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BioInform s Funding Update: Some Recent NIH Awards in Bioinformatics: Dec 1, 2003

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A Homotopy Method for Predicting the Lowest Energy Conformations of Proteins. Start date: Sept. 2003. Expires: Sept. 2005. Amount: $45,725. Principal investigator: Daniel Dunlavy. Institution: University of Maryland College Park. NIH institute: NLM.

Proposes a new computational technique for predicting the state of lowest energy for proteins called the homotopy method, which creates a mapping of low energy states between two sequences of amino acids and follows this mapping from the state of lowest energy of one sequence to the lowest state of energy of the other. The goal of the project is to implement the homotopy method for use with data from the Protein Data Bank in order to map the lowest energy state of proteins with known tertiary structure to the lowest energy state of proteins with unknown tertiary structure.


Biostatistics and Bioinformatics. Start date: Sept. 2003. Expires: Aug. 2008. Amount: NA. Principal investigator: Seng-Jaw Soong. Institution: University of Alabama at Birmingham. NIH institute: NCI.

Establishes a core facility to provide specialized statistical and bioinformatics services to the research projects of the Cooperative Specialized Center for Nutrient-Gene Interaction in Cancer (CNGI) at the University of Alabama. The core will provide statistical expertise in study design, as well as existing and newly developed analytical techniques for microarray data and epidemiological studies, among other goals.


Genomics and Proteomics in High-Dimensional Biology. Start date: Sept. 2003. Expires: Aug. 2008. Amount: NA. Principal investigator: David Allison. Institution: University of Alabama at Birmingham. NIH institute: NCI.

Proposal to develop statistical methods for the design and analysis of high-dimensional biological studies, including experiments involving any combination of thousands of genetic polymorphisms, gene expression levels, protein measurements, or exposure variables as in the case of nutrient or toxicology studies.


Developing tools for finding novel full-length sequences. Start date: March 2004. Expires: NA. Amount: $41,608. Principal investigator: Thomas Bair. Institution: University of Iowa. NIH institute: NHGRI.

Supports development of classification techniques for identifying full-length cDNA clones based on single-pass 5’ EST data. The pipeline will use primarily homology-based methods to identify ESTs that should be selected for full insert sequencing and assembly. Software will also be developed to identify ESTs that are candidates for full-length sequencing that do not have evidence for this assignment from homology to known genes.

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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.