# #+LATEX_CLASS_OPTIONS: [10pt,breaklinks]
* Experience
+** Team Lead Data Engineering at Bayer Crop Science \hfill 2018--Present
++ Hired, managed, and developed team of 5+ Data Engineers, Systems
+ Administrators, and Business Analysts working within the Biologics
+ R&D unit of Bayer Crop Science enabling data capture, data
+ integration, and operationalization of data analysis pipelines
++ Developed and supervised implementation of data capture,
+ integration, and analysis strategies to increase the value of
+ genomics, metabolomics, transcriptomics, spectroscopic, phenotypic
+ (/in vitro/ and /in planta/), and fermentation/formulation process
+ data for discovery and development
++ Lead the development of multiple tools in python and R while
+ coaching, mentoring, and developing multiple developers and
+ engineers
++ Served as a key collaborator on multiple cross-function and
+ cross-divisional projects, including leading the architecture of a
+ life science collaboration using serverless architecture to provide
+ machine-learning estimates of critical parameters from
+ spectrographic measurements
+** Debian Developer \hfill 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 [[https://bugs.debian.org][Debbugs]], a perl and SQL-based issue-tracker with ≥ 100
+ million entries with web, REST, and SOAP interfaces.
++ Provided vendor-level support for complex systems integration issues
+ on Debian GNU/Linux systems.
** Research Scientist at UIUC \hfill 2015--2017
-+ Epigenetic modifications associated with PTSD, the genomic basis of
- the development of parturition in mammals, and detecting adverse
- pregnancy outcomes using urinary exosomes.
++ 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 ([[https://bluewaters.ncsa.illinois.edu/][Blue Waters]])
** Postdoctoral Researcher at USC \hfill 2013--2015
-+ Identifying genes and causal alleles associated with Systemic Lupus
- Erythematosus using genome-wide association, next-generation
- sequencing, computational and biochemical approaches.
++ 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 \hfill 2010--2012
-+ Identifying genes which are associated with Systemic Lupus
- Erythematosus using prior information and targeted trio-based
- studies.
-** Debian Developer \hfill 2004--Present
-+ \emph{Debian Project}, Developer; Technical Committee Member
- (2010--2016), Technical Committee Chair (2015--2016).
-
++ 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.
+** Independent Systems Administrator \hfill 2004--2018
++ 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.
++ 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) \hfill UC Riverside
- + Cell, Molecular and Developmental Biology.
+** Doctor of Philosophy (PhD) in Cell, Molecular and Developmental Biology \hfill UC Riverside
** Batchelor of Science (BS) in Biology \hfill UC Riverside
* Skills
-** 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
-** Mentoring and Leadership
+** Leadership and Mentoring
++ Lead
+ Mentored graduate students and Outreachy and Google Summer of Code
interns
+ Former chair of Debian's Technical Committee
+ Head developer behind https://bugs.debian.org
** Software Development
-+ Languages: perl, R, C, C++, python, groovy, sh, make
-+ Collaborative Development: git, travis, continuous integration,
- automated testing
++ Languages: python, R, perl, C, C++, python, groovy, sh (bash, POSIX,
+ and zsh), make
++ Collaborative Development: git, Jira, github actions, Aha!, travis,
+ continuous integration, automated testing, continuous deployment
+ Web, Mobile: Shiny, jQuery, JavaScript
+ Databases: Postgresql (PL/SQL), SQLite, Mysql, NoSQL
+** Big Data
++ Parallel and Cloud Computing (slurm, torque, AWS, OpenStack, Azure)
++ Inter-process communication: MPI, OpenMP
++ Filestorage: Gluster, CEFS, GPFS, Lustre
++ Linux system administration
+** Applications and Daemons
++ Web: apache, ngix, varnish (load balancing/caching), REST, SOAP,
+ Tomcat
++ SQL servers: PostgreSQL, MySQL, SQLite, oracle
++ Build Tools: GNU make, cmake
++ Continuous Integration/Deployment: codebuild, travis, jenkins,
+ github actions
++ Virtualization: libvirt, KVM, qemu, VMware, docker
++ Statistics: R, SAS
++ VCS: git, mercurial, subversion
++ Mail: postfix, exim, sendmail, spamassassin
++ Configuration Infrastructure: puppet, hiera, etckeeper, git
++ Documentation: \LaTeX, confluence, emacs, MarkDown, MediaWiki, ikiwiki, trac
++ Monitoring: munin, nagios, icinga, prometheus
++ Issue Tracking: Debbugs, Request Tracker, Trac, JIRA
+ Office Software: Gnumeric, Libreoffice, \LaTeX, Word, Excel,
Powerpoint
+** Networking
+ + Hardware, Linux routing and firewall experience, ferm, DHCP,
+ openvpn, bonding, NAT, DNHS, SNMP, IPv4, and IPv6.
+** Operating systems
+ + GNU/Linux (Debian, Ubuntu, Red Hat)
+ + Windows
+ + MacOS
** 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
+** 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) using R and SAS.
++ Addressing confounders and batch effects
++ Reproducible research
+* Authored Open Source Software
+ *[[http://bugs.debian.org][Debbugs]]*: Bug tracking software for the Debian GNU/Linux
distribution. [[https://bugs.debian.org]]
+ *[[http://git.donarmstrong.com/r/CairoHacks.git][CairoHacks]]*: Bookmarks and Raster images for large PDF plots in R.
+ *[[http://rzlab.ucr.edu/function2gene/][Function2Gene]]*: Gene selection tool based on literature mining which
enables Bayesian approaches to significance testing.
+ *[[http://rzlab.ucr.edu/scripts/wheel/wheel.cgi?sequence=ABCDEFGHIJLKMNOP&submit=Submit][Helical Wheel Projections]]*: Web-based tool to draw helical wheel
- protein projections. [[http://rzlab.ucr.edu/scripts/wheel]]
+ protein projections.
* Publications and Presentations
-+ 24 peer-reviewed publications cited over 1800 times:
++ 24 peer-reviewed publications cited over 3000 times:
https://dla2.us/pubs
+ Publication record in GWAS, expression analysis of microarrays, SLE,
GBM, epigenetics, comparative evolution of mammals, and lipid
membranes
-+ H index of 11
++ H index >= 20
+ Multiple presentations on EWAS of PTSD, genetics of SLE, and Open
Source: https://dla2.us/pres