I am a computational biologist and software developer with a strong interest in single-cell techniques, systems biology and mathematical modeling. I am also passionate about developing open source software that is of use to the scientific community.
GAMBIT (Genomic Approximation Method for Bacterial Identification and Tracking) is a software tool for the rapid taxonomic identification of microbial pathogens from WGS data. It has been in regular use at multiple state‑ and county‑level public health labs across the US for several years, where it has been used to diagnose actual patients.
- Publication in PLoS One
- Project home page
- Project documentation
- Automated workflow to reproduce figures and results in paper
- Masters in Biological and Medical Informatics, University of California, San Francisco (2020)
- BS in Molecular Biology, Santa Clara University (2012)
- Bioinformatics Researcher and Software Developer, Independent Researcher (Jun 2020 - present)
- Graduate Student, University of California, San Francisco (Sep 2017 - Mar 2020)
- Bioinformatics Analyst and Software Developer, Independent Contractor (Jan 2017 - Dec 2017)
- Application Developer / Data Analyst, Primity Bio (Jan 2015 - Jan 2017)
- Life Science Research Associate, Primity Bio (Jul 2012 - Dec 2014)
Lumpe, J., Gumbleton, L., Gorzalski, A., Libuit, K., Varghese, V., Lloyd, T., Tadros, F., Arsimendi, T., Wagner, E., Stephens, C., Sevinsky, J., Hess, D., & Pandori, M. (2023). Gambit (genomic approximation method for bacterial identification and tracking): A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification. PLOS ONE, 18(2), 1–22. https://doi.org/10.1371/journal.pone. 0277575
Newberry, R. W., Arhar, T., Costello, J., Hartoularos, G. C., Maxwell, A. M., Naing, Z. Z. C., Pittman, M., Reddy, N. R., Schwarz, D. M. C., Wassarman, D. R., Wu, T. S., Barrero, D., Caggiano, C., Catching, A., Cavazos, T. B., Estes, L. S., Faust, B., Fink, E. A., Goldman, M. A., … Kampmann, M. (2020). Robust sequence determinants of 𝛼‑Synuclein toxicity in yeast implicate membrane binding. ACS chemical biology, 15(8), 2137–2153. https://doi.org/10.1021/acschembio.0c00339
Sheikh, A. I., Caswell, D., Dick, C., Gang, S., Jarrell, J., Kohli, A., Lieu, A., Lumpe, J., Garrett, M., Parker, J., & Stephens, C. (2013). Regulation of d‑galacturonate metabolism in caulobacter crescentus by HumR, a LacI‑family transcriptional repressor. Advances in bioscience and biotechnology, 4(10), 63–74. https://doi.org/10.4236/abb.2013.410A3008