[[!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 + 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 + 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 # 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 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