Resume

Microbiology PhD with 9+ years experience in applying data science and statistics to biological problems. Skilled leader of teams with diverse backgrounds and varied training. Expertise in next-generation sequencing from experimental design to publication. Effective communicator with formal teaching experience. Specific skills include:

DataSoftwareStatistics
  • Transcriptomics: RNA-seq
  • Genetics: MegaEX, Omni, whole exome
  • Epigenetics: ATAC-seq, bisulfite seq
  • Proteomics: MS/MS
  • Microbiome: 16S, 18S, ITS, meta-transcriptomics
  • AWS
  • Git, GitHub
  • R, Rmd, Shiny
  • samtools, bedtools
  • STAR, BWA, bowtie
  • PLINK, vcftools
  • mothur, QIIME
  • Linear, PLS, LASSO, latent regression
  • Un/supervised machine learning
  • PCA, NMDS, tSNE
  • Sparse data imputation
  • Data visualization

Experience


07/2019 - present — Bioinformatician, Allergy and Infectious Diseases, U. of Washington

  • Analyze human transcriptomic, epigenetic, and genetic datasets including quality assessment, and statistical tests
  • Develop novel pipelines for integrated ‘omics analysis
  • Lead a team of 3 core bioinformaticians as well as mentor post-docs and students in related groups
  • Administrator AWS Organization (6 users)

04/2021 - present — Genomic data specialist, San Mateo County Public Health Lab (part-time)

  • Genome assembly, variant tracking, and outbreak assessment of COVID-19 clinical samples

08/2017 - 06/2019 — Post-doctoral research fellow, Microbiology & Immunology, U. of British Columbia

  • Directed Experiential Data Science for Undergraduate Cross-disciplinary Education ([EDUCE](https://educe-ubc.github.io/)) including a team of 3 teaching assistants
  • Designed and implemented data science curriculum in 7 courses
  • [ECOSCOPE](http://ecoscope.ubc.ca/) fellow coordinating and teaching data science workshops for industry and academic partners

07/2016 - 06/2017 — Post-doctoral research associate, Bacteriology/Sociology, U. of Wisconsin-Madison

  • Investigated relationships between the human gut microbiome and longterm behaviors in the Wisconsin Longitudinal Study ([WLS](https://www.ssc.wisc.edu/wlsresearch/))
  • Navigated large, longitudinal survey databases

08/2011 - 06/2016 — Graduate research assistant, Bacteriology, U. of Wisconsin-Madison

  • Designed and implemented amplicon sequence analysis pipelines
  • Collaborated effectively with diverse international researchers resulting in first and corresponding author publications
  • Mentored high school, undergraduate, and graduate students

08/2008 - 05/2011 — Undergraduate research assistant, Biology, U. of Puget Sound

  • Thesis: Investigating maltose metabolism in *Bdellovibrio bacteriovorus*

Education


2011 - 2016 — Ph.D. Microbiology, U. of Wisconsin-Madison, Madison, WI. GPA: 4.00

2007 - 2011 — B.S. Molecular and cellular biology, Minor mathematics, U. of Puget Sound, Tacoma, WA. GPA: 3.84

Select publications


Dill-McFarland KA*, Tang Z*, Kemis JH, Kerby RL, Chen G, Palloni A, Sorenson T, Rey FE†, Herd P†. 2019. Close social relationships correlate with human gut microbiota composition. Sci Rep 9: 703. doi: 10.1038/s41598-018-37298-9GitHub

Dill-McFarland KA, Weimer PJ, Breaker JD, Suen G. 2019. Diet influences early microbiota development in dairy calves without long-term impacts on milk production. Appl Environ Microbiol 85(2): e02141-18. doi: 10.1128/AEM.02141-18GitHub

Dill-McFarland KA, König SG, Mazel F, Oliver DC, McEwen LM, Hong KY, Hallam SJ. 2021. An integrated, modular approach to data science education in microbiology. PLoS Comput Biol 17(2): e1008661. doi: 10.1371/journal.pcbi.1008661GitHub

*co-first authors
Full publication list

Notable accomplishments


2017, 2018, 2019 — Session moderator/convener at the American Society for Microbiology (ASM) Microbe meeting

2016 — Microbiome Digest’s Best Microbiome Paper

2016 — Sigrid Leirmo Memorial Award for peer mentorship and support

2009, 2010 — American Society for Microbiology Undergraduate Fellow

Contact


University of Washington, Division of Allergy and Infectious Diseases, Box 358061
kadm [at] uw.edu
@kdillmcfarland