Author

Kyle Medley

University of WashingtonORCID 0000-0002-9135-0844Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Approach:experimental assay· 6 Research Focus:software / tool· 6 Research Focus:benchmarking· 3 Approach:statistical model· 2 Assay:metabolomics· 1 Research Focus:variant calling· 1 Research Focus:variant effect prediction· 1

Frequent Co-Authors

Herbert M. SauroiD· 7 shared Kiri ChoiiD· 4 shared Caroline Cannistra· 2 shared Joseph Hellerstein· 2 shared Frank BergmanniD· 1 shared Jaya KrishnaniD· 1 shared Jenna L. PersonsiD· 1 shared Joseph L. HellersteiniD· 1 shared

Activity by Year

2015-2022 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 15 mutual co-author links

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7 shared papersSystems Biology

Herbert M. SauroORCID

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Author profile →

8 papers

Recent·Most cited

Resilience in a Natural Model of Metabolic Dysfunction Through Changes in Longevity and Ageing-Related Metabolites

Kyle Medley, Jenna L. Persons, Tathagata Biswas, Luke A. Olsen, Robert Peuß, Jaya Krishnan, Shaolei Xiong, 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.

eLife · May 20, 2022Peer-reviewedSystems Biology

libsbmljs - Enabling Web--Based SBML Tools

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.

Biosystems · Apr 24, 2020Peer-reviewedSystems Biology

Accelerated Biochemical Kinetic Model Fitting via the Asynchronous, Generalized Island Method

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.

bioRxiv · Oct 6, 2019 · PreprintSystems Biology

A Portable Structural Analysis Library for Reaction Networks

Yosef Bedaso, Frank Bergmann, Kiri Choi, Kyle Medley, 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.

Biosystems · Jul 1, 2018Peer-reviewedSystems Biology

Tellurium Notebooks - An Environment for Dynamical Model Development, Reproducibility, and Reuse

Kyle Medley, Kiri Choi, Matthias König, Lucian P. Smith, Stanley Gu, Joseph L. Hellerstein, Stuart C. Sealfon, Herbert M. Sauro

Tellurium Notebook enables reproducible and reusable dynamical models in systems biology by integrating community standards and literate coding practices.

PLoS Computational Biology · Jun 15, 2018Peer-reviewedSystems Biology

Tellurium: A Python Based Modeling and Reproducibility Platform for Systems Biology

Kiri Choi, J. Kyle Medley, Caroline Cannistra, Matthias König, Lucian Smith, Kaylene Stocking, Herbert M. Sauro

Tellurium provides a Python-based platform for systems biology modeling, simulation, and reproducibility using SBML and other standards.

bioRxiv · Jun 2, 2016 · PreprintSystems Biology

A portable library to support the SBML Layout Extension

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.

bioRxiv · Jan 5, 2016 · PreprintSystems Biology

SimpleSBML: A Python package for creating and editing SBML models

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.

bioRxiv · Oct 30, 2015 · PreprintSystems Biology