Don Armstrong/ Resumé

Experience

Career Synopsis & Outlook

  • A proven, transformative leader of teams that enable businesses to harness the value of scientific and business data to achieve business goals in biotechnology and other biology-adjacent industries.
  • Significant experience mentoring, coaching, managing, and leading managers and individual contributors from the entry level to principal level, enabling them to develop into their full potential as leaders and contributors.
  • Extensive scientific, computational, analytical, and business background coupled with a history of effective communication with diverse audiences enables bridging the needs and requirements of challenging stakeholders and earning their trust and buy-in even in complex, highly regulated environments.
  • Seeking opportunities to grow, lead, and transform organizations with a larger scope and greater impact.

Director of Data Science and Analytics at Ginkgo Bioworks 2022--Present

  • Directed a geographically distributed team of managers who lead teams of data engineers, system administrators, statisticians, bioinformaticians, and scientists at the PhD level working within the Ag business unit of Ginkgo Bioworks
  • Accountable for the data architecture, engineering, management, and governance of all data within the Ag Business unit, including complex modalities of research and development data from genomics to complex phenotypic data, including chemistry, production, systems biology, and business data.
  • Accountable for cost centers totalling $10 M annually, including budgeting, procurement, vendor relationships, and policy compliance.
  • Hired and developed team members in data science, bioinformatics, data engineering, software engineering, and statistics using coaching, mentorship, and teaching approaches.
  • Accountable (and frequently responsible) for all R&D IT applications in a business unit, including vendor selection, architectural decisions, deployment, and development where appropriate.
  • Championed modern approaches to data governance and data stewardship principles across multiple life-science and business functions.
  • Lead the development of multiple cloud-based serverless and container-based applications in AWS and GCP with multiple API and UI interfaces written in python and javascript to enable the management of data, with dbt, airflow, postgresql, and snowflake handling data storage and plumbing roles.
  • Key leadership role in multiple mergers and acquisitions, specializing in R&D business applications and data-adjacent systems.
  • Extensive collaborations with scientific, business, and customer leaders attest to my excellent communication and interpersonal skills.

Team Lead Data Engineering at Bayer Crop Science 2018--2022

  • 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 using AWS, python, postgresql, R, and
  • Lead the development of multiple systems while coaching, mentoring, and developing software and data 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.

Debian Developer 2004--Present

  • 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.

Research Scientist at UIUC 2015--2017

  • Architected and engineered systems to store, retrieve, and analyze complex R&D data including behavioral healthcare data (PTSD), genomic, epigenomic, and other phenotypic healthcare data (pre-eclampsia), while maintaining compliance with data privacy regulations including HIPAA and institutional review boards.
  • 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 ([[https://bluewaters.ncsa.illinois.edu/][Blue Waters]])

Postdoctoral Researcher at USC 2013--2015

  • 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.

Postdoctoral Researcher at UCR 2010–2012

  • 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.

Education

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

Skills

Leadership and Mentoring

  • Lead managers and teams of PhD-level scientists in multiple scientific and industrial programs.
  • Mentorship of multiple employees, graduate students, and undergraduates throughout career, helping them to fully develop their potential and thrive.
  • Chair or lead of multiple initiatives and committees, including aligning highly cross-functional and diverse stakeholders.

Data Governance/Management/Engineering

  • Leadership and implementation of data governance and management programs across multiple functions within Ginkgo and Bayer.
  • Establishment of Metadata and master data management standards and frameworks in life science and business domains.
  • Snowflake, dbt, Airflow

Bioinformatics, Genomics, and Epigenomics

  • 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

Statistics

  • 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

Software Development

  • Languages: python, R, perl, C, C++, 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, RDS
  • Cloud: AWS, Azure, GCP, OpenStack
  • Infrastructure as Code: AWS Cloudformation, Terraform, puppet, etckeeper, hieara

Big Data

  • Parallel and Cloud Computing (slurm, torque, AWS, OpenStack, Azure)
  • Inter-process communication: MPI, OpenMP
  • Filestorage: Gluster, CEFS, GPFS, Lustre
  • Linux system administration

Applications and Daemons

  • Web: apache, ngix, varnish (load balancing/caching), REST, SOAP, Tomcat
  • Build Tools: GNU make, cmake
  • Virtualization: libvirt, KVM, qemu, VMware, docker
  • VCS: git, mercurial, subversion
  • Mail: postfix, exim, sendmail, spamassassin
  • Configuration Infrastructure: puppet, hiera, etckeeper, git
  • Documentation: LaTeX, confluence, emacs, MarkDown, MediaWiki, ikiwiki, trac
  • Monitoring: munin, nagios, icinga, prometheus
  • Issue Tracking: Debbugs, Request Tracker, Trac, JIRA
  • Office Software: Gnumeric, Libreoffice, LaTeX, Word, Excel, Powerpoint

Networking

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

    Operating systems

  • GNU/Linux (Debian, Ubuntu, Red Hat)

  • Windows
  • MacOS

Communication

  • Strong written communication skills as evidenced by publication record.
  • Proven experience communicating with cross-functional and diverse teams and stakeholders at all organizational levels.
  • Strong verbal and presentation skills as evidenced by presentation, leadership, and teaching record

Authored Open Source Software

  • Debbugs: Bug tracking software for the Debian GNU/Linux distribution.
  • CairoHacks: Bookmarks and Raster images for large PDF plots in R.
  • Function2Gene: Gene selection tool based on literature mining which enables Bayesian approaches to significance testing.
  • Helical Wheel Projections: Web-based tool to draw helical wheel protein projections.

Publications and Presentations

  • 24 peer-reviewed publications cited over 4000 times: https://dla2.us/pubs
  • Publication record in GWAS, transcriptomics, SLE, GBM, epigenetics, comparative evolution of mammals, and lipid membranes
  • H index >= 21
  • Multiple presentations on EWAS of PTSD, genetics of SLE, and Open Source: https://dla2.us/pres

Funding and Awards

Grants

  • 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

Scholarships and Fellowships

  • 2001–2003: University of California, Riverside Doctoral Fellowship
  • 1997–2001: Regents of the University of California Scholarship.

Academic Information

You can also read my Curriculum Vitæ (pdf), Research Statement (pdf), and Teaching Statement (pdf).

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