konkelzach@pm.me

EDUCATION

PhD, Translational Plant Sciences: Computational & Evolutionary Genomics
2018 - 2023: The Ohio State University
Dissertation: On Molecular Symbiosis and the Evolution of Fungal Genome Architecture
Translational Plant Sciences PhD Fellow
Ohio Agricultural Research and Development Center Associate
University Fellow
BS, Biology: Ecology; Chemistry minor
2013 - 2017: Oregon State University
Cum laude


EXPERIENCE

Ruby Bio, Inc.
2023 - 2024: Bioinformatics and Genomics Science Consultant
Integrative -omics (metabolomics, transcriptomics, and genomics) to identify and engineer expression of biosynthetic pathways
Dr. Jonathan Jacob’s Emerging Infectious Disease Ecology Lab
2023 - Now: Postdoctoral Researcher
Investigating how transposon-mediated gene loss influences genome evolution, host-switching, and ecological niche switching.
Central NGS data standardization, database management, and adapting Mycotools software suite to accomodate 100,000s prokaryote genomes
Dr. Jason Slot’s Fungal Evolutionary Genomics Lab
2018 - 2023: Computational Biologist Research Fellow
Big data genomics and phylogenomics analysis to study the evolution of fungal gene cluster architecture
Algorithm development using mathematical/statistical modeling of evolutionary processes underlying biosynthetic gene cluster detection
Integrative genomics-metabolomics algorithm development to identify novel natural products by synthesizing phylogenetic and tandem mass spectrometry analysis
Mycology lecturer and teaching assistant
Practical Computing for Biology lecturer and teaching assistant
Cold Spring Harbor Laboratory
2022: Programming for Biology selected teaching assistant
Cascadia Labs
2017 - 2018: Quality Control Analytical Chemist
Oregon (ORELAP) accredited quantitation
LC-MS/MS, HPLC-UV, GC-MS, GC-FID analytical method development
Dr. Sandra Loesgen’s Natural Product Drug Discovery Lab
2014 – 2017: Natural Product Drug Discovery Analytical Chemist
Isolation and structure elucidation of fungal-derived antimicrobial compounds
LC-MS, HPLC-UV analytical method development


PUBLICATIONS

Google scholar
1. Konkel, Z., Kubatko, K., Slot, J. C. (2024). CLOCI: Unveiling cryptic fungal gene clusters with generalized detection. Nucleic Acids Research
2. Konkel, Z., Slot, J. C. (2023). Mycotools: An Automated and Scalable Platform for Comparative Genomics. bioRxiv (preprint)
3. Roman-Reyna, V., Sharma, A., Toth, H., Konkel, Z., Omiotek, N., Murthy, S., Faith, S., Slot, J. C., Hand, F. P., Goss, E., Jacobs, J. M. (2023). Live tracking of a plant pathogen outbreak reveals rapid and successive, multidecade episome reduction. bioRxiv (preprint).
4. Sierra-Patev, S., Byoungnam, M., Naranjo-Ortiz, M., Looney, B., Konkel, Z., Slot, J. C., Sakamoto, Y., Steenwyk, J. L., Rokas, A., Carro, J., Camarero, S., Ferreira, P., Molpeceres, G., Ruiz-Duenas, F. J., Serrano, A., Henrissat, B., Drula, E., Hughes, K. W., Mata, J. L., Ishikawa, N. K., Vargas-Isla, R., Ushijima, S., Smith, C. A., Donoghue, J., Ahrendt, S., Andreopoulos, W., He, G., LaButti, K., Lipzen, A., Ng, V., Riley, R., Sandor, L., Barry, K., Martinez, A. T., Xiao, Y., Gibbons, J. G., Terashima, K., Grigoriev, I. V., Hibbett, D. (2023). A global phylogenomic analysis of the shiitake genus Lentinula. Proceedings of the National Academy of Sciences
5. Scott, K., Konkel, Z., Gluck-Thaler, E., Valero David, G. E., Simmt, C. F., Grootmyers, D., Chaverri, P., Slot, J. C. (2023). Endophyte genomes support greater metabolic gene cluster diversity compared with non-endophytes in Trichoderma. PLoS ONE (Accepted)
6. Valero David, G. E., Emanuel, I. B., Konkel, Z. M., Martin, D., Slot, J. C. (2022). First report of Colletotrichum sansevieriae causing Anthracnose of Snake Plant (Dracaena trifasciata) in Ohio and its Draft Genome. Plant Disease
7. Emanuel, I. B., Konkel, Z. M., Scott, K. L., Valero David, G. E., Slot, J. C., Hand, F. P. (2022). Whole-Genome Sequence Data for the Holotype Strain of Diaporthe ilicicola, a Fungus Associated with Latent Fruit Rot in Deciduous Holly. Microbiology Resource Announcements
8. Gluck-Thaler, E., Ralston, T., Konkel, Z. M., Ocampos, C. G., Ganeshan, V. D., Dorrance, A. E., Niblack, T. L., Wood, C. W., Slot, J. C., Lopez-Nicora, H. D., Vogan, A. A. (2022). Giant Starship Elements Mobilize Accessory Genes in Fungal Genomes. Molecular Biology and Evolution
9. Franco, M. E. E., Wisecaver, J. H., Arnold, E. A., Ju, Y., Slot, J. C., Ahrendt, S., Moore, L. P., Eastman, K. E., Scott, K., Konkel, Z., Mondo, S. J., Kuo, A., Hayes, R. D., Haridas, S., Andreopoulos, B., Riley, R., LaButti K., Pnagilinan J., Lipzen, A., Amirebrahimi, M., Yan, J., Adam, C., Keymanesh, K., Ng, V., Louie, K., Northen, T., Drula, E., Henrissat, B., Hsieh, H., Youens-Clark, K., Lutzoni, F., Miadlikowska, J., Eastwood, D. C., Hamelin, R. C., Grigoriev, I. V., U’Ren, J. M. (2022). Ecological generalism drives hyperdiversity of secondary metabolite gene cluster in xylarialean endophytes. New Phytologist
10. Konkel, Z., Scott, K., Slot, J. C. (2021). Draft Genome Sequence of the Termite-Associated “Cuckoo Fungus,” Athelia (Fibularhizoctonia) sp. TMB Strain TB5. Microbiology Resource Announcements
11. Adpressa, D. A., Connolly, L. R., Konkel, Z. M., Neuhaus, G. F., Chang, X. L., Pierce, B. R., Smith, K. M., Freitag, M., Loesgen, S. (2019). A metabolomics-guided approach to discovery Fusarium graminearum metabolites after removal of a repressive histone modification. Fungal Genetics and Biology


HIGHLIGHTED SKILLSETS

Method (Citation)
Phylogenomics (1, 2, 3, 4, 5, 6, 9)
Biosynthetic gene cluster identification/bioactive gene discovery (1, 2, 4, 5, 9, 10)
RNA-seq and transcriptomic analysis (4)
Metabolomics and analytical method development (11)
Multi-omic analysis (4, 11)
Linux (1, 2, 3, 4, 5, 6, 7, 8, 9, 10)
Python (1, 2, 3, 4, 5, 6, 7, 8, 9, 10)
R (2, 4)
Eukaryote genome annotation (5, 6, 7, 9, 10)
Large-scale, automated comparative genomic analysis (1, 2, 4, 5, 8)
Statistics (2, 5)


ACHIEVEMENTS & FUNDING

Translational Plant Sciences Research Fellowship
2020 - 2023: Center for Applied Plant Sciences
Best Poster Award
2022: Gordon Research Conference – Fungal Genetics
Director’s Associateship Award
2019: Ohio Agricultural Research and Development Center
Regeneron Scholarship
2019: Cold Spring Harbor Laboratory – Programming for Biology Workshop 2019
Mentor-Student Travel Award
2019: Mycological Society of America
University Fellowship
2018: The Ohio State University 2018
Best Oral Presentation
2017: Oregon State University – Microbiology Colloquium
URISC Grant
2016: Oregon State University
Doc Gilfillan Award
2016: Oregon State University – College of Science
Robert’s Scholarship
2015-2017: Oregon Scholarship Access Commission


PRESENTATIONS

Emerging Infectious Disease Symposium - The Ohio State University
2024: Talk
Methods for Biological Analysis Workshop - University of Madison-Wisconsin
2024: Workshop
Fungal Supergroup Seminar - University of Madison-Wisconsin
2023: Talk
Gordon Research Conference Fungal Cellular and Molecular Biology*
2022: Poster
Asilomar Fungal Genetics Conference
2022: Poster
North Central Coordinating Committee Workshop
2022: Talk
Center for Applied Plant Sciences Seminar - The Ohio State University
2019: Talk
Ohio Mass Spectrometry and Metabolomics Symposium
2019: Talk
Franklinton Fridays Halloween Seminar
2019: Talk
Mycological Society of America Conference
2019: Poster
Northwest Regional Meeting of the American Chemical Society
2017: Poster (declined)
Volcano Conference
2017: Poster
Microbiology Colloquium - Oregon State University*
2017: Talk
Celebrating Undergraduate Excellence Seminar - Oregon State University
2016: Talk
Hatfield Marine Science Center Research Symposium
2016: Poster


* Best presentation award


Teaching Experience

Programming for Biology Workshop
2022: Cold Spring Harbor Laboratory
Emerging Fungal Pathogens
2022: The Ohio State University
Practical Computing for Biology
2021: The Ohio State University
Mycology
2018 - 2019: The Ohio State University