Olfactory Coding and Decision Making

Organisms navigate their surroundings using information inferred from the spatially and temporally complex odor plume. I am interested in understanding the principle behind the neural processing of how a brain encodes, perceives, and makes decisions accordingly.

1. 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.

Dynamics of Chemosensory Receptors

The olfactory signals are generated through a complex ligand-receptor binding process between odorants and olfactory receptors. I build models to explain and characterize the dynamics of chemosensory signal generation.

1. 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.

Structure to Function in Neural Processing

The spatial distribution and structures of neurons are diverse. These physical properties shape the complex neural dynamics observed in the brain which are poorly understood. I study the structure-function relationship in neural processing using large-scale data analysis that utilizes the latest connectomics and reconstruction datasets. Integrating the concepts from information theory, I use compartmental neuron models to understand the effect of structural properties on the function of single neurons and small neural circuits.

1. 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.

2. 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.

3. 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.

Softwares/Algorithms for Biological Systems

Biological processes are complex, requiring advanced software tools and algorithms to understand. I develop tools to analyze biological networks such as biochemical reactions, neural networks, and signaling networks. I am also interested in high-throughput optimization algorithms, network inference techniques, and novel clustering algorithms for biological systems. I work to improve model reuse and reproducibility in biological models.

1. 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.

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

3. 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.