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Funding Update: NSF Bioinformatics Awards Through Dec. 6, 2003


“Regulography” — Quantitative Reconstruction of Transcriptional Regulatory Networks. Start date: Dec. 1, 2003. Expires: Oct. 31, 2007. Expected total amount: $2,528,019. Principal investigator: James Liao. Sponsor: University of California, Los Angeles.

Project to reconstruct the structure and dynamics of transcriptional regulatory networks based on gene expression data from microarray experiments and other information, such as protein interactions with DNA, other proteins, and RNA. The goal is to create an integrated analytical and IT framework, incorporating methodology and databases, to deduce transcriptional network structure and dynamics, which can be applied to define the signal transduction pathways perturbed by unknown drug effects, toxic compound challenges, and mutations. The grantees are using Saccharomyces cerevisiae as the model eukaryote for verification of the approach.

Theory and Software Infrastructure for a Scalable Systems Biology. Start date: Dec. 15, 2003. Expires: Nov. 30, 2007. This grant is awarded to three investigative teams:

  • California Institute of Technology. Principal investigator: John Doyle. Expected total amount: $1,300,000.
  • University of California, Santa Barbara. Principal investigator: Mustafa Khammash. Expected total amount: $575,000.
  • University of California, San Francisco. Principal investigator: Carol Gross. Expected total amount: $275,000.

Collaborative project to develop the theoretical foundation and information technology infrastructure to support progress in systems biology. Goals include augmenting existing bioinformatics and modeling and simulation approaches with a better understanding of the organizational principles underlying network complexity, including connections with molecular details, and using this understanding to advance mainstream experimental biology.

Use of a Visual Programming Environment to Promote Bioinformatics Education. Start date: Jan. 1, 2004. Expires: June 30, 2004. Expected total amount: $100,000. Principal investigator: Maciek Sasinowski. Sponsor: Incogen.

SBIR Phase I project to create a visual programming environment for bioinformatics education. The work will be based on Incogen’s VIBE (Visual Integrated Bioinformatics Environment) software. Expected users of the resulting educational software will be individual bioinformatics professors and students, as well as departments and universities that offer bioinformatics degrees.


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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.