Author
University of WashingtonORCID 0000-0002-9135-0844Unclaimed ORCID profile · follow to get notified of new preprints
8 papers
Recent·Most cited
Kyle Medley, Jenna L. Persons, Tathagata Biswas…·Nicolas Rohner
This study uses metabolomics to compare long- and short-term fasting responses in cave-dwelling and surface-dwelling Mexican tetra, identifying metabolic differences linked to resilience and longevity.
Kyle Medley, Joseph Hellerstein, Herbert M. Sauro
The paper introduces libsbmljs, a JavaScript/WebAssembly library for handling SBML models in web environments, enabling browser-based tools and simulations without server-side processing.
Kyle Medley, Shaik Asifullah, Joseph Hellerstein, Herbert M. Sauro
The paper introduces an asynchronous, generalized island method for accelerating biochemical kinetic model fitting, achieving super-linear speedups and improved fit quality.
Yosef Bedaso, Frank Bergmann, Kiri Choi…·Herbert M. Sauro
The paper introduces a portable software library, libStructural, for structural analysis of reaction networks, supporting conservation analysis, flux dependency analysis, and elementary modes enumeration.
Kyle Medley, Kiri Choi, Matthias König…·Herbert M. Sauro
Tellurium Notebook enables reproducible and reusable dynamical models in systems biology by integrating community standards and literate coding practices.
Kiri Choi, J. Kyle Medley, Caroline Cannistra…·Herbert M. Sauro
Tellurium provides a Python-based platform for systems biology modeling, simulation, and reproducibility using SBML and other standards.
J Kyle Medley, Kiri Choi, Herbert M Sauro
This paper introduces libSBNW, a library for generating and editing SBML layout information, with C and Python APIs and open-source availability.
Caroline Cannistra, Kyle Medley, Herbert M. Sauro
SimpleSBML simplifies SBML model creation and editing in Python by providing one-command operations for adding model elements and supporting SBML levels 2 and 3.