# #+LATEX_CLASS_OPTIONS: [10pt,breaklinks]
* Experience
- + \emph{Debian Project}, Developer; Technical Committee
- Member (2010--2016), Technical Committee Chair (2015--2016).
+** Debian Developer \hfill 2004--Present
- + Developing and designing software and hardware
- requirements. Deploying and maintaining enterprise-level systems for
- web, email, and data storage backends using MySQL and other
- solutions.
+++ 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.
+** Independent Systems Administrator \hfill 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.
** 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.
** 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.
-
+ + 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 \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.
-** Independent Systems Administrator \hfill 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) \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
-** Statistics
-+ Statistical modeling (regression, inference, prediction, and
- learning in very large (> 1TB) datasets)
-+ Addressing confounders and batch effects
-+ Reproducible research
+** Programming Languages
+ + [[http://r-project.org][R]], [[http://www.perl.org][Perl]], sh (bash, POSIX, and zsh), SQL, PL/SQL, C/C++, HTML, CSS,
+ javascript
+** Applications and Daemons
+ + Web: apache, ngix, varnish, REST, SOAP
+ + SQL servers: PostgreSQL, MySQL (including failover and replication)
+ + VCS: git, subversion
+ + Mail: postfix, exim, sendmail, spamassassin
+ + Configuration Infrastructure: puppet, etckeeper, git
+ + Documentation: \LaTeX, emacs, MarkDown, MediaWiki, ikiwiki, trac
+ + Monitoring: munin, nagios, icinga, prometheus
+ + Issue Tracking: Debbugs, Request Tracker, Trac
+ + Statistics: R, SAS
+ + Office Software: Gnumeric, Libreoffice, \LaTeX, Word, Excel,
+ Powerpoint
+ + Virtualization libvirt, KVM, qemu, VMware
+** 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 (5.0-10)
+ + MacOS (10-10.13)
+** Statistics
+ + Statistical modeling in very large datasets
+ + Addressing confounders and batch effects
+ ** 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
** Big Data
+ Parallel and Cloud Computing (slurm, torque, AWS, OpenStack, Azure)
+ Inter-process communication: MPI, OpenMP
projects / resume.git / commitdiff