From b4ab7669dabbff33fcfd2c2279ae50cea55195ff Mon Sep 17 00:00:00 2001 From: Don Armstrong Date: Sun, 25 Feb 2018 13:32:19 -0800 Subject: [PATCH] update my resume --- resume.mdwn | 202 ++++++++++++++++++++++++++++++++-------------------- 1 file changed, 124 insertions(+), 78 deletions(-) diff --git a/resume.mdwn b/resume.mdwn index 26f2117..6443b38 100644 --- a/resume.mdwn +++ b/resume.mdwn @@ -1,119 +1,165 @@ [[!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. -+ **[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. - - ++ *[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: - -+ 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: ++ 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 -- 2.39.2