4 #+AUTHOR: Don L. Armstrong
6 #+LATEX_CLASS: dlaresume
7 # #+LATEX_CLASS_OPTIONS: [10pt,breaklinks]
10 ** Research Scientist at UIUC \hfill 2015--2017
11 + Primarily responsible for the planning, design, organization,
12 execution, and analysis of multiple complex epidemiological studies
13 involving epigenomics, transcriptomics, and genomics of diseases of
14 pregnancy and post-traumatic stress disorder.
15 + Published results in scientific publications and presented results
16 orally at major scientific conferences.
17 + Wrote and completed grants, including budgeting, scientific
18 direction, project management, and reporting.
19 + Mentored graduate students and collaborated with internal and
21 + Performed literature review, training, and applied new techniques to
22 maintain abreast of current scientific literature, principles of
23 scientific research, and modern statistical methodology.
24 + Wrote software and designed relational databases using R, perl, C,
25 SQL, make, and very large computational systems.
26 ** Postdoctoral Researcher at USC \hfill 2013--2015
27 + Primarily responsible for the design, execution, and analysis of an
28 epidemiological study to identify genomic variants associated with
29 systemic lupus erythematosus using targeted deep sequencing.
30 + Designed, budgeted, configured, maintained, and supported a secure
31 linux analysis cluster (MPI/torque) with a shared filesystem (NFS
32 over gluster) for statistical analyses.
33 + Wrote multiple pieces of software to reproducibly analyze and
34 archive large datasets resulting from genomic sequencing.
35 + Coordinated with clinicians, molecular biologists, and biologists to
36 produce analyses and major reports.
37 ** Postdoctoral Researcher at UCR \hfill 2010--2012
38 + Primarily responsible for the execution and analysis of an
39 epidemiological study to identify genomic variants associated with
40 systemic lupus erythematosus using prior information and array based
41 approaches in a trio and cross sectional study of individuals from
42 the Los Angeles and greater United States.
43 + Wrote and maintained multiple software components to reproducibly
45 ** Debian Developer \hfill 2004--Present
46 + Maintained, managed configurations, and resolved issues in multiple
47 packages written in R, perl, python, scheme, C++, and C.
48 + Resolved technical conflicts, developed technical standards, and
49 provided leadership as the elected chair of the Technical Committee.
50 + Developer of [[https://bugs.debian.org][Debbugs]], a perl and SQL-based issue-tracker with ≥ 100
51 million entries with web, REST, and SOAP interfaces.
52 ** Independent Systems Administrator \hfill 2004--Present
53 + Researched, recommended, budgeted, designed, deployed, configured,
54 operated, and monitored highly-available high-performance enterprise
55 hardware and software for web applications, authentication, backup,
57 + Provided vendor-level support for complex systems integration issues
58 on Debian GNU/Linux systems.
59 + Full life-cycle support of medium and small business networking
60 infrastructure, including VPN, network security, wireless networks,
61 routing, DNS, DHCP, and authentication.
63 ** Doctor of Philosophy (PhD) in Cell, Molecular and Developmental Biology \hfill UC Riverside
64 ** Batchelor of Science (BS) in Biology \hfill UC Riverside
67 ** Genomics and Epigenomics
68 + NGS and array-based Genomics and Epigenomics of complex human
69 diseases using RNA-seq, targeted DNA sequencing, RRBS, Illumina
70 bead arrays, and Affymetrix microarrays from sample collection to
72 + Reproducible, scalable bioinformatics analysis using make,
73 nextflow, and cwl based workflows on cloud- and cluster-based
74 systems on terabyte-scale datasets
75 + Alignment, annotation, and variant calling using existing and custom
76 software, including GATK, bwa, STAR, and kallisto.
77 + Correcting for and experimental design to overcome multiple
78 testing, confounders, and batch effects using Bayesian and
79 frequentist methods approaches
80 + Using evolutionary genomics to identify causal human variants
82 + Statistical modeling (regression, inference, prediction, and
83 learning in very large (> 1TB) datasets)
84 + Addressing confounders and batch effects
85 + Reproducible research
87 + Parallel and Cloud Computing (slurm, torque, AWS, OpenStack, Azure)
88 + Inter-process communication: MPI, OpenMP
89 + Filestorage: Gluster, CEFS, GPFS, Lustre
90 + Linux system administration
91 ** Mentoring and Leadership
92 + Mentored graduate students and Outreachy and Google Summer of Code
94 + Former chair of Debian's Technical Committee
95 + Head developer behind https://bugs.debian.org
96 ** Software Development
97 + Languages: perl, R, C, C++, python, groovy, sh, make
98 + Collaborative Development: git, travis, continuous integration,
100 + Web, Mobile: Shiny, jQuery, JavaScript
101 + Databases: Postgresql (PL/SQL), SQLite, Mysql, NoSQL
102 + Office Software: Gnumeric, Libreoffice, \LaTeX, Word, Excel,
105 + Strong written communication skills as evidenced by publication
107 + Strong verbal and presentation skills as evidenced by presentation
109 # ** Consortia Involvement
110 # + *H3A Bionet*: Generating workflows and cloud resources for H3 Africa
111 # + *Psychiatric Genomics Consortium*: Identification of epigenetic
112 # variants which are correlated with PTSD.
113 # + *SLEGEN*: System lupus erythematosus genetics consortium.
115 + *[[http://bugs.debian.org][Debbugs]]*: Bug tracking software for the Debian GNU/Linux
116 distribution. [[https://bugs.debian.org]]
117 + *[[http://git.donarmstrong.com/r/CairoHacks.git][CairoHacks]]*: Bookmarks and Raster images for large PDF plots in R.
118 + *[[http://rzlab.ucr.edu/function2gene/][Function2Gene]]*: Gene selection tool based on literature mining which
119 enables Bayesian approaches to significance testing.
120 + *[[http://rzlab.ucr.edu/scripts/wheel/wheel.cgi?sequence=ABCDEFGHIJLKMNOP&submit=Submit][Helical Wheel Projections]]*: Web-based tool to draw helical wheel
121 protein projections. [[http://rzlab.ucr.edu/scripts/wheel]]
122 * Publications and Presentations
123 + 24 peer-reviewed publications cited over 1800 times:
125 + Publication record in GWAS, expression analysis of microarrays, SLE,
126 GBM, epigenetics, comparative evolution of mammals, and lipid
129 + Multiple presentations on EWAS of PTSD, genetics of SLE, and Open
130 Source: https://dla2.us/pres
134 + 2017 R Consortium: *[[https://www.r-consortium.org/blog/2017/04/03/q1-2017-isc-grants][Adding Linux Binary Builders to R-Hub]]* Role:
136 + 2015 Blue Waters Allocation Grant: *Making ancestral trees using Bayesian
137 inference to identify disease-causing genetic variants* Role:
139 + *Tracking placenta and uterine funciton using urinary extracellular vesicles* (R21
140 RFA-HD-16-037) Role: Key Personnel
141 + *NIAMS* R01-AR045650-04 *Genetics of Childhood Onset SLE* to Chaim O. Jacob.
143 ** Scholarships and Fellowships
144 + 2001--2003: University of California, Riverside Doctoral Fellowship
145 + 1997--2001: Regents of the University of California Scholarship.