X-Git-Url: https://git.donarmstrong.com/?p=don.git;a=blobdiff_plain;f=resume.mdwn;h=6443b3816ff3985856b29becd6bd35543fc85ced;hp=a4a9b2ca75d875391cd1fb0a0143384f66123c0b;hb=b4ab7669dabbff33fcfd2c2279ae50cea55195ff;hpb=5e1f47a06e05aea04f15a6145dd711af71d1d169 diff --git a/resume.mdwn b/resume.mdwn index a4a9b2c..6443b38 100644 --- a/resume.mdwn +++ b/resume.mdwn @@ -1,50 +1,166 @@ -[[!meta title="Curriculum Vitæ, Research Statement, and Teaching Statement"]] +[[!meta title="Resumé"]] -Introduction ------------- +# 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 ++ Doctor of Philosophy (PhD) in Cell, Molecular and Developmental Biology at UC Riverside ++ Batchelor of Science (BS) in Biology at UC Riverside -A brief statement of my research interests and teaching mission -follows, and my [Curriculum Vitæ](resume/curriculum_vitae) -([pdf](resume/dla-cv.pdf)), -[Research Statement](resume/research_statement) -([pdf](resume/research_statement.pdf)), and -[Teaching Statement](resume/teaching_statement) -([pdf](resume/teaching_statement.pdf)) are also available. +# 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 ++ 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 ++ Using evolutionary genomics to identify causal human variants +## Statistics ++ 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 (slurm, torque, AWS, OpenStack, Azure) ++ Inter-process communication: MPI, OpenMP ++ Filestorage: Gluster, CEFS, GPFS, Lustre ++ 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 ++ 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 +## 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] +# Publications and Presentations ++ 24 peer-reviewed publications cited over 1800 times: + https://dla2.us/pubs ++ H index of 11 ++ Numerous invited talks on EWAS of PTSD, genetics of SLE, and Open + Source: https://dla2.us/pres -For my contact information or additional references, please e-mail - - -Research Focus --------------- - -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_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 +