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Funding Update: NSF Bioinformatics Grants Awarded Dec. 21, 2011 — Feb. 24, 2012

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Predicting and Mining Phenome-Genome Association across Species
Start Date: Aug. 1, 2012
Expires: July 31, 2017
Awarded Amount to Date: $83,847
Principal Investigator: Rui Kuang
Sponsor: University of Minnesota, Twin Cities

Supports the development of computational methods that will be used to predict and understand phenome-genome association across multiple species. According to the investigators, the project will yield a web portal called Phenome-Genome Explorer as well as a collection of tools that researchers could use to prioritize genes and test their association with phenotypes. Specifically, the methods will be used to study associations in ovarian and lung cancer phenotypes as well as the growth phenotypes of Arabidopsis thaliana to identify genes that govern seedling de-etiolation and seed development.


A Modular, Community Based Design Platform for Synthetic Biology (Clotho)
Start Date: May 1, 2012
Expires: April 30, 2015
Awarded Amount to Date: $357,234; $92,042
Principal Investigators: Douglas Densmore; John Anderson
Sponsors: Trustees of Boston University; University of California, Berkeley

The funds will support the development of the Clotho software platform for synthetic biology. According to the abstract, Clotho links biological databases to user-created apps through a common interface that reflects a data model specifically tailed to synthetic biology. These apps can then be used to “create design flows covering high level specification of biological functionality all the way down to basic sample tracking and laboratory management.”


Exploring the 3D Structure Organization of Genomes
Start Date: April 1, 2012
Expires: March 31, 2017
Awarded Amount to Date: $163,504
Principal Investigator: Douglas Densmore
Sponsor: University of Southern California

The funds will be used to develop methods to study the three-dimensional spatial organization of genomes. It will include tools to combine large-scale data sources; identify functional units in the 3D structures; and characterize structural elements in genome architectures through image analysis.


The Scan

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.

Lupus Heterogeneity Highlighted With Single-Cell Transcriptomes

Using single-cell RNA sequencing, researchers in Nature Communications tracked down immune and non-immune cell differences between discoid lupus erythematosus and systemic lupus erythematosus.

Rare Disease Clues Gleaned From Mobile Element Insertions in Exome Sequences

With an approach called MELT, researchers in the European Journal of Human Genetics uncovered mobile element insertions in exomes from 3,232 individuals with or without developmental or neurological abnormalities.

Team Tracks Down Potential Blood Plasma Markers Linked to Heart Failure in Atrial Fibrillation Patients

Researchers in BMC Genomics found 10 differentially expressed proteins or metabolites that marked atrial fibrillation with heart failure cases.