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

Experience


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

  • Lead a team of bioinformaticians in the analysis of ‘omics data for multiple research groups across the Dept of Medicine
  • Director of the Human Immunology Project Consortium ( [HIPC](https://immunespace.org/) ) Data Management and Analysis Core
  • Develop, standardize, and publish 'omics workflows in R packages and other software
  • Contribute to scientific grants and publications

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


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, Mitchell K, Batchu S, Segnitz RM, Benson B, Janczyk T, Cox MS, Mayanja-Kizza HA, Boom WH, Benchek P, Stein C, Hawn TR, Altman MC. 2023. kimma: Flexible linear mixed effects modeling with kinship for RNA-seq data. Bioinformatics. 39(5):btad279. doi: 10.1093/bioinformatics/btad279 — GitHub

Jackson DJ, Bacharier LB, Gergen PJ … Dill-McFarland KA … Altman MC, US NIAID Inner City Asthma Consortium. 2022. Mepolizumab for urban children with exacerbation-prone eosinophilic asthma in the USA (MUPPITS-2): a randomised, double-blind, placebo-controlled, parallel-group trial. Lancet 400(10351): 502-511 doi: 10.1016/S0140-6736(22)01198-9

Dill-McFarland KA, Schwartz JT, Zhao H, Shao B, Fulkerson PC, Altman MC, Gill MA. 2022. Eosinophil-mediated suppression and Anti-IL-5 enhancement of plasmacytoid dendritic cell interferon responses in asthma. J Allergy Clin Immunol. Epub ahead of print. doi: 10.1016/j.jaci.2022.03.025 — GitHub

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