Kelly L. Sovacool

Bioinformatician developing open source software

Contact:   sovacool [at] umich.edu

View a PDF version of my CV:   https://sovacool.dev/latex-cv/vitae_KLS.pdf

Skills

Education

Dates Degree Institution
2018-2023 PhD Bioinformatics University of Michigan, Dept. of Computational Medicine and Bioinformatics
Advisor: Patrick D. Schloss
2014-2018 BS Biology University of Kentucky, Dept. of Biology
Minor: Computer Science
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Research Experience

Dates Title Lab Description
2023-present Bioinformatics Software Engineer II Frederick National Laboratory for Cancer Research Develop and maintain open source bioinformatics workflows on the CCR Collaborative Bioinformatics Resource core team to support researchers at the National Cancer Institute.
2019-2023 Graduate Student Researcher Schloss Lab, Dept. of Microbiology and Immunology,
University of Michigan 		Developed, benchmarked, and maintained bioinformatics workflows and software packages in R & Python. Built machine learning pipelines for human gut microbiome classification problems in colorectal cancer and C. difficile infection. Published findings as reproducible papers in open access journals. Collaborated with other scientists on microbiome projects. Mentored junior lab members.
2018-2019 Rotation Student Researcher Program in Biomedical Sciences,
University of Michigan 		Worked in several different bioinformatics labs to find the best mentorship fit.
2015-2018 Undergraduate Lab Assistant Moseley Bioinformatics Lab, Dept. of Molecular and Cellular Biochemistry,
University of Kentucky 		Developed a Python package for comparative genomics. Identified sets of orthologous and paralogous gene products to facilitate collinearity analysis and detection of gene duplication events.
2016-2018 BIO395 Independent Research Student Weisrock Lab, Dept. of Biology,
University of Kentucky 		Developed bash scripts and a SNP calling pipeline in Snakemake. Population structure analysis of the Ambystoma tigrinum species complex. Bayesian species delimitation of the Desmognathus fuscus species complex.
2015-2016 Undergraduate Lab Assistant Jaromczyk Lab, Dept. of Computer Science,
University of Kentucky 		Maintained the Epichloë festucae genome project database. Analyzed RNA-seq data of Chenopodium quinoa and coffee ringspot virus.
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Service

Dates Title Organization Description
2025-present Co-Founder | Tech Lead Your Neighborhood Scientist Your Neighborhood Scientist cultivates community-based conversations around science, science policy, and scientists through a newsletter and blog.
2019-2022 Executive Committee Member: Open Source Technical Lead Girls Who Code at U-M DCMB Plan, apply for funding, develop curriculum, and maintain resources to teach introductory Python programming & data science to young women+. Facilitate collaborative development and maintenance of our open source teaching resources. Organize our year-round Club and annual Data Science Summer Experience for high school women+.
2019-2022 Organizer and Maintainer U-M Carpentries Co-lead development & maintenance of a curriculum for workshops teaching programming skills for reproducible research. Maintain the website, develop curriculum, and organize workshops. Collaborate with U-M Women in Science and Engineering to organize workshops for women+.
2021-2023 Mentor Schloss Lab Mentor an undergraduate student in building reproducible machine learning models to predict C. difficile infection severity from gut microbiome composition.
2021-2022 CoderSpaces co-host U-M ISR Data Science Hub Hold office hours at a weekly virtual help session for data science practitioners
2021-present Peer reviewer   PLOS ONE (1), JOSS (2)
2019-2021 Graduate Student Coordinator U-M Data Analysis Networking Group Organize monthly meetings & a one-day symposium for researchers to sharpen their data analysis skills. Apply for funding through a Rackham Interdisciplinary Workshop grant.
2009-present Volunteer Sound Engineer various churches and non-profit organizations Mix FOH, monitors, recording, and live stream.
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Teaching

Date Title Organization where Event(s)
2025 Aug Workshop Instructor Norwegian University of Science and Technology NTNU, Trondheim, Norway Health AI in R Workshop
2023 Jan-Apr Graduate Student Instructor U-M Dept. of Computational Medicine & Bioinformatics University of Michigan, Ann Arbor, MI BIOINF 576: Tool Development for Bioinformatics. Develop curriculum and teach students the principles of software development in R & Python. Topics: software design, implementation, testing, documentation, issue tracking, peer review, and release.
2022 Jun Instructor   Virtual Intro to R & RNA-Seq Workshop for ASM Microbe conference attendees
2019-2022 Facilitator & Capstone Project Mentor Girls Who Code at U-M DCMB University of Michigan, Ann Arbor, MI Weekly Club during the school year and week-long Summer Experience for high schoolers to learn Python for data science
2018-2022 Workshop Instructor & Helper U-M Carpentries University of Michigan, Ann Arbor, MI 2-day Software Carpentry workshops teaching computational skills for reproducible research
2019 Apr DNA Day Ambassador Michigan DNA Day Pioneer High School, Ann Arbor, MI Epigenetics & Scientific Journeys
2019 Mar Workshop helper Graduate Society of Black Engineers and Scientists University of Michigan, Ann Arbor, MI Data Visualization with Python Workshop
2019 Mar Capstone Activity Leader Females Excelling More in Math, Engineering, & the Sciences University of Michigan, Ann Arbor, MI Binary Numbers through Ozobots with GWC at U-M DCMB
2012-2018 Tutor freelance   for high school and college students in Biology, Calculus, Chemistry, Computer Science, and Bioinformatics.
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Publications

Last updated: August 21, 2025

* Indicates co-first author.

Date Article Authors badges
2023 Aug Machine Learning Classification by Fitting Amplicon Sequences to Existing OTUs. mSphere Armour CR, Sovacool KL, Close WL, Topçuoğlu BD, Wiens J, Schloss PD
2022 Jul Intestinal Inflammation Reversibly Alters the Microbiota to Drive Susceptibility to Clostridioides Difficile Colonization in a Mouse Model of Colitis. mBio Barron MR, Sovacool KL, Abernathy-Close L, Vendrov KC, Standke AK, Bergin IL, Schloss PD, Young VB
2022 Feb OptiFit: An Improved Method for Fitting Amplicon Sequences to Existing OTUs. mSphere Sovacool KL, Westcott SL, Mumphrey MB, Dotson GA, Schloss PD
2022 Jan Developing and Deploying an Integrated Workshop Curriculum Teaching Computational Skills for Reproducible Research. JOSE *Lapp Z, *Sovacool KL, Lesniak N, King D, Barnier C, Flickinger M, Krüger J, Armour CR, Lapp MM, Tallant J, Diao R, Oneka M, Tomkovich S, Anderson JM, Lucas SK, Schloss PD
2021 Dec Teaching Python for Data Science: Collaborative Development of a Modular & Interactive Curriculum. JOSE *Duda M, *Sovacool KL, Farzaneh N, Nguyen VK, Haynes SE, Falk H, Furman KL, Walker LA, Diao R, Oneka M, Drotos AC, Woloshin A, Dotson GA, Kriebel A, Meng L, Thiede SN, Lapp Z, Wolford BN
2021 May Mikropml: User-Friendly R Package for Supervised Machine Learning Pipelines. JOSS *Topçuoğlu BD, *Lapp Z, *Sovacool KL, Snitkin E, Wiens J, Schloss PD
2021 Apr Geography Is More Important than Life History in the Recent Diversification of the Tiger Salamander Complex. PNAS Everson KM, Gray LN, Jones AG, Lawrence NM, Foley ME, Sovacool KL, Kratovil JD, Hotaling S, Hime PM, Storfer A, Parra-Olea G, Percino-Daniel R, Aguilar-Miguel X, O’Neill EM, Zambrano L, Shaffer HB, Weisrock DW
2020 Aug Ten Simple Rules to Increase Computational Skills among Biologists with Code Clubs. PLoS Comput Biol Hagan AK, Lesniak NA, Balunas MJ, Bishop L, Close WL, Doherty MD, Elmore AG, Flynn KJ, Hannigan GD, Koumpouras CC, Jenior ML, Kozik AJ, McBride K, Rifkin SB, Stough J, Sovacool KL, Sze MA, Tomkovich S, Topcuoglu BD, Schloss PD
2016 Aug Processing RNA-Seq Data of Plants Infected with Coffee Ringspot Virus. BMC Bioinform Goodin MM, Farman M, Inocencio H, Jang C, Jaromczyk JW, Moore N, Sovacool KL
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Google Scholar logo

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Presentations

Talks

Date Title Event Location
Aug 2025 Tips & Tricks for Reproducible R Projects R Ladies Trondheim Trondheim, Norway
Feb 2025 Introduction to GitHub Actions for Analysts & Engineers BTEP Coding Club NCI CCR Bioinformatics Training & Education Program (virtual)
Apr 2024 Organizing and documenting NGS pipelines on GitHub ABCS Programmer’s Corner NCI at Frederick (virtual)
Jun 2023 Improving Machine Learning Models for Microbiome Analysis and Democratizing Data Science Along the Way PhD Defense University of Michigan
Nov 2022 Predicting C. difficile infection severity from the taxonomic composition of the gut microbiome Bioinformatics Student Research Hour University of Michigan
Feb 2022 Intro to git & GitHub Seminar for the KG Jebsen Center for Genetic Epidemiology Norwegian University of Science and Technology (Virtual)
Mar 2021 OptiFit: a fast method for fitting amplicon sequences to existing OTUs Bioinformatics Student Research Hour University of Michigan (Virtual)
Apr 2018 Developing a Global Homology Analysis for Comparative Genomics Systems Biology and Omics Integration Seminar University of Kentucky
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Posters

Date Title Event Location
Jun 2022 Predicting the severity of C. difficile infections from the taxonomic composition of the gut microbiome ASM Microbe Washington, DC
Jun 2020 OptiFit: a fast method for fitting amplicon sequences to existing OTUs ASM Microbe Virtual
Apr 2018 Developing a Global Homology Analysis for Comparative Genomics Showcase for Undergraduate Scholars University of Kentucky
Apr 2018 Developing a Global Homology Analysis for Comparative Genomics National Conference on Undergraduate Research University of Central Oklahoma
Apr 2016 Processing RNA-seq Reads of Plants Infected with the Coffee Ringspot Virus Showcase for Undergraduate Scholars University of Kentucky
Apr 2016 Processing RNA-seq Reads of Plants Infected with the Coffee Ringspot Virus UT-KBRIN Bioinformatics Summit Cadiz, KY
Apr 2015 The Effect of Meditation on Performance Showcase for Undergraduate Scholars University of Kentucky
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Awards

Grants

Dates Title Institution Amount
2022 Conference Travel Grant Rackham Graduate School
University of Michigan 		$900
2020-2021 Rackham Interdisciplinary Workshop Grant Rackham Graduate School
University of Michigan 		$500
2020 Conference Travel Grant Rackham Graduate School
University of Michigan 		$800
2019-2020 Rackham Interdisciplinary Workshop Grant Rackham Graduate School
University of Michigan 		$500
2019-2021 NIH T32 Bioinformatics Training Program Fellow Bioinformatics Graduate Program
University of Michigan 		 
2017 Oswald Research & Creativity Award
2nd place in Biological Sciences 		Office of Undergraduate Research
University of Kentucky 		$200
2017 Summer Research Grant Office of Undergraduate Research
University of Kentucky 		$2,000
2014-2018 Presidential Scholarship University of Kentucky out-of-state full tuition
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Honors

Dates Title Institution
2018 Graduated Cum Laude with Departmental Honors in Biology University of Kentucky
2018 Biology Undergraduate Research Award Nominee University of Kentucky
2014-2018 Lewis Honors College University of Kentucky
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Open Source Contributions

CCBR pipeliner
software
nextfow
snakemake
cancer research
Suite of pipelines for multi-omics data analysis, purpose-built for NCI researchers
Co-author and maintainer

mikropml
software
machine learning
R
User-Friendly R Package for Supervised Machine Learning Pipelines
Co-author and maintainer

schtools
software
microbiome
R
Schloss Lab tools for reproducible microbiome research
Co-author and maintainer

mikropml snakemake workflow
software
snakemake
machine learning
R
Python
Snakemake template for building reusable and scalable machine learning pipelines with mikropml
Co-author and maintainer

mothur
software
microbiome
C++
Command-line tool for processing microbial amplicon sequence data
Contributor

mothur snakemake workflow
software
microbiome
snakemake
R
Python
Snakemake template for reproducible microbial amplicon sequence analysis with mothur
Co-author

U-M Software Carpentry
Curriculum
R
Unix Shell
git
Workshop
Intro to R, the Unix shell, and git for workshops on reproducible research.
Co-author and maintainer

Girls Who Code at U-M DCMB
Curriculum
Python
Data Science
Intro to Python for Data Science via Live-Coding for Girls Who Code clubs.
Co-author and maintainer

Code Clubs
Code Club
Tutorials
Short coding tutorials for lab meetings
Contributor

U-M DANG!
Reproducibility
Tutorials
repro-packs: Organizing projects for reproducibility and headache prevention.
Author

Intro to R & RNA-seq
Curriculum
R
RNA-seq
Workshop
Workshop for 2022 ASM Microbe attendees
Contributor
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Continuing Education

Date Title Organization Location
Jan 2020 Building Tidy Tools workshop at rstudio::conf Rstudio, PBC San Francisco, CA
Dec 2019 Winter School in Research Software Engineering US Research Software Sustainability Institute Seattle, WA
Jun 2019 Software Carpentry Instructor Training The Carpentries University of Michigan
May 2019 PyCon Education Summit & Conference The Python Software Foundation Cleveland, OH
Apr 2019 MICROBIOL 612.2 Riffomonas Minimal R Workshop University of Michigan
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