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NIH Grants in Bioinformatics Awarded May 2005 -- June 2005

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Xenbase: a Xenopus Model Organism Database. Start date: May 15, 2005. Expires: Feb. 28, 2010. Amount: $410,755. Principal investigator: Peter Vize. Institution: University of Calgary. NIH institute: NICHD.

Project will create a model organism database dedicated to storing and interlinking Xenopus data. Over 400,000 Xenopus EST's are available, the Xenopus genome project has generated over 1.6 billion base pairs, over 500 whole mount sets of gene expression patterns are available, some 20,000 publications and an enormous amount of anatomical and histological data exists. The database will store, annotate, and analyze biological data on both Xenopus laevis and X. tropicalis.


High Performance Computing Cluster. Start date: June 1, 2005. Expires: May 31, 2005. Amount: $1,985,558. Principal investigator: RM Townsend. Institution: Cold Spring Harbor Laboratory. NIH institute: NCRR.

Proposal to improve and expand the computing infrastructure at Cold Spring Harbor Laboratory to meet the computational and data storage requirements for microarray experiments and comparative techniques in bioinformatics.


Raw Sequencing Data Processing and Base Calling. Start date: June 1, 2005. Expires: May 31, 2005. Amount: $171,653. Principal investigator: Cristian Domnisoru. Institution: University of St. Thomas. NIH institute: NHGRI.

Funds development of a software application for processing raw data obtained using DNA capillary electrophoresis sequencing machines and identifying the DNA bases in order to achieve an overall higher accuracy over existing techniques. The specific aims are to: collect a large number of data files (approximately 50,000), create a database including the correct base calls associated with each of the data files, develop a methodology for comparing the results of two base callers and incorporate the confidence values associated with each call into the assessment method, develop novel algorithms for processing the raw data, incorporate into the base-calling a model for the peak amplitudes, improve the current base-spacing model, and test the base-caller with the proposed database.


A Computer Cluster for Computational Biology. Start date: June 1, 2005. Expires: May 31, 2005. Amount: $500,000. Principal investigator: Ron Elber. Institution: Cornell University Ithaca. NIH institute: NCRR. Funds a computer cluster for computational biology and bioinformatics at Cornell University. The cluster will have 256 dual nodes connected with Giganet switches.


Supporting Expression Analysis Users with GenePattern. Start date: June 1, 2005. Expires: May 31, 2009. Amount: $467,013. Principal investigator: Jill Mesirov. Institution: Massachusetts Institute of Technology. NIH institute: NIGMS.

Supports continued development of the GeneCluster and GenePattern microarray analysis packages. Aims include continuing user support for the packages, enhancing GenePattern to better support users and their research, and continuing software maintenance of the packages.


Bayesian Methods for Mapping Complex Epistatic Genes. Start date: June 1, 2005. Expires: May 31, 2010. Amount: $240,308. Principal investigator: Nengjun Yi. Institution: University of Alabama at Birmingham. NIH institute: NIGMS.

Proposal to develop statistical methodologies and computer software for identifying multiple genes with complex interaction patterns using the Bayesian framework and Markov chain Monte Carlo algorithms.


Computational Reconstruction of Disease Pathways. Start date: June 1, 2005. Expires: Nov. 30, 2005. Amount: $99,324. Principal investigator: Andrej Bugrim. Institution: GeneGo. NIH institute: NIGMS.

Funds development of technology for automated functional analysis of large sets of high-throughput molecular data in the framework of human pathways. The proposed approach will allow rapid reconstruction of unique pathway/network motifs that closely correlate with given condition, disease, or phenotype. These networks could then serve as means for finding/validating drug targets and biomarkers, predicting response to a treatment, and designing a new generation of diagnostic tools, according to the grantees.


Genetic Network Inference with Combinational Phenotypes. Start date: June 21, 2005. Expires: May 31, 2010. Amount: $387,233. Principal investigator: Andrea Califano. Institution: Columbia University Health Sciences. NIH institute: NCI.

Proposal to develop methods for the reverse engineering of cellular genetic circuits from gene expression data. The investigators propose to reconstruct the genetic circuitry of human B-cells by coupling three distinct components: 1) an information theoretic method for the inference of cellular networks from microarray profile data for a large number of distinct cellular and molecular phenotypes; a synthetic network simulation framework for the assessment of the performance of the reverse engineering under a variety of constraints and conditions, such as noise and network complexity; and an adaptive learning method that will iteratively apply optimal perturbations to the biological system, which will allow refining the cellular network model over time.


Reconstructing Regulation Networks of Meiosis in Silico. Start date: July 1, 2005. Expires: June 30, 2005. Amount: $336,559. Principal investigator: Wei Wang. Institution: University of California San Diego. NIH institute: NIGMS.

Proposal to develop new bioinformatics methods for reconstructing the transcriptional network regulating yeast sporulation, which consists of meiosis and spore morphogenesis, by integrating genomic data from different sources. The specific aims are: to develop a new bioinformatics method to accurately construct transcription modules; to construct transcription modules of budding yeast sporulation using the above algorithm; and to predict transcription modules and network topologies of sporulation in six newly sequenced yeast genomes based on the network of budding yeast.

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The Scan

Genetic Risk Factors for Hypertension Can Help Identify Those at Risk for Cardiovascular Disease

Genetically predicted high blood pressure risk is also associated with increased cardiovascular disease risk, a new JAMA Cardiology study says.

Circulating Tumor DNA Linked to Post-Treatment Relapse in Breast Cancer

Post-treatment detection of circulating tumor DNA may identify breast cancer patients who are more likely to relapse, a new JCO Precision Oncology study finds.

Genetics Influence Level of Depression Tied to Trauma Exposure, Study Finds

Researchers examine the interplay of trauma, genetics, and major depressive disorder in JAMA Psychiatry.

UCLA Team Reports Cost-Effective Liquid Biopsy Approach for Cancer Detection

The researchers report in Nature Communications that their liquid biopsy approach has high specificity in detecting all- and early-stage cancers.