1 [[!meta title="Resumé"]]
4 ## Research Scientist at UIUC 2015--2017
5 + Primarily responsible for the planning, design, organization,
6 execution, and analysis of multiple complex epidemiological studies
7 involving epigenomics, transcriptomics, and genomics of diseases of
8 pregnancy and post-traumatic stress disorder.
9 + Published results in scientific publications and presented results
10 orally at major scientific conferences.
11 + Wrote and completed grants, including budgeting, scientific
12 direction, project management, and reporting.
13 + Mentored graduate students and collaborated with internal and
15 + Performed literature review, training, and applied new techniques to
16 maintain abreast of current scientific literature, principles of
17 scientific research, and modern statistical methodology.
18 + Wrote software and designed relational databases using R, perl, C,
19 SQL, make, and very large computational systems.
20 ## Postdoctoral Researcher at USC 2013--2015
21 + Primarily responsible for the design, execution, and analysis of an
22 epidemiological study to identify genomic variants associated with
23 systemic lupus erythematosus using targeted deep sequencing.
24 + Designed, budgeted, configured, maintained, and supported a secure
25 linux analysis cluster (MPI/torque) with a shared filesystem (NFS
26 over gluster) for statistical analyses.
27 + Wrote multiple pieces of software to reproducibly analyze and
28 archive large datasets resulting from genomic sequencing.
29 + Coordinated with clinicians, molecular biologists, and biologists to
30 produce analyses and major reports.
31 ## Postdoctoral Researcher at UCR 2010--2012
32 + Primarily responsible for the execution and analysis of an
33 epidemiological study to identify genomic variants associated with
34 systemic lupus erythematosus using prior information and array based
35 approaches in a trio and cross sectional study of individuals from
36 the Los Angeles and greater United States.
37 + Wrote and maintained multiple software components to reproducibly
39 ## Debian Developer 2004--Present
40 + Maintained, managed configurations, and resolved issues in multiple
41 packages written in R, perl, python, scheme, C++, and C.
42 + Resolved technical conflicts, developed technical standards, and
43 provided leadership as the elected chair of the Technical Committee.
44 + Developer of [Debbugs](https://bugs.debian.org), a perl and SQL-based issue-tracker with ≥ 100
45 million entries with web, REST, and SOAP interfaces.
46 ## Independent Systems Administrator 2004--Present
47 + Researched, recommended, budgeted, designed, deployed, configured,
48 operated, and monitored highly-available high-performance enterprise
49 hardware and software for web applications, authentication, backup,
51 + Provided vendor-level support for complex systems integration issues
52 on Debian GNU/Linux systems.
53 + Full life-cycle support of medium and small business networking
54 infrastructure, including VPN, network security, wireless networks,
55 routing, DNS, DHCP, and authentication.
57 + Doctor of Philosophy (PhD) in Cell, Molecular and Developmental Biology at UC Riverside
58 + Batchelor of Science (BS) in Biology at UC Riverside
62 + Reproducible, scalable analyses using *R*, *perl*, and python with
63 workflows on cloud- and cluster-based systems on terabyte-scale
65 + Experimental design and correction to overcome multiple testing,
66 confounders, and batch effects using Bayesian and frequentist
68 + Design, development, and deployment of algorithms and data-driven
69 products, including APIs, reports, and interactive web applications
70 + Statistical modeling (regression, inference, prediction/forecasting,
71 time series, and machine learning in very large (> 1TB) datasets)
72 + Data mining, cleaning, processing and quality assurance of data
73 sources and products using tidydata formalisms
74 + Visualization using *R*, ggplot, Shiny, and custom written routines.
75 ## Software Development
76 + Languages: perl, R, C, C++, python, groovy, sh, make
77 + Collaborative Development: git, travis, continuous integration,
79 + Web, Mobile: Shiny, jQuery, JavaScript
80 + Databases: Postgresql (PL/SQL), SQLite, Mysql, NoSQL
81 + Office Software: Gnumeric, Libreoffice, \LaTeX, Word, Excel,
83 ## Genomics and Epigenomics
84 + NGS and array-based Genomics and Epigenomics of complex human
85 diseases using RNA-seq, targeted DNA sequencing, RRBS, Illumina
86 bead arrays, and Affymetrix microarrays from sample collection to
88 + Reproducible, scalable bioinformatics analysis using make,
89 nextflow, and cwl based workflows on cloud- and cluster-based
90 systems on terabyte-scale datasets
91 + Alignment, annotation, and variant calling using existing and custom
92 software, including GATK, bwa, STAR, and kallisto.
93 + Correcting for and experimental design to overcome multiple
94 testing, confounders, and batch effects using Bayesian and
95 frequentist methods approaches
96 + Using evolutionary genomics to identify causal human variants
98 + Statistical modeling (regression, inference, prediction, and
99 learning in very large (> 1TB) datasets)
100 + Addressing confounders and batch effects
101 + Reproducible research
103 + Parallel and Cloud Computing (slurm, torque, AWS, OpenStack, Azure)
104 + Inter-process communication: MPI, OpenMP
105 + Filestorage: Gluster, CEFS, GPFS, Lustre
106 + Linux system administration
107 ## Genomics and Epigenomics
108 + Linkage and association-based mapping of complex phenotypes using
109 next-generation sequencing and arrays
110 + Alignment, annotation, and variant calling using existing and custom
112 ## Mentoring and Leadership
113 + Mentored graduate students and Outreachy and Google Summer of Code
115 + Former chair of Debian's Technical Committee
117 + Strong written communication skills as evidenced by publication
119 + Strong verbal and presentation skills as evidenced by presentation
121 ## Consortia Involvement
122 + *H3A Bionet*: Generating workflows and cloud resources for H3 Africa
123 + *Psychiatric Genomics Consortium*: Identification of epigenetic
124 variants which are correlated with PTSD.
125 + *SLEGEN*: System lupus erythematosus genetics consortium.
127 + *[Debbugs](http://bugs.debian.org)*: Bug tracking software for the Debian GNU/Linux
128 distribution. [https://bugs.debian.org]
129 + *[CairoHacks](https://git.donarmstrong.com/r/CairoHacks.git)*: Bookmarks and Raster images for large PDF plots in R.
130 + *[Function2Gene](http://rzlab.ucr.edu/function2gene/)*: Gene selection tool based on literature mining which
131 enables Bayesian approaches to significance testing.
132 + *[Helical Wheel Projections](http://rzlab.ucr.edu/scripts/wheel/wheel.cgi?sequence=ABCDEFGHIJLKMNOP&submit=Submit)*: Web-based tool to draw helical wheel
133 protein projections. [http://rzlab.ucr.edu/scripts/wheel]
134 # Publications and Presentations
135 + 24 peer-reviewed publications cited over 1800 times:
138 + Numerous invited talks on EWAS of PTSD, genetics of SLE, and Open
139 Source: https://dla2.us/pres
143 + 2017 R Consortium: *[Adding Linux Binary Builders to R-Hub](https://www.r-consortium.org/blog/2017/04/03/q1-2017-isc-grants)* Role:
145 + 2015 Blue Waters Allocation Grant: *Making ancestral trees using Bayesian
146 inference to identify disease-causing genetic variants* Role:
148 + *Tracking placenta and uterine funciton using urinary extracellular vesicles* (R21
149 RFA-HD-16-037) Role: Key Personnel
150 + *NIAMS* R01-AR045650-04 *Genetics of Childhood Onset SLE* to Chaim O. Jacob.
152 ## Scholarships and Fellowships
153 + 2001--2003: University of California, Riverside Doctoral Fellowship
154 + 1997--2001: Regents of the University of California Scholarship.
156 #Academic Information
158 You can also read my [curriculum_vitae](Curriculum Vitæ)
159 ([dla-cv.pdf](pdf)), [research_statement](Research Statement)
160 ([research_statement.pdf](pdf)),
161 and [teaching_statement](Teaching Statement)
162 ([teaching_statement.pdf](pdf)).
164 For my contact information or additional references, please e-mail
165 <don@donarmstrong.com>