From: Don Armstrong Date: Thu, 11 May 2017 03:28:32 +0000 (-0700) Subject: update resume X-Git-Url: https://git.donarmstrong.com/?p=don.git;a=commitdiff_plain;h=53f0738631b271a4f5e5072b019cf14da04f8c32 update resume --- diff --git a/resume.mdwn b/resume.mdwn index 14d54df..78ce684 100644 --- a/resume.mdwn +++ b/resume.mdwn @@ -1,50 +1,109 @@ [[!meta title="Curriculum Vitæ, Research Statement, and Teaching Statement"]] -Introduction ------------- - -A brief statement of my research interests and teaching mission -follows, and 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)) are also available. - -For my contact information or additional references, please e-mail - +# Education +## UC Riverside ++ **PhD** in Cell, Molecular and Developmental Biology ++ **BS** in Biology +# 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 ++ 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 ++ Addressing confounders and batch effects ++ Reproducible research +## Big Data ++ Parallel and Cloud Computing ++ Inter-process communication: MPI, OpenMP, Hadoop ++ Filestorage: Gluster, CEFS, GPFS, Lustre ++ Cloud based-infrastructure: Azure, AWS, Docker, cloud-init ++ Debian GNU/Linux system administration +## 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 +## Communication ++ Strong written communication skills as evidenced by publication + record ++ Strong verbal and presentation skills as evidenced by presentation + and teaching record -Research Focus --------------- +# 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. \emph{Debian Project}, Developer; Technical Committee + Member (2010--Present), Technical Committee Chair (2015--2016). +# Authored Software ++ **[Debbugs](http://bugs.debian.org)**: Bug tracking software for the Debian GNU/Linux + distribution. [https://bugs.debian.org] ++ **[CairoHacks](http://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 ++ H index of 11 ++ Multiple presentations on EWAS of PTSD, genetics of SLE, and Open + Source: [https://dla2.us/pres] -My primary research focus is developing and using bioinformatics -techniques to identify causes and mechanisms underlying human -diseases, such as Systemic Lupus Erythematosus (SLE). I have -identified multiple novel genes associated with SLE using both -genome-wide association studies and trio-based studies in targeted -regions. In collaborative work, I have identified a causal variant in -NCF2 -([rs17849502](http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=rs17849502)) -using both *in silico* and *in vitro* approaches. I am currently -working on identifying causal variants in additional associated genes -using targeted deep sequencing using high-throughput variant analysis -pipelines to prioritize variants for additional *in silico* and *in -vitro* experiments. In the future, utilizing my extensive -bioinformatic and software development experience, I will head a -development group working on techniques for the storage, alignment, -and analysis of terabytes (eventually petabytes) of next-generation -sequencing data from collaborations studying human-relevant diseases -and biological systems. +# 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: + Primary Investigator ++ **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. + 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 +------------ -Teaching Mission ----------------- - -While teaching, my primary mission is to have my students experience -the excitement of scientific discovery for themselves. Secondarily, I -use that excitement to keep them engaged and interested in the -material. While a graduate student at UC Riverside, I was a teaching -assistant for [Introductory Biology, Genetics, Molecular Biology, and -Developmental Biology](http://www.biology.ucr.edu/courses/UGcourses.html) +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)). +For my contact information or additional references, please e-mail +