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Basics
| Name | Joseph J. Gardner |
| Label | Principal Scientist, Bioinformatics Platform Manager |
| joseph.j.gardner@gmail.com | |
| Url | https://insilijo.github.io/ |
| Summary | Strategic bioinformatics leader with 8+ years of experience translating multi-omic and real world data into actionable insights across wide scientific applications using end-to-end software development and AI. Combines PhD-level technical expertise with business acumen to support portfolio growth, BD diligence, and commercial strategy. Outside of work, I'm passionate about operationalizing food justice at a local level for dignified and sustainable public access to fresh, nutritious produce. |
Work
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2023 - Present Principal Scientist and Bioinformatics Platform Manager
Metabolon
I lead a small team to cross-functionally translate commercial and scientific needs into stable, interpretable, and secure software applications for the largest, highest-quality provider of metabolomics data in the world. I perform functions spanning design, product, marketing, sales, and competitive intelligence in addition to direct technical implementation. Major initiatives include leading a microbiome launch, supporting tabular multiomics integration, pathways visualizations, spectral delivery support, and cheminformatics workflows.
- 90% reduction in client-facing errors in the first month after being given ownership of the platform
- Ideation, development, and deployment of pathway visualization, enrichment, and microbiome analysis tools
- Led evaluation of the chemical library against public libraries to justify strategic decision for spectral release
- Observed and quantified consultant operations to prioritize workflow and software improvements
- Proposed and executed cheminformatics workflows leading to closure of high-value deals
- Responsible for generating sales collateral and disseminating competitive and product knowledge internally as the representative of the competitive technical intelligence team
- Directly responsible for over $4M in revenue in the quarter since deployment of projects I've led and delivered
- Track record of talent development with all reports executing their projects and being promoted to higher roles
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2022 - 2022 Computational Biologist 1-2 + Consultant
Rheos Medicines
Used network modeling approaches and multi-omics to analyze autoimmune inflammatory diseases to predict individual patient response to treatement.
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2022 - 2023 Senior Data Scientist
General Metabolics
Generated cheminformatics workflows and client-facing tools for a rapid, scalable metabolomics assay.
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2019 - 2022 Computational Biologist
Joyn Bio
Worked with a small team to create high-throughput synthetic biology pipelines to engineer microbes for agricultural applicaitons.
Volunteer
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2025 - Present Boston, Massachusetts
Board Member and Volunteer
Fresh Start Food Network
Operationalized food justice at a local level for dignified and sustainable public access to fresh, nutritious produce.
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2022 - 2025 Boston, Massachusetts
Advisory Board Member and Volunteer
The Centre Food Hub
Operationalized food justice at a local level for dignified and sustainable public access to fresh, nutritious produce.
Education
Publications
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2023 Investigating the unique ability of Trichodesmium to fix carbon and nitrogen simultaneously using MiMoSA
mSystems
Joseph J. Gardner, Bri-Mathias Hodge, Nanette R. Boyle
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2019 Multiscale Multiobjective Systems Analysis (MiMoSA): an advanced metabolic modeling framework for complex systems
Scientific Reports
Joseph J. Gardner, Bri-Mathias Hodge, Nanette R. Boyle
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2019 Multiscale, Multiparadigm Metabolic Modeling of the Keystone Diazotrophic Cyanobacterium, Trichodesmium erythraeum
Colorado School of Mines
Joseph J. Gardner, Bri-Mathias Hodge, Nanette R. Boyle
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2017 The use of genome-scale metabolic network reconstruction to predict fluxes and equilibrium composition of N-fixing versus C-fixing cells in a diazotrophic cyanobacterium, Trichodesmium erythraeum
BMC Systems Biology
Joseph J. Gardner, Bri-Mathias Hodge, Nanette R. Boyle
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2016 Omics in Chlamydomonas for Biofuel Production
Lipids in Plant and Algae Development
Hanna R. Aucoin and Joseph J. Gardner, Nanette R. Boyle
Skills
| Computational Biology and Scientific Informatics | |
| Workflow Managers (Snakemake, Nextflow) | |
| Databases (Reactome, KEGG, HMDB, UniProt, ChEBI, StringDB, GenBank, PDB, GEO, GO) | |
| Modeling and Simulation (cobraPy, Cytoscape, networkx, igraph, Repast ABM) | |
| Metabolomics (FBA, MetaboAnalyst, mixomics) | |
| Transcriptomics (DeSeq, limma, edgeR) | |
| Proteomics (Pyteomics, pyOpenMS) | |
| Cheminformatics (xcms, pyOpenMS, mzMine, rdkit) | |
| Metagenomics (Taxprofiler, AmpliSeq) |
| Data Science | |
| Databases (SQL, parquet, APIs) | |
| Visualization (ggplot, Seaborn, plotly, Tableau, Metabase, RShiny, Dash) | |
| Notebooks (Jupyter, R md) | |
| Python (scikit-learn, pandas, numpy, scipy, pyomo, statsmodels, grakel) | |
| R (limma, edgeR, tidyverse) | |
| Other (MatLab, MiniTab, Excel) |
| Product and Project Management | |
| Stakeholder alignment | |
| Gantt charting | |
| Stagegating | |
| Jira | |
| GitHub | |
| Product wireframing | |
| Figma | |
| draw.io | |
| RACI designations | |
| Executive communication |
| Full-Stack Engineering | |
| Languages (Python, R, JavaScript, HTML, C#, HTMX, node.js) | |
| DevOps (Lambda, SNS/SQS, EC2, Docker/Containerization, Git/GitHub Actions, ADO) | |
| Platforms (Django, Metabase, Tableau) | |
| Compliance (ISO, Change Requests, SOPs) | |
| Architecture (ERDs, Process Flow, Service vs Monolith, Caching/redis) | |
| Philosophies (Agile, Shapeup, Kanban, Test-driven) |
| Strategy | |
| Competitive intelligence | |
| Sales collateral generation | |
| Internal communications | |
| Public speaking | |
| Market forecasting | |
| Marketing technical liaising | |
| Mentorship |
Interests
| Book Club |
| Interior Design and DIY |
| Camping and Hiking |
| Skiing |
| Writing |
| Board Games |
| Photography |
| Ice hockey |
| Food justice |
| Running |
Projects
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Fresh Start Food Network
Fresh Start Food Network sources, reclaims, and distributes vast tons of fresh produce that would otherwise go to waste and provides it to underserved neighborhoods in the Boston metro area.