[[!meta title="Resumé"]]

# 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.

## 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
+ 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.

## 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](https://bugs.debian.org), 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
+ 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](https://bluewaters.ncsa.illinois.edu/))

## 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 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

## 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++, 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

## 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
+ Strong verbal and presentation skills as evidenced by presentation,
  leadership, and teaching record

# Authored Open Source Software
+ *[Debbugs](http://bugs.debian.org)*: Bug tracking software for the Debian GNU/Linux
   distribution. 
+ *[CairoHacks](http://git.donarmstrong.com/r/CairoHacks.git)*: 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

# Funding and Awards
## Grants
+ 2017 R Consortium: *[Adding Linux Binary Builders to R-Hub](https://www.r-consortium.org/blog/2017/04/03/q1-2017-isc-grants)* 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](curriculum_vitae)
([pdf](dla-cv.pdf)), [Research Statement](research_statement)
([pdf](research_statement.pdf)),
and [Teaching Statement](teaching_statement)
([pdf](teaching_statement.pdf)).

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