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NSF Bioinformatics Grants Awarded Feb. 29 — April 3, 2008

Building a Network of Plant Metabolic Pathway Databases and Communities. Start date: March 15, 2008. Expires: Feb. 28, 2009. Awarded amount to date: $486,674. Principal investigator: Seung Rhee. Sponsor: Carnegie Institution of Washington.
Supports the creation of a network of plant metabolism databases called PlantCyc, which will contain pathways from many plants, supported by experimental evidence for pathways, reactions, or enzymes. PlantCyc will be “initialized” with data from currently available plant metabolism databases such as AraCyc, TomatoCyc, RiceCyc, MedicagoCyc, and Soybase, according to the grant abstract. It will be used in conjunction with the MetaCyc metabolic pathway database as a reference database for creating multiple plant pathway genome databases. To build these databases, “putative enzyme sequences will be identified for each organism using several sequence analysis methods and Pathway Tools software will be used to generate the initial PGDBs from the annotated sequences,” the abstract states. “As each PGDB is built, all of the pathways and enzymes in the new PGDB will be validated and added to PlantCyc, and subsequently curated.”

Integrated Approaches to Mapping Genome to Phenome. Start date: April 15, 2008. Expires: March 31, 2009. Awarded amount to date: $123,499. Principal investigator: Xianghong Zhou. Sponsor: University of Southern California.
Funds the development of integrated approaches for genome-to-phenome mapping. The project will use genomics data, particularly public microarray data, together with the associated phenotypic and environmental context information “to reconstruct the biological basis of phenotypes,” according to the grant abstract. The investigators note in the abstract that “traditional association studies have been relatively successful at relating genetic polymorphisms to phenotypes. However, they have met difficulties in elucidating the gene-gene interactions that contribute to complex phenotypes.” The goal of the project, therefore, is to develop methods for deriving genome-wide molecular networks of genotype-phenotype associations, termed “phenomic associations.”

Computational Tools for Population Biology. Start date: May 1, 2008. Expires: April 30, 2013. Awarded amount to date: $504,930. Principal investigator: Tanya Berger-Wolf. Sponsor: University of Illinois at Chicago.
Supports a project to develop a computational framework for the emerging field of computational population biology. The investigators plan to develop techniques for inferring genetic relationships in wildlife populations and using them to predict genetic diversity; computational methods for analyzing dynamic social interactions, focusing on prediction of interaction patterns and dynamic processes within populations; and techniques for combining the genetic and the social structures of a population and across species to identify global ecological processes.

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The Scan

Unique Germline Variants Found Among Black Prostate Cancer Patients

Through an exome sequencing study appearing in JCO Precision Oncology, researchers have found unique pathogenic or likely pathogenic variants within a cohort of Black prostate cancer patients.

Analysis of Endogenous Parvoviral Elements Found Within Animal Genomes

Researchers at PLOS Biology have examined the coevolution of endogenous parvoviral elements and animal genomes to gain insight into using the viruses as gene therapy vectors.

Saliva Testing Can Reveal Mosaic CNVs Important in Intellectual Disability

An Australian team has compared the yield of chromosomal microarray testing of both blood and saliva samples for syndromic intellectual disability in the European Journal of Human Genetics.

Octopus Brain Complexity Linked to MicroRNA Expansions

Investigators saw microRNA gene expansions coinciding with complex brains when they analyzed certain cephalopod transcriptomes, as they report in Science Advances.