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NSF Bioinformatics Grants Oct. 22 — Nov. 25, 2006

Matrix Algorithms for Data Clustering and Nonlinear Dimension Reduction. Start date: Aug. 15, 2006. Expires: Aug. 31, 2007. Awarded amount to date: $146,342. Principal investigator: Hongyuan Zha. Sponsor: Georgia Tech Research Corporation.
Funds the investigation of statistical and computational methods for “simultaneous clustering of data matrices and their extensions to handle data hypercubes using spectral techniques,” according to the grant abstract. The goal of the project is to develop clustering algorithms that can, for example, find subsets of genes that behave similarly across subsets of conditions. The techniques are based on spectral methods for simultaneous clustering of data matrices and will have applications in bioinformatics and text analysis.

OpenBio Workbench for Sharing of Mathematical Models in Drug Discovery. Start date: Jan. 1, 2007. Expires June 30, 2007. Expected total amount: $100,000. Principal investigator: Taeshin Park. Sponsor: RES Group.
Phase I SBIR to test the feasibility of a software platform called OpenBio Workbench that will enable drug discovery researchers to access and share mathematical models and model results. According to the grant abstract, broad adoption of modeling has been limited “because the current practice requires programming and computational skills not typically possessed by researchers in biological sciences.” The project will develop a code-generation technology that will “transform models from diverse heterogeneous sources into a Web-enabled GUI-driven form that can be readily used without the required modeling skills,” the abstract states.

Machine Vision-Based Quantification of Plant Growth and Development. Start date: Nov. 1, 2006. Expires: Nov. 30, 2007. Awarded amount to date: $567,885. Principal investigator: Edgar Spalding. Sponsor: University of Wisconsin, Madison.
Supports a pilot project to develop machine-vision technology for discovering phenotypes in mutant or naturally varying populations of plants. Project participants are developing a screening platform that employs electronic CCD cameras, robotic positioning devices, and custom computational tools to quantify and mathematically characterize the growth and development of structures such as roots, stems, and leaves. During the pilot phase, hardware, custom algorithms, and data management will be assembled into a platform that will be tested by screening root growth and gravitropism in a selected set of Arabidopsis mutants and recombinant inbred lines. The results will be linked to the TAIR database. The raw data will be available for the image-analysis community to assist in the development of new algorithms and classification techniques.

U.S. Contribution to the International Solanaceae Genome Effort. Start date: Dec. 1, 2006. Expires: Nov. 30, 2007. Awarded amount to date: $1,535,497. Principal investigator: James Giovannoni. Sponsor: Boyce Thompson Institute.
Supports the development of clone and informatic resources as part of an international consortium to sequence the euchromatin of all twelve tomato chromosomes. The project will provide a central repository and web interface for all sequence and annotation data and will develop integrated bioinformatics for genomic research in the Solanaceae and related taxa through the SOL Genome Network database ( This will include computationally mapping ESTs and other gene sequences from related species, such as potato, eggplant, pepper, and coffee, onto the tomato reference sequence in order to generate predictive sequence maps for those species.

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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.