X-Git-Url: https://git.donarmstrong.com/?p=don.git;a=blobdiff_plain;f=resume.mdwn;h=6497721cc42c5a14122092a440dc5dea48d989c1;hp=14d54dfa0d7d7590f26f1f23e837f6c987975a4b;hb=HEAD;hpb=b20cbd7935cfe0dd174f69904345445a75967cd9 diff --git a/resume.mdwn b/resume.mdwn index 14d54df..43e34c0 100644 --- a/resume.mdwn +++ b/resume.mdwn @@ -1,50 +1,192 @@ -[[!meta title="Curriculum Vitæ, Research Statement, and Teaching Statement"]] +[[!meta title="Resumé"]] -Introduction ------------- +# 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. -A brief statement of my research interests and teaching mission -follows, and 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)) are also available. +## 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. -For my contact information or additional references, please e-mail - +## 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 -Research Focus --------------- - -My primary research focus is developing and using bioinformatics -techniques to identify causes and mechanisms underlying human -diseases, such as Systemic Lupus Erythematosus (SLE). I have -identified multiple novel genes associated with SLE using both -genome-wide association studies and trio-based studies in targeted -regions. In collaborative work, I have identified a causal variant in -NCF2 -([rs17849502](http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=rs17849502)) -using both *in silico* and *in vitro* approaches. I am currently -working on identifying causal variants in additional associated genes -using targeted deep sequencing using high-throughput variant analysis -pipelines to prioritize variants for additional *in silico* and *in -vitro* experiments. In the future, utilizing my extensive -bioinformatic and software development experience, I will head a -development group working on techniques for the storage, alignment, -and analysis of terabytes (eventually petabytes) of next-generation -sequencing data from collaborations studying human-relevant diseases -and biological systems. - - -Teaching Mission ----------------- - -While teaching, my primary mission is to have my students experience -the excitement of scientific discovery for themselves. Secondarily, I -use that excitement to keep them engaged and interested in the -material. While a graduate student at UC Riverside, I was a teaching -assistant for [Introductory Biology, Genetics, Molecular Biology, and -Developmental Biology](http://www.biology.ucr.edu/courses/UGcourses.html) +## 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 +