CV

Education

• B.S. in Natural Resources – Ecology – and Management, Iowa State, 2007
• M.S. in Ecology and Evolution, Iowa State, 2009
• Ph.D in Evolutionary Genetics, University of Nebraska-Lincoln, 2016

Work experience and deliverables

• 2020-2023: Bioinformatics Lead, Checkerspot Inc.
  • Assembled and annotated a microbial (algal) genome into two chromosome scale, phased haploid genomes
  • Built custom nextflow pipelines to leverage AWS batch cloud computing resources to conduct comparative transcriptomics, differential expression analyses, genome assembly and resequencing, and annotation and functional prediction
• 2016-2020: Postdoc in Plant Adaptation and Evolution, UC-Davis
  • Conceived of and carried out population genetic association tests to identify candidate adaptation genes in maize landraces
  • Coordinated collaboration between researchers at six different institutions in order to validate candidate adaptation genes with data from RNA-sequencing, chromatin accessibility, phospholipid variation between environments, and trait performance in drought and heat experiments.

Skills

• General Computational Biology
  • Unix
  • R
  • Python
  • git
  • Nextflow
  • AWS
  • HPC (SLURM)
• General Communications and Teamwork
  • MS Excel/Numbers/gSheets
  • Powerpoint/gSlides
  • MS Word/gDocs
  • LaTeX
  • Jupyter notebooks
  • Google colab

Publications

Selective sorting of ancestral introgression in maize and teosinte along an elevational cline.

Calfee, Erin, et al. "Selective sorting of ancestral introgression in maize and teosinte along an elevational cline." PLoS genetics 17.10 (2021): e1009810.

An adaptive teosinte mexicana introgression modulates phosphatidylcholine levels and is associated with maize flowering time

Barnes, A.C., Rodríguez-Zapata, F., Juárez-Núñez, K.A., Gates, D.J., Janzen, G.M., Kur, A., Wang, L., Jensen, S.E., Estévez-Palmas, J.M., Crow, T.M. and Kavi, H.S., 2022. An adaptive teosinte mexicana introgression modulates phosphatidylcholine levels and is associated with maize flowering time. Proceedings of the National Academy of Sciences , 119(27), p.e2100036119.

Development and Large-Scale Production of Human Milk Fat Analogue by Fermentation of Microalgae

Zhao, Xinhua, et al. "Development and Large-Scale Production of Human Milk Fat Analogue by Fermentation of Microalgae." Frontiers in Nutrition 11: 1341527.