Profile Picture

Amy Glen

Research Scientist, Knowledge Graphs at Phenome Health

Ph.D. in Computer Science

knowledge graphs
bioinformatics
data engineering
graph algorithms
data integration

I'm a computer scientist working on tools to help make better use of biomedical data. In particular, my research focuses on biomedical knowledge graphs—building them, serving them, and reasoning across them.

I currently lead knowledge graph development at Phenome Health as a Research Scientist, where I'm designing and driving efforts to integrate and serve a large-scale biomedical knowledge graph to support genomic and phenomic analysis.

Before that, I spent six years on the NIH's NCATS Biomedical Data Translator project, serving as an architect and primary technical lead for our team's biomedical knowledge graph and reasoning engine at Oregon State University.

Earlier in my career, I worked in industry on knowledge management projects in the life sciences, in roles ranging from analyst to product manager to software engineer. I've co-founded companies focused on enhancing biomedical literature search tools with integrated clinical trial information and providing evidence-focused competitive intelligence for digital therapeutics.

Beyond my professional work, I'm honored to be a member of the University of Vermont Athletic Hall of Fame for my achievements in cross-country skiing, including a national collegiate championship.

Ph.D. Computer Science Oregon State University 2020 - 2024
B.A. Biology University of Vermont 2009 - 2012

Highlighted works

Experience

knowledge graphs
bioinformatics
data engineering
graph algorithms
data integration
2014 2015 2016 2017 2018 2019 2020 2021 2022 2023 2024 2025
Research Scientist, Knowledge Graphs
Phenome Health
Co-founder, Principal, Engineering & Product
PloverAI
VP of Product, Co-founder
Chief Technology & Product Officer, Co-founder
DTxIntelligence
Postbaccalaureate Researcher
Analyst Programmer
Graduate Researcher/Fellow
Postdoctoral Scholar
Oregon State University
Scientific Writer
Cardiovascular Product Manager
cvPipeline
Intern
Analyst
VR Analytical
See my CV for more details.

Publications

2025 PloverDB: A high-performance platform for serving biomedical knowledge graphs as standards-compliant web APIs
A. K. Glen, E. W. Deutsch, S. A. Ramsey
Bioinformatics
2024 Generating biomedical knowledge graphs from knowledge bases, registries, and multiomic data
G. Qin, K. Narsinh, Q. Wei, J. C. Roach, A. Joshi, S. L. Goetz, S. T. Moxon, M. H. Brush, C. Xu, Y. Yao, A. K. Glen, E. D. Morris, A. Ralevski, R. Roper, B. Belhu, Y. Zhang, I. Shmulevich, J. Hadlock, and G. Glusman
bioRxiv
2024 MicrobiomeKG: Bridging microbiome research and host health through knowledge graphs
S. L. Goetz, A. K. Glen, and G. Glusman
bioRxiv
2024 Computational methods for integrating and querying biomedical knowledge to facilitate translational science
A. K. Glen. Ph.D. dissertation. Embargoed for publication until September 2025.
Oregon State University
2023 ARAX: A graph-based modular reasoning tool for translational biomedicine
A. K. Glen*, C. Ma*, L. Mendoza, F. Womack, E. C. Wood, M. Sinha, L. Acevedo, L. G. Kvarfordt, R. C. Peene, S. Liu, A. S. Hoffman, J. C. Roach, E. W. Deutsch*, S. A. Ramsey*, and D. Koslicki*
Bioinformatics
2022 RTX-KG2: A system for building a semantically standardized knowledge graph for translational biomedicine
E. C. Wood*, A. K. Glen*, L. G. Kvarfordt, F. Womack, L. Acevedo, T. S. Yoon, C. Ma, V. Flores, M. Sinha, Y. Chodpathumwan, A. Termehchy, J. C. Roach, L. Mendoza, A. S. Hoffman, E. W. Deutsch, D. Koslicki, and S. A. Ramsey
BMC Bioinformatics
2022 Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science
D. R. Unni, S. A. T. Moxon, M. Bada, M. Brush, R. Bruskiewich, J. H. Caufield, P. A. Clemons, V. Dancik, M. Dumontier, K. Fecho, G. Glusman, J. J. Hadlock, N. L. Harris, A. Joshi, T. Putman, G. Qin, S. A. Ramsey, K. A. Shefchek, H. Solbrig, K. Soman, A. E. Thessen, M. A. Haendel, C. Bizon, C. J. Mungall, and The Biomedical Data Translator Consortium
Clinical and Translational Science
2022 Progress toward a universal biomedical data translator
K. Fecho, A. E. Thessen, S. E. Baranzini, C. Bizon, J. J. Hadlock, S. Huang, R. T. Roper, N. Southall, C. Ta, P. B. Watkins, M. D. Williams, H. Xu, W. Byrd, V. Dančík, M. P. Duby, M. Dumontier, G. Glusman, N. L. Harris, E. W. Hinderer, G. Hyde, A. Johs, A. I. Su, G. Qin, Q. Zhu, and The Biomedical Data Translator Consortium
Clinical and Translational Science
2021 Structural generalizability: The case of similarity search
Y. Chodpathumwan, A. Termehchy, S. A. Ramsey, A. Shrestha, A. Glen, and Z. Liu
ACM SIGMOD
* These authors contributed equally to the work.

Beyond work

I grew up in Anchorage, Alaska, and have always enjoyed spending time outdoors. In my earlier years, I competed as a professional cross-country skier. These days, I still ski, though mostly downhill, and I'm also a big fan of mountain biking.

I live in the Oregon Cascades with a few too many animals (see below), who never fail to keep things interesting.

NCAA Skiing Championships, Bozeman, MT, 2012.
Whistler, BC, 2023.
Burlington, VT, 2023.
NCAA Skiing Championships, Bozeman, MT, 2012.
Oakridge, OR, 2023.
Mt. Bachelor, OR, 2022.
Dead Mountain, OR, 2023.
Oakridge, OR, 2024.