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BioInform s Funding Update: NSF Awards in Bioinformatics through July 19, 2003

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Design and Development of a Unified Object-Oriented Software Platform for Biomolecular Computations. Start date: July 1, 2003. Expires: Dec. 31, 2003. Expected total amount: $100,000. Principal investigator: Jeyapandian Kottalam. Sponsor: Kuyilan BioSoft.

Phase I SBIR supports the design and construction of an object-oriented software development platform in Java for sequence manipulations, storage in relational databases, molecular mechanics computations, and three-dimensional structure visualization of protein and DNA.


A Bioinformatics System for GCxGC-MS (Comprehensive Two-Dimensional Gas Chromatography). Start date: July 1, 2003. Expires: Dec. 31, 2003. Expected total amount: $100,000. Principal investigator: Stephen Reichenbach. Sponsor: GC Imaging.

Phase I SBIR supports development of a bioinformatics system for analyzing data from two-dimensional gas chromatography with mass spectrometry. The proposed software will provide a graphical user interface, data handling methods, a manipulation language, and a metadata schema for GCxGC-MS data.


Improving Overlap-Finding Techniques for Whole-Genome Shotgun Data. Start date: July 15, 2003. Expires: June 30, 2005. Expected total amount: $99,375. Principal investigator: James Yorke. Sponsor: University of Maryland, College Park.

Project will focus on producing a robust set of overlapping genome fragments, using a combination of error-correction techniques and a method for localizing fragments to ensure that both fragments come from the same vicinity of the genome.


Robust Tools for Biological Sequence Analysis. Start date: Aug. 1, 2003. Expires: Aug. 31, 2007. Expected total amount: $500,498. Principal investigator: John Kececioglu. Sponsor: University of Arizona.

Project to develop a suite of open source software tools for aligning protein sequences, especially those of whole genomes. The program will focus on two issues: very specifically aligning small areas of protein sequences and less specifically aligning many sequences together.


The Ribosomal Database Project: Automation, Integration, and Education. Start date: Aug. 1, 2003. Expires: July 31, 2008. Expected total amount: $750,000. Principal investigator: James Tiedje. Sponsor: Michigan State University.

Project to create a repository of ribosomal (rRNA) sequences that will provide automated sequence harvesting, alignment, and annotation procedures along with new phylogeny and ecology tools.


Algorithmic Problems in Haplotyping, Oligonucleotide Fingerprinting, and NMR Peak Assignment. Start date: Sept. 1, 2003. Expires: Aug. 31, 2006. Expected total amount: $200,000. Principal investigator: Tao Jiang. Sponsor: University of California, Riverside.

Project will address three algorithmic problems in computational biology: inferring haplotype configurations from genotype data based on the Mendelian law of inheritance; resolving missing values in cluster analysis for oligonucleotide fingerprinting; and assigning NMR peaks to individual amino acids.


ARCiB — Accessible Retired Computers in Biology. Start date: Sept. 1, 2003. Expires: Aug. 31, 2006. Expected total amount: $95,272. Principal investigator: Herbert Bernstein. Sponsor: Dowling College.

Project will build an archiving facility to preserve “previous but still very useful” versions of software for processing biological data. There is also a component for maintaining outdated pieces of hardware to act as a testbed for backward compatibility of new programs.


Algorithms for the Discovery and Geometric-Matching of Hierarchical 3-D Templates of Functional Sites in Protein Structures. Start date: Sept. 1, 2003. Expires: Aug. 31, 2006. Expected total amount: $896,527. Principal investigator: Olivier Lichtarge. Sponsor: Baylor College of Medicine.

Project to develop algorithms to identify functional sites in protein structures using the Evolutionary Trace method, which uses evolutionary data to identify key functional residues in proteins.


Developing an Integrated Toolkit to Explore Code/Genome Interaction. Start date: Nov. 1, 2003. Expires: Oct. 31, 2006. Expected total amount: $548,302. Principal investigator: Stephen Freeland. Sponsor: University of Maryland, Baltimore County.

Grant supports development of web-based software with improved algorithms for homology detection, synthetic gene design, and predicting protein structure from sequence data. Among other functions, the software will predict the relative rates at which amino acids interchange over evolutionary time.

 

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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.