Features
Get A Demo
Plans
Sign Up
Login
All Federal Grant Awards
Help
Project Grant 1947257
Award Date
9/1/20
Completion Date
8/31/24
Dollars Obligated
$235K
Overview
Activity
6
Transactions
6
Subawards
Federal Agency
Division of Information and Intelligent Systems
Awardee
Milwaukee School Of Engineering (M6RCJVHKTHJ5)
Federal Grant Program
47.070
Assistance Type
Project Grant
Place of Performance
Milwaukee, WI 53202, USA
Description
Update #1
CRII: III: RUI: ASSOCIATION TESTING AND INVERSION DETECTION WITHOUT REFERENCE GENOMES
Posted 6/11/20, 12:00 AM
Mod #
Description
Reason For Modification
Federal Obligation
(Click to sort descending)
Date
(Click to sort ascending)
Not listed
CRII: III: RUI: ASSOCIATION TESTING AND INVERSION DETECTION WITHOUT REFERENCE GENOMES -THE LAST DECADE HAS SEEN THE COST OF DNA SEQUENCING PLUMMET. CONSEQUENTLY, THE POTENTIAL TO SEQUENCE THE GENOME OF EVERY LIVING ORGANISM IS WITHIN OUR GRASP. GENOME ASSEMBLIES OFTEN REQUIRE SIGNIFICANT POLISHING, WHICH IS OFTEN A MANUAL AND LABOR-INTENSIVE PROCESS. NEW METHODS ARE NEEDED TO DIRECTLY ANALYZE FRAGMENTED OR UNASSEMBLED GENOMIC DATA. ANALYSIS OF THESE GENOMES INCLUDE THE IDENTIFICATION OF PHYSICAL REARRANGEMENTS SUCH AS INVERSIONS. LARGE INVERSIONS HAVE SIGNIFICANT IMPACTS ON THE BIOLOGY OF ORGANISMS AND THEIR EVOLUTION. EXISTING COMPUTATIONAL METHODS FOR IDENTIFYING INVERSIONS HAVE BEEN PRIMARILY TESTED ON AND DEVELOPED FOR WELL-STUDIED, REFERENCE GENOMES. THIS PROJECT SEEKS TO DEVELOP NEW INVERSION DETECTION AND ASSOCIATION TESTING METHODS SUITABLE FOR THE LARGE AND GROWING NUMBER OF FRAGMENTED AND/OR UNASSEMBLED GENOMES THAT ARE BECOMING AVAILABLE. UNDERGRADUATE RESEARCH ASSISTANTS WILL BE FUNDED AS ACTIVE COLLABORATORS ON THE PROJECT. SO-CALLED K-MER METHODS HAVE BECOME POPULAR IN THE LAST DECADE FOR THE ANALYSIS OF UNASSEMBLED GENOMICS OR METAGENOMICS DATA. THIS PROJECT SEEKS TO UTILIZE K-MERS, UNSUPERVISED LEARNING, AND ASSOCIATION TESTING TO IDENTIFY INVERSIONS IN FRAGMENTED OR POORLY ASSEMBLED POPULATION GENOMICS DATA. SINCE MILLIONS OF ASSOCIATION TESTS WILL BE RUN PER DATA SET, THE METHODS WILL BE ACCELERATED USING GPUS. THE RESULTING METHOD AND SOFTWARE WILL BE DEVELOPED IN CONJUNCTION WITH UNDERGRADUATE RESEARCH ASSISTANTS AND RELEASED UNDER AN OPEN-SOURCE LICENSE. THIS AWARD REFLECTS NSF'S STATUTORY MISSION AND HAS BEEN DEEMED WORTHY OF SUPPORT THROUGH EVALUATION USING THE FOUNDATION'S INTELLECTUAL MERIT AND BROADER IMPACTS REVIEW CRITERIA.
$12.0k
4/24/24
Not listed
CRII: III: RUI: ASSOCIATION TESTING AND INVERSION DETECTION WITHOUT REFERENCE GENOMES -THE LAST DECADE HAS SEEN THE COST OF DNA SEQUENCING PLUMMET. CONSEQUENTLY, THE POTENTIAL TO SEQUENCE THE GENOME OF EVERY LIVING ORGANISM IS WITHIN OUR GRASP. GENOME ASSEMBLIES OFTEN REQUIRE SIGNIFICANT POLISHING, WHICH IS OFTEN A MANUAL AND LABOR-INTENSIVE PROCESS. NEW METHODS ARE NEEDED TO DIRECTLY ANALYZE FRAGMENTED OR UNASSEMBLED GENOMIC DATA. ANALYSIS OF THESE GENOMES INCLUDE THE IDENTIFICATION OF PHYSICAL REARRANGEMENTS SUCH AS INVERSIONS. LARGE INVERSIONS HAVE SIGNIFICANT IMPACTS ON THE BIOLOGY OF ORGANISMS AND THEIR EVOLUTION. EXISTING COMPUTATIONAL METHODS FOR IDENTIFYING INVERSIONS HAVE BEEN PRIMARILY TESTED ON AND DEVELOPED FOR WELL-STUDIED, REFERENCE GENOMES. THIS PROJECT SEEKS TO DEVELOP NEW INVERSION DETECTION AND ASSOCIATION TESTING METHODS SUITABLE FOR THE LARGE AND GROWING NUMBER OF FRAGMENTED AND/OR UNASSEMBLED GENOMES THAT ARE BECOMING AVAILABLE. UNDERGRADUATE RESEARCH ASSISTANTS WILL BE FUNDED AS ACTIVE COLLABORATORS ON THE PROJECT. SO-CALLED K-MER METHODS HAVE BECOME POPULAR IN THE LAST DECADE FOR THE ANALYSIS OF UNASSEMBLED GENOMICS OR METAGENOMICS DATA. THIS PROJECT SEEKS TO UTILIZE K-MERS, UNSUPERVISED LEARNING, AND ASSOCIATION TESTING TO IDENTIFY INVERSIONS IN FRAGMENTED OR POORLY ASSEMBLED POPULATION GENOMICS DATA. SINCE MILLIONS OF ASSOCIATION TESTS WILL BE RUN PER DATA SET, THE METHODS WILL BE ACCELERATED USING GPUS. THE RESULTING METHOD AND SOFTWARE WILL BE DEVELOPED IN CONJUNCTION WITH UNDERGRADUATE RESEARCH ASSISTANTS AND RELEASED UNDER AN OPEN-SOURCE LICENSE. THIS AWARD REFLECTS NSF'S STATUTORY MISSION AND HAS BEEN DEEMED WORTHY OF SUPPORT THROUGH EVALUATION USING THE FOUNDATION'S INTELLECTUAL MERIT AND BROADER IMPACTS REVIEW CRITERIA.
$24.0k
6/13/23
Not listed
CRII: III: RUI: ASSOCIATION TESTING AND INVERSION DETECTION WITHOUT REFERENCE GENOMES
$12.6k
12/13/21
Not listed
CRII: III: RUI: ASSOCIATION TESTING AND INVERSION DETECTION WITHOUT REFERENCE GENOMES
$0
5/19/21
Not listed
CRII: III: RUI: ASSOCIATION TESTING AND INVERSION DETECTION WITHOUT REFERENCE GENOMES
$12.6k
1/7/21