Summary
I am currently working as a Bioinformatics Software Engineer at LanzaTech where I develop bioinformatics software and pipelines that empower scientists to engineer microorganisms that can produce useful chemicals sustainably.
Python is my native programming language, but I've also written a decent amount of JavaScript, HTML, CSS, and Swift. I use other tools like bash, docker, git, and AWS daily. I love to learn new technologies and use those tools to address practical needs.
I currently live in Skokie, IL and in my spare time I enjoy hiking, learning Japanese, building iOS apps, and strength training.
See below and check out my
LinkedIn for more info.
Skills: What can I do?
Software Development
- 🧬 Develop Scientific Software: For example, I helped develop the MINE Database, to unlock new modes of scientific inquiry. I have also used backend frameworks like flask to build web APIs, one which also uses celery to schedule tasks across distributed workers in AWS.
- 🫱🏻🫲🏽 Communicate Effectively, esp. with Scientists: With a STEM PhD and as a former scientist myself, I can collaborate effectively with key stakeholders on science teams during the development process.
- ✍🏻 Communicate and document effectively: I am always focused on documenting my code via docstrings, type annotations, descriptive variable names, etc. The joy I get from cleaning up messy code is like no other and highly motivating. I have also used tools like Sphinx to generate API documentation for python libraries.
- 📊 Data visualization: I love thinking about ways to visualize data to meet user requirements. I am most experienced with python libraries such as matplotlib, seaborn, and bokeh. I have also used tools like streamlit to create interactive dashboards.
- ☁ AWS: I have practical experience with EC2, S3, and RDS and am familiar with networking concepts (VPNs, security groups, etc.). I have also used AWS CodeDeploy to deploy apps to production. I am currently working on obtaining the Solutions Architect AWS Associate Certification.
- 🏭 High-Performance Computing: I have used the Slurm Workload Manager to submit jobs on supercomputing clusters. For example, I used the Quest supercomputing cluster at Northwestern University to predict MS2 spectra for millions of compounds in parallel.
- 🫙 Containerization: I frequently use Docker to containerize my applications and have recently started diving deeper into docker compose.
- 🐚 Scripting: I am very familiar with bash scripting, as it is often used in bioinformatics applications. I have also dabbled in bat scripting for Windows.
- 💾 Build and query databases: I have experience building and working with MySQL (e.g. with python's sqlalchemy driver) as well as MongoDB (e.g. with pymongo driver) databases.
- 💻 Contribute to frontend development: I'm familiar with vanilla JavaScript as well as basic HTML and CSS and have built basic user interfaces for APIs I've developed. I built this site using Jekyll + HTML/CSS.
- 🧹 Collaborate using git, GitHub, and Jira: submit issues, make commits, merge changes, review and submit pull requests, use features like interactive rebase to keep commit history clean. I have used these tools for both solo projects as well as collaborative projects.
- 📱 Develop iOS applications using SwiftUI: As a side project, I'm currently working on my first iPhone app - a crossword game for Japanese language learners (see blog for details).
Scientific Background
- 💭 Design & Analysis of Experiments: I absolutely love working with experimentalists to design experiments and analyses that best answer the most pressing questions. I have experience with both frequentist statistics as well as Bayesian statistical modeling.
- 🤖 Machine Learning/AI: Analyze complex datasets and make predictions. For example, I built a random forest regressor model using scikit-learn to predict chromatographic retention times in order to annotate unknown compounds in a metabolomics dataset.
- 🧬 Bioinformatics: I have experience processing and analyzing large NGS, transcriptomics, proteomics, and metabolomics datasets.
- 🧪 Cheminformatics: I have used tools like RDKit and mordred to process, analyze, and interpret chemical data.
- 🧮 Mathematical Modeling: I have used Genome-scale Models (GEMs) to make predictions using cobrapy. I have also developed kinetic metabolic models, using both deterministic (e.g. ODE) and stochastic (e.g. Kinetic Monte Carlo) kinetic modeling approaches.
- ✍🏻 Scientific Writing: I clearly communicate my science to the rest of the world or company. My work has been published in Bioinformatics, PLoS Computational Biology, and Nature Biotechnology.
Professional Experience
LanzaTech (Skokie, IL) - Feb 2024 - Now
Bioinformatics Software Engineer, AI & Computational Biology
LanzaTech (Skokie, IL) - July 2022 - Jan 2024
Scientist, AI & Modeling
Northwestern University (Evanston, IL) - 2016 - 2022
PhD Candidate in Chemical & Biological Engineering
LanzaTech (Skokie, IL) - June 2018 - Dec 2018
Computational Biology Intern
Wood Laboratory at Ohio State (Columbus, OH) - 2014 - 2016
Undergraduate Researcher
Ohio State University (Columbus, OH) - 2013 - 2015
Undergraduate Teaching Assistant
DuPont (Circleville, OH) - Summer 2013
Manufacturing Technology Engineer Intern
Education
Northwestern University (Evanston, IL) - Sep 2016 - June 2022
Ph.D. Chemical & Biological Engineering
Advisors: Keith Tyo & Linda Broadbelt
Thesis: Computational Approaches for Enhanced Metabolomics Annotation and DNA-based Biorecording and Data Storage
Ohio State University (Columbus, OH) - Sep 2011 - Dec 2015
B.S. Chemical & Biomolecular Engineering
Minors: Biomedical Engineering, German
GPA: 3.82
Circleville High School (Circleville, OH) - 2007 - 2011
Valedictorian (GPA: 4.55)
Honors & Awards
ARCS Scholar Award (renewed twice) - 2017, 2018, 2019
Biotechnology Training Program Trainee - 2017, 2018
Undergraduate Research Award - 2015
Honda-OSU Math Medal Award - 2011
Columbus Dispatch Scholar-Athlete Runner-Up Male - 2011
National Merit Finalist - 2011
High School Valedictorian - 2011
Teaching Experience
Northwestern University (Evanston, IL)
ChBE 373 - Global Health & Biotechnology (TA) - F2019
ChBE 477 - Bioseparations (TA) - S2017, S2018, S2019
Ohio State University (Columbus, OH)
CBE 2420 - Transport Phenomena I - F2013, F2014, F2015
Organizations
Northwestern University (Evanston, IL)
Graduate Student Forum - 2017 - 2018
Ohio State University (Columbus, OH)
Phi Kappa Tau Fraternity, Gamma Chapter
- Vice President - 2013 - 2015
- Secretary - 2012
- Founding Father - 2012
Publications
Primary Research
Shebek K, Strutz J, Broadbelt L, Tyo K (2023)
Pickaxe: a Python library for the prediction of novel metabolic reactions
BMC Bioinformatics 24:106
Strutz J, Shebek K, Broadbelt L, Tyo K (2022)
MINE 2.0: enhanced biochemical coverage for peak identification in untargeted metabolomics.
Bioinformatics, 38(13):3484-3487.
Liew EF, Nogle R, Abdalla T, Rasor BJ, Canter C, Jensen RO, Wang L, Strutz J, ..., Köpke M (2022)
Carbon-negative production of acetone and isopropanol by gas fermentation at industrial pilot scale.
Nature Biotechnology, 40:335-344.
Bhan NJ, Callisto A, Strutz J, Glaser J, Kalhor R, Boyden E, Church G, Kording K, Tyo KEJ (2021)
Recording Temporal Signals with Minutes Resolution Using Enzymatic DNA Synthesis.
Journal of the American Chemical Society, 143:16630-16640.
St. John P, Strutz J, Broadbelt LJ, Tyo KEJ, Bomble YJ (2019)
Bayesian inference of metabolic kinetics from genome-scale multiomics data.
PLoS Computational Biology, 15(11):e1007424.
Reviews and Opinions
Strutz J, Martin J, Greene J, Broadbelt L, Tyo K (2019)
Metabolic kinetic modeling provides insight into complex biological questions, but hurdles remain.
Current Opinion in Biotechnology, 59:24-30.
Book Chapters and Technical Reports (Non-peer Reviewed)
Jeffryes J, Strutz J, Henry C, Tyo KEJ (2019)
Metabolic in silico network expansions to predict and exploit enzyme promiscuity.
Methods in Molecular Biology, 1927:11-21.
Rosenfeld, D, Liew, F, Kopke, M, Gao, A, Harris, A, Mueller, A, Nagaraju, S, Smith, A, Tran, L, O'Brien, J, Tyo, K, Martin, J, Strutz, J, Metz, J. The Dow Chemical Company (2019)
Bio-syngas to Fatty Alcohols (C6-14) as a Pathway to Fuels.
Presentations, Panels, & Talks
November 28, 2023 - Northwestern University Data Science Nights Career Panel - Virtual
Participated in a career panel for data science students considering a career in industry
October 27, 2023 - Northwestern University Center for Synthetic Biology Career Panel - Chicago, IL
Participated in a career panel for synthetic biology graduate students considering a career in industry
February 24, 2022 - PhD Student Seminar - Evanston, IL
“Exploring the Uncharted Biochemical Universe: Predicting Metabolites across Scales”
September 10, 2021 - Central US SynBio Workshop - Evanston, IL
“MINE 2.0: Enhanced biochemical coverage for peak identification in untargeted metabolomics” (poster)
October 7, 2020 - ARCS Fun at Five - Evanston, IL
“Using DNA as a medium for recording biological signals”
September 10, 2020 - Central US SynBio Workshop - Online
“Kinetic Monte Carlo Modeling of ssDNA Extension via Terminal deoxynucleotidyl Transferase” (poster)
May 8, 2020 - Virtual Podium 2020 - Online
“MINEs: Open Access Databases of Computationally Predicted Enzyme Products for Untargeted Metabolomics”
September 12, 2019 - Central US SynBio Workshop - Madison, WI
“Prediction of Liquid Chromatography Retention Times for Metabolite Identification” (poster)
May 21, 2019 - Mini-Symposium on Microbial Lignin Valorization - NREL - Golden, CO
“Discovery of Novel Metabolites and Gene Functions in Aromatic-Degrading Organisms (Proposed Work)”
October 31, 2018 - AIChE Annual Meeting - Pittsburgh, PA
“Addition of Thermodynamic Constraints to a Scalable Kinetic Modeling Framework”
March 4, 2018 - ARCS Illinois Chapter Meet & Greet - Evanston, IL
“Improving the Environmental Sustainability of Biorefineries: Engineering a Bacterium to Eat Plants”
June 26, 2017 - Mini-Symposium on Microbial Lignin Valorization - NREL - Golden, CO
“Modeling Catabolism of Lignin-Derived Aromatics in Acinetobacter baylyi ADP1”