Big Data for Biosurveillance
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Mathematical Modeling for the Subtyping of PulseNet Pathogens

The Centers for Disease Control and Prevention (CDC) has announced intentions to award a sole source contract to Emory University for Amplicon Phasing through Mathematical Modeling for the Subtyping of PulseNet Pathogens in Stool.

Emory’s Department of Mathematics and Computer Science will develop mathematical modeling software for subtyping amplicons to their pathogen strain of origin when multiple pathogen strains or closely related organisms are present in the sample.

The software shall estimate the number of strains present in the original sample and assign alleles for each locus in the subtyping schema to a strain. The software shall also provide a measurement of the confidence in the strain number and allele assignments, and perform tasks with subtyping schema that contains thousands of amplified loci and computing hardware resources within a specified time frame.

The award is on behalf of the CDC’s National Center for Emerging and Zoonotic Infectious Diseases (NCEZID).

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