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[don.git] / resume.mdwn

[[!meta title="Resumé"]]

# Experience
## Career Synopsis & Outlook 
+ A proven, transformative leader of teams that enable businesses to
  harness the value of scientific and business data to achieve
  business goals in biotechnology and other biology-adjacent
  industries.
+ Significant experience mentoring, coaching, managing, and leading
  managers and individual contributors from the entry level to
  principal level, enabling them to develop into their full potential
  as leaders and contributors.
+ Extensive scientific, computational, analytical, and business
  background coupled with a history of effective communication with
  diverse audiences enables bridging the needs and requirements of
  challenging stakeholders and earning their trust and buy-in even in
  complex, highly regulated environments.
+ Seeking opportunities to grow, lead, and transform organizations
  with a larger scope and greater impact.

## Director of Data Science and Analytics at Ginkgo Bioworks  2022--Present 
+ Directed a geographically distributed 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 [Ginkgo Bioworks](https://www.ginkgobioworks.com)
+ Accountable for the data architecture, engineering, management, and
  governance of all data within the Ag Business unit, including
  complex modalities of research and development data from genomics to
  complex phenotypic data, including chemistry, production, systems
  biology, and business data.
+ 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, software engineering, and statistics using
  coaching, mentorship, and teaching approaches.
+ Accountable (and frequently responsible) for all R&D IT applications
  in a business unit, including vendor selection, architectural
  decisions, deployment, and development where appropriate.
+ Championed modern approaches to data governance and data stewardship
  principles across multiple life-science and business functions.
+ Lead the development of multiple cloud-based serverless and
  container-based applications in AWS and GCP with multiple API and UI
  interfaces written in python and javascript to enable the management
  of data, with dbt, airflow, postgresql, and snowflake handling data
  storage and plumbing roles.
+ Key leadership role in multiple mergers and acquisitions,
  specializing in R&D business applications and data-adjacent systems.
+ Extensive collaborations with scientific, business, and customer
  leaders attest to my excellent communication and interpersonal
  skills.

## Team Lead Data Engineering at Bayer Crop Science  2018--2022
+ 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 using AWS, python, postgresql, R, and 
+ Lead the development of multiple systems while coaching, mentoring,
  and developing software and data 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 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.
+ Provided vendor-level support for complex systems integration issues
  on Debian GNU/Linux systems.

## Research Scientist at UIUC 2015--2017
+ Architected and engineered systems to store, retrieve, and analyze
  complex R&D data including behavioral healthcare data (PTSD),
  genomic, epigenomic, and other phenotypic healthcare data
  (pre-eclampsia), while maintaining compliance with data privacy
  regulations including HIPAA and institutional review boards.
+ 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 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 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 at UC Riverside
+ Batchelor of Science (BS) in Biology at UC Riverside

# Skills
## Leadership and Mentoring
+ 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.

## Data Governance/Management/Engineering
+ Leadership and implementation of data governance and management
  programs across multiple functions within Ginkgo and Bayer.
+ Establishment of Metadata and master data management standards and
  frameworks in life science and business domains.
+ Snowflake, dbt, Airflow

## Bioinformatics, 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
+ Using evolutionary genomics to identify causal human variants

## Statistics
+ Statistical modeling (regression, inference, prediction, and machine
  learning in very large (> 1TB) datasets) using R and python.
+ Correcting & experimental design to overcome multiple testing,
  confounders, and batch effects (both Bayesian and frequentist)
+ Reproducible research

## Software Development
+ 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, 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
+ Filestorage: Gluster, CEFS, GPFS, Lustre
+ Linux system administration

## Applications and Daemons
+ Web: apache, ngix, varnish (load balancing/caching), REST, SOAP,
  Tomcat
+ Build Tools: GNU make, cmake
+ 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
+ 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.
+ Proven experience communicating with cross-functional and diverse
  teams and stakeholders at all organizational levels.
+ Strong verbal and presentation skills as evidenced by presentation,
  leadership, and teaching record

# Authored Open Source Software
+ *[Debbugs](http://bugs.debian.org)*: Bug tracking software for the Debian GNU/Linux
   distribution.
+ *[CairoHacks](http://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.

# Publications and Presentations
+ 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 >= 21
+ Multiple presentations 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 Vitæ](curriculum_vitae)
([pdf](dla-cv.pdf)), [Research Statement](research_statement)
([pdf](research_statement.pdf)),
and [Teaching Statement](teaching_statement)
([pdf](teaching_statement.pdf)).

For my contact information or additional references, please e-mail
<don@donarmstrong.com>