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Funding Update: Apr 1, 2011 (rev. 1)


NSF Bioinformatics Grants Awarded Feb. 10, 2011 — April 1, 2011

Synthetic Sequence Designs for Real Biology
Start Date: April 15, 2011
Expires: March 31, 2014
Awarded Amount to Date: $497,915
Principal Investigator: Steven Skiena
Sponsor: State University of New York, Stony Brook

The grant abstract states that the funds will be used to "unify, generalize, and expand" algorithmic design techniques for synthetic biology into a set of tools to address experimental problems in microbiology. As part of the project, the investigators will develop algorithms for "the large-scale design of diverse coding sequences [that] will allow researchers to exploit array-based synthesis technologies and assay their performance" as well as "build on restriction-site placement algorithms to produce a web-accessible genome factorization tool."

Model-based Reconstruction of Ancient Biological Networks
Start Date: April 01, 2011
Expires: March 31, 2012
Awarded Amount to Date: $79,620
Principal Investigator: Carleton Kingsford
Sponsor: University of Maryland, College Park

Supports the development of new algorithms for recovering ancient biological networks from present-day networks as well as the creation of "realistic" computational models of network evolution. Specifically, the algorithms will be used to find "precursor networks of a single network at various points in time and to find the common ancestor network of several extant organisms."

Sparse-sampling inference for functional proteomics, metabolomics, and ionomics
Start Date: April 01, 2011
Expires: March 31, 2014
Awarded Amount to Date: $323,983
Principal Investigator: Olga Vitek
Sponsor: Purdue University

The funds will be used to develop statistical and computational tools for functional proteomics, metabolomics, and ionomics that will address three aims. These include accurate identification and quantification of proteins, metabolites, and ions from high-throughput experiments; joint interpretation and integration of heterogeneous datasets; and optimal design of global and targeted follow-up experiments.

Scalable Computational Models for Multicellular Systems Biology
Start Date: April 01, 2011
Expires: March 31, 2014
Awarded Amount to Date: $592,331
Principal Investigator: Curtis Huttenhower
Sponsor: Harvard University

Supports a project that aims to provide a general framework for genomic data mining in multicellular systems, particularly microbial communities and their interactions with metazoan tissues, with a simple interface for summarizing thousands of genome-scale datasets. The investigators will also develop satellite models for machine learning in which core properties and parameters are modified on an as-needed basis.

Computational Methods for Analyzing Large-Scale Genomic Changes in Mammalian Genomes
Start Date: March 01, 2011
Expires: February 29, 2012
Awarded Amount to Date: $125,000
Principal Investigator: Jian Ma
Sponsor: University of Illinois, Urbana-Champaign

The funds will be used to develop new ancestral genome reconstruction algorithms that handle rearrangements, duplications, and large insertions and deletions at different resolutions in a single framework. The abstract states that the approach "focuses on building better synteny blocks between genomes and using these blocks in a hierarchical method to develop new reconstruction algorithms that are then refined to smaller blocks and dealing with incomplete lineage sorting." These tools will be used to improve genome assemblies based on next-generation sequencing reads as well as to investigate genomic regions that are affected by changes in the genome.

Bioinformatic FPGA Appliance
Start Date: March 01, 2011
Expires: February 28, 2013
Awarded Amount to Date: $500,000
Principal Investigator: Vincent Natoli
Sponsor: Stone Ridge Technology

The funds will be used to build a field programmable gate array-based bioinformatics tool for processing DNA sequence data faster, at lower cost, and with less power.

Computational Analysis of Metagenomic Sequencing Data
Start Date: February 15, 2011
Expires: January 31, 2014
Awarded Amount to Date: $608,732
Principal Investigator: Ting Chen, Jed Fuhrman, Fengzhu Sun
Sponsor: University of Southern California, University Park

Supports the development of computational tools, such as better base-calling and SNP-calling methods and accurate clustering methods, that can detect microbial organisms' genome sequences in environmental samples and help understand "the diversity, and the temporal and spatial patterns of microbial communities." The investigators plan to develop mathematical, statistical, and computational tools to address biological questions such as which organisms are present in an environmental sample; what are the genetic variants of the organisms present; and how do the organisms change in the affected community, among others

OpenWetWare: A Collaborative Tool for Biological Knowledge Management and Dissemination
Start Date: May 3, 2010
Expires: April 30, 2011
Awarded Amount to Date: $209,644
Principal Investigator: Drew Endy
Sponsor: Stanford University

The funds will enhance an existing biological knowledge resource known as Open WetWare that enables researchers to "organize and disseminate protocols, interim and negative results, and contextual metadata generated during the execution of bench biology research." Specifically, the investigators will "establish leadership and technical infrastructure under a sustainable model, develop additional tools for expanding the types and organization of knowledge that is managed by the system, and implement a Wiki-based framework for distributing and supporting the software."

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