Chase

Posts by Chase:

Summary

Chase is a Postdoctoral Research Associate at the University of Wisconsin-Madison where he was awarded and partially funded by a T32 Fellowship in the Computation and Informatics in Biology and Medicine (CIBM) training program. Chase completed a PhD in Pharmacognosy with Dr. Brian Murphy at the University of Illinois at Chicago where he was awarded and funded by an NIH F31 fellowship

Chase has >10 years of lab and computational experience surrounding natural products. Non-comprehensively, this spans analytical chemistry/biochemistry/microbiology method development and R&D at a small enzyme and probiotic manufacturer, to mass spectrometry method and software development in grad school, to engineering large scale genome mining and metagneomic software for drug discovery.

Chase would like to spend more time outdoors this year– kayaking, scuba diving, cycling, etc.

More info can be found at https://chasemc.github.io.

Education

University of Illinois at Chicago | Chicago, IL | PhD in Pharmacognosy | 2015 - 2020

Berry College | Mount Berry, GA | B.S. in Biochemisty | 2008 - 2012

Experience

University of Wisconsin-Madison | Postdoctoral Fellow/Associate (Computational Biology, Data Science, Drug Discovery) | 2020 - present

Deerland Probiotics & Enzymes | R&D Tech | 2013 - 2015

(image created with DALL·E 3)

Publications

(1)

Mullowney, M. W.; Duncan, K. R.; Elsayed, S. S.; Garg, N.; Hooft, J. J. J. van der; Martin, N. I.; Meijer, D.; Terlouw, B. R.; Biermann, F.; Blin, K.; Durairaj, J.; Gorostiola González, M.; Helfrich, E. J. N.; Huber, F.; Leopold-Messer, S.; Rajan, K.; Rond, T. de; Santen, J. A. van; Sorokina, M.; Balunas, M. J.; Beniddir, M. A.; Bergeijk, D. A. van; Carroll, L. M.; Clark, C. M.; Clevert, D.-A.; Dejong, C. A.; Du, C.; Ferrinho, S.; Grisoni, F.; Hofstetter, A.; Jespers, W.; Kalinina, O. V.; Kautsar, S. A.; Kim, H.; Leao, T. F.; Masschelein, J.; Rees, E. R.; Reher, R.; Reker, D.; Schwaller, P.; Segler, M.; Skinnider, M. A.; Walker, A. S.; Willighagen, E. L.; Zdrazil, B.; Ziemert, N.; Goss, R. J. M.; Guyomard, P.; Volkamer, A.; Gerwick, W. H.; Kim, H. U.; Müller, R.; Wezel, G. P. van; Westen, G. J. P. van; Hirsch, A. K. H.; Linington, R. G.; Robinson, S. L.; Medema, M. H. Artificial Intelligence for Natural Product Drug Discovery. Nat. Rev. Drug Discov. 2023, 22 (11), 895–916. https://doi.org/10.1038/s41573-023-00774-7.

(2)

Rees, E. R.; Uppal, S.; Clark, C. M.; Lail, A. J.; Waterworth, S. C.; Roesemann, S. D.; Wolf, K. A.; Kwan, J. C. Autometa 2: A Versatile Tool for Recovering Genomes from Highly-Complex Metagenomic Communities. bioRxiv, 2023, 2023.09.01.555939. https://doi.org/10.1101/2023.09.01.555939.

(3)

Waterworth, S. C.; Rees, E. R.; Clark, C. M.; Carlson, S.; Miller, I. J.; Puglisi, M.; Kwan, J. C. Elevated Expression of Srp RiPPs Across Bacterial Phyla in Marine Sponges. bioRxiv, 2023, 2023.06.09.544420. https://doi.org/10.1101/2023.06.09.544420.

(4)

Clark, C. M.; Nguyen, L.; Pham, V. C.; Sanchez, L. M.; Murphy, B. T. Automated Microbial Library Generation Using the Bioinformatics Platform IDBac. Molecules 2022, 27 (7). https://doi.org/10.3390/molecules27072038.

(5)

Clark, C. M.; Hernandez, A.; Mullowney, M. W.; Fitz-Henley, J.; Li, E.; Romanowski, S. B.; Pronzato, R.; Manconi, R.; Sanchez, L. M.; Murphy, B. T. Relationship Between Bacterial Phylotype and Specialized Metabolite Production in the Culturable Microbiome of Two Freshwater Sponges. ISME Communications 2022, 2 (1), 1–8. https://doi.org/10.1038/s43705-022-00105-8.

(6)

Elfeki, M.; Mantri, S.; Clark, C. M.; Green, S. J.; Ziemert, N.; Murphy, B. T. Evaluating the Distribution of Bacterial Natural Product Biosynthetic Genes Across Lake Huron Sediment. ACS Chem. Biol. 2021, 16 (11), 2623–2631. https://doi.org/10.1021/acschembio.1c00653.

(7)

Leao, T. F.; Clark, C. M.; Bauermeister, A.; Elijah, E. O.; Gentry, E. C.; Husband, M.; Oliveira, M. F.; Bandeira, N.; Wang, M.; Dorrestein, P. C. Quick-Start Infrastructure for Untargeted Metabolomics Analysis in GNPS. Nat Metab 2021, 3 (7), 880–882. https://doi.org/10.1038/s42255-021-00429-0.

(8)

Clark, C. M.; Murphy, B. T.; Sanchez, L. M. A Call to Action: The Need for Standardization in Developing Open-Source Mass Spectrometry-Based Methods for Microbial Subspecies Discrimination. mSystems 2020, 5 (1). https://doi.org/10.1128/mSystems.00813-19.

(9)

Costa, M. S.; Clark, C. M.; Ómarsdóttir, S.; Sanchez, L. M.; Murphy, B. T. Minimizing Taxonomic and Natural Product Redundancy in Microbial Libraries Using MALDI-TOF MS and the Bioinformatics Pipeline IDBac. J. Nat. Prod. 2019, 82 (8), 2167–2173. https://doi.org/10.1021/acs.jnatprod.9b00168.

(10)

Clark, C. M.; Costa, M. S.; Conley, E.; Li, E.; Sanchez, L. M.; Murphy, B. T. Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data. J. Vis. Exp. 2019, No. 147. https://doi.org/10.3791/59219.

(11)

Braesel, J.; Clark, C. M.; Kunstman, K. J.; Green, S. J.; Maienschein-Cline, M.; Murphy, B. T.; Eustáquio, A. S. Genome Sequence of Marine-Derived Streptomyces Sp. Strain F001, a Producer of Akashin a and Diazaquinomycins. Microbiol Resour Announc 2019, 8 (19). https://doi.org/10.1128/MRA.00165-19.

(12)

Clark, C. M.; Costa, M. S.; Sanchez, L. M.; Murphy, B. T. Coupling MALDI-TOF Mass Spectrometry Protein and Specialized Metabolite Analyses to Rapidly Discriminate Bacterial Function. Proceedings of the National Academy of Sciences, 2018, 115, 4981–4986. https://doi.org/10.1073/pnas.1801247115.