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R01 GM081070

Funded outputs count: 29
Funder award ID: R01 GM081070
OpenAlex ID: G798009823
Recent advances in biomedical simulations: a manifesto for model engineering
2019 · Joseph L. Hellerstein, Stanley Gu, et al. · F1000Research · 20
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Tellurium: An extensible python-based modeling environment for systems and synthetic biology
2018 · Kiri Choi, J. Kyle Medley, et al. · Biosystems · 164
Inferring Reaction Networks using Perturbation Data
2018 · Kiri Choi, Joesph Hellerstein, et al. · bioRxiv (Cold Spring Harbor Laboratory) · 4
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A Portable Structural Analysis Library for Reaction Networks
2018 · Yosef Bedaso, Frank T. Bergmann, et al. · Biosystems · 4
Synthetic Biology: Engineering Living Systems from Biophysical Principles
2017 · Bryan A. Bartley, Kyung Kim, et al. · Biophysical Journal · 39
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Control and regulation of pathways via negative feedback
2017 · Herbert M. Sauro · Journal of The Royal Society Interface · 51
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Engineering Living Systems: Closing the Loop in the Design-Build-Test Cycle using the Semantic Web
2017 · Bryan Bartley · ResearchWorks at the University of Washington (University of Washington)
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SED-ML web tools: generate, modify and export standard-compliant simulation studies
2016 · Frank T Bergmann, David Nickerson, et al. · Bioinformatics · 9
phraSED-ML: A paraphrased, human-readable adaptation of SED-ML
2016 · Kiri Choi, Lucian P. Smith, et al. · Journal of Bioinformatics and Computational Biology · 13
Editorial Reproducibility of Computational Models
2016 · A. Erdemir, H. M. Sauro · IEEE Transactions on Biomedical Engineering · 2
Guidelines for Reproducibly Building and Simulating Systems Biology Models
2016 · J. Kyle Medley, Arthur P. Goldberg, et al. · IEEE Transactions on Biomedical Engineering · 29
A portable library to support the SBML Layout Extension
2016 · J Kyle Medley, Kiri Choi, et al. · bioRxiv (Cold Spring Harbor Laboratory) · 1
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SimpleSBML: A Python package for creating and editing SBML models
2015 · Caroline Cannistra, Kyle Medley, et al. · bioRxiv (Cold Spring Harbor Laboratory) · 6
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libRoadRunner: a high performance SBML simulation and analysis library
2015 · Endre T. Somogyi, Jean-Marie Bouteiller, et al. · Bioinformatics · 150
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COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project
2014 · Frank T Bergmann, Richard Adams, et al. · BMC Bioinformatics · 170
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A Reappraisal of How to Build Modular, Reusable Models of Biological Systems
2014 · Maxwell L. Neal, Michael T. Cooling, et al. · PLoS Computational Biology · 49
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SBML and CellML translation in Antimony and JSim
2013 · Lucian P. Smith, Erik Butterworth, et al. · Bioinformatics · 18
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A C library for retrieving specific reactions from the BioModels database
2013 · M. L. Neal, M. Galdzicki, et al. · Bioinformatics · 6
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Computational tools for metabolic engineering
2012 · Wilbert B. Copeland, Bryan A. Bartley, et al. · Metabolic Engineering · 98
A case of unrecognized maternal PTH resistance and severe impact on neonatal bone mineralisation
2012 · Subash Sivaraman, R.V. Rao, et al.
Minimum Information About a Simulation Experiment (MIASE)
2011 · Dagmar Waltemath, Richard Adams, et al. · PLoS Computational Biology · 168
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SBML2TikZ: supporting the SBML render extension in LaTeX
2010 · Si Yuan Shen, Frank Bergmann, et al. · Bioinformatics · 8
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Computer-aided design of biological circuits using tinkercell
2010 · Deepak Chandran, Frank T. Bergmann, et al. · Bioengineered Bugs · 36
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Antimony: a modular model definition language
2009 · Lucian P. Smith, Frank T. Bergmann, et al. · Bioinformatics · 129
TinkerCell: modular CAD tool for synthetic biology
2009 · Deepak Chandran, Frank T Bergmann, et al. · Journal of Biological Engineering · 186
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