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NSF Bioinformatics Grants, April 16 -- May 13, 2006

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Multi-Way Semilinear Methods with Applications to Microarray Data. Start date: July 1, 2006. Expires: June 30, 2009. Expected total amount: $139,586. Principal investigator: Cun-Hui Zhang. Sponsor: Rutgers University New Brunswick.

Supports development of statistical models, methods, and theory for normalization and significance analysis of microarray data and similar applications. The grantees have proposed and developed a two-way semilinear model for normalization and analysis of cDNA microarray data, and the current project will extend and further develop this methodology.


Identification and Modeling of Cells. Start date: July 1, 2006. Expires: June 30, 2007. Expected total amount: $239,993. Principal investigator: Er-Wei Bai. Sponsor: University of Iowa.

Funds development of an identification method for cell modeling. The approach will build a mathematical model based on cells' physiological and electrical properties and then validate the model experimentally.


Mapping Biological Networks. Start date: May 15, 2006. Expires: April 30, 2007. Expected total amount: $527,452. Principal investigator: Joel Bader. Sponsor: Johns Hopkins University.

Supports development of methods to predict specific interactions between protein transcription factors and DNA regulatory elements purely from genome sequence and inferred protein structure using all-atom, explicit solvent simulations of transcription factors bound to DNA. New algorithms will be developed for protein-DNA simulations and binding site predictions. In a complementary effort, the human protein-protein interaction network will be analyzed at the domain level and the topological organization of protein subunits within protein complexes will be predicted.


Theoretical Studies of Protein Folding. Start date: May 15, 2006. Expires: April 30, 2007. Expected total amount: $861,773. Principal investigator: Harold A. Scheraga. Sponsor: Cornell University.

Project intends to gain an understanding of how inter-residue interactions determine the three-dimensional structure of a globular protein and the pathways from the unfolded polypeptide chain to the final folded conformation. The researchers will use a physics-based approach that is based solely on the global optimization of a potential energy function, without the use of secondary-structure predictions, homology modeling, or threading.

 

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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.