--- /dev/null
-** Debian Developer \hfill 2004--Present
-+ \emph{Debian Project}, Developer; Technical Committee Member
- (2010--2016), Technical Committee Chair (2015--2016).
+ #+OPTIONS: ^:nil
+ #+OPTIONS: toc:nil
+ #+TITLE: Resume
+ #+AUTHOR: Don L. Armstrong
+ #+LATEX_CMD: xelatex
+ #+LATEX_CLASS: dlaresume
+ # #+LATEX_CLASS_OPTIONS: [10pt,breaklinks]
+
+ * Experience
++** Debian Developer \hfill 2004--Present
+++ \emph{Debian Project}, Developer; Technical Committee
++ Member (2010--2016), Technical Committee Chair (2015--2016).
++** Independent Systems Administrator \hfill 2004--Present
+++ Developing and designing software and hardware
++ requirements. Deploying and maintaining enterprise-level systems for
++ web, email, and data storage backends using MySQL and other
++ solutions.
+ ** Research Scientist at UIUC \hfill 2015--2017
+ + 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 \hfill 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 \hfill 2010--2012
+ + Identifying genes which are associated with Systemic Lupus
+ Erythematosus using prior information and targeted trio-based
+ studies.
-** 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
+
+ * Education
+ ** Doctor of Philosophy (PhD) \hfill UC Riverside
+ + Cell, Molecular and Developmental Biology.
+ ** Batchelor of Science (BS) in Biology \hfill UC Riverside
+
+ * Skills
-+ Statistical modeling (regression, inference, prediction, and
- learning in very large (> 1TB) datasets)
-+ Addressing confounders and batch effects
-# + Reproducible research
++** Programming Languages
++ + [[http://r-project.org][R]], [[http://www.perl.org][Perl]], sh (bash, POSIX, and zsh), SQL, PL/SQL, C/C++, HTML, CSS,
++ javascript
++** Applications and Daemons
++ + Web: apache, ngix, varnish, REST, SOAP
++ + SQL servers: PostgreSQL, MySQL (including failover and replication)
++ + VCS: git, subversion
++ + Mail: postfix, exim, sendmail, spamassassin
++ + Configuration Infrastructure: puppet, etckeeper, git
++ + Documentation: \LaTeX, emacs, MarkDown, MediaWiki, ikiwiki, trac
++ + Monitoring: munin, nagios, icinga, prometheus
++ + Issue Tracking: Debbugs, Request Tracker, Trac
++ + Statistics: R, SAS
++ + Office Software: Gnumeric, Libreoffice, \LaTeX, Word, Excel,
++ Powerpoint
++ + Virtualization libvirt, KVM, qemu, VMware
++** 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 (5.0-10)
++ + MacOS (10-10.13)
+ ** Statistics
-+ Filestorage: Gluster, CEFS, GPFS, Lustre
-+ Linux system administration
++ + Statistical modeling in very large datasets
++ + Addressing confounders and batch effects
+ ** Big Data
+ + Parallel and Cloud Computing (slurm, torque, AWS, OpenStack, Azure)
+ + Inter-process communication: MPI, OpenMP
-** 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
+++ Filestorage: Gluster, CEFS, GPFS, Lustre, FC, iSCSI
+ ** Mentoring and Leadership
+ + 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
-+ Publication record in GWAS, expression analysis of microarrays, SLE,
- GBM, epigenetics, comparative evolution of mammals, and lipid
- membranes
+ ** 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
+ + *[[http://bugs.debian.org][Debbugs]]*: Bug tracking software for the Debian GNU/Linux
+ distribution. [[https://bugs.debian.org]]
+ + *[[http://git.donarmstrong.com/r/CairoHacks.git][CairoHacks]]*: Bookmarks and Raster images for large PDF plots in R.
+ + *[[http://rzlab.ucr.edu/function2gene/][Function2Gene]]*: Gene selection tool based on literature mining which
+ enables Bayesian approaches to significance testing.
+ + *[[http://rzlab.ucr.edu/scripts/wheel/wheel.cgi?sequence=ABCDEFGHIJLKMNOP&submit=Submit][Helical Wheel Projections]]*: 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
+ + Multiple presentations on EWAS of PTSD, genetics of SLE, and Open
+ Source: https://dla2.us/pres
+
+ * Funding and Awards
+ ** Grants
+ + 2017 R Consortium: *[[https://www.r-consortium.org/blog/2017/04/03/q1-2017-isc-grants][Adding Linux Binary Builders to R-Hub]]* 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.
+
+
+
projects / resume.git / commitdiff