Experience

Team Lead Data Engineering at Ginkgo Bioworks 2022–Present

Lead and manged team of data engineers, system administrators, statisticians, bioinformaticians, and scientists at the PhD level working within the AgBio unit of Ginkgo Bioworks.
Mentored and coached team members in data science, bioinformatics, data engineering, and statistics.
Key leadership role in successful merger of AgBio unit with Ginkgo, including all relevant R&D business applications and data-adjacent systems.

Hired, managed, and developed team of 5+ Data Engineers, Systems Administrators, and Business Analysts working within the Biologics R&D unit of Bayer Crop Science enabling data capture, data integration, and operationalization of data analysis pipelines
Developed and supervised implementation of data capture, integration, and analysis strategies to increase the value of genomics, metabolomics, transcriptomics, spectroscopic, phenotypic (/in vitro/ and /in planta/), and fermentation/formulation process data for discovery and development
Lead the development of multiple systems while coaching, mentoring, and developing developers and engineers
Served as a key collaborator on multiple cross-function and cross-divisional projects, including leading the architecture of a life science collaboration using serverless architecture to provide machine-learning estimates of critical parameters from spectrographic measurements
Established and developed network of internal and external contacts for technical implementation of Bayer program goals.

Maintained, managed configurations, and resolved issues in multiple packages written in R, perl, python, scheme, C++, and C.
Resolved technical conflicts, developed technical standards, and provided leadership as the elected chair of the Technical Committee.
Developer of Debbugs, a perl and SQL-based issue-tracker with ≥ 100 million entries with web, REST, and SOAP interfaces.
Provided vendor-level support for complex systems integration issues on Debian GNU/Linux systems.

Planning, design, organization, execution, and analysis of multiple complex epidemiological studies involving epigenomics, transcriptomics, and genomics of diseases of pregnancy and post-traumatic stress disorder.
Published results in scientific publications and presented results orally at major scientific conferences.
Wrote and completed grants, including budgeting, scientific direction, project management, and reporting.
Mentored graduate students and collaborated with internal and external scientists.
Performed literature review, training, and applied new techniques to maintain abreast of current scientific literature, principles of scientific research, and modern statistical methodology.
Wrote software and designed relational databases using R, perl, C, SQL, make, and very large computational systems (Blue Waters)

Design, execution, and analysis of an epidemiological study to identify genomic variants associated with systemic lupus erythematosus using targeted deep sequencing.
Wrote multiple pieces of software to reproducibly analyze and archive large datasets resulting from genomic sequencing.
Coordinated with clinicians, molecular biologists, and biologists to produce analyses and major reports.

Executed and analyzed an epidemiological study to identify genomic variants associated with systemic lupus erythematosus using prior information and array based approaches in a trio and cross sectional study of individuals from the Los Angeles and greater United States.
Wrote and maintained multiple software components to reproducibly perform the analyses.

Doctor of Philosophy (PhD) in Cell, Molecular and Developmental Biology at UC Riverside
Batchelor of Science (BS) in Biology at UC Riverside

Lead teams of PhD and MD scientists in multiple scientific and industrial programs
Mentored graduate students and Outreachy and Google Summer of Code interns
Former chair of Debian's Technical Committee
Head developer behind https://bugs.debian.org

NGS and array-based Genomics and Epigenomics of complex human diseases using RNA-seq, targeted DNA sequencing, RRBS, Illumina bead arrays, and Affymetrix microarrays from sample collection to publication
Reproducible, scalable bioinformatics analysis using make, nextflow, and cwl based workflows on cloud- and cluster-based systems on terabyte-scale datasets
Alignment, annotation, and variant calling using existing and custom software, including GATK, bwa, STAR, and kallisto
Using evolutionary genomics to identify causal human variants

Statistical modeling (regression, inference, prediction, and machine learning in very large (> 1TB) datasets) using R and python.
Correcting & experimental design to overcome multiple testing, confounders, and batch effects (both Bayesian and frequentist)
Reproducible research

Languages: python, R, perl, C, C++, python, groovy, sh (bash, POSIX, and zsh), make
Collaborative Development: git, Jira, gitlab CI/CD, github actions, Aha!, continuous integration & deployment, automated testing
Web, Mobile: Shiny, jQuery, JavaScript
Databases: Postgresql (PL/SQL), SQLite, Mysql, NoSQL

Hardware, Linux routing and firewall experience, ferm, DHCP, openvpn, bonding, NAT, DNHS, SNMP, IPv4, and IPv6.

Strong written communication skills as evidenced by publication record
Strong verbal and presentation skills as evidenced by presentation, leadership, and teaching record

Debbugs: Bug tracking software for the Debian GNU/Linux distribution.
CairoHacks: Bookmarks and Raster images for large PDF plots in R.
Publications and Presentations
24 peer-reviewed publications cited over 3000 times: https://dla2.us/pubs
Publication record in GWAS, transcriptomics, SLE, GBM, epigenetics, comparative evolution of mammals, and lipid membranes
H index >= 20
Multiple presentations on EWAS of PTSD, genetics of SLE, and Open Source: https://dla2.us/pres

2017 R Consortium: Adding Linux Binary Builders to R-Hub Role: Co-PI
2015 Blue Waters Allocation Grant: Making ancestral trees using Bayesian inference to identify disease-causing genetic variants Role: Primary Investigator
Tracking placenta and uterine funciton using urinary extracellular vesicles (R21 RFA-HD-16-037) Role: Key Personnel
NIAMS R01-AR045650-04 Genetics of Childhood Onset SLE to Chaim O. Jacob. Role: Key Personnel

For my contact information or additional references, please e-mail don@donarmstrong.com