# #+LATEX_CLASS_OPTIONS: [10pt,breaklinks]
* Experience
-** Team Lead Data Engineering at Ginkgo Bioworks \hfill 2022--Present
-+ Lead and manged team of data engineers, system administrators,
- statisticians, bioinformaticians, and scientists at the PhD level
- working within the AgBio unit of Ginkgo Bioworks.
-+ Mentored and coached team members in data science, bioinformatics,
- data engineering, and statistics.
-+ Key leadership role in successful merger of AgBio unit with Ginkgo,
- including all relevant R&D business applications and data-adjacent
- systems.
+** Director of Data Science and Analytics at Ginkgo Bioworks \hfill 2022--Present
++ Directed a team of managers who lead teams of data engineers, system
+ administrators, statisticians, bioinformaticians, and scientists at
+ the PhD level working within the Ag business unit of [[https://www.ginkgobioworks.com][Ginkgo Bioworks]].
++ Accountable for cost centers totalling $10 M annually, including
+ budgeting, procurement, vendor relationships, and policy compliance.
++ Hired and developed team members in data science, bioinformatics,
+ data engineering, and statistics using coaching, mentorship, and
+ teaching approaches.
++ Accountable (and frequently responsible) for all R&D IT applications
+ in the Ag BU, including vendor selection, architectural decisions,
+ deployment, and development where appropriate.
++ Championed the adoption of data governance and data stewardship
+ principles, including new tools and ways of working.
++ Lead the development of multiple cloud-based serverless and
+ container-based applications with multiple API and UI interfaces,
+ including project management as well as contractor and vendor
+ oversight.
++ Key leadership role in multiple mergers and acquisitions,
+ specializing in R&D business applications and data-adjacent systems.
** Team Lead Data Engineering at Bayer Crop Science \hfill 2018--2022
+ Hired, managed, and developed team of 5+ Data Engineers, Systems
Administrators, and Business Analysts working within the Biologics
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
+ genomics, metabol\-omics, transcript\-omics, spectroscopic, phenotypic
(/in vitro/ and /in planta/), and fermentation/formulation process
data for discovery and development
+ Lead the development of multiple systems while coaching, mentoring,
life science collaboration using serverless architecture to provide
machine-learning estimates of critical parameters from
spectrographic measurements
-+ Established and developed network of internal and external contacts
- for technical implementation of Bayer program goals.
** Debian Developer \hfill 2004--Present
+ Maintained, managed configurations, and resolved issues in multiple
packages written in R, perl, python, scheme, C++, and C.
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
-+ Design, execution, and analysis of an epidemiological study to
- identify genomic variants associated with systemic lupus
- erythematosus using targeted deep sequencing.
-+ 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
-+ Executed and analyzed 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.
+# ** Postdoctoral Researcher at USC \hfill 2013--2015
+# + Design, execution, and analysis of an epidemiological study to
+# identify genomic variants associated with systemic lupus
+# erythematosus using targeted deep sequencing.
+# + 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
+# + Executed and analyzed 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.
* Education
-** Doctor of Philosophy (PhD) in Cell, Molecular and Developmental Biology \hfill UC Riverside
-** Batchelor of Science (BS) in Biology \hfill UC Riverside
++ Doctor of Philosophy (PhD) in Cell, Molecular and Developmental Biology \hfill UC Riverside
++ Batchelor of Science (BS) in Biology \hfill UC Riverside
* Skills
** Leadership and Mentoring
-+ Lead teams of PhD and MD scientists in multiple scientific and
- industrial programs
-+ 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
++ Lead managers and teams of PhD-level scientists in multiple
+ scientific and industrial programs.
++ Mentorship of multiple employees, graduate students, and
+ undergraduates throughout career, helping them to fully develop
+ their potential and thrive.
++ Chair or lead of multiple initiatives and committees, including
+ aligning highly cross-functional and diverse stakeholders.
** Bioinformatics, Genomics, and Epigenomics
+ NGS and array-based Genomics and Epigenomics of complex human
diseases using RNA-seq, targeted DNA sequencing, RRBS, Illumina
confounders, and batch effects (both Bayesian and frequentist)
+ Reproducible research
** Software Development
-+ Languages: python, R, perl, C, C++, python, groovy, sh (bash, POSIX,
++ Languages: python, R, perl, C, C++, groovy, sh (bash, POSIX,
and zsh), make
+ Collaborative Development: git, Jira, gitlab CI/CD, github actions,
Aha!, continuous integration & deployment, automated testing
+ Web, Mobile: Shiny, jQuery, JavaScript
-+ Databases: Postgresql (PL/SQL), SQLite, Mysql, NoSQL
++ Databases: Postgresql (PL/SQL), SQLite, Mysql, NoSQL, RDS
++ Cloud: AWS, Azure, GCP, OpenStack
++ Infrastructure as Code: AWS Cloudformation, Terraform, puppet,
+ etckeeper, hieara
** Big Data
+ Parallel and Cloud Computing (slurm, torque, AWS, OpenStack, Azure)
+ Inter-process communication: MPI, OpenMP
+ Virtualization: libvirt, KVM, qemu, VMware, docker
+ 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
+ *[[http://rzlab.ucr.edu/scripts/wheel/wheel.cgi?sequence=ABCDEFGHIJLKMNOP&submit=Submit][Helical Wheel Projections]]*: Web-based tool to draw helical wheel
protein projections.
* Publications and Presentations
-+ 24 peer-reviewed publications cited over 3000 times:
++ 24 peer-reviewed publications cited over 4000 times:
https://dla2.us/pubs
+ Publication record in GWAS, transcriptomics, SLE, GBM, epigenetics,
comparative evolution of mammals, and lipid membranes
-+ H index >= 20
++ H index >= 21
+ Multiple presentations on EWAS of PTSD, genetics of SLE, and Open
Source: https://dla2.us/pres
-* Funding and Awards
-** Grants
-+ 2017 R Consortium: *[[https://www.r-consortium.org/blog/2017/04/03/q1-2017-isc-grants][Adding Linux Binary Builders to R-Hub]]* 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.
+# * Funding and Awards
+# ** Grants
+# + 2017 R Consortium: *[[https://www.r-consortium.org/blog/2017/04/03/q1-2017-isc-grants][Adding Linux Binary Builders to R-Hub]]* 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.
projects / resume.git / commitdiff