Education and Experience


Informatics Leader, Genomic Diversity Facility, Cornell University. July 2014-present.
Research Associate, Bioinformatics Facility, Cornell University. August 2012-present.
Postdoctoral Researcher, Cornell University. March 2012-August 2012.
Postdoctoral Researcher, UMass Amherst. 2011-2012.
PhD Evolution, Ecology and Population Biology, Washington University in St. Louis. 2010.
MS Microbiology and Molecular Genetics, Michigan State University. 2004.
BS Microbiology and Molecular Genetics, Michigan State University. 2004.

Current Research


The Genomic Diversity Facility in Cornell's Biotechnology Resource Center provides Genotyping-by-Sequencing (GBS) project design and optimization, GBS sample preparation (library production), GBS data generation (DNA sequencing), GBS data analysis, consultation, workshops and training. Find out more about the Genomic Diversity Facility

Past Research


Grapevine cultivar improvement (VitisGen)


VitisGen is a large, multi-disciplinary, collaborative project focused on decreasing the time, effort and cost involved in developing the next generation of grapes. Read more about VitisGen

Grapevine breeding is complicated by high levels of heterozygosity in an outcrossing species. These complications pose a challenge to researchers using genotyping-by-sequencing (GBS) data to create high density linkage maps. I have designed a genetic map creation pipeline (HetMapps) suitable for high density GBS data from bi-parental F1 grapevine families. The pipeline can be used for linkage group creation and phasing of a large number of markers with high amounts of missing data (a hallmark of GBS data). The method includes options for synteny (reference genome assisted) linkage group creation and de-novo linkage group creation, and does not require parental genotypes.
The output of this pipeline has been validated in five grapevine families with shared parents, and is currently being used in the VitisGen project for map creation in dozens of VitisGen grapevine families for mapping a suite of different traits.

Related Publications:
Grapevine powdery mildew resistance and susceptibility loci identified on a high-resolution SNP map

Yeast Population Genetics


Genetic evidence suggests that strains of Saccharomyces cerevisiae used to make wine may be domesticated. Although S. cerevisiae has been isolated from trees, soil, indigenous fermentations and clinical sources as well as vineyards and wine fermentations, the genetic variation that exists within the vineyard and grape must strains is a subset of the genetic variation that exists within the species as a whole. While a bottleneck pattern is consistent with domestication, it could also be the consequence of a complex population history rather than adaptation to wine making. To distinguish between these hypothesis I investigated genetic and phenotypic variation between vineyard and non-vineyard strains of S. cerevisiae.
If vineyard strains are locally adapted we expect selection to limit gene flow between sympatric vineyard and arboreal isolates. To address this question, I collected and characterized yeast from grapes, trees and soil at vineyard and non-vineyard locations during the grape harvest season.
Domestication is typically characterized by a suite of adaptive traits referred to as the 'domestication syndrome.' Potential domestication traits in S. cerevisiae could include growth and fermentation phenotypes that lead to fitness differences, as well as differential production of metabolic products that affect wine aroma and flavor. I measured growth rate as a proxy for fitness over varying environments, and also completed sensory analyses using wines fermented from vineyard strains, oak tree strains, and other Saccharomyces species.

Related Publications:
Genomic sequence diversity and population structure of Saccharomyces cerevisiae assessed by RAD-seq
Mixing of vineyard and oak-tree ecotypes of Saccharomyces cerevisiae in North American Vineyards
Divergence in wine characteristics produced by wild and domesticated strains of Saccharomyces cerevisiae
Genetic and Phenotypic Differentiation between Winemaking and Wild Strains of Saccharomyces cerevisiae