[[!meta title="Resumé"]]
+# Experience
+## Research Scientist at UIUC 2015--2017
++ Primarily responsible for the planning, design, organization,
+ execution, and analysis of multiple complex epidemiological studies
+ involving epigenomics, transcriptomics, and genomics of diseases of
+ pregnancy and post-traumatic stress disorder.
++ Published results in scientific publications and presented results
+ orally at major scientific conferences.
++ Wrote and completed grants, including budgeting, scientific
+ direction, project management, and reporting.
++ Mentored graduate students and collaborated with internal and
+ external scientists.
++ Performed literature review, training, and applied new techniques to
+ maintain abreast of current scientific literature, principles of
+ scientific research, and modern statistical methodology.
++ Wrote software and designed relational databases using R, perl, C,
+ SQL, make, and very large computational systems.
+## Postdoctoral Researcher at USC 2013--2015
++ Primarily responsible for the design, execution, and analysis of an
+ epidemiological study to identify genomic variants associated with
+ systemic lupus erythematosus using targeted deep sequencing.
++ Designed, budgeted, configured, maintained, and supported a secure
+ linux analysis cluster (MPI/torque) with a shared filesystem (NFS
+ over gluster) for statistical analyses.
++ Wrote multiple pieces of software to reproducibly analyze and
+ archive large datasets resulting from genomic sequencing.
++ Coordinated with clinicians, molecular biologists, and biologists to
+ produce analyses and major reports.
+## Postdoctoral Researcher at UCR 2010--2012
++ Primarily responsible for the execution and analysis of an
+ epidemiological study to identify genomic variants associated with
+ systemic lupus erythematosus using prior information and array based
+ approaches in a trio and cross sectional study of individuals from
+ the Los Angeles and greater United States.
++ Wrote and maintained multiple software components to reproducibly
+ perform the analyses.
+## Debian Developer 2004--Present
++ Maintained, managed configurations, and resolved issues in multiple
+ packages written in R, perl, python, scheme, C++, and C.
++ Resolved technical conflicts, developed technical standards, and
+ provided leadership as the elected chair of the Technical Committee.
++ Developer of [Debbugs](https://bugs.debian.org), a perl and SQL-based issue-tracker with ≥ 100
+ million entries with web, REST, and SOAP interfaces.
+## Independent Systems Administrator 2004--Present
++ Researched, recommended, budgeted, designed, deployed, configured,
+ operated, and monitored highly-available high-performance enterprise
+ hardware and software for web applications, authentication, backup,
+ email, and databases.
++ Provided vendor-level support for complex systems integration issues
+ on Debian GNU/Linux systems.
++ Full life-cycle support of medium and small business networking
+ infrastructure, including VPN, network security, wireless networks,
+ routing, DNS, DHCP, and authentication.
# Education
-## UC Riverside
-+ **PhD** in Cell, Molecular and Developmental Biology
-+ **BS** in Biology
++ Doctor of Philosophy (PhD) in Cell, Molecular and Developmental Biology at UC Riverside
++ Batchelor of Science (BS) in Biology at UC Riverside
# Skills
+## Data Science
++ Reproducible, scalable analyses using *R*, *perl*, and python with
+ workflows on cloud- and cluster-based systems on terabyte-scale
+ datasets
++ Experimental design and correction to overcome multiple testing,
+ confounders, and batch effects using Bayesian and frequentist
+ methods
++ Design, development, and deployment of algorithms and data-driven
+ products, including APIs, reports, and interactive web applications
++ Statistical modeling (regression, inference, prediction/forecasting,
+ time series, and machine learning in very large (> 1TB) datasets)
++ Data mining, cleaning, processing and quality assurance of data
+ sources and products using tidydata formalisms
++ Visualization using *R*, ggplot, Shiny, and custom written routines.
+## Software Development
++ Languages: perl, R, C, C++, python, groovy, sh, make
++ Collaborative Development: git, travis, continuous integration,
+ automated testing
++ Web, Mobile: Shiny, jQuery, JavaScript
++ Databases: Postgresql (PL/SQL), SQLite, Mysql, NoSQL
++ Office Software: Gnumeric, Libreoffice, \LaTeX, Word, Excel,
+ Powerpoint
## 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
-
## Statistics
-+ Statistical modeling
++ Statistical modeling (regression, inference, prediction, and
+ learning in very large (> 1TB) datasets)
+ Addressing confounders and batch effects
+ 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
+## Genomics and Epigenomics
++ Linkage and association-based mapping of complex phenotypes using
+ next-generation sequencing and arrays
++ Alignment, annotation, and variant calling using existing and custom
+ software
## Mentoring and Leadership
+ Mentored graduate students and Outreachy and Google Summer of Code
interns
-+ Chairperson of the Debian Technical Committee
-+ Head developer behind https://bugs.debian.org
-
-## Software Development
-+ Languages: perl, R, C, C++, python, groovy, assembly, sh, make
-+ Collaborative Development: git, travis, continuous integration,
- automated testing
-+ Databases: Postgresql (PL/SQL), SQLite, Mysql
-
++ Former chair of Debian's Technical Committee
## Communication
+ Strong written communication skills as evidenced by publication
record
+ Strong verbal and presentation skills as evidenced by presentation
and teaching record
-
-# 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 using urinary exosomes.
-
-## 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
-+ 2004–Present. *Debian Project*, Developer; Technical Committee
- Member (2010–2016), Technical Committee Chair (2015–2016).
-
+## 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.
# Authored Software
-+ **[Debbugs](http://bugs.debian.org)**: Bug tracking software for the Debian GNU/Linux
- distribution. <https://bugs.debian.org>
-+ **[CairoHacks](https://git.donarmstrong.com/r/CairoHacks.git)**:
- Bookmarks and Raster images for large PDF plots in R.
-+ **[Function2Gene](http://rzlab.ucr.edu/function2gene/)**: Gene
- selection tool based on literature mining which enables Bayesian
- approaches to significance testing.
-+ **[Helical Wheel Projections](http://rzlab.ucr.edu/scripts/wheel/wheel.cgi?sequence=ABCDEFGHIJLKMNOP&submit=Submit)**:
- Web-based tool to draw helical wheel protein projections.
- <http://rzlab.ucr.edu/scripts/wheel>
-
++ *[Debbugs](http://bugs.debian.org)*: Bug tracking software for the Debian GNU/Linux
+ distribution. [https://bugs.debian.org]
++ *[CairoHacks](https://git.donarmstrong.com/r/CairoHacks.git)*: Bookmarks and Raster images for large PDF plots in R.
++ *[Function2Gene](http://rzlab.ucr.edu/function2gene/)*: Gene selection tool based on literature mining which
+ enables Bayesian approaches to significance testing.
++ *[Helical Wheel Projections](http://rzlab.ucr.edu/scripts/wheel/wheel.cgi?sequence=ABCDEFGHIJLKMNOP&submit=Submit)*: Web-based tool to draw helical wheel
+ protein projections. [http://rzlab.ucr.edu/scripts/wheel]
# Publications and Presentations
-+ 20 peer-reviewed refereed publications cited over 1700 times:
- <https://dla2.us/pubs>
-+ Publication record in GWAS, expression analysis of microarrays,
- epigenetics, comparative evolution of mammals, and lipid membranes
++ 24 peer-reviewed publications cited over 1800 times:
+ https://dla2.us/pubs
+ H index of 11
-+ Multiple presentations on EWAS of PTSD, genetics of SLE, and Open
- Source: <https://dla2.us/pres>
++ Numerous invited talks on EWAS of PTSD, genetics of SLE, and Open
+ Source: https://dla2.us/pres
# Funding and Awards
## Grants
-+ 2017 R Consortium:
- **[Adding Linux Binary Builders to R-Hub](https://www.r-consortium.org/blog/2017/04/03/q1-2017-isc-grants)**
- Role: Co-PI
-+ 2015 Blue Waters Allocation Grant: **Making ancestral trees using Bayesian
- inference to identify disease-causing genetic variants** Role:
++ 2017 R Consortium: *[Adding Linux Binary Builders to R-Hub](https://www.r-consortium.org/blog/2017/04/03/q1-2017-isc-grants)* Role:
+ Co-PI
++ 2015 Blue Waters Allocation Grant: *Making ancestral trees using Bayesian
+ inference to identify disease-causing genetic variants* Role:
Primary Investigator
-+ **Tracking placenta and uterine funciton using urinary extracellular vesicles** (R21
++ *Tracking placenta and uterine funciton using urinary extracellular vesicles* (R21
RFA-HD-16-037) Role: Key Personnel
-+ **NIAMS** R01-AR045650-04 **Genetics of Childhood Onset SLE** to Chaim O. Jacob.
++ *NIAMS* R01-AR045650-04 *Genetics of Childhood Onset SLE* to Chaim O. Jacob.
Role: Key Personnel
-
## Scholarships and Fellowships
+ 2001--2003: University of California, Riverside Doctoral Fellowship
+ 1997--2001: Regents of the University of California Scholarship.
#Academic Information
-You can also read my [Curriculum Vitæ](curriculum_vitae)
-([pdf](dla-cv.pdf)), [Research Statement](research_statement)
-([pdf](research_statement.pdf)),
-and [Teaching Statement](teaching_statement)
-([pdf](teaching_statement.pdf)).
+You can also read my [curriculum_vitae](Curriculum Vitæ)
+([dla-cv.pdf](pdf)), [research_statement](Research Statement)
+([research_statement.pdf](pdf)),
+and [teaching_statement](Teaching Statement)
+([teaching_statement.pdf](pdf)).
For my contact information or additional references, please e-mail
<don@donarmstrong.com>
projects / don.git / blobdiff