# Ryan Nelson > Software Engineer Location: Somerville, Massachusetts, United States Profile: https://flows.cv/ryannelson I'm a prolific creator and budding computational biologist with an optimistic view of the future. I speak right-brain and left-brain and am currently tackling challenging computational problems in protein design. ## Work Experience ### Software Engineer III, Scientific Computing & Orchestration @ Generate:Biomedicines Jan 2025 – Present | Somerville, Massachusetts, United States ### Software Engineer II, Scientific Computing & Orchestration @ Generate:Biomedicines Jan 2025 – Jan 2025 | Somerville, Massachusetts, United States ### Software Engineer II, Machine Learning Operations @ Generate:Biomedicines Jan 2024 – Jan 2024 | Somerville, Massachusetts, United States ### Bioinformatics Engineer I, Machine Learning Operations @ Generate:Biomedicines Jan 2024 – Jan 2024 | Somerville, Massachusetts, United States ### Bioinformatics Engineer I, Computational Protein Generation @ Generate:Biomedicines Jan 2022 – Jan 2024 | Somerville, Massachusetts, United States ### Graduate Researcher, Hiller Lab @ Carnegie Mellon University Jan 2021 – Jan 2022 | Pittsburgh, PA - Worked with research scientists in the Hiller Lab to document the complex, multi-step wet-lab protocol used to isolate prokaryotic extracellular vesicles (EV) from Streptococcus pneumoniae - Designed novel experimental protocols for shifting EV purification and validation steps to a remote, automated lab facility (Emerald Cloud Lab) while also updating protocols to reduce manual labor and accommodate changes in equipment - Managed all steps of the project to date, bringing the project from an idea to the point at which experiments can be run on samples ### Data Science Intern @ Zymergen Jan 2021 – Jan 2021 | Remote - Analyzed model performance and developed alternative models to leverage untapped data sources to improve the prediction of fermentation yield from high-throughput screening (HTS) data - Created python module to generate time series datasets and performance metrics from strain engineering data captured over a program's lifecycle and used it to analyze production ML models - Studied how different QC threshold values impacted the data normalization model for a strain engineering program and presented recommendations to the scientific team - Introduced novel approaches to predicting yield in strain engineering programs, including models leveraging Active Learning / Bayesian Optimization and hierarchical clustering - Interfaced with LIMS to extract experiment results - Used advanced data visualization techniques like swarm plots and ridgeline plots to communicate results to lab scientists - Mentored high school student from the SMASH Rising Scholar-Intern program in their summer internship at Zymergen ### Senior Data Engineer @ Target Jan 2019 – Jan 2020 | Greater Minneapolis-St. Paul Area - Led the modernization of team’s tech stack and data pipeline patterns for migration to Hadoop 3 and Spark, collaborating across functional groups to define standards and clear roadblocks - Wrote high throughput data pipelines and unit tests using Spark Scala - Researched and internally published a series of data-driven performance tuning guides for Spark Scala - Contributed novel Scala classes to Target's Data Engineering Group to handle common design patterns (Spark session generator for multiple build environments, wrapper for Scallop to allow unit testing, wrapper for parsing/validation of config files) ### Data Engineer @ Target Jan 2018 – Jan 2019 | Greater Minneapolis-St. Paul Area - Developed and supported data pipelines using Bash, SQL, and Hadoop stack (Hive, Oozie, Sqoop) to ingest and process over 10 billion records (2 TB) per day into Hadoop and Hive via a Kubernetes cluster - Built and maintained all DevOps components for my team (GitHub, Drone CI, Jenkins) - Created and taught a Bash training course required for all engineers in the Data Engineering Group - Collaborated on a multicultural team, evenly divided between India and the United States - Invented a breakthrough diagramming system to communicate complex pipelines designs to product owners and engineering managers ### Implementation Consultant Intern @ Fast Enterprises, LLC Jan 2017 – Jan 2017 | Lakewood, CO - Leveraged company VB.NET codebase to generate registration cards for the State of Colorado - Significantly reduced database reads for registrations by utilizing shared objects over individual queries ### Town Architect @ Las Catalinas, Costa Rica Jan 2014 – Jan 2015 | Guanacaste, Costa Rica - Managed the planning and urban design for all current and future phases of the 1200-acre development - Communicated design strategies between civil engineering, management, and architecture groups - Created in-field solutions for projects under construction and improvements to completed parts of town. - Authored documents and systems to improve the development process. - Guided the design of all buildings as the leading member of the Architectural Review Committee. ### Architectural Designer @ Union Studio Architecture & Community Design Jan 2013 – Jan 2014 | Providence, Rhode Island ### Architectural Intern @ Krier Kohl Architects Jan 2012 – Jan 2012 | Berlin, Germany ### Teaching Assistant (Freshman Graphics II - Drafting) @ University of Notre Dame Jan 2012 – Jan 2012 | Notre Dame, Indiana ### Summer Fellow @ Duany Plater-Zyberk & Company Jan 2011 – Jan 2011 | Miami, FL ### Summer Intern @ EAPC Architects Engineers Jan 2009 – Jan 2009 ## Education ### Master's degree in Computational Biology Carnegie Mellon University ### (non-degree) in Mathematics University of North Dakota ### Bachelor’s Degree in Computer Science North Dakota State University ### Bachelor of Architecture (BArch) in Architecture & Urban Design University of Notre Dame ### High School Diploma Saint Mary's Central High School ## Contact & Social - LinkedIn: https://linkedin.com/in/ryan-nelson-b335933a --- Source: https://flows.cv/ryannelson JSON Resume: https://flows.cv/ryannelson/resume.json Last updated: 2026-03-31