4 #+AUTHOR: Don L. Armstrong
6 #+LATEX_CLASS: dlaresume
7 # #+LATEX_CLASS_OPTIONS: [10pt,breaklinks]
10 ** Research Scientist at UIUC \hfill 2015--2017
11 + Epigenetic modifications associated with PTSD, the genomic basis of
12 the development of parturition in mammals, and detecting adverse
13 pregnancy outcomes using urinary exosomes.
14 ** Postdoctoral Researcher at USC \hfill 2013--2015
15 + Identifying genes and causal alleles associated with Systemic Lupus
16 Erythematosus using genome-wide association, next-generation
17 sequencing, computational and biochemical approaches.
18 ** Postdoctoral Researcher at UCR \hfill 2010--2012
19 + Identifying genes which are associated with Systemic Lupus
20 Erythematosus using prior information and targeted trio-based
22 ** Debian Developer \hfill 2004--Present
23 + \emph{Debian Project}, Developer; Technical Committee Member
24 (2010--2016), Technical Committee Chair (2015--2016).
27 ** Doctor of Philosophy (PhD) \hfill UC Riverside
28 + Cell, Molecular and Developmental Biology.
29 ** Batchelor of Science (BS) in Biology \hfill UC Riverside
32 ** Genomics and Epigenomics
33 + *NGS* and array-based Genomics and Epigenomics of complex human
34 diseases using *RNA-seq*, targeted DNA sequencing, *RRBS*, Illumina
35 bead arrays, and Affymetrix microarrays from sample collection to
37 + Reproducible, scalable bioinformatics analysis using make,
38 *nextflow*, and *cwl* based workflows on cloud- and cluster-based
39 systems on terabyte-scale datasets
40 + Alignment, annotation, and variant calling using existing and custom
41 software, including *GATK*, *bwa*, *STAR*, and *kallisto*.
42 + Correcting for and experimental design to overcome multiple
43 testing, confounders, and batch effects using Bayesian and
44 frequentist methods approaches
45 # + Using evolutionary genomics to identify causal human variants
47 + Statistical modeling (regression, inference, prediction, and
48 learning in very large (> 1TB) datasets)
49 + Addressing confounders and batch effects
50 # + Reproducible research
52 + Parallel and Cloud Computing (slurm, torque, AWS, OpenStack, Azure)
53 + Inter-process communication: MPI, OpenMP
54 + Filestorage: Gluster, CEFS, GPFS, Lustre
55 + Linux system administration
56 ** Mentoring and Leadership
57 + Mentored graduate students and Outreachy and Google Summer of Code
59 + Former chair of Debian's Technical Committee
60 + Head developer behind https://bugs.debian.org
61 ** Software Development
62 + Languages: perl, R, C, C++, python, groovy, sh, make
63 + Collaborative Development: git, travis, continuous integration,
65 + Web, Mobile: Shiny, jQuery, JavaScript
66 + Databases: Postgresql (PL/SQL), SQLite, Mysql, NoSQL
67 + Office Software: Gnumeric, Libreoffice, \LaTeX, Word, Excel,
70 + Strong written communication skills as evidenced by publication
72 + Strong verbal and presentation skills as evidenced by presentation
74 # ** Consortia Involvement
75 # + *H3A Bionet*: Generating workflows and cloud resources for H3 Africa
76 # + *Psychiatric Genomics Consortium*: Identification of epigenetic
77 # variants which are correlated with PTSD.
78 # + *SLEGEN*: System lupus erythematosus genetics consortium.
80 + *[[http://bugs.debian.org][Debbugs]]*: Bug tracking software for the Debian GNU/Linux
81 distribution. [[https://bugs.debian.org]]
82 + *[[http://git.donarmstrong.com/r/CairoHacks.git][CairoHacks]]*: Bookmarks and Raster images for large PDF plots in R.
83 + *[[http://rzlab.ucr.edu/function2gene/][Function2Gene]]*: Gene selection tool based on literature mining which
84 enables Bayesian approaches to significance testing.
85 + *[[http://rzlab.ucr.edu/scripts/wheel/wheel.cgi?sequence=ABCDEFGHIJLKMNOP&submit=Submit][Helical Wheel Projections]]*: Web-based tool to draw helical wheel
86 protein projections. [[http://rzlab.ucr.edu/scripts/wheel]]
87 * Publications and Presentations
88 + 24 peer-reviewed publications cited over 1800 times:
90 + Publication record in GWAS, expression analysis of microarrays, SLE,
91 GBM, epigenetics, comparative evolution of mammals, and lipid
94 + Multiple presentations on EWAS of PTSD, genetics of SLE, and Open
95 Source: https://dla2.us/pres
99 + 2017 R Consortium: *[[https://www.r-consortium.org/blog/2017/04/03/q1-2017-isc-grants][Adding Linux Binary Builders to R-Hub]]* Role:
101 + 2015 Blue Waters Allocation Grant: *Making ancestral trees using Bayesian
102 inference to identify disease-causing genetic variants* Role:
104 + *Tracking placenta and uterine funciton using urinary extracellular vesicles* (R21
105 RFA-HD-16-037) Role: Key Personnel
106 + *NIAMS* R01-AR045650-04 *Genetics of Childhood Onset SLE* to Chaim O. Jacob.
108 ** Scholarships and Fellowships
109 + 2001--2003: University of California, Riverside Doctoral Fellowship
110 + 1997--2001: Regents of the University of California Scholarship.