-[[!meta title="Curriculum Vitæ, Research Statement, and Teaching Statement"]]
+[[!meta title="Resumé"]]
-Introduction
-------------
+# 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.
++ 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.
+## 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.
++ 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.
++ 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
-A brief statement of my research interests and teaching mission
-follows, and my [Curriculum Vitæ](resume/curriculum_vitae)
-([pdf](resume/dla-cv.pdf)),
-[Research Statement](resume/research_statement)
-([pdf](resume/research_statement.pdf)), and
-[Teaching Statement](resume/teaching_statement)
-([pdf](resume/teaching_statement.pdf)) are also available.
+# 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
+## 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.
++ Correcting for and experimental design to overcome multiple
+ testing, confounders, and batch effects using Bayesian and
+ frequentist methods approaches
++ 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
++ Reproducible research
+## 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
+## Mentoring and Leadership
++ Mentored graduate students and Outreachy and Google Summer of Code
+ interns
++ Former chair of Debian's Technical Committee
+## 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.
+# 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
++ 24 peer-reviewed publications cited over 1800 times:
+ https://dla2.us/pubs
++ H index of 11
++ Numerous invited talks on EWAS of PTSD, genetics of SLE, and Open
+ Source: https://dla2.us/pres
-For my contact information or additional references, please e-mail
-<don@donarmstrong.com>
-
-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.
+# 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
-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)
+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)).
+For my contact information or additional references, please e-mail
+<don@donarmstrong.com>
projects / don.git / blobdiff