Jared Lumpe Email & Phone Number

San Francisco, CA, US

Sunnyvale, CA, US

• Collaborate with the rest of the bioinformatics team to create computational pipelines for multiplexed PCR assay design, developing new methods as well as organizing existing ones into automated workflows.
• Contribute to development of the team's Python software suite. Led efforts to apply industry best practices, such as comprehensive automated testing.
• Developed and applied a unit testing framework for the Snakemake workflow manager.
• Manage the team's computational infrastructure.
• Assist team in assay design tasks.

• Developed GAMBIT, a software tool for taxonomic identification of bacterial pathogens from WGS data.
• Research was published in PLoS One in February 2023.
• Tool 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.

San Francisco, California, US

• Developed software and methods to improve development and calibration of systems biology models.
• Incorporated elements of ensemble modeling, global parameter sensitivity analysis, and automated model reduction to attempt to better explore the space of possible models for a given system.
• Worked on developing a more complete and accurate dynamic model of the yeast PKA signaling network.
• Used automated optimal experimental design to derive dynamic perturbations to a biological system that yield the most informative response for the purposes of model selection and fitting.

Santa Clara, California, US

Created methods and tools for analyzing high-throughput, high-dimensional flow cytometry data sets. Developed database and web application to annotate, validate, and store experimental data and later correlate across experiments, leading to a many-fold decrease in analysis time.

Santa Clara, California, US

Headed a project to develop a high-throughput assay panel for the discovery of effective new tyrosine kinase inhibitors.

Santa Clara, CA, US

• Studied hexuronate metabolism in C. crescentus
• Research focused on a lac repressor analogue believed to act on several operons within the hexose isomerase pathway
• Verified binding of repressor protein to operator sequence through mobility shift assays and studied the regulatory effect of galacturonate and other sugars on binding affinity
• Used PCR site-directed mutagenesis to design vectors for expression of a recombinant version of the protein in E. coli, and worked on developing a purification protocol using FPLC
• Research culminated in a paper submitted to the Journal of Bacteriology

Santa Clara, CA, US

• Evolution of the anthocyanin biosynthetic pathway in plants of the Brassicaceae genus (mustards)
• Compared rate and direction of molecular evolution in different stages of the pathway
• Used BioEdit and ClustalW to perform multiple sequence alignments
• Constructed phylogenetic trees by Bayesian inference and maximum likelihood methods and used PAML to compute dN/dS ratios

Santa Clara, CA, US

• Performed assays to measure non-template-directed nucleotide addition and template-switching activity on various oligonucleotide substrates
• Studied similar activity in HIV Reverse Transcriptase hoping to gain insight into possible new antiretroviral drugs
• Developed protocols for the cloning, expression and purification of E. coli polymerase II and IV and HIV reverse transcriptase.

Master'S Degree, Biological And Medical Informatics

Bachelor Of Science (Bs), Cellular And Molecular Biology