in Bioinformatics: Jul 19, 2004

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Compact Encoding of Genomes using Delta Compression. Start date: June 2004. Expires: October 2004. Amount: $149,519. Principal investigator: Callum Bell. Institution: SeiraD. NIH institute: NHGRI.

Phase I SBIR proposal to test the feasibility of a new system for storing complete genome sequences based on applying delta compression to DNA sequence strings, which will allow an entire genome to be represented by a set of differences between a reference genome and a version genome. The method is expected to achieve 60-120 fold compression over a text representation of DNA.


Exact Inference Software for Correlated Categorical Data. Start date: June 2004. Expires: November 2004. Amount: $100,459. Principal investigator: Pralay Senchaudhuri. Institution: Cytel Software. NIH institute: NCRR.

Phase I SBIR supports development of computer software to perform small-sample exact inference for correlated categorical data for use in biomedical research.


Improved Modeling of RNA/DNA Hybridization. Start date: June 2004. Expires: December 2004. Amount: $119,365. Principal investigator: Hyung Lee. Institution: DNA Software. NIH institute: NHGRI.

Phase I SBIR funds an enhancement to DNA Software’s Oligonucleotide Modeling Platform platform to incorporate knowledge of thermodynamics and kinetics of nucleic acid folding and hybridization in order to improve the accuracy of RNA-DNA hybridization predictions.


NF-kappaB in B Tumor Cell: A Systems Biology Approach. Start date: June 2004. Expires: May 2007. Amount: $41,068. Principal investigator: Markus Covert. Institution: California Institute of Technology. NIH institute: NCI

Proposal to investigate the interactions of the upstream signal transducing proteins that regulate NF-kappaB activity in B cells, using a combined computational/experimental approach.


Parallel Computer. Start date: July 2004. Expires: June 2005. Amount: $1,526,201. Principal investigator: Jason Moore. Institution: Vanderbilt University. NIH institute: NCRR.

Proposal to build a 824-processor Beowulf computer system to support biomedical research at Vanderbilt University Medical School. The proposed system will be added to a 270-processor parallel computer that was recently installed as part of Vanderbilt’s new Scientific Computing Center.


FPGA-Based Computational Accelerators. Start date: July 2004. Expires: June 2006. Amount: $157,191. Principal investigator: Martin Herbordt. Institution: Boston University, Charles River Campus. NIH institute: NCRR

Proposal to augment PCs with FPGA-based, computational coprocessors for use in bioinformatics and computational biology applications. The projected deliverable is a factor of 100 to 1,000 speed-up over a PC for a wide variety of applications, together with an environment for the creation of new applications by ordinary programmers.


Management Software for Genetic Analysis (GeMS). Start date: July 2004. Expires: December 2004. Amount: $100,000. Principal investigator: Thomas Geraghty. Institution: Immunogenomics. NIH institute: NCRR

Phase I SBIR supports development of a genetics management system that is applicable in a general way to the management of data acquired from automatic DNA sequencers. The resource will support three types of data acquisition: PCR resequencing for SNP discovery and genotyping; shotgun sequencing projects; and genotyping methods that use capillary-based data acquisition.


Detection of natural selection from DNA sequence data. Start date: July 2004. Expires: June 2007. Amount: $100,860. Principal investigator: Richard Lewontin. Institution: Harvard University. NIH institute: NIGMS.

Project will use large-scale computer simulation of populations to ask under what conditions current statistical tests can actually detect selection and under what conditions an apparent detection of natural selection is really a consequence of the fact that populations deviate in various ways from the underlying assumptions of the tests about population history and structure.


Creating software tools for whole genome comparison. Start date: July 2004. Expires: June 2007. Amount: $105,071. Principal investigator: John Karro. Institution: Pennsylvania State University, University Park. NIH institute: NHGRI

Supports development of new software tools to align three or more whole-genome sequences.


Intelligent Aids for Proteomic Data Mining. Start date: July 2004. Expires: June 2009. Amount: $122,697. Principal investigator: Vanathi Gopalakrishnan. Institution: University of Pittsburgh at Pittsburgh. NIH institute: NIGMS.

Proposal to develop computational aids for mining proteomic data from high-throughput techniques like SELDI-TOF mass spectrometry. Project aims include developing a wrapper-based machine learning tool and augmenting the tool with prior knowledge such as heuristic rules and relationships in the data.


G Protein Networks: Modeling, Simulation and Analysis. Start date: July 2004. Expires: June 2009. Amount: $140,400. Principal investigator: Marc Turcotte. Institution: University of Texas Southwestern Medical Center, Dallas. NIH institute: NIGMS.

Supports development of a computational model of signaling in a G protein module (receptor, heterotrimeric G protein, GTPase-activating protein, effector) to evaluate how elementary interactions within the module combine to produce its characteristic kinetic and dynamic behaviors.


OligoArray Design Software Development. Start date: August 2004. Expires: July 2006. Amount: NA. Principal investigator: Erdogan Gulari. Institution: University of Michigan, Ann Arbor. NIH institute: NIGMS.

Funds development of a software package dedicated to the design of oligonucleotides to make DNA microarrays for gene expression and genotyping analysis. This package will be built on the latest knowledge of the thermodynamics of DNA hybridization on chips.


Bayesian methods for analyzing genetic diversity. Start date: August 2004. Expires: July 2007. Amount: $126,000. Principal investigator: Kent Holsinger. Institution: University of Connecticut, Storrs. NIH institute: NIGMS.

Project will extend previously developed Bayesian methods to describe patterns of genetic variation in complex, hierarchically structured populations.


A Novel Probabilistic Engine for Virtual Screening. Start date: September 2004. Expires: February 2005. Amount: NA. Principal investigator: Richard Fine. Institution: Biocomputing Group. NIH institute: NIGMS

Phase I SBIR funds development of a probabilistic computational engine for docking-based virtual screening based on Markov random fields (MRFs), which have proven successful in other fields such as computer vision.

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