CV

Education

• Ph.D in Bioengineering, UC Berkeley/UCSF Joint Program, March 2020
  • National Science Foundation Graduate Research Fellow
• B.S. in Biochemistry and Molecular Biology, UC Davis, 2015

Work experience

• 04/2020 – Present. Research Scientist, Protein Design; Nautilus Biotechnology
• 04/2016 – 03/2020. Graduate Student Researcher, Tanja Kortemme Lab, UCSF
  • Developed (Py)Rosetta to implement an innovative strategy to assemble thousands of possible protein binding sites for arbitrary small molecules de novo as part of my dissertation research
  • Designed and screened libraries of small-molecule responsive sgRNAs using FACS and characterized hits using flow cytometry to control Cas9 activity in Escherichia coli
• 01/2016 – 03/2016. Rotation Student, Michelle Chang Lab, UC Berkeley
  • Assay development for high-throughput screening and engineering of C-C bond forming enzymes
• 08/2015 – 12/2015. Rotation Student, John Dueber Lab, UC Berkeley
  • Developed and implemented an assay to screen a panel of acetyltransferase enzymes I selected for activity on a target substrate to produce a base-labile indigo precursor in Escherichia coli
• 03/2014 – 11/2014. Team Member, iGEM Competition Team, UC Davis
  • Selected and characterized a panel of aldehyde dehydrogenases with various substrate specificity profiles for an enzyme-linked electrochemical biosensor to quantitatively evaluate olive oil composition
• 04/2013 – 08/2015. Undergraduate Researcher, Justin Siegel Lab, UC Davis
  • Purified and kinetically characterized a series of active site mutants of a mannitol 2-dehydrogenase

Selected Fellowships and Awards

• 04/2015 – Fellow, National Science Foundation Graduate Research Fellowship Program
• 06/2015 – UC Davis Ronald and Lydia Baskin Award for Excellence in Biological Sciences Research
• 11/2014 – Grand Prize, 2014 International Genetically Engineered Machine Competition
• 03/2014 – Honorable Mention, Barry M. Goldwater Scholarship
• 03/2014 – R. Bryan Miller Undergraduate Award for Excellence in Chemistry Research

Skills

COMPUTATIONAL

Programming. Python, C++, JavaScript, Docker, GitHub, Jupyter, LATEX

Software. Rosetta Macromolecular Modeling Suite, Avogadro, OpenEye Omega, RDKit, ProDy, Gurobi, Graphviz

Full Stack. Amazon Web Services (Elastic Beanstalk), Django, jQuery, MySQL, PostgreSQL, SQLite3, HTML, CSS

NGS. bcl2fastq, CutAdapt, Jellyfish

HPC. Amazon Web Services (Batch, EC2), Sun Grid Engine

EXPERIMENTAL

Engineering. Phage Display and Panning, Fluorescence-Activated Cell Sorting (FACS)

Characterization. Protein Expression and Purification, Flow Cytometry, ELISA, Enzyme Kinetics, Plate Reader Assays

DNA Assembly. Golden Gate, Gibson, HiFi, Restriction/Ligation, SOE PCR, Kunkel Mutagenesis

Molecular Biology. PCR, Gel Electrophoresis, SDS-Page, Western Blot

Model Systems. E. coli, S. cerevisiae

Publications

New Protein Design Methods for De Novo Small Molecule Binding Sites

Lucas JE, Kortemme T (2020) New computational protein design methods for de novo small molecule binding sites. PLOS Computational Biology 16(10): e1008178. https://doi.org/10.1371/journal.pcbi.1008178

Controlling CRISPR-Cas9 with ligand-activated and ligand-deactivated sgRNAs

Kundert K, Lucas JE, Watters KE, Fellmann C, Ng AH, Heineike BM, Fitzsimmons CM, Oakes BL, Qu J, Prasad N, Rosenberg OS, Savage DF, El-Samad H, Doudna JA, Kortemme T. Controlling CRISPR-Cas9 with ligand-activated and ligand-deactivated sgRNAs. Nat Commun. 2019 May 9;10(1):2127. doi: 10.1038/s41467-019-09985-2.

Flex ddG: Rosetta Ensemble-Based Estimation of Changes in Protein–Protein Binding Affinity upon Mutation

Barlow KA, Ó Conchúir S, Thompson S, Suresh P, Lucas JE, Heinonen M, Kortemme T. Flex ddG: Rosetta Ensemble-Based Estimation of Changes in Protein-Protein Binding Affinity upon Mutation. J Phys Chem B. 2018 doi: 10.1021/acs.jpcb.7b11367.

Quantitative functional characterization of conserved molecular interactions in the active site of mannitol 2‐dehydrogenase

Lucas, J.E. and Siegel, J.B. (2015), Quantitative functional characterization of conserved molecular interactions in the active site of mannitol 2‐dehydrogenase. Protein Science, 24: 936-945. doi:10.1002/pro.2669

Talks

De Novo Ligand Binding Site Design for Improved Biosensors

February 15, 2019

Talk at Mission Bay Conference Center at UCSF, San Francisco, California

De Novo Ligand Binding Site Design for Improved Biosensors

August 08, 2019

Talk at Sleeping Lady, Leavenworth, Washington

Service and leadership

• 01/2018 – 03/2018. Member, Faculty Search - Student Committee, UC Berkeley
  • Interviewed and evaluated faculty candidates for the Department of Bioengineering at UC Berkeley