Controlling E. coli Gene Expression Noise. - Kyung Hyuk Kim; Kiri Choi; Bryan Bartley; Herbert M. Sauro (IEEE Trans. Biomed. Circuits Syst., 2015)

phraSED-ML: A paraphrased, human-readable adaptation of SED-ML. - Kiri Choi; Lucian P. Smith; J. Kyle Medley; Herbert M. Sauro (J. Bioinform. Comput. Biol., 2016)

Synthetic Biology Open Language (SBOL) Version 2.1.0. - Jacob Beal; Robert Sidney Cox III; Raik Grünberg; James Alastair McLaughlin; Tramy Nguyen; Bryan Bartley; Michael Bissell; Kiri Choi; Kevin Clancy; Chris Macklin; Curtis Madsen; Goksel Misirli; et al. (J. Integr. Bioinform., 2016)

A portable structural analysis library for reaction networks. - Yosef Bedaso; Frank T. Bergmann; Kiri Choi; Kyle Medley; Herbert M. Sauro (Biosyst., 2018)

Tellurium: An extensible python-based modeling environment for systems and synthetic biology. - Kiri Choi; J. Kyle Medley; Matthias König 003; Kaylene Stocking; Lucian P. Smith; Stanley Gu; Herbert M. Sauro (Biosyst., 2018)

Synthetic Biology Open Language (SBOL) Version 2.2.0. - Robert Sidney Cox III; Curtis Madsen; James Alastair McLaughlin; Tramy Nguyen; Nicholas Roehner; Bryan Bartley; Jacob Beal; Michael Bissell; Kiri Choi; Kevin Clancy; Raik Grünberg; Chris Macklin; et al. (J. Integr. Bioinform., 2018)

Tellurium notebooks - An environment for reproducible dynamical modeling in systems biology. - J. Kyle Medley; Kiri Choi; Matthias König 003; Lucian P. Smith; Stanley Gu; Joseph L. Hellerstein; Stuart C. Sealfon; Herbert M. Sauro (PLoS Comput. Biol., 2018)

Synthetic Biology Open Language (SBOL) Version 2.3. - Curtis Madsen; Ángel Goñi-Moreno; Umesh P; Zachary Palchick; Nicholas Roehner; Christian Atallah; Bryan Bartley; Kiri Choi; Robert Sidney Cox III; Thomas E. Gorochowski; Raik Grünberg; Chris Macklin; et al. (J. Integr. Bioinform., 2019)

BioSimulators: a central registry of simulation engines and services for recommending specific tools. - Bilal Shaikh; Lucian P. Smith; Dan Vasilescu; Gnaneswara Marupilla; Michael Wilson; Eran Agmon; Henry Agnew; Steven S. Andrews; Azraf Anwar; Moritz E. Beber; Frank T. Bergmann; David Brooks 006; et al. (CoRR, 2022)

BioSimulators: a central registry of simulation engines and services for recommending specific tools. - Bilal Shaikh; Lucian P. Smith; Dan Vasilescu; Gnaneswara Marupilla; Michael Wilson; Eran Agmon; Henry Agnew; Steven S. Andrews; Azraf Anwar; Moritz E. Beber; Frank T. Bergmann; David Brooks 006; et al. (Nucleic Acids Res., 2022)

Neural Information Processing and Computations of Two-Input Synapses. - Soon Ho Kim; Junhyuk Woo; Kiri Choi; Moo Young Choi; Kyungreem Han (Neural Comput., 2022)

libRoadRunner 2.0: a high performance SBML simulation and analysis library. - Ciaran M. Welsh; Jin Xu; Lucian P. Smith; Matthias König 003; Kiri Choi; Herbert M. Sauro (Bioinform., 2023)

Polymer Physics-Based Classification of Neurons. - Kiri Choi; Won Kyu Kim; Changbong Hyeon (Neuroinformatics, 2023)