4 #+AUTHOR: Don Armstrong
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7 #+LATEX_CLASS_OPTIONS: [10pt,breaklinks]
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12 {\color{headings}\fontsize{24pt}{24pt}\selectfont {\textsc{\textbf{\myauthor}}}}
14 \href{mailto:\myemail}{\myemail} \hfill
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17 \href{https://github.com/dondelelcaro}{https://github.com/dondelelcaro}
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27 % Address and contact block
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30 \href{https://dla2.us/res}{\qrcode[tight,level=L,nolink,height=0.6in]{https://dla2.us/res}}
38 + *PhD* in Cell, Molecular and Developmental Biology
41 ** Genomics and Epigenomics
42 + *NGS* and array-based Genomics and Epigenomics of complex human
43 diseases using *RNA-seq*, targeted DNA sequencing, *RRBS*, Illumina
44 bead arrays, and Affymetrix microarrays from sample collection to
46 + Reproducible, scalable bioinformatics analysis using make,
47 *nextflow*, and *cwl* based workflows on cloud- and cluster-based
48 systems on terabyte-scale datasets
49 + Alignment, annotation, and variant calling using existing and
50 custom-written software, including *GATK*, *bwa*, *STAR*, and
52 + Correcting for and experimental design to overcome multiple
53 testing, confounders, and batch effects using Bayesian and
54 frequentist methods approaches
55 # + Using evolutionary genomics to identify causal human variants
57 + Statistical modeling (regression, inference, prediction, and
58 learning in very large (> 1TB) datasets)
59 + Addressing confounders and batch effects
60 # + Reproducible research
62 + Parallel and Cloud Computing (slurm, torque, AWS, OpenStack, Azure)
63 + Inter-process communication: MPI, OpenMP
64 + Filestorage: Gluster, CEFS, GPFS, Lustre
65 + Linux system administration
66 ** Mentoring and Leadership
67 + Mentored graduate students and Outreachy and Google Summer of Code
69 + Former chair of Debian's Technical Committee
70 + Head developer behind https://bugs.debian.org
71 ** Software Development
72 + Languages: perl, R, C, C++, python, groovy, sh, make
73 + Collaborative Development: git, travis, continuous integration,
75 + Web, Mobile: Shiny, jQuery, JavaScript
76 + Databases: Postgresql (PL/SQL), SQLite, Mysql, NoSQL
77 + Office Software: Gnumeric, Libreoffice, \LaTeX, Word, Excel,
80 + Strong written communication skills as evidenced by publication
82 + Strong verbal and presentation skills as evidenced by presentation
84 # ** Consortia Involvement
85 # + *H3A Bionet*: Generating workflows and cloud resources for H3 Africa
86 # + *Psychiatric Genomics Consortium*: Identification of epigenetic
87 # variants which are correlated with PTSD.
88 # + *SLEGEN*: System lupus erythematosus genetics consortium.
93 \begin{minipage}[t]{0.0in}
98 \begin{minipage}[t]{0.55\textwidth}
102 ** Research Scientist at UIUC
103 + 2015--Present. University of Illinois at Urbana-Champaign. Epigenetic
104 modifications associated with PTSD, the genomic basis of the
105 development of parturition in mammals, and detecting adverse
106 pregnancy outcomes using urinary exosomes.
107 ** Postdoctoral Researcher at USC
108 + 2013--2015. Identifying genes and causal alleles associated with
109 Systemic Lupus Erythematosus using genome-wide association,
110 next-generation sequencing, computational and biochemical
112 ** Postdoctoral Researcher at UCR
113 + 2010--2012. Identifying genes which are associated with Systemic
114 Lupus Erythematosus using prior information and targeted trio-based
117 + 2004--Present. \emph{Debian Project}, Developer; Technical Committee
118 Member (2010--2016), Technical Committee Chair (2015--2016).
120 + *[[http://bugs.debian.org][Debbugs]]*: Bug tracking software for the Debian GNU/Linux
121 distribution. [[https://bugs.debian.org]]
122 + *[[http://git.donarmstrong.com/r/CairoHacks.git][CairoHacks]]*: Bookmarks and Raster images for large PDF plots in R.
123 + *[[http://rzlab.ucr.edu/function2gene/][Function2Gene]]*: Gene selection tool based on literature mining which
124 enables Bayesian approaches to significance testing.
125 + *[[http://rzlab.ucr.edu/scripts/wheel/wheel.cgi?sequence=ABCDEFGHIJLKMNOP&submit=Submit][Helical Wheel Projections]]*: Web-based tool to draw helical wheel
126 protein projections. [[http://rzlab.ucr.edu/scripts/wheel]]
127 * Publications and Presentations
128 + 20 peer-reviewed refereed publications cited over 1700 times:
130 + Publication record in GWAS, expression analysis of microarrays,
131 epigenetics, comparative evolution of mammals, and lipid membranes
133 + Multiple presentations on EWAS of PTSD, genetics of SLE, and Open
134 Source: https://dla2.us/pres
138 + 2017 R Consortium: *[[https://www.r-consortium.org/blog/2017/04/03/q1-2017-isc-grants][Adding Linux Binary Builders to R-Hub]]* Role:
140 + 2015 Blue Waters Allocation Grant: *Making ancestral trees using Bayesian
141 inference to identify disease-causing genetic variants* Role:
143 + *Tracking placenta and uterine funciton using urinary extracellular vesicles* (R21
144 RFA-HD-16-037) Role: Key Personnel
145 + *NIAMS* R01-AR045650-04 *Genetics of Childhood Onset SLE* to Chaim O. Jacob.
147 ** Scholarships and Fellowships
148 + 2001--2003: University of California, Riverside Doctoral Fellowship
149 + 1997--2001: Regents of the University of California Scholarship.