Staff Profiles

Ryan Spangler, M.S.

Machine Learning Engineer

Ryan is currently working as a Machine Learning Engineer in the Modeling team at the Allen Institute for Cell Science. He was previously at the Stanford School for Bioengineering as a Software Engineer in Markus Covert’s lab helping to build and design a whole-cell simulation of E. coli, and other biological systems. He graduated from Portland State University with a Masters in Systems Science where he studied Information Theory, Systems Dynamics and Computational Neuroscience. Ryan is looking forward to making discoveries in the realm of biological systems.


Research Interests

Ryan is focused on deriving the fundamental principles of living systems. To achieve this end, he draws from inspiration across fields and disciplines: Biology, Computer Science, Mathematics, Philosophy, Systems Science, Game Design and Physics. Ryan works on various modeling, simulation and deep learning projects throughout the Institute, as well as guiding decisions about computational infrastructure and distributed computing. 


  • Systems Science
  • Biological Modeling
  • Simulation Engine Design
  • Computational Architecture

Research Programs

  • Nuclear Morphogenesis

Selected Publications

A Multi-Scale Approach to Modeling E. coli Chemotaxis

September 29, 2020

Agmon E, Spangler RK

Simultaneous cross-evaluation of heterogeneous E. coli datasets via mechanistic simulation

July 24, 2020

Macklin DN, Ahn-Horst TA, Choi H, Ruggero NA, Carrera J, Mason JC, Sun G, Agmon E, DeFelice MM, Maayan I, Lane K, Spangler RK, Gillies TE, Paull ML, Akhter S, Bray SR, Weaver DS, Keseler IM, Karp PD, Morrison JH, Covert MW