[[!meta title="Resumé"]]
# Experience
-## Research Scientist at UIUC 2015--2017
-+ Primarily responsible for the 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.
+## 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
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.
-
-## Postdoctoral Researcher at USC 2013--2015
-+ Primarily responsible for the design, execution, and analysis of an
- epidemiological study to identify genomic variants associated with
- systemic lupus erythematosus using targeted deep sequencing.
-+ Designed, budgeted, configured, maintained, and supported a secure
- linux analysis cluster (MPI/torque) with a shared filesystem (NFS
- over gluster) for statistical analyses.
+ 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
-+ Primarily responsible for the execution and analysis of 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.
+## 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.
-## 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.
-
-## Independent Systems Administrator 2004--Present
-+ Researched, recommended, budgeted, designed, deployed, configured,
- operated, and monitored highly-available high-performance enterprise
- hardware and software for web applications, authentication, backup,
- email, and databases.
-+ Provided vendor-level support for complex systems integration issues
- on Debian GNU/Linux systems.
-+ Full life-cycle support of medium and small business networking
- infrastructure, including VPN, network security, wireless networks,
- routing, DNS, DHCP, and authentication.
-
# Education
+ Doctor of Philosophy (PhD) in Cell, Molecular and Developmental Biology at UC Riverside
+ Batchelor of Science (BS) in Biology at UC Riverside
# Skills
-## Data Science
-+ Reproducible, scalable analyses using *R*, *perl*, and python with
- workflows on cloud- and cluster-based systems on terabyte-scale
- datasets
-+ Experimental design and correction to overcome multiple testing,
- confounders, and batch effects using Bayesian and frequentist
- methods
-+ Design, development, and deployment of algorithms and data-driven
- products, including APIs, reports, and interactive web applications
-+ Statistical modeling (regression, inference, prediction/forecasting,
- time series, and machine learning in very large (> 1TB) datasets)
-+ Data mining, cleaning, processing and quality assurance of data
- sources and products using tidydata formalisms
-+ Visualization using *R*, ggplot, Shiny, and custom written routines.
-
-## Software Development
-+ Languages: perl, R, C, C++, python, groovy, sh, make
-+ Collaborative Development: git, travis, continuous integration,
- automated testing
-+ Web, Mobile: Shiny, jQuery, JavaScript
-+ Databases: Postgresql (PL/SQL), SQLite, Mysql, NoSQL
-+ Office Software: Gnumeric, Libreoffice, \LaTeX, Word, Excel,
- Powerpoint
+## 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
-## Genomics and Epigenomics
+## 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.
+ 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.
-+ Correcting for and experimental design to overcome multiple
- testing, confounders, and batch effects using Bayesian and
- frequentist methods approaches
+ software, including GATK, bwa, STAR, and kallisto
+ Using evolutionary genomics to identify causal human variants
## Statistics
-+ Statistical modeling (regression, inference, prediction, and
- learning in very large (> 1TB) datasets)
-+ 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 (slurm, torque, AWS, OpenStack, Azure)
+ Inter-process communication: MPI, OpenMP
+ Filestorage: Gluster, CEFS, GPFS, Lustre
+ Linux system administration
-## Genomics and Epigenomics
-+ Linkage and association-based mapping of complex phenotypes using
- next-generation sequencing and arrays
-+ Alignment, annotation, and variant calling using existing and custom
- software
+## 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
-## Mentoring and Leadership
-+ Mentored graduate students and Outreachy and Google Summer of Code
- interns
-+ Former chair of Debian's Technical Committee
+## 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
-
-## Consortia Involvement
-+ *H3A Bionet*: Generating workflows and cloud resources for H3 Africa
-+ *Psychiatric Genomics Consortium*: Identification of epigenetic
- variants which are correlated with PTSD.
-+ *SLEGEN*: System lupus erythematosus genetics consortium.
++ Strong verbal and presentation skills as evidenced by presentation,
+ leadership, and teaching record
-# Authored Software
+# Authored Open Source 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
-+ 24 peer-reviewed publications cited over 1800 times:
+ 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
-+ H index of 11
-+ Numerous invited talks on EWAS of PTSD, genetics of SLE, and Open
++ 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
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
-You can also read my [curriculum_vitae](Curriculum Vitæ)
-([dla-cv.pdf](pdf)), [research_statement](Research Statement)
-([research_statement.pdf](pdf)),
-and [teaching_statement](Teaching Statement)
-([teaching_statement.pdf](pdf)).
+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>
projects / don.git / blobdiff