-[[!meta title="Curriculum Vitæ, Research Statement, and Teaching Statement"]]
+[[!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
-## UC Riverside
-+ **PhD** in Cell, Molecular and Developmental Biology
-+ **BS** in Biology
++ Doctor of Philosophy (PhD) in Cell, Molecular and Developmental Biology at UC Riverside
++ Batchelor of Science (BS) in Biology at UC Riverside
# Skills
-## Genomics and Epigenomics
-+ Genomics and Epigenomics of complex human diseases including
- PTSD, Systemic Lupus Erythematosus, and Alzheimer's Disease using
- cross-sectional and longitudinal experimental designs
-+ Correcting for and experimental design to overcome multiple
- testing, confounders, and batch effects using Bayesian and
- frequentist methods approaches
-+ Reproducible, scalable analysis using workflows on cloud- and
- cluster-based systems on terabyte-scale datasets
+## 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
-+ Addressing confounders and batch effects
++ 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
-+ Inter-process communication: MPI, OpenMP, Hadoop
++ Parallel and Cloud Computing (slurm, torque, AWS, OpenStack, Azure)
++ Inter-process communication: MPI, OpenMP
+ Filestorage: Gluster, CEFS, GPFS, Lustre
-+ Cloud based-infrastructure: Azure, AWS, Docker, cloud-init
-+ Debian GNU/Linux system administration
-
-## Mentoring and Leadership
-+ Mentored graduate students and Outreachy and Google Summer of Code
- interns
-+ Chairperson of the Debian Technical Committee
-+ Head developer behind https://bugs.debian.org
-
-## Software Development
-+ Languages: perl, R, C, C++, python, groovy, assembly, sh, make
-+ Collaborative Development: git, travis, continuous integration,
- automated testing
-+ Databases: Postgresql (PL/SQL), SQLite, Mysql
++ 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
- and teaching record
-
-# Experience
-## Research Scientist at UIUC
-+ 2015–Present. University of Illinois at Urbana-Champaign. Epigenetic
- modifications associated with PTSD, the genomic basis of the
- development of parturition in mammals, and detecting adverse
- pregnancy outcomes using urinary exosomes.
-
-## Postdoctoral Researcher at USC
-+ 2013–2015. Identifying genes and causal alleles associated with
- Systemic Lupus Erythematosus using genome-wide association,
- next-generation sequencing, computational and biochemical
- approaches.
-
-## Postdoctoral Researcher at UCR
-+ 2010–2012. Identifying genes which are associated with Systemic
- Lupus Erythematosus using prior information and targeted trio-based
- studies.
-
-## Debian Developer
-+ 2004–Present. *Debian Project*, Developer; Technical Committee
- Member (2010–2016), Technical Committee Chair (2015–2016).
-
-# Authored Software
-+ **[Debbugs](http://bugs.debian.org)**: Bug tracking software for the Debian GNU/Linux
- distribution. <https://bugs.debian.org>
-+ **[CairoHacks](https://git.donarmstrong.com/r/CairoHacks.git)**:
- Bookmarks and Raster images for large PDF plots in R.
-+ **[Function2Gene](http://rzlab.ucr.edu/function2gene/)**: Gene
- selection tool based on literature mining which enables Bayesian
- approaches to significance testing.
-+ **[Helical Wheel Projections](http://rzlab.ucr.edu/scripts/wheel/wheel.cgi?sequence=ABCDEFGHIJLKMNOP&submit=Submit)**:
- Web-based tool to draw helical wheel protein projections.
- <http://rzlab.ucr.edu/scripts/wheel>
-
-# Publications and Presentations
-+ 20 peer-reviewed refereed publications cited over 1700 times:
- <https://dla2.us/pubs>
-+ Publication record in GWAS, expression analysis of microarrays,
- epigenetics, comparative evolution of mammals, and lipid membranes
-+ H index of 11
++ 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>
+ 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:
++ 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
++ *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.
++ *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.
++ 2001–2003: University of California, Riverside Doctoral Fellowship
++ 1997–2001: Regents of the University of California Scholarship.
-#Academic Information
+# Academic Information
You can also read my [Curriculum Vitæ](curriculum_vitae)
([pdf](dla-cv.pdf)), [Research Statement](research_statement)
projects / don.git / blobdiff