Merge branch 'master' into jobs/data_scientist

diff --cc don_armstrong_resume.org
index 0000000000000000000000000000000000000000,9604e257ca88b4a8603a7ad2c370e0c49e0ad877..5dcfff3f74b200fd14cbd55cc04a8c59d29cdb0f
mode 000000,100644..100644
--- /dev/null
--- 2/don_armstrong_resume.org
+++ b/don_armstrong_resume.org
@@@ -1,0 -1,113 +1,109 @@@
 -** 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
+ #+OPTIONS: ^:nil
+ #+OPTIONS: toc:nil
+ #+TITLE: Resume
+ #+AUTHOR: Don L. Armstrong
+ #+LATEX_CMD: xelatex
+ #+LATEX_CLASS: dlaresume
+ # #+LATEX_CLASS_OPTIONS: [10pt,breaklinks]
+ 
+ * Experience
+ ** 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.
+ ** Debian Developer \hfill 2004--Present
+ + \emph{Debian Project}, Developer; Technical Committee Member
+   (2010--2016), Technical Committee Chair (2015--2016).
+ 
+ * Education
+ ** Doctor of Philosophy (PhD) \hfill UC Riverside
+  + Cell, Molecular and Developmental Biology.
+ ** Batchelor of Science (BS) in Biology \hfill UC Riverside
+ 
+ * Skills
 -+ Head developer behind https://bugs.debian.org
 -** 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
++** 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
+ ** 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
 -+ 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
 -+ Multiple presentations on EWAS of PTSD, genetics of SLE, and Open
+ + H index of 11
+++ Numerous invited talks 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.
+ 
+ 
+