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#+TITLE: Resume
-#+AUTHOR: Don Armstrong
+#+AUTHOR: Don L. Armstrong
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+* Experience
+** Research Scientist at UIUC \hfill 2015--2017
++ Epigenetic modifications associated with PTSD, the genomic basis of
+ the development of parturition in mammals, and detecting adverse
+ pregnancy outcomes using urinary exosomes.
+** Postdoctoral Researcher at USC \hfill 2013--2015
++ Identifying genes and causal alleles associated with Systemic Lupus
+ Erythematosus using genome-wide association, next-generation
+ sequencing, computational and biochemical approaches.
+** Postdoctoral Researcher at UCR \hfill 2010--2012
++ Identifying genes which are associated with Systemic Lupus
+ Erythematosus using prior information and targeted trio-based
+ studies.
+** Debian Developer \hfill 2004--Present
++ \emph{Debian Project}, Developer; Technical Committee Member
+ (2010--2016), Technical Committee Chair (2015--2016).
* Education
-** UC Riverside
-+ *PhD* in Cell, Molecular and Developmental Biology
-+ *BS* in Biology
+** Doctor of Philosophy (PhD) \hfill UC Riverside
+ + Cell, Molecular and Developmental Biology.
+** Batchelor of Science (BS) in Biology \hfill UC Riverside
+
* Skills
** Genomics and Epigenomics
-+ Genomics and Epigenomics of complex human diseases including
- PTSD, Systemic Lupus Erythematosus, and Alzheimer's Disease using
- cross-sectional and longitudinal experimental designs
++ *NGS* and array-based Genomics and Epigenomics of complex human
+ diseases using *RNA-seq*, targeted DNA sequencing, *RRBS*, Illumina
+ bead arrays, and Affymetrix microarrays from sample collection to
+ publication.
++ Reproducible, scalable bioinformatics analysis using make,
+ *nextflow*, and *cwl* based workflows on cloud- and cluster-based
+ systems on terabyte-scale datasets
++ Alignment, annotation, and variant calling using existing and custom
+ software, including *GATK*, *bwa*, *STAR*, and *kallisto*.
+ Correcting for and experimental design to overcome multiple
testing, confounders, and batch effects using Bayesian and
frequentist methods approaches
-+ Reproducible, scalable analysis using workflows on cloud- and
- cluster-based systems on terabyte-scale datasets
-+ Using evolutionary genomics to identify causal human variants
+# + Using evolutionary genomics to identify causal human variants
** Statistics
-+ Statistical modeling
++ Statistical modeling (regression, inference, prediction, and
+ learning in very large (> 1TB) datasets)
+ Addressing confounders and batch effects
-+ Reproducible research
+# + Reproducible research
** Big Data
-+ Parallel and Cloud Computing
-+ Inter-process communication: MPI, OpenMP, Hadoop
++ Parallel and Cloud Computing (slurm, torque, AWS, OpenStack, Azure)
++ Inter-process communication: MPI, OpenMP
+ Filestorage: Gluster, CEFS, GPFS, Lustre
-+ Cloud based-infrastructure: Azure, AWS, Docker, cloud-init
-+ Debian GNU/Linux system administration
++ Linux system administration
** Mentoring and Leadership
+ Mentored graduate students and Outreachy and Google Summer of Code
interns
-+ Chairperson of the Debian Technical Committee
++ Former chair of Debian's Technical Committee
+ Head developer behind https://bugs.debian.org
** Software Development
-+ Languages: perl, R, C, C++, python, groovy, assembly, sh, make
++ Languages: perl, R, C, C++, python, groovy, sh, make
+ Collaborative Development: git, travis, continuous integration,
automated testing
-+ Databases: Postgresql (PL/SQL), SQLite, Mysql
++ Web, Mobile: Shiny, jQuery, JavaScript
++ Databases: Postgresql (PL/SQL), SQLite, Mysql, NoSQL
++ Office Software: Gnumeric, Libreoffice, \LaTeX, Word, Excel,
+ Powerpoint
+** Communication
++ Strong written communication skills as evidenced by publication
+ record
++ Strong verbal and presentation skills as evidenced by presentation
+ and teaching record
# ** Consortia Involvement
# + *H3A Bionet*: Generating workflows and cloud resources for H3 Africa
# + *Psychiatric Genomics Consortium*: Identification of epigenetic
# variants which are correlated with PTSD.
# + *SLEGEN*: System lupus erythematosus genetics consortium.
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-* Experience
-** Research Scientist at UIUC
-+ 2015--Present. University of Illinois at Urbana-Champaign. Epigenetic
- modifications associated with PTSD, the genomic basis of the
- development of parturition in mammals, and detecting adverse
- pregnancy outcomes.
-** Postdoctoral Researcher at USC
-+ 2013--2015. Identifying genes and causal alleles associated with
- Systemic Lupus Erythematosus using genome-wide association,
- next-generation sequencing, computational and biochemical
- approaches.
-** Postdoctoral Researcher at UCR
-+ 2010--2012. Identifying genes which are associated with Systemic
- Lupus Erythematosus using prior information and targeted trio-based
- studies.
-** Debian Developer with the Debian Project
-+ 2004--Present. \emph{Debian Project}, Developer; Technical Committee
- Member (2010--Present), Technical Committee Chair (2015--2016).
* Authored Software
+ *[[http://bugs.debian.org][Debbugs]]*: Bug tracking software for the Debian GNU/Linux
distribution. [[https://bugs.debian.org]]
enables Bayesian approaches to significance testing.
+ *[[http://rzlab.ucr.edu/scripts/wheel/wheel.cgi?sequence=ABCDEFGHIJLKMNOP&submit=Submit][Helical Wheel Projections]]*: Web-based tool to draw helical wheel
protein projections. [[http://rzlab.ucr.edu/scripts/wheel]]
-* Publications
-+ 20 peer-reviewed refereed publications cited over 1700 times
-+ Publication record in GWAS, expression analysis
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+* Publications and Presentations
++ 24 peer-reviewed publications cited over 1800 times:
+ https://dla2.us/pubs
++ Publication record in GWAS, expression analysis of microarrays, SLE,
+ GBM, epigenetics, comparative evolution of mammals, and lipid
+ membranes
++ H index of 11
++ Multiple presentations on EWAS of PTSD, genetics of SLE, and Open
+ Source: https://dla2.us/pres
* Funding and Awards
** Grants
+ 2015 Blue Waters Allocation Grant: *Making ancestral trees using Bayesian
inference to identify disease-causing genetic variants* Role:
Primary Investigator
-+ BD2K Mentored Career Development Award: *Predicting individualized*
- *chemotherapeutic treatment outcomes using large multi-omics and*
- *clinical datasets* (K01 RFA-ES-16-002) (under review) Role: PI
-+ *Mechanism of PR Resistance in Endometriosis* (R01 RFA-HD-16-036)
- (under review) Role: Co-PI
+ *Tracking placenta and uterine funciton using urinary extracellular vesicles* (R21
- RFA-HD-16-037) (under review) Role: Key Personnel
-+ *Molecular Transducers of Physical Activity Bioinformatics Center*
- (U24 RFA-RM-15-012) (under review) Role: Key Personnel
+ RFA-HD-16-037) Role: Key Personnel
+ *NIAMS* R01-AR045650-04 *Genetics of Childhood Onset SLE* to Chaim O. Jacob.
Role: Key Personnel
-** Conference Awards
-+ 2007 FOCIS Trainee Award
-+ 2009 FOCIS Trainee Award
** Scholarships and Fellowships
+ 2001--2003: University of California, Riverside Doctoral Fellowship
+ 1997--2001: Regents of the University of California Scholarship.
-* Service
-** Consortiums
-+ *H3A Bionet*: Generating workflows and cloud resources for
- bioinformatics analysis as part of the H3 Africa consortium
-+ *Psychiatric Genomics Consortium*: Identification of epigenetic
- variants which are correlated with PTSD.
-+ *SLEGEN*: System lupus erythematosus genetics consortium.
-** Mentoring
-+ *Laren Riesche*: Differential methylation of marmoset placentas
- using RRBS. Statistical training and bioinformatics training
- resulting in PhD in Nursing. 2016-2017.
-+ *Christine Y. Chan*: Ancestral trees for disease predictions. 2016
-+ *[[https://developers.google.com/open-source/gsoc/2006/][Phillip Kern]]*: GUI for Debian's bug tracking system.
-+ *[[https://gnome.org/opw/][Virginia King]]*: Improving documentation of Debian's Bug Tracking system.
-** Reviewing
-+ /Ad hoc/ reviewer for PLoS One.
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