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BioInform s Funding Update: Recent NIH Awards in Bioinformatics: Nov 1, 2004

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An Optical Map-Assisted Assembler. Start date: Sept. 2004. Expires: March 2005. Amount: $99,767. Principal investigator: Christie Robertson. Institution: Geospiza. NIH institute: NHGRI.

Phase I SBIR supports development of a map-assisted assembler in which data from optical mapping are integrated into a re-engineered Phrap assembler.


Genomic Pathway Storage, Documentation in Graph-like Structures. Start date: Sept. 2004. Expires: March 2005. Amount: $100,000. Principal investigator: Ronald Blanford. Institution: Alodar Systems. NIH institute: NHGRI.

Phase I SBIR supports development of tools that will link repositories of biochemical pathway information via a graph-like annotation system.


Fast Biosequence Annotation via Reconfigurable Hardware. Start date: Sept. 2004. Expires: Aug. 2006. Amount: $156,462. Principal investigator: Jeremy Buhler. Institution: BECS Technology. NIH institute: NHGRI.

Proposal to construct a hardware-based biosequence accelerator that combines the flexibility of reconfigurable FPGA logic with a new architecture that ties the comparison logic closely to an array of hard disks.


Toward a Computation Center for Biomolecular Complexes. Start date: Sept. 2004. Expires: July 2007. Amount: $645,999. Principal investigator: Wah Chiu. Institution: Baylor College of Medicine. NIH institute: NCRR.

Supports computational resources to study the structural biology of biomolecular complexes larger than 0.5 megaDaltons.


Predicting Impact of Mutations on Proteins. Start date: Sept. 2004. Expires: Aug. 2007. Amount: $42,976. Principal investigator: Rachel Karchin. Institution: University of California, San Francisco. NIH institute: NIGMS.

Project will develop a computational method to predict the functional effects of non-synonymous SNPs using a combination of features derived from multiple sequence alignments, experimental structures , and comparative models.


Comparative Cross-Species Genomic Analysis System. Start date: Sept. 2004. Expires: Aug. 2007. Amount: $350,000. Principal investigator: Simon Kasif. Institution: Boston University Charles River Campus. NIH Institute: NHGRI.

Proposal to develop a general computational framework for comparative analysis of genomic sequences based on evidence integration frameworks.


The ProPhylER Database and Web Resource. Start date: Sept. 2004. Expires: Aug. 2007. Amount: $467,580. Principal investigator: Arend Sidow. Institution: Stanford University. NIH institute: NHGRI

Supports development of the ProPhylER (Protein Phylogeny and Evolutionary Rates) database, which will include quantitative estimates of local constraint on orthologs and closely related paralogs.


Application of Bioinformatics to Retinal Gene Regulation. Start date: Sept. 2004. Expires: Aug. 2007. Amount: $163,500. Principal investigator: Jiang Qian. Institution: Johns Hopkins University. NIH institute: NEI.

Supports development of two algorithms to help decipher transcriptional regulatory networks: one for discovering cis-regulatory motifs and another for predicting transcription factor targets.


Detecting relations among heterogeneous genomic datasets. Start date: Sept. 2004. Expires: Aug. 2007. Amount: $400,000. Principal investigator: William Noble. Institution: University of Washington. NIH institute: NHGRI.

Funds development of a computational framework for integrating and drawing inferences from heterogeneous data using concepts from machine learning.


Developing Genome Fingerprint Scanning for Proteomics. Start date: Sept. 2004. Expires: Aug. 2007. Amount: $313,502. Principal investigator: Michael Giddings. Institution: University of North Carolina, Chapel Hill. NIH institute: NCRR.

Funds development of the Genome Fingerprint Scanning program, which can match MS and MS/MS data directly to raw, unannotated sequence to identify proteins and locate novel genes.


Technology Development for a Molecular Biology Knowledge-Base. Start date: Sept. 2004. Expires: Sept. 2007. Amount: $577,307. Principal investigator: Lawrence Hunter. Institution: University of Colorado Health Sciences Center. NIH institute: NLM.

Proposal to use computational technology and human-curated knowledge resources to build a computational knowledgebase of molecular biology.


Informatics for Integrating Biology and the Bedside. Start date: Sept. 2004. Expires: July 2009. Amount: $3,925,000. Principal investigator: Isaac Kohane. Institution: Brigham and Women’s Hospital. NIH institute: NLM.

Funds development of a scalable computational and organizational framework for conducting clinical research in and across large multidisciplinary academic medical centers that “fully exploits the fruit of the genomic revolution for clinical practice.”


Center for Computational Biology (CCB). Start date: Sept. 2004. Expires: July 2009. Amount: $3,925,000. Principal investigator: Arthur Toga. Institution: University of California, Los Angeles. NIH institute: NCRR.

Supports a new Center for Computational Biology with the goals of applying computational and mathematical approaches to the study of genes, cells, systems, and the whole brain.


Computational Tools for Neutron Protein Crystallography. Start date: Sept. 2004. Expires: Aug. 2009. Amount: NA. Principal investigator: Paula Langan. Institution: University of California/Los Alamos National Laboratory. NIH institute: NIGMS.

Project to develop a set of computational tools for neutron protein crystallography.


Genetic Regulatory Networks: Comp. & Ext. Investigations. Start date: Sept. 2004. Expires: Aug. 2009. Amount: $218,950. Principal investigator: Ily Shmulevich. Institution: University of Texas MD Anderson Cancer Center. NIH institute: NIGMS.

Project to model the genetic regulatory system and infer the model structure and parameters from gene expression data.


MIT EECS/Whitehead/Broad Training Program in Computational Biology. Start date: Sept. 2004. Expires: Aug. 2009. Amount: $43,476. Principal investigator: David Gifford. Institution: Massachusetts Institute of Technology. NIH institute: NIDDK.

Supports a new interdisciplinary research training program in computational biology as a collaborative effort between MIT, the Whitehead Institute, and the Broad Institute.


Statistical Methods for the Analysis of Microarray Data. Start date: Sept. 2004. Expires: Aug. 2009. Amount: $224,957. Principal investigator: Debashis Ghosh. Institution: University of Michigan, Ann Arbor. NIH institute: NIGMS.

Funds development of statistical procedures for modeling complex high-dimensional biological data with an emphasis toward incorporating functional biological knowledge. Methods will be developed for assessing the role of functional pathways based on integration of gene expression and pathway data.

 

Filed under

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.