Resume

Microbiology PhD with 10+ years experience applying data science and statistics to biological problems. Expertise in multi-omics from experimental design to publication. Skilled leader with Project Management Professional (PMP) training and teams with diverse backgrounds and varied training. Effective communicator with formal teaching experience. Specific skills include:

DataSoftwareStatistics
  • Transcriptomics: RNA-seq, scRNA-seq
  • Genetics: MegaEX, lpWGS, WGS
  • Epigenetics: ATAC-seq, bisulfite seq
  • Proteomics: MS/MS
  • Microbiome: 16S, 18S, ITS, meta-transcriptomics
  • AWS
  • Git, GitHub
  • R, Rmd, Shiny
  • python, Jupyter
  • STAR, BWA, bowtie
  • Seurat, scanpy, STARsolo
  • PLINK, vcftools
  • mothur, QIIME
  • Linear, additive, PLS, LASSO, latent regression
  • Un/supervised machine learning
  • PCA, NMDS, tSNE
  • Sparse data imputation
  • Data visualization

Experience


01/2024 - present — Director, Bioinformatics Core, U. of Washington

  • UWISDOM: U of Washington Informatics, Systems immunology, and Data Omics in Medicine, https://uwisdom.github.io/index.html
  • Manage a portfolio of 10+ projects and 5+ bioinformaticians
  • Develop and maintain shared code base in R and python
  • Interface with the UW community to identify and fill bioinformatic needs
  • Serve as the primary Bioinformatician on select projects

08/2024 - present — Bioinformatics consultant, EuropaDX

  • Europa Data eXplorer (EuropaDX™) is a cloud-based data exploration platform that enables scientists to easily manage, process, visualize and share large multiomics datasets, https://europadx.com/
  • Develop production ready unix, R, and python code for omics analysis, particularly bulk and single-cell RNAseq

07/2023 - present — Bioinformatics consultant, Seattle Biosoftware

  • Fulfill customer requests for R and python based omics analysis, particularly data visualization

07/2021 - 12/2023 — Senior Bioinformatician, Allergy and Infectious Diseases, U. of Washington

  • Lead a team of bioinformaticians analyzing 'omics data across diverse research fields
  • Develop software (R packages) and reproducible workflows (snakemake, Rmarkdown)
  • Multi-omics and integrated data analyses

07/2019 - 06/2021 — Bioinformatician, Allergy and Infectious Diseases, U. of Washington

  • Analyze human transcriptomic, epigenetic, and genetic datasets including quality assessment, statistical tests, and visualization
  • Mentor researchers and students as Founder and Chair of the Bioinformatics Group at South Lake Union ( [BIGslu](https://github.com/BIGslu) ) and Informatics for TB ( [i4TB](https://seatrac.uw.edu/training/i4TBworkinggroup) )

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

  • Directed the Experiential Data Science for Undergraduate Cross-disciplinary Education ( [EDUCE](https://educe-ubc.github.io/) ) program
  • 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


2023 - 2024 — Project Management Professional (PMP) Certificate, U. of Washington, Seattle, WA. Project Management Institute (PMI) certification Jan 2025

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, et al. 2025. Genome-wide association study in Brazil identifies risk factor-adjusted genetic susceptibility to pulmonary tuberculosis with cell-specific gene expression effects. medRvix doi: 10.1101/2025.03.13.25323932 — GitHub

Dill-McFarland KA, et al. 2023. kimma: Flexible linear mixed effects modeling with kinship for RNA-seq data. Bioinformatics. doi: 10.1093/bioinformatics/btad279 — GitHub

Cox MS, Dill-McFarland KA, et al. 2024. Multi-omic latent variable data integration reveals multicellular structure pathways associated with resistance to tuberculin skin test (TST)/interferon gamma release assay (IGRA) conversion in Uganda. BMC Genomics. doi: 10.1186/s12864-025-11407-1 — bioRvix doi: 10.1101/2024.11.05.622020

Full publication list

Notable accomplishments


2017, 2018, 2019, 2022 — Session convener 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
kadm [at] uw.edu
@kdillmcfarland