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


Principled Methods for Very Large-Scale Causal Discovery. Amount: $199,320. Start date: Aug. 2003. Expires: July 2006. Principal investigator: Constantin Aliferis. Institution: Vanderbilt University. NIH Institute: NLM.

Project to develop methods for very large-scale principled causal discovery that scale up to massive datasets such as the ones found in bioinformatics, electronic patient records, and bibliographic systems. Algorithms will be applied to gene expression data from patients with lung cancer and data from a large epidemiologic analysis of factors that influence development of breast cancer in patients with non-invasive breast disease.


Comparative Approaches to Bio-knowledge Discovery. Amount: $396,250. Start date: Aug. 2003. Expires: July 2006. Principal Investigator: Junhyong Kim. Institution: University of Pennsylvania. NIH Institute: NIGMS.

Supports an organization at the University of Pennsylvania and the Children’s Hospital of Philadelphia that will serve as a central conduit of biomedical computing research for three schools and six research institutes. Four projects will be funded in the first year: pattern discovery in comparative genomics; computational phylogeny reconstruction; comparative text mining for cancer research; and a comparative informatics approach to sickle-cell disease.


Computational Approaches to Disease Causes and Treatment. Amount: NA. Start date: Aug. 2003. Expires: July 2006. Principal investigator: Aidong Zhang. Institution: State University of New York at Buffalo. NIH Institute: NIGMS.

Supports a National Program of Excellence in Biomedical Computing with the theme, “Novel Data Mining Algorithms for Applications in Genomics” with a focus on the development of novel techniques for storing, managing, analyzing, modeling and visualizing multi-dimensional data sets. Computational projects will include data integration and data mining of clinical data and genomic data; pharmacodynamic analysis of drug-responsive gene expression changes; and chemi-genetic approaches to mapping regulatory pathways.


Integrated Methods to Discover Novel Disease Pathways. Amount: $235,381. Start date: Aug. 2003. Expires: Jan. 2004. Principal investigator: Richard Del Mastro. Institution: Genome Therapeutics. NIH Institute: NIA.

Project to create an “integrated knowledge workbench” to integrate genes with no experimental functional data within protein interaction network maps. A subset of 1,241 genes has already been identified to populate a prototype database.


Infrastructure equipment for gene expression analysis. Amount: $188,256. Start date: Aug. 2003. Expires: July 2004. Principal investigator: Sorin Draghici. Institution: Wayne State University. NIH Institute: NCRR.

Funds the purchase of a dedicated SunFire server to support a campus-wide enterprise system for the collection, storage, management, and analysis of the microarray data generated by the large group of NIH funded PIs currently undertaking gene expression experiments. The server is a SunFire V880 with eight 750 MHz CPUs with 8 MB memory.


The CRW Project: A Comparative Database of RNA Molecules. Amount: 220,715. Start date: Sept. 2003. Expires: Aug. 2007. Principal investigator: Robin Gutell. Institution: University of Texas, Austin. NIH Institute: NIGMS.

Supports curation and maintenance of the Comparative RNA Website (CRW) and database, which currently contains approximately 14,500 rRNA, group I and II intron, and tRNA sequences, nearly 450 secondary structure and conservation diagrams, alignments for these sequences, nucleotide frequency information, and a database of introns in the rRNAs.


Maintenance and Development of RepeatMasker and Gestalt. Amount: NA. Start date: Aug. 2003. Expires: June 2006. Principal investigator: Arian Smit. Institution: Institute for Systems Biology. NIH Institute: NHGRI.

Funds maintenance and further development of RepeatMasker, a computational tool for identification and characterization of interspersed repeats, and the Gestalt graphical user interface for detailed visualization of RepeatMasker results in their genomic context.


Bioinformatics of a Gene Interaction Map. Amount: NA. Start date: Jan. 2004. Expires: NA. Principal investigator: Daniel Yuan. Institution: Johns Hopkins University. NIH Institute: NHGRI.

Project will test a novel microarray design for sharpening the precision of experimental results and develop an object database for facilitating access to functional genomic data across multiple levels of abstraction.

Institution: Johns Hopkins University. Amount: NA. Start date: Jan. 2004. Expires: NA. NIH Institute: NHGRI.


In Silico Analysis of Ocular Genes and Proteins. Amount: NA. Start date: Aug. 2003. Expires: July 2007. Principal investigator: John Michon. Institution: Duke University. NIH Institute: NEI.

Project for in silico analysis of genes and their protein products expressed in ocular tissues using statistical and machine learning techniques.


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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.