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.
21 ## Postdoctoral Researcher at USC 2013--2015
22 + Primarily responsible for the design, execution, and analysis of an
23 epidemiological study to identify genomic variants associated with
24 systemic lupus erythematosus using targeted deep sequencing.
25 + Designed, budgeted, configured, maintained, and supported a secure
26 linux analysis cluster (MPI/torque) with a shared filesystem (NFS
27 over gluster) for statistical analyses.
28 + Wrote multiple pieces of software to reproducibly analyze and
29 archive large datasets resulting from genomic sequencing.
30 + Coordinated with clinicians, molecular biologists, and biologists to
31 produce analyses and major reports.
33 ## Postdoctoral Researcher at UCR 2010--2012
34 + Primarily responsible for the execution and analysis of an
35 epidemiological study to identify genomic variants associated with
36 systemic lupus erythematosus using prior information and array based
37 approaches in a trio and cross sectional study of individuals from
38 the Los Angeles and greater United States.
39 + Wrote and maintained multiple software components to reproducibly
42 ## Debian Developer 2004--Present
43 + Maintained, managed configurations, and resolved issues in multiple
44 packages written in R, perl, python, scheme, C++, and C.
45 + Resolved technical conflicts, developed technical standards, and
46 provided leadership as the elected chair of the Technical Committee.
47 + Developer of [Debbugs](https://bugs.debian.org), a perl and SQL-based issue-tracker with ≥ 100
48 million entries with web, REST, and SOAP interfaces.
50 ## Independent Systems Administrator 2004--Present
51 + Researched, recommended, budgeted, designed, deployed, configured,
52 operated, and monitored highly-available high-performance enterprise
53 hardware and software for web applications, authentication, backup,
55 + Provided vendor-level support for complex systems integration issues
56 on Debian GNU/Linux systems.
57 + Full life-cycle support of medium and small business networking
58 infrastructure, including VPN, network security, wireless networks,
59 routing, DNS, DHCP, and authentication.
62 + Doctor of Philosophy (PhD) in Cell, Molecular and Developmental Biology at UC Riverside
63 + Batchelor of Science (BS) in Biology at UC Riverside
67 + Reproducible, scalable analyses using *R*, *perl*, and python with
68 workflows on cloud- and cluster-based systems on terabyte-scale
70 + Experimental design and correction to overcome multiple testing,
71 confounders, and batch effects using Bayesian and frequentist
73 + Design, development, and deployment of algorithms and data-driven
74 products, including APIs, reports, and interactive web applications
75 + Statistical modeling (regression, inference, prediction/forecasting,
76 time series, and machine learning in very large (> 1TB) datasets)
77 + Data mining, cleaning, processing and quality assurance of data
78 sources and products using tidydata formalisms
79 + Visualization using *R*, ggplot, Shiny, and custom written routines.
81 ## Software Development
82 + Languages: perl, R, C, C++, python, groovy, sh, make
83 + Collaborative Development: git, travis, continuous integration,
85 + Web, Mobile: Shiny, jQuery, JavaScript
86 + Databases: Postgresql (PL/SQL), SQLite, Mysql, NoSQL
87 + Office Software: Gnumeric, Libreoffice, \LaTeX, Word, Excel,
90 ## Genomics and Epigenomics
91 + NGS and array-based Genomics and Epigenomics of complex human
92 diseases using RNA-seq, targeted DNA sequencing, RRBS, Illumina
93 bead arrays, and Affymetrix microarrays from sample collection to
95 + Reproducible, scalable bioinformatics analysis using make,
96 nextflow, and cwl based workflows on cloud- and cluster-based
97 systems on terabyte-scale datasets
98 + Alignment, annotation, and variant calling using existing and custom
99 software, including GATK, bwa, STAR, and kallisto.
100 + Correcting for and experimental design to overcome multiple
101 testing, confounders, and batch effects using Bayesian and
102 frequentist methods approaches
103 + Using evolutionary genomics to identify causal human variants
106 + Statistical modeling (regression, inference, prediction, and
107 learning in very large (> 1TB) datasets)
108 + Addressing confounders and batch effects
109 + Reproducible research
112 + Parallel and Cloud Computing (slurm, torque, AWS, OpenStack, Azure)
113 + Inter-process communication: MPI, OpenMP
114 + Filestorage: Gluster, CEFS, GPFS, Lustre
115 + Linux system administration
117 ## Genomics and Epigenomics
118 + Linkage and association-based mapping of complex phenotypes using
119 next-generation sequencing and arrays
120 + Alignment, annotation, and variant calling using existing and custom
123 ## Mentoring and Leadership
124 + Mentored graduate students and Outreachy and Google Summer of Code
126 + Former chair of Debian's Technical Committee
129 + Strong written communication skills as evidenced by publication
131 + Strong verbal and presentation skills as evidenced by presentation
134 ## Consortia Involvement
135 + *H3A Bionet*: Generating workflows and cloud resources for H3 Africa
136 + *Psychiatric Genomics Consortium*: Identification of epigenetic
137 variants which are correlated with PTSD.
138 + *SLEGEN*: System lupus erythematosus genetics consortium.
141 + *[Debbugs](http://bugs.debian.org)*: Bug tracking software for the Debian GNU/Linux
142 distribution. [https://bugs.debian.org]
143 + *[CairoHacks](https://git.donarmstrong.com/r/CairoHacks.git)*: Bookmarks and Raster images for large PDF plots in R.
144 + *[Function2Gene](http://rzlab.ucr.edu/function2gene/)*: Gene selection tool based on literature mining which
145 enables Bayesian approaches to significance testing.
146 + *[Helical Wheel Projections](http://rzlab.ucr.edu/scripts/wheel/wheel.cgi?sequence=ABCDEFGHIJLKMNOP&submit=Submit)*: Web-based tool to draw helical wheel
147 protein projections. [http://rzlab.ucr.edu/scripts/wheel]
149 # Publications and Presentations
150 + 24 peer-reviewed publications cited over 1800 times:
153 + Numerous invited talks on EWAS of PTSD, genetics of SLE, and Open
154 Source: https://dla2.us/pres
158 + 2017 R Consortium: *[Adding Linux Binary Builders to R-Hub](https://www.r-consortium.org/blog/2017/04/03/q1-2017-isc-grants)* Role:
160 + 2015 Blue Waters Allocation Grant: *Making ancestral trees using Bayesian
161 inference to identify disease-causing genetic variants* Role:
163 + *Tracking placenta and uterine funciton using urinary extracellular vesicles* (R21
164 RFA-HD-16-037) Role: Key Personnel
165 + *NIAMS* R01-AR045650-04 *Genetics of Childhood Onset SLE* to Chaim O. Jacob.
168 ## Scholarships and Fellowships
169 + 2001--2003: University of California, Riverside Doctoral Fellowship
170 + 1997--2001: Regents of the University of California Scholarship.
172 # Academic Information
174 You can also read my [Curriculum Vitæ](curriculum_vitae)
175 ([pdf](dla-cv.pdf)), [Research Statement](research_statement)
176 ([pdf](research_statement.pdf)),
177 and [Teaching Statement](teaching_statement)
178 ([pdf](teaching_statement.pdf)).
180 For my contact information or additional references, please e-mail
181 <don@donarmstrong.com>