Resume

zkonkel@tuta.com · LinkedIn · GitHub · Google Scholar

Experience

Bioinformatics Engineer II

Theiagen Genomics · 2025 – Present

Develop microbial pathogen genomics pipelines for public health bioinformatics, contributing to team-led pipeline development, cloud job deployment, automated analysis, and AI integration for government and private partners.

Postdoctoral Researcher

Dr. Jonathan Jacobs’s Emerging Infectious Disease Ecology Lab · 2023 – 2025

Investigated how transposon-mediated gene loss shapes genome evolution, host switching, and ecological niche switching. Led NGS data standardization and database management, and scaled the Mycotools suite to 100,000s of prokaryote genomes.

Bioinformatics and Genomics Science Consultant

Ruby Bio, Inc. · 2023 – 2024

Integrated metabolomics, transcriptomics, and genomics to identify and engineer expression of biosynthetic pathways.

Computational Biologist Research Fellow

Dr. Jason Slot’s Fungal Evolutionary Genomics Lab · 2018 – 2023

Studied the evolution of fungal gene cluster architecture through large-scale genomics and phylogenomics. Developed statistical models of evolutionary processes for biosynthetic gene cluster detection, and built integrative genomics–metabolomics methods that pair phylogenetics with tandem mass spectrometry to discover novel natural products.

Quality Control Analytical Chemist

Cascadia Labs · 2017 – 2018

Performed ORELAP-accredited quantitation and developed LC-MS/MS, HPLC-UV, GC-MS, and GC-FID analytical methods.

Natural Product Drug Discovery Analytical Chemist

Dr. Sandra Loesgen’s Natural Product Drug Discovery Lab · 2014 – 2017

Isolated and elucidated the structures of fungal-derived antimicrobial compounds, and developed LC-MS and HPLC-UV analytical methods.

Education

PhD, Translational Plant Sciences: Computational & Evolutionary Genomics

The Ohio State University · 2018 – 2023

Dissertation: On Molecular Symbiosis and the Evolution of Fungal Genome Architecture. University Fellow, Translational Plant Sciences PhD Fellow, and Ohio Agricultural Research and Development Center Director’s Associate.

BS, Biology: Ecology; Chemistry minor

Oregon State University · 2013 – 2017 · Cum laude

Skills

• Genomics: phylogenomics, large-scale automated comparative genomics, biosynthetic gene cluster detection, eukaryote genome annotation, RNA-seq/transcriptomics, multi-omics
• Computation: Python, R, Linux, statistics, collaborative software development
• Analytical chemistry: LC-MS/MS, GC-MS, HPLC-UV, GC-FID method development; metabolomics; natural product structure elucidation

Selected Publications

Full list on Google Scholar.

• Merfa, M. V., … Konkel, Z., … Jacobs, J. M. (2026). Effector loss and gain drives host range at a fitness cost. PLoS Pathogens
• Rutter, B., … Konkel, Z., Slot, J. C., … Brand, A. C. (2026). Evolution, structure and function of the putative biosynthetic gene cluster of the fungal secondary metabolite myriocin, a potent inhibitory sphingolipid. Communications Biology
• Konkel, Z., Slot, J. C. (2026). Generalized gene cluster detection using CLOCI. Methods in Molecular Biology
• Baltrus, D. A., … Konkel, Z., Jacobs, J. M. (2026). Independent, ongoing clade-specific expansions of IS5 elements in Pseudomonas syringae. Microbial Genomics
• Cope-Arguello, M. L., Li, J., Konkel, Z., … Lowe-Power, T. M. (2026). The EPS-I exopolysaccharide transforms Ralstonia wilt pathogen biofilms into viscoelastic fluids for rapid dissemination in planta. PNAS
• Konkel, Z., Kubatko, L., Slot, J. C. (2024). CLOCI: Unveiling cryptic fungal gene clusters with generalized detection. Nucleic Acids Research
• Roman-Reyna, V., … Konkel, Z., … Jacobs, J. M. (2024). Live tracking of a plant pathogen outbreak reveals rapid and successive, multidecade plasmid reduction. mSystems
• Konkel, Z., Slot, J. C. (2023). Mycotools: An automated and scalable platform for comparative genomics. bioRxiv
• Sierra-Patev, S., … Konkel, Z., … Hibbett, D. (2023). A global phylogenomic analysis of the shiitake genus Lentinula. PNAS
• Gluck-Thaler, E., Ralston, T., Konkel, Z., … Vogan, A. A. (2022). Giant Starship elements mobilize accessory genes in fungal genomes. Molecular Biology and Evolution

Teaching

• Programming for Biology (selected teaching assistant) · Cold Spring Harbor Laboratory · 2022
• Emerging Fungal Pathogens · The Ohio State University · 2022
• Practical Computing for Biology (lecturer and teaching assistant) · The Ohio State University · 2021
• Mycology (lecturer and teaching assistant) · The Ohio State University · 2018 – 2019

Selected Presentations

• Emerging Infectious Disease Symposium, The Ohio State University · Talk · 2024
• Methods for Biological Analysis Workshop, University of Wisconsin–Madison · Workshop · 2024
• Fungal Supergroup Seminar, University of Wisconsin–Madison · Talk · 2023
• Gordon Research Conference: Fungal Cellular and Molecular Biology · Poster (Best Poster Award) · 2022
• Center for Applied Plant Sciences Seminar, The Ohio State University · Talk · 2019
• Ohio Mass Spectrometry and Metabolomics Symposium · Talk · 2019

Selected Awards

• Best Poster Award · Gordon Research Conference, Fungal Genetics · 2022
• Translational Plant Sciences Research Fellowship · Center for Applied Plant Sciences · 2020 – 2023
• Regeneron Scholarship · Cold Spring Harbor Laboratory, Programming for Biology · 2019
• Mentor-Student Travel Award · Mycological Society of America · 2019
• Best Oral Presentation · Oregon State University Microbiology Colloquium · 2017