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Publications

* indicates equal contribution

K. Choi, W.K. Kim, C. Hyeon. In Press. “Unveiling the Odor Representation in the Inner Brain of Drosophila through Compressed Sensing.” 10.1101/2023.07.19.549810.

W.K. Kim, K. Choi, C. Hyeon, S.J. Jang. 2023. “General Chemical Reaction Network Theory for GPCR-Based Olfactory Sensing: Elucidation of Odorant Mixture Effects and Agonist–Synergist Threshold.” J. Phys. Chem. Lett. 14 (XXX), 8412–8420. 10.1021/acs.jpclett.3c02310.

C. Welsh, J. Xu, L. Smith, M. König, K. Choi, H.M. Sauro. 2023. “libRoadRunner 2.0: A High-Performance SBML Simulation and Analysis Library.” Bioinformatics. 39 (1), btac770. 10.1093/bioinformatics/btac770.

K. Choi, W.K. Kim, C. Hyeon. 2022. “Polymer physics-based classification of neurons.” Neuroinformatics. 21, 177–193. 10.1007/s12021-022-09605-3.

K. Choi, W.K. Kim, C. Hyeon. 2022. “Olfactory responses of Drosophila are encoded in the organization of projection neurons.” eLife. 11, e77748. 10.7554/eLife.77748.

S.H. Kim, J.H. Woo, K. Choi, M.Y. Choi, K. Han. 2022. “Neural information processing and computations of two-input synapses.” Neural Computation. 34 (10), 2102–2131. 10.1162/neco_a_01534.

B. Shaikh, L.P. Smith, D. Vasilescu, G. Marupilla, M. Wilson, E. Agmon, H. Agnew, S.S. Andrews, A. Anwar, M.E. Beber, F.T. Bergmann, D. Brooks, L. Brusch, L. Calzone, K. Choi, …, J.R. Karr. 2022. “BioSimulators: a web-based registry of simulation engines and services for multiscale modeling.” Nucleic Acids Research. 50 (W1), W108–W114. 10.1093/nar/gkac331.

J.H. Woo, K. Choi, S.H. Kim, K. Han, M.Y. Choi. 2022. “The structural aspects of neural dynamics and information flow.” Front Biosci.-Landmark. 27 (1), 15. 10.31083/j.fbl2701015.

J.H. Woo*, K. Choi*, S.H. Kim, K. Han, M.Y. Choi. 2021. “Characterization of multiscale logic operations in the neural circuits.” Front Biosci.-Landmark. 26 (10), 723–739. 10.52586/4983.

K. Choi, J.R. Karr, H.M. Sauro. 2020. “Status and Challenges of Reproducibility in Computational Systems and Synthetic Biology.” In Systems Medicine: Integrative, Qualitative and Computational Approaches. Amsterdam, Netherlands: Elsevier. 3, 406–412. 10.1016/B978-0-12-801238-3.11525-9.

C. Madsen, A.G. Moreno, P. Umesh, Z. Palchick, N. Roehner, C. Atallah, B. Bartley, K. Choi, …, A. Wipat. 2019. “Synthetic Biology Open Language (SBOL) Version 2.3.” J. Integr. Bioinform. 16 (2). 10.1515/jib-2019-0025.

J. Hellerstein, S. Gu, K. Choi, H.M. Sauro. 2019. “Recent Advances in Biomedical Simulations: A Manifesto for Model Engineering.” F1000Research. 8. 10.12688/f1000research.15997.1.

B. Bartley, K. Choi, M. Samineni, Z. Zundel, T. Nguyen, C.J. Myers, H.M. Sauro. 2018. “pySBOL: A Python Package for Genetic Design Automation and Standardization.” ACS Synthetic Biology. 8 (7), 1515–1518. 10.1021/acssynbio.8b00336.

K. Choi. 2018. “Robust approaches to generating reliable predictive models in systems biology.” In Systems Biology. Cham, Switzerland: Springer. 301–312. 10.1007/978-3-319-92967-5_15.

K. Choi, J.K. Medley, M. König, K. Stocking, L. Smith, S. Gu, H.M. Sauro. 2018. “Tellurium: An Extensible Python-based Modeling Environment for Systems and Synthetic Biology.” BioSystems. 171, 74–79. 10.1016/j.biosystems.2018.07.006.

J.K. Medley, K. Choi, M. König, L. Smith, S. Gu, J. Hellerstein, S.C. Sealfon, H.M. Sauro. 2018. “Tellurium Notebooks - An Environment for Dynamical Model Development, Reproducibility, and Reuse.” PLOS Comp. Biol. 14 (6), e1006220. 10.1371/journal.pcbi.1006220.

Y. Bedaso, F.T. Bergmann, K. Choi, J.K. Medley, H.M. Sauro. 2018. “A Portable Structural Analysis Library for Reaction Networks.” BioSystems. 169–170, 20–25. 10.1016/j.biosystems.2018.05.008.

R.S. Cox III, C. Madsen, J.A. McLaughlin, T. Nguyen, N. Roehner, B. Bartley, J. Beal, M. Bissell, K. Choi, …, A. Wipat . 2018. “Synthetic Biology Open Language (SBOL) Version 2.2.0.” J. Integr. Bioinform. 15 (1), 30–132. 10.1515/jib-2018-0001.

J. Beal, R. Cox, R. Grunberg, J. McLaughlin, T. Nguyen, B. Bartley, M. Bissell, K. Choi, …, A. Wipat. 2016. “Synthetic Biology Open Language (SBOL) Version 2.1.0.” J. Integr. Bioinform. 13 (3), 291. 10.1515/jib-2016-291.

K. Choi, L. Smith, J.K. Medley, H.M. Sauro. 2016. “phraSED-ML: A paraphrased, human-readable adaptation of SED-ML.” J. Bioinform. Comput. Biol. 14 (6), 1650035. 10.1142/S0219720016500359.

K.H. Kim, K. Choi, B. Bartley, H.M. Sauro. 2015. “Controlling E. coli Gene Expression Noise.” IEEE Trans. Biomed. Circuits Syst. 9 (4), 497–504. 10.1109/TBCAS.2015.2461135.

B.-B. Koo, K. Choi, I. Ronen, J.M. Lee, D.S. Kim. 2010. “Quantitative Mapping of Diffusion Characteristics under the Cortical Surface.” Magn. Reson. Imaging. 28 (8), 1175–1182. 10.1016/j.mri.2010.03.020.

K.D. Yoon, M.H. Yang, Y.-W. Chin, Y. Kim, H.R. Kim, K. Choi, …, J.W. Kim. 2009. “Development of Gradient Centrifugal Partition Chromatography Method and Its Application for the Isolation of 3,5-Dimethoxyphenanthrene-2,7-diol and Batatasin-I from Dioscorea opposite.” Natural Product Sciences. 15, 144–150. 10.1093/bioinformatics/btac770.