Hello and welcome to my website! My name is Nolan Nichols, and I'm a seasoned bioinformatics professional with a background in software engineering, data science, computational biology. Over the years, I've worked in various capacities, from academia to industry-leading biotech companies. I'm passionate about leveraging my expertise to design and implement innovative solutions that accelerate biomedical research and help unlock the secrets of human genetics and brain development.
My particular interest lies in the future of large language models, AI, and knowledge graphs with their combined potential to drive progress in biomedical research and uncover the secrets of human genetics and brain development. I am committed to leveraging my expertise to design and implement state-of-the-art solutions that contribute to advancements in the biotech industry.
Education
Bachelor of Arts in Psychology
Lewis and Clark College | Portland, OR | 2003 – 2005
Ph.D., Biomedical and Health Informatics
University of Washington | Seattle, WA | 2009 – 2014
Professional Experience
Associate Director of Platform Engineering
Maze Therapeutics | South San Francisco, CA | March 2023 – Present
- Currently leading a talented team of data engineers and DevOps professionals to develop cutting-edge data strategies and platforms.
- Designed and implemented a data lake and knowledge graph for clinico-genomic datasets with powerful analytics interfaces.
- Developed a data science platform for computational biology analyses, incorporating containerized workflows and literate programming.
Senior Software Engineer
Maze Therapeutics | South San Francisco, CA | November 2019 – February 2023
- Established the enterprise cloud architecture based on AWS best practices.
- Implemented GitOps strategies using tools such as GitHub, Terraform, Kubernetes/Helm, and ArgoCD.
Bioinformatics Software Engineer III
Genentech | South San Francisco, CA | August 2019 – November 2019
- Designed metadata standards and implemented a data portal for analysis ready, multi-omics datasets from clinical trials patients.
Bioinformatics Software Engineer II
Genentech | South San Francisco, CA | January 2017 – July 2019
- Designed and implemented study access controls, user interfaces, and data release processes for a large-scale clinical genomics database of clinical trials patients with whole genome sequencing.
- Developed a platform supporting reproducible science by unobtrusively capturing data, code, provenance, and metadata for computational biology workflows.
Postdoctoral Fellow
Department of Psychiatry and Behavioral Sciences, Stanford University | Palo Alto,
CA
Center for Health Sciences, SRI International | Menlo Park, CA\
January 2015 – October 2016
- Worked collaboratively with an interdisciplinary team of biomedical scientists to design and implement an informatics framework to streamline brain research on adolescent development.
- Designed, developed, and provided ongoing user-driven improvement for data integration software for a large study on adolescent brain development.
- Applied the principles developed during the NCANDA study to guide the informatics of a 10,000 subject study on adolescent brain development.
Predoctoral Fellow
Biomedical and Health Informatics, University of Washington | Seattle, WA\ September 2009 – December 2014
- Co-founded, designed, and collaboratively managed the development of an open data exchange standard to harmonize and integrate brain data repositories using semantic technology.
- Developed a distributed computing framework to track data provenance in brain imaging workflows using the NIDM data exchange standard based on the PROV ontology.
- Extended the Foundational Model of Anatomy (FMA) ontology with a knowledge representation approach to capture white matter connectivity in the human brain.
Clinical Data Manager
CCBR-Synarc | San Francisco, CA | May 2008 – June 2009
- Managed medical imaging data and case report form information using SQL for over 10 stage II and III neurology and oncology clinical trials.
- Developed and implemented data transfer specifications to/from pharmaceutical information systems.
- Gathered requirements from Operations to design and implement data quality tools using SQL and MS Access.
Research Analyst
Department of Psychiatry and Behavioral Sciences, Stanford University | Palo Alto, CA\ Center for Health Sciences, SRI International | Menlo Park, CA | October 2006 – May 2008
- Acquired anatomical and functional MRI data from clinical populations and administered a 10-hour battery of standardized neuropsychological tests.
- Developed and managed a database for cognitive measures, IRB documentation, and imaging metadata.
Data Analyst
Herbert and Louis, LLC | Wilsonville, OR | December 2005 – July 2006
- Conducted qualitative analysis of survey data and reported results on the prevalence of gambling in the state of Oregon and demographics of dually diagnosed homeless persons in Portland.