Derek Gagnon
Scientist
San Diego, CA
derek.gagnon.16@gmail.com
https://www.linkedin.com/in/derek-gagnon-028bab99/
Computer Skills
- Data Processing
- Data Extraction
- Unstructured data mining
- Pandas/Numpy
- Functional Scripting
- Data Visualization (e.g. matplotlib)
- Instrument Test Automation
- Scikit-learn
- Spectral Simulation
- Data Import/Export
- Functional Scripting
- Figure Generation
- Powerpoint
- Word
- Excel
- Pivot Tables
- Conditional IF
- Array Formulas
- LabVIEW
- Unix/Linux Environment
- Shell Scripting
- Widnows Environment
Lab Skills
- Electron Paramagnetic Resonance (EPR/ESR)
- Nuclear Magnetic Resonance (NMR)
- FTIR
- Fluorescence
- UV/Vis and Circular Dichroism
- Protein X-ray Crystallography
- HPLC/FPLC
- Mass Spec
- E. coli Protein Expression
- in vitro Protein Expression (IVTT)
- IEX/SEC/IMAC Protein Purification
- Analysis of Routine Sequencing Data
- PCR Mutagenesis
- Aseptic Techniques
- Gel Electrophoresis
- DNA Purification
- Diafiltration
- Cryogen Handling
- Schlenk-Line
- Instrument Programming and Automation (Python/LabVIEW)
- mm-Wave/Microwave/Radio Frequency Instrument Troubleshooting/Maintenance
- Standard chemistry/biochemistry lab instrument maintenance
Interests
- Rock Climbing
- Hiking
- Camping
- Volleyball
Work Experience
Research Scientist Electronic Biosciences, San Diego CA
October 2020 - Present
- Mined existing dataset for insights into nanopore sensor design
- Upgrading from py2.7 to py3.8 and maintenance to py3.10
- Refactored codebase to improve maintainability and extensibility
- Designed and setup new SQL database to track samples and data
- Simulation and analysis of time domain electrical signals
- In vitro protein expression and purification
- Writing SOPs and reports
- Process improvements in production and mutation decisions of proteins
Postdoctoral Researcher University of California, San Diego CA
January 2019 - February 2020
- Python scripts to automate extraction of data from computational results
- Computational design, analysis, and modeling of protein-protein interactions
- Automation of data extraction from scientific instrumentations (Python)
- Assay development (mass spec, UV/Vis, chromatography)
- Manuscript and grant writing
- Training and mentoring of junior colleagues
Postdoctoral Researcher University of California, Davis CA
September 2018 - December 2018
Graduate Student Researcher University of California, Davis CA
December 2012 - August 2018
- Simulation and modeling of data (electron paramagnetic resonance - Matlab and Python)
- Custom models for analysis and simulation of data
- Production of software tools to automate extraction of data from computational models
- Augmenting software for simulation and modeling (adding new capabilities)
- Helped successfully acquire >$3 million in grant funding through NIH and NSF, lead on a $1.5 million grant for instrument development + additional university support
- Independently saved a cumulative of $39,000+ in direct costs and 12+ months of equipment downtime by diagnosing problems, reverse engineering commercial systems, and performing repairs in house on several occasions
- Design and construction of new, and maintenance/repair/upgrade of existing analytical instrumentation and helium liquefaction systems
- Liaison with contractors and facilities management to ensure needs are properly communicated for continued operation and expansion of laboratory facilities/equipment
Research Technician I Florida Institute of Technology, Melbourne FL
May 2012 - August 2012
- Writing code to automate output of commercial quantum property calculation software (Spartan and Gaussian) and convert data for input to in house developed code
- Simulating data collected from scanning tunneling microscopy
- Assisting graduate students and researchers in daily research needs: chemical/solvent purification, analytical instrument training/support, scientific calculations/programming
Undergraduate Researcher Florida Institute of Technology, Melbourne FL
September 2008 - April 2012
- Fluorescence, UV/Vis, and FTIR characterization of candidate hydrazine sensors elucidating molecular reasons for lack of specificity
- Circular dichroism characterization of DNA secondary structures stabilized by small molecules
- Synthesis of small molecule natural product analogues of tryptanthrin for structure-activity relationship studies and spectroscopic characterization
- Scanning tunneling microscopy to probe molecular orbitals of tryptanthrin and analogues, developing techniques to measure tunneling currents in ionic liquids and highly polar solvents
Education
Masters Data Science National University
2023 - present
Online Coursework w/ Emphasis in AI/ML
Ph.D. Physical Chemistry UC Davis
2012 - 2018
Electron Paramagnetic Studies of Radical S-Adenosyl-L-Methionine Enzyme Intermediates and Manganese Binding Proteins
Advisor: Prof. R.D. Britt
Research Accomplishments
- Trapping of short-lived enzyme radical intermediates
- Characterization of metals bound to proteins relevant at the host-pathogen interface
- Peter A. Rock Graduate Fellowship in Chemistry (2016)
- Three first author publications, four co-author publications, and presented research talks or posters at 12 conferences
Teaching Accomplishments
- 5 Quarters as a Chemistry TA (Lab/Discussion)
- Part of a team developing active teaching methods to reform Gen Chem curriculum
- Taught and maintained safe laboratory environment for students
B.Sc. Chemistry-Research Florida Institute of Technology
2008 - 2012
Major in Chemistry with Undergraduate Thesis
Thesis Research
- Spectrocopic characterization turn-on fluorescence hydrazine sensors
- Analysis of strong and weak hydrogen bonding ligands that disrupt fluorescence quenching
Other Research/Activities
- Circular dichroism characterization of DNA secondary structures stabilized by small molecules
- Synthesis of small molecule natural product analogues of tryptanthrin for structure-activity relationship studies and spectroscopic characterization
- Scanning tunneling microscopy to probe molecular orbitals of tryptanthrin and analogues, developing techniques to measure tunneling currents in ionic liquids and highly polar solvents
- Teaching assistant for physical chemistry labs
Publications and Presentations
Publications
Kakkis, A.; Gagnon, D. M.; Esselborn, J.; Britt, R. D.; Tezcan, F. A. Metal‐Templated Design of Chemically Switchable Protein Assemblies with High‐Affinity Coordination Sites Angew. Chem., 132 (49):22124-22128, December 2020.
Rutledge, H. L.; Rittle, J.; Williamson, L. M.; Xu, W. A.; Gagnon, D. M.; Tezcan, F. A. Redox-Dependent Metastability of the Nitrogenase P-Cluster. J. Am. Chem. Soc., 141 (25):10091-10098, June 2019.
Hadley, R. C.; Gagnon, D. M.; Ozarowski, A.; Britt, R. D.; Nolan, E. M. Murine Calprotectin Coordinates Mn(II) at a Hexahistidine Site with Ca(II)-Dependent Affinity. Inorg. Chem., 58 (20):13578-13590, October 2019.
Gagnon, D. M.; Hadley, R. C.; Ozarowski, A.; Nolan, E. M.; Britt, R. D. High-Field EPR Spectroscopic Characterization of Mn(II) Bound to the Bacterial Solute-Binding Proteins MntC and PsaA. J. Phys. Chem. B, 123 (23):4929-4934, June 2019.
Gagnon, D. M.; Stich, T. A.; Mehta, A. P.; Abdelwahed, S. H.; Begley, T. P.; Britt, R. D. An Aminoimidazole Radical Intermediate in the Anaerobic Biosynthesis of the 5,6-Dimethylbenzimidazole Ligand to Vitamin B12. J. Am. Chem. Soc., 140 (40):12798-12807, October 2018.
Hadley, R. C.; Gagnon, D. M.; Brophy, M. B.; Gu, Y.; Nakashige, T. G.; Britt, R. D.; Nolan, E. M. Biochemical and Spectroscopic Observation of Mn(II) Sequestration from Bacterial Mn(II) Transport Machinery by Calprotectin. J. Am. Chem. Soc., 140 (1):110-113, January 2018.
Stich, T. A.; Gagnon, D. M.; Anderson, B. L.; Nocera, D. G.; Britt, R. D. EPR Spectroscopic Characterization of a Jahn-Teller Distorted ( C 3 v → C s ) Four-Coordinate Chromium(V) Oxo Species. Isr. J. Chem., 56 (9-10):864-871, October 2016. [Invited Contribution]
Gagnon, D. M.; Brophy, M. B.; Bowman, S. E. J.; Stich, T. A.; Drennan, C. L.; Britt, R. D.; Nolan, E. M. Manganese Binding Properties of Human Calprotectin under Conditions of High and Low Calcium: X-Ray Crystallographic and Advanced Electron Paramagnetic Resonance Spectroscopic Analysis. J. Am. Chem. Soc., 137 (8):3004-30016, March 2015.
Oral Presentations
Understanding How Proteins Control Radical Reactivity Chemical Biology Innovation Group (CBIG), Davis CA, May 2018
A Radical Intermediate in the Biosynthesis of Aminofutalosine by MqnE Gordon Research Seminar on Bioinorganic Chemistry, Ventura CA, January 2017
Poster Presentations
Electron Paramagnetic Resonance Studies of Trapped Radical Intermediates in the Radical S-adenosyl-L-methionine Enzyme MqnE Gordon Research Seminar on Bioinorganic Chemistry, Ventura CA, January 2018
Electron Paramagnetic Resonance Studies of Trapped Radical Intermediates in the Radical S-adenosyl-L-methionine Enzyme MqnE Gordon Research Conference on Metals in Biology, Ventura CA, January 2018
Radical Intermediates in Radical S-adenosyl-L-methionine Enzymes Characterized with Electron Paramagnetic Resonance R. Brian Miller Symposium, Davis CA, March, 2017
Radical Intermediates in Radical S-adenosyl-L-methionine Enzymes Characterized with Electron Paramagnetic Resonance Gordon Research Seminar on Bioinorganic Chemistry, Ventura CA, January, 2017
Radical Intermediates in Radical S-adenosyl-L-methionine Enzymes Characterized with Electron Paramagnetic Resonance Gordon Research Conference on Metals in Biology, Ventura CA, January, 2017
A Radical Intermediate in the Anaerobic Synthesis of the Lower Ligand to Vitamin B12 Gordon Research Seminar on Bioinorganic Chemistry, Ventura CA, January, 2016
A Radical Intermediate in the Anaerobic Synthesis of the Lower Ligand to Vitamin B12 Gordon Research Conference on Metals in Biology, Ventura CA, January, 2016
Manganese Binding Properties of Human Calprotectin Under Conditions of High and Low Calcium: X-ray Crystallographic and Advanced Electron Paramagnetic Resonance Spectroscopic Analysis Gordon Research Seminar on Metals in Biology, Ventura CA, January, 2015
Electron Paramagnetic Resonance (EPR) Spectroscopy in the mm-Wave Regime Davis mm-Wave Research Conference, Davis CA, October, 2014
EPR Spectroscopic Studies of the Mn(II) Binding Site in Human Calprotectin Frontiers in Metallobiochemistry, State College PA, May 2014