Resume/CV

The interactive version of my hybrid Resume/CV/coverletter. Many sections have clickable links. Enjoy.

Justin D Vrana

PhD • Bioengineer • Software Engineer
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Seattle, WA

Strengths

Cross-functional problem solving
Creativity
Technical leadership

Skills

Languages
Python
Java
JavaScript
TypeScript
BASH
SQL
Ruby
Groovy
C++
Web Technologies
React
FastAPI
Ruby-on-Rails
JSF
Next.js
Flask
Plotly/Dash
Infrastructure
Kubernetes
AWS Serverless (Lambda, ECS)
AWS EKS
Database
PostgreSQL
redis
AWS s3
AWS EFS
Mysql
Neo4j
MongoDb
Data engineering
Dagster
NextFlow
Airflow
Data modeling
PyTorch
pandas
numpy
scikit-learn
SciPy
matplotlib
Software Engineering
Agile
code-review
test-driven development
CI/CD
Productivity
Docker
docker-compose
Jupyter/IPython
LaTeX
JIRA
git
ML & Optimization
Deep reinforcement learning
Graph neural networks
Monte Carlo
Regularization
Probabilistic Modeling
Wetlab
mammalian cell culture
lentivirus transfection
yeast engineering
molecular cloning
NGS
nanopore

Other Passions

ice hockey, rock climbing, snowboarding, biking

Summary

Dynamic and innovative full-stack software engineer and scientist with over a decade of experience in biotechnology and software development. Proven track record in designing and implementing advanced bioinformatics pipelines, machine learning algorithms, and full-stack applications to enhance research and development in biotechnology. Adept at leading cross-functional teams to deliver scalable solutions and accelerate the transition from designs to practical applications.

Professional Highlights

Developed critical software for a national DARPA program, translating complex cell designs into executable lab processes, significantly boosting operational efficiency.
Led the modernization of data infrastructure at Just-Evotec, transitioning from basic Jupyter Notebooks to advanced workflow orchestration platforms.
Designed and constructed the largest known engineered genetic circuit in eukaryotes as of 2017, using engineered CRISPR transcription factors and supporting it with robust mathematical models.
Co-authored 14 publications, demonstrating strong collaboration skills across biotech disciplines.

Education

PhD, Bioengineering
2014-2021
University of Washington
Seattle, WA
Advisor: Eric Klavins, Professor and Chair of Electrical Engineering
BS, Chemistry & Philosophy
2007-2010
University of Wisconsin-Madison
Madison, WI
Honors in the Major, Graduated with Distinction, Dean's List (4 yrs)
Certificate, Computer Science
2009-2010
University of Wisconsin-Madison
Madison, WI
Supplementary Online Courses
Coursera: Neural Networks and Deep Learning, Probabilistic Graphical Models, Deep Learning (Hyperparameter Tuning, Regularization, Optimization), Structuring Machine Learning Projects
KodeKloud: Kubernetes Administrator, Kubernetes Developer

Experience

Full-Stack Software Engineer
2021-present
Just-Evotec Biologics (Seattle, WA)
Seattle, WA
  • Engineered serverless computing infrastructure and data pipelines optimizing antibody discovery processes using yeast and phage-display technologies.
  • Developed full-stack solutions for real-time data visualization, browsing, and pipeline executions, integrating LIMS databases with REST and GraphQL APIs.
  • Automated bioinformatics pipelines for next-generation and long-read sequencing, enhancing data processing efficiency and accuracy. Reduced NGS pipeline computation time from days to less than 1 hour.
PhD Graduate Researcher
2014-2021
University of Washington
Seattle, WA
Lab of Eric Klavins, Dept. of Electrical Engineering
  • Designed CRISPR tools and biosensors for yeast and mammalian cells; built largest published genetic circuits (circa 2017) in eukaryotes.
  • Developed mathematical models and simulations of cell behaviors.
  • Developed deep reinforcement learning algorithms for genetic circuit design, using graph neural networks for cell state modeling from RNA-seq data.
PhD Graduate Researcher - DARPA
2019-2021
DARPA - Synergistic Design and Discovery (SD2)
Seattle, WA
  • Led cell manufacturing, innovating software to optimize lab steps for strain construction; achieved significant throughput increases and cost reductions.
  • Constructed over 400 genetically engineered yeast strains, integrating software with cloud labs to streamline operations. 5-fold increase in strain construction throughput & 4-fold reduction in material and labor costs.
  • Captured laboratory metadata and performed simulations and analysess to estimate lead-time and costs for stake holders.
  • Facilitated cross-functional collaborations to enhance generation of AI-ready biological datasets.
Co-Founder and Software Lead
2019-2021
Global Impact (OLASimple)
Seattle, WA
cofounded non-profit company to develop assays easy to detect HIV drug-resistence
  • Spearheaded technical direction and authored software for tablet application for automated user-guidance. Utilizes image processing and digital lab protocol generation.
  • Secured NSF iCorp grant and led user testing and diagnostic and software validation in Kenya and Mexico.
Amazon Catalyst Fellow
2017-2018
University of Washington
Seattle, WA
Developed digitally guided workflows for designing mammalian cell lines and experimental assays..
Workflow Developer and Consultant
2016-2017
University of Washington
Seattle, WA
UW-Biofab
  • Founding member of UW-BIOFAB, creating software to guide lab techs through molecular cloning, yeast strain construction, and mammalian cell culturing
  • Consulted team on scientific validity of experiments and procedure.
Research Assistant
2011-2014
University of Colorado-Denver
Aurora, CO
Lab of Chandra Tucker
Invented light-inducible gene expression systems and developed software for optogenetic control, contributing to enhanced cellular manipulation techniques.
Research Assistant
2008-2011
University of Wisconsin-Madison
Madison, WI
Lab of David C Schwartz, Department of Chemistry and Genetics
Performed data analysis on high-throughput genomic mapping data, utilizing university computing clusters for data-intensive operations.
Research Intern
2010-2011
University of Wisconsin-Madison
Madison, WI
Lab of Brian Pfleger, Dept. of Chemical and Biological Engineering
Developed a recombination-based genetic circuit in E. coli for detecting sequential environmental inputs and a bacterial peptide delivery system for probiotic therapy
Undergraduate Research Scholar
2008-2009
University of Wisconsin-Madison
Madison, WI
Lab of Lingjun Li, Dept. of Chemistry
Used MALDI TOF/TOF mass spectrometry to analyze peptide-level responses to environmental stress in crustaceans.
Undergraduate Researcher
2007-2008
University of Wisconsin-Madison
Madison, WI
Lab of Mark Brownfield, School of Veterinary Medicine
Used immunohistochemistry to identify location of serotonin receptor variants in rat brain and adrenal glands.

Publications (14)

>1000 citations, h-index 12
Robustness and reproducibility of simple and complex synthetic logic circuit designs using a DBTL loop
Cummins B, Vrana J, Moseley RC, Eramian H, Deckard A, Fontanarrosa P, Bryce D, Weston M, Zheng G, Nowak J,
Synthetic Biology, 2023
Implementation of an interactive mobile application to pilot a rapid assay to detect HIV drug resistance mutations in Kenya
Vrana JD, Panpradist N, Higa N, Ko D, Ruth P, Kanthula R, Lai JJ, Yang Y, Sakr SR, Chohan B,
PLOS Global Public Health, 2022
Highly-automated, high-throughput replication of yeast-based logic circuit design assessments
Goldman RP, Moseley R, Roehner N, Cummins B, Vrana JD, Clowers KJ, Bryce D, Beal J, DeHaven M, Nowak J,
Synthetic Biology, 2022
Computational prediction of synthetic circuit function across growth conditions
Cummins B, Moseley RC, Deckard A, Weston M, Zheng G, Bryce D, Nowak J, Gameiro M, Gedeon T, Mischaikow K,
bioRxiv, 2022
Aquarium: open-source laboratory software for design, execution and data management
Vrana J, de Lange O, Yang Y, Newman G, Saleem A, Miller A, Cordray C, Halabiya S, Parks M, Lopez E,
Synthetic Biology, 2021
Simpler and faster Covid-19 testing: Strategies to streamline SARS-CoV-2 molecular assays
Panpradist N, Wang Q, Ruth PS, Kotnik JH, Oreskovic AK, Miller A, Stewart SW, Vrana J, Han PD, Beck IA,
EBioMedicine, 2021
OLA-Simple: A software-guided HIV-1 drug resistance test for low-resource laboratories
Panpradist N, Beck IA, Vrana J, Higa N, McIntyre D, Ruth PS, So I, Kline EC, Kanthula R, Wong-On-Wing A,
EBioMedicine, 2019
Digital logic circuits in yeast with CRISPR-dCas9 NOR gates
Gander MW, Vrana JD, Voje WE, Carothers JM, Klavins E,
Nature communications, 2017
Peripheral nervous system defects in a mouse model for peroxisomal biogenesis disorders
Hanson MG, Fregoso VL, Vrana JD, Tucker CL, Niswander LA,
Developmental biology, 2014
An optimized optogenetic clustering tool for probing protein interaction and function
Taslimi A, Vrana JD, Chen D, Borinskaya S, Mayer BJ, Kennedy MJ, Tucker CL,
Nature communications, 2014
Benchmarking of optical dimerizer systems
Pathak GP, Strickland D, Vrana JD, Tucker CL,
ACS synthetic biology, 2014
Optogenetic control of cell function using engineered photoreceptors
Pathak GP, Vrana JD, Tucker CL,
Biology of the Cell, 2013
Rapid profiling of disease alleles using a tunable reporter of protein misfolding
Pittman AM, Lage MD, Poltoratsky V, Vrana JD, Paiardini A, Roncador A, Cellini B, Hughes RM, Tucker CL,
Genetics, 2012
Light-dependent, Dark-promoted Interaction between Arabidopsis Cryptochrome 1 and Phytochrome B Proteins
Hughes RM, Vrana JD, Song J, Tucker CL,
Journal of Biological Chemistry, 2012

Conferences, Talks, & Book Chapters

Software systems for automated manufacturing of engineered organisms
Vrana J,
(PhD Dissertation) University of Washington, 2021
Aquarium: the laboratory operating system (Version v2. 5.0)
Keller B, Vrana J, Miller A, Newman G, Klavins E,
(open-source software) Zenodo, 2019
Aquarium: a laboratory operating system for reproducible experimental design and execution
Vrana J, Strickland D, Keller B, Lopez E, Halabiya S, Corday C, Klavins E,
(conference) SIMB Annual Meeting and Exhibition 2019, 2019
Design and Characterization of Orthogonal Pol II gRNA Expression Systems for dCas9 Transcriptional Repression Networks in S. Cerevisiae
Voje W, Gander MW, Vrana J, Klavins E, Carothers J,
(conference) 2017 AIChE Annual Meeting, 2017
Tools for controlling protein interactions using light
Tucker CL, Vrana JD, Kennedy MJ,
(book chapter) Current Protocols in Cell Biology, 2014
Optical control of protein-protein interactions to modulate cellular function
Taslimi A, Pathak G, Vrana JD, Tucker CL,
(conference) CLEO: 2013, 2013

Awards

I-Corp Grant
2018
National Science Foundation (NSF)
$100K Amazon Catalyst Grant
2017
Amazon & UW CoMotion
Best Idea with Global Reach
2018
Foster School of Business, University of Washington
Final 16 Business Plan Competition
2018
Foster School of Business, University of Washington
1st Place, CNS Sandbox Competition
2015
Foster School of Business, University of Washington
Gold Award
2010
iGEM
William F. Vilas Grant
2007-2010
Anthony Delorenzo Grant
2007-2011