-Resume
-======
+[[!meta title="Resumé"]]
-[Don Armstrong](http://www.donarmstrong.com/)
+# 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
-<don@donarmstrong.com>
-
-<http://www.donarmstrong.com>
-
-[Phone contact information available via e-mail.]
+# 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
-I am a practitioner of the art of solving problems as elegantly and
-practically as possible. I seek to enhance my abilities to solve
-problems in the digital realm by learning (and inventing where
-appropriate) new methods and techniques, and to help others achieve
-their goals by removing or smoothing over ponderous obstacles in their
-path. If you have difficult problems for which a digital approach
-seems appropriate, I'm the person to talk to to find a solution.
+# 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.
-Education
-----------
-* Doctor of Philosophy in Cell, Molecular and Developmental Biology from [UC Riverside](http://www.ucr.edu), 2008
-* Bachelor of Science in [Biology](http://bio.ucr.edu) from [UC Riverside](http://www.ucr.edu), 2001
-* Graduate, Scholar with Distinction from [Marina High School](http://www.hbuhsd.k12.ca.us/mhs/), 1997
+#Academic Information
-Experience
-----------
-* July 2002-July 2003: Researcher for Socratech, LLC
- * Affymetrix Gene Microarray Analysis using R, and Perl.
- * Custom designed cell, tissue and data tracking system in perl
- * Analysis of MA results using Gene Ontology
- * Literature minining using custom designed Perl scripts to search pubmed.
-* Jun. 2000-Jun 2001: Computer Resource Coordinator for [UC Riverside](http://www.ucr.edu)
- * Network administration/design of a 2000+ node network
- * developed web based registration system using bash, dhcp, perl, php and mysql
- * Developed network monitoring system
- ([rnm](http://rnm.sourceforge.net)) using php, mysql, perl, and
- snmp.
- * Supervised a staff of 13 RCCs<LI>Administration of 7+ Unix Servers (Apache,ISC DHCP, MySQL, mod_perl, slash)
- <LI>Computer Lab Administration (NT)
- <LI>Developed a printer recharge/tracking system using card readers, perl, mysql, and lpr-ng
- <LI>Developed a customer-tech Help Request System/Billing System using php, mysql, smtp, and perl
-
-Skills
-------
+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)).
-
-Projects
---------
-[Current projects|projects]
-
-References
-----------
-Available Upon Request.
+For my contact information or additional references, please e-mail
+<don@donarmstrong.com>
projects / don.git / blobdiff