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BioInform s Funding Update: NSF Bioinformatics Awards to May 22, 2004

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New Development on Nonparametric Modeling and Inferences with Biological Applications. Start date: June 2004. Expires: May 2007. This grant is awarded to three investigative teams:

  • University of California, Davis. Principal investigator: Hans-Georg Mueller. Expected total amount: $282,000.
  • Princeton University. Principal investigator: Jianqing Fan. Expected total amount: $552,000.
  • University of Wisconsin Madison. Principal investigator: Chunming Zhang. Expected total amount: $216,000.

Proposal to develop semi-parametric and non-parametric approaches to solve statistical problems in computational biology, including normalization and analysis of microarray and proteomic data, covariate effects on longitudinal and functional data, and prediction of individual response trajectories.


Computational Design of Proteins. Start date: May 2004. Expires: March 2007. Expected total amount: $170,000. Principal investigator: Tracy Handel. Sponsor: University of California, Berkeley.

Funds the development of computational methods to design novel proteins. As a demonstration of a practical application, natural proteins containing disulfide bonds will be redesigned to remove the disulfide bonds.


Modeling of Graphs, Networks and Trees for Genomic Applications: High-Dimensional Model Search. Start date: July 2004. Expires: June 2009. Expected total amount: $364,000. Principal investigator: Mike West. Sponsor: Duke University

Supports development of computational tools for statistical modeling with applications in functional genomics. The researchers will investigate models and computational methods for very large-scale graphical models — especially Gaussian graphical models and very sparse model structures — as representatives of the structure and patterns of association between biological variables from observed and experimental data. The research is coupled with an integrated collection of genomic studies that provide data, biological collaborators, and applications in functional genomics in several areas of cancer and cardiovascular biology, pathway studies in cell cycle regulation and oncogenesis, cancer proteomics, transcription regulation, and other areas.


Multi-study Genomic Data Analysis. Start date: May 2004. Expires: April 2009. Expected total amount: $365,126. Principal investigator: Giovanni Parmigiani. Sponsor: Johns Hopkins University.

Project to develop statistical approaches for multi-study genomic data analysis. Specific targets include the application of meta-analysis tools used in medicine and social sciences to the field of genomics, metrics for evaluating reproducibility of expression measurements across different platforms, and approaches for deriving and validating common expression scales across platforms.


Sufficient Dimension Reduction for High Dimensional Data with Applications in Bioinformatics. Start date: July 2004. Expires: June 2007. This grant is awarded to two investigative teams:

  • Pennsylvania State University, University Park. Principal investigator: Hongyuan Zha. Expected total amount: $85,067.
  • University of Minnesota, Twin Cities. Principal investigator: Ralph Cook. Expected total amount: $88,173.

A proposal to develop optimal dimension reduction methods with an emphasis on bioinformatics applications. The new optimal reduction methods will permit investigators to derive model-free tests of conditional independence, which are “roughly” equivalent to t-tests on coefficients in model-based linear regression, according to the researchers.


Greater Philadelphia Bioinformatics Alliance. Start date: May 2004. Expires: April 2006. Expected total amount: $295,926. Principal investigator: Aydin Tozeren. Sponsor: Drexel University

Supports development of a “virtual network” of universities, industry, government agencies, and venture capitalists in southeast Pennsylvania to promote computational biology in the region. Partners include Drexel University, Pennsylvania State University Great Valley, Temple University, Thomas Jefferson University, the University of Pennsylvania, University of the Sciences in Philadelphia, Children’s Hospital of Philadelphia, Fox Chase Cancer Research Center, Wistar Institute, and the Biotechnology Greenhouse Corporation. Objectives include developing and maintaining a skilled workforce; catalyzing innovation in bioinformatics; and fostering an infrastructure for commercialization of innovation.

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The Scan

Study Tracks Off-Target Gene Edits Linked to Epigenetic Features

Using machine learning, researchers characterize in BMC Genomics the potential off-target effects of 19 computed or experimentally determined epigenetic features during CRISPR-Cas9 editing.

Coronary Artery Disease Risk Loci, Candidate Genes Identified in GWAS Meta-Analysis

A GWAS in Nature Genetics of nearly 1.4 million coronary artery disease cases and controls focused in on more than 200 candidate causal genes, including the cell motility-related myosin gene MYO9B.

Multiple Sclerosis Contributors Found in Proteome-Wide Association Study

With a combination of genome-wide association and brain proteome data, researchers in the Annals of Clinical and Translational Neurology tracked down dozens of potential multiple sclerosis risk proteins.

Quality Improvement Study Compares Molecular Tumor Boards, Central Consensus Recommendations

With 50 simulated cancer cases, researchers in JAMA Network Open compared molecular tumor board recommendations with central consensus plans at a dozen centers in Japan.