Publications | IN/SBLab

*indicates equal contribution

Bifurcation Enhances Temporal Information Encoding in the Olfactory Periphery
K. Choi, W. Rosenbluth**, I.R. Graf, N. Kadakia, T. Emonet
PRX Life. 2, 043011 (2024)
10.1103/PRXLife.2.043011
Unveiling the Odor Representation in the Inner Brain of Drosophila through Compressed Sensing
K. Choi, W.K. Kim, C. Hyeon
Physical Review Research. 6 (2), 023298 (2024)
10.1103/PhysRevResearch.6.023298

General Chemical Reaction Network Theory for GPCR-Based Olfactory Sensing: Elucidation of Odorant Mixture Effects and Agonist–Synergist Threshold
W.K. Kim, K. Choi, C. Hyeon, S.J. Jang
J. Phys. Chem. Lett. 14 (XXX), 8412–8420 (2023)
10.1021/acs.jpclett.3c02310
libRoadRunner 2.0: A High-Performance SBML Simulation and Analysis Library C. Welsh, J. Xu, L. Smith, M. König, K. Choi, H.M. Sauro
Bioinformatics. 39(1), btac770 (2023)
10.1093/bioinformatics/btac770

Polymer physics-based classification of neurons.
K. Choi, W.K. Kim, C. Hyeon
Neuroinformatics. 21(1), 177-193 (2022)
10.1007/s12021-022-09605-3
Olfactory responses of Drosophila are encoded in the organization of projection neurons.
K. Choi, W.K. Kim, C. Hyeon
eLife. 11, e77748 (2022)
10.7554/eLife.77748
Neural information processing and computations of two-input synapses.
S.H. Kim, J.H. Woo, K. Choi, M.Y. Choi, K. Han
Neural Computation. 34 (10), 2102–2131 (2022)
10.1162/neco_a_01534
BioSimulators: a web-based registry of simulation engines and services for multiscale modeling
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
Nucleic Acids Research. 50 (W1), W108–W114 (2022)
10.1093/nar/gkac331
The structural aspects of neural dynamics and information flow
J.H. Woo, K. Choi, S.H. Kim, K. Han, M.Y. Choi
Front Biosci.-Landmark. 27 (1), 15 (2022)
10.31083/j.fbl2701015

Characterization of multiscale logic operations in the neural circuits
J.H. Woo, K. Choi, S.H. Kim, K. Han, M.Y. Choi
Front Biosci.-Landmark. 26 (10), 723–739 (2021)
10.52586/4983
Status and Challenges of Reproducibility in Computational Systems and Synthetic Biology
K. Choi, J.R. Karr, H.M. Sauro
In Systems Medicine: Integrative, Qualitative and Computational Approaches. Amsterdam, Netherlands: Elsevier. 3, 406–412 (2021)
10.1016/B978-0-12-801238-3.11525-9

Synthetic Biology Open Language (SBOL) Version 2.3
C. Madsen, A.G. Moreno, P. Umesh, Z. Palchick, N. Roehner, C. Atallah, B. Bartley, K. Choi, …, A. Wipat
J. Integr. Bioinform. 16 (2) (2019)
10.1515/jib-2019-0025
Recent Advances in Biomedical Simulations: A Manifesto for Model Engineering
J. Hellerstein, S. Gu, K. Choi, H.M. Sauro
F1000Research. 8 (2019)
10.12688/f1000research.15997.1

pySBOL: A Python Package for Genetic Design Automation and Standardization
B. Bartley, K. Choi, M. Samineni, Z. Zundel, T. Nguyen, C.J. Myers, H.M. Sauro
ACS Synthetic Biology. 8 (7), 1515–1518
10.1021/acssynbio.8b00336
Robust approaches to generating reliable predictive models in systems biology
K. Choi
In Systems Biology. Cham, Switzerland: Springer. 301–312 (2018)
10.1007/978-3-319-92967-5_15
Tellurium: An Extensible Python-based Modeling Environment for Systems and Synthetic Biology
K. Choi, J.K. Medley, M. König, K. Stocking, L. Smith, S. Gu, H.M. Sauro
BioSystems. 171, 74–79 (2018)
10.1016/j.biosystems.2018.07.006
Tellurium Notebooks - An Environment for Dynamical Model Development, Reproducibility, and Reuse
J.K. Medley, K. Choi, M. König, L. Smith, S. Gu, J. Hellerstein, S.C. Sealfon, H.M. Sauro
PLOS Comp. Biol. 14 (6), e1006220 (2018)
10.1371/journal.pcbi.1006220
A Portable Structural Analysis Library for Reaction Networks
Y. Bedaso, F.T. Bergmann, K. Choi, J.K. Medley, H.M. Sauro
BioSystems. 169–170, 20–25 (2018)
10.1016/j.biosystems.2018.05.008
Synthetic Biology Open Language (SBOL) Version 2.2.0
R.S. Cox III, C. Madsen, J.A. McLaughlin, T. Nguyen, N. Roehner, B. Bartley, J. Beal, M. Bissell, K. Choi, …, A. Wipat
J. Integr. Bioinform. 15 (1), 30–132 (2018)
10.1515/jib-2018-0001

Synthetic Biology Open Language (SBOL) Version 2.1.0
J. Beal, R. Cox, R. Grunberg, J. McLaughlin, T. Nguyen, B. Bartley, M. Bissell, K. Choi, …, A. Wipat
J. Integr. Bioinform. 13 (3), 291 (2016)
10.1515/jib-2016-291
phraSED-ML: A paraphrased, human-readable adaptation of SED-ML
K. Choi, L. Smith, J.K. Medley, H.M. Sauro
J. Bioinform. Comput. Biol. 14 (6), 1650035 (2016)
10.1142/S0219720016500359

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

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

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
K.D. Yoon, M.H. Yang, Y.-W. Chin, Y. Kim, H.R. Kim, K. Choi, …, J.W. Kim
Natural Product Sciences. 15, 144–150 (2009)
10.1093/bioinformatics/btac770

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