Summary
I am a scientist turned software engineer - my mission is to empower scientists by crafting high-quality software and building maintainable, scalable infrastructure. I currently work 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.
I currently live in the Chicago area with my wife, Ayana, and our two cats, Miko and Lupin.
See below and check out my
LinkedIn for more info.
Skills: What can I do?
I've loosely divided my skillset into four categories:
Software Development - Crafting high-quality code to support scientific research
Data Infrastructure - Building and maintaining scalable data infrastructure
Scientific Background - Using my scientific background to inform the development process
Other - Miscellaneous skills and interests
Software Development
- 🧬 Scientific Software Development: In my current role, I develop and maintain a suite of 10+ bioinformatics pipelines comprising 100+ (mostly open-source) bioinformatics tools to process genomics datasets. I also built a web app that constructs 1000s of mathematical models daily and validates these models against in-house scientific datasets.
- 👨🏻💻 Write Web App Backends & APIs: I've written and contributed to many web backends & REST APIs - I've used flask, Django, Next.js, and FastAPI (which I love using for quick prototypes).
- 💻 Contribute to Frontend Development: I'm familiar with vanilla JavaScript, Typescript, as well as basic HTML and CSS. I've built simple user interfaces for APIs I've developed. I built this site using Jekyll + HTML/CSS (code here). I have also contributed to projects that use Vue on the frontend.
- 🧠 Deploy AI & LLM Tools: I've built RAG pipelines (using Haystack) to allow users to quickly query 1000+ internal documents supporting critical business processes. I've also made some minor contributions to Haystack itself.
- 🐳 Containerize Apps: I frequently use Docker (often with Docker Compose) to containerize applications to improve reproducibility.
- 🐚 Write Shell Scripts: I am very comfortable with bash scripting (which is particularly common in bioinformatics). I have also dabbled in bat scripting for Windows.
- 🧹 Collaborate Using git & GitHub: I use git & GitHub daily to submit issues, make commits, merge changes, and review and submit pull requests. I like to use interactive rebase to keep the commit history clean. Lazygit is my best friend.
- ✍🏻 Communicate and Document Effectively: I prioritize writing readable code in order to clearly communicate the code's purpose. The joy I get from cleaning up messy code is like no other and highly motivating. I also use tools like Sphinx to write API documentation for python libraries.
Data Infrastructure
- 🛠️ Build Maintainable Data Infrastructure: In my current role, I used Ansible to rearchitect 3 on-prem linux servers used for compute-heavy bioinformatics workloads - I designed a standardized data architecture, optimized storage resources, improved security, and increased reproducibility of bioinformatics pipelines.
- 💾 Design and Query Databases: I have experience designing small databases (~5-10 tables) from scratch. I have also worked with large legacy databases (100+ tables). I have experience with PostgreSQL, MySQL, as well as MongoDB.
- ☁ Optimize AWS Resources: I use AWS daily (especially EC2, ECS, S3, and RDS), and I am always looking for ways to optimize existing infrastructure (In my current role, I reduced costs for some AWS accounts by more than 50% while meeting business requirements). In 2025, I passed the AWS Solutions Architect exam at the Associate level.
- 🔒 Prioritize Cybersecurity: I've configured on-prem linux servers with security measures like SSH hardening and proper permissions & access control. I've implemented SSO on web app frontends and backends. See this PR where I added a new auth-related feature to an open-source LLM chat app.
- 📈 Build Dashboards to Bolster Observability: I've used the OpenTelemetry Collector to send metrics to Grafana cloud. I've built dashboards in Grafana to track key metrics for products I (and others) have built. I've also built Grafana dashboards to monitor resource usage of on-prem servers.
Scientific Background
- 🫱🏻🫲🏽 Communicate Effectively (especially 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.
- ✍🏻 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.
- 📊 Data Visualization: I love thinking about ways to visualize data to meet user requirements. I am experienced with python libraries such as matplotlib, seaborn, and bokeh. I have also used tools like streamlit to create interactive dashboards.
- 🏭 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 molecules in parallel.
- 💭 Design & Analysis of Experiments: I enjoy working with scientists 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.
- 🧮 Mathematical Modeling: I have used linear programming techniques to make metabolic state predictions for bacteria. I have also developed kinetic metabolic models, using both deterministic (e.g. ODE) and stochastic (e.g. Kinetic Monte Carlo) methods.
- 🤖 Machine Learning: During my PhD, I built a random forest regressor model using scikit-learn to predict chromatographic retention times in order to help identify unknown molecules in a metabolomics dataset.
- 🧬 Bioinformatics: I have experience processing and analyzing large genomics & transcriptomics datasets (e.g. alignment, variant calling, assembly & annotation). I also have experience processing and annotating metabolomics datasets.
- 🧪 Cheminformatics: I have used tools like RDKit and mordred to process, analyze, and interpret chemical data.
Other
- 📱 Develop iOS applications: I develop iPhone apps on the side - currently, the apps I've built just live on my phone (I build them primarily for my own use), but I might release some in the future (see blog for more details).
- 🏋️♂️ Strength Training: I love optimizing my strength training protocols. I've been lifting weights for 10+ years and am obsessed with the science behind strength gain and muscle growth.
- 🇯🇵 Japanese: I've been learning Japanese for 10+ years now (and I still suck, but I enjoy it). I've put in over 1,000 hours reading & listening to Japanese.
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
Co-advised by Keith Tyo & Linda Broadbelt
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
Biomedical Engineering Minor
German Minor
Circleville High School (Circleville, OH) - 2007 - 2011
Valedictorian
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
Callisto A, Strutz J, Leeper K, Kalhor R, Church G, Tyo KEJ, Bhan N (2024)
Post-translational digital data encoding into the genomes of mammalian cell populations.
bioRxiv (in review)
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”