Journals
(+equally contributed authors, *corresponding author)

2025

1. Kang, J.+*, Matsuoka, T+. and Tateno, M. (2025), Identification of CO-binding modes in the CuB site of bovinecytochrome c oxidase by spatial mapping of binding energy. FEBS J. https://doi.org/10.1111/febs.70115

2024

1. Jiyoung Kang and Hae-Jeong Park*, Integration of Partially Observed Multimodal and Multiscale Neural Signals for Estimating a Neural Circuit Using Dynamic Causal Modeling, PLoS Comput Biol 20(12): e1012655, https://doi.org/10.1371/journal.pcbi.1012655 

2.  Eun Lee*, and Jiyoung Kang*, A comparison between the Coleman homophily index and BA-homophily metric with a random network of unequal group sizes, Journal of the Korean Physical Society (2024). doi: https://doi.org/10.1007/s40042-024-01013-x

3.  Jiyoung Kang*, Ensemble-based community detection for dynamic networks. J. Korean Phys. Soc.(2024). https://doi.org/10.1007/s40042-024-01224-2

2023

1.    Jinseok Eo+, Jiyoung Kang+, Tak Youn, Hae-Jeong Park*, Neuropharmacological computational analysis of longitudinal electroencephalograms in clozapine-treated patients with schizophrenia using hierarchical dynamic causal modeling, NeuroImage (2023), doi:https://doi.org/10.1016/j.neuroimage.2023.120161  

2.  Donghyeok Kim+, Eun Lee+, and Jiyoung Kang+*, A Comprehensive Evaluation of Entropy-Based Directionality Estimation Method, Journal of the Korean Physical Society (2023) https://doi.org/10.1007/s40042-023-00903-w.

2022-

1.     Hae-Jeong Park*+, Jinseok Eo+, Chongwon Pae, Junho Son, Sung Min Park, and Jiyoung Kang*, State-dependent effective connectivity in resting-state fMRI, Front. Neural Circuits. 2021, doi: 10.3389/fncir.2021.719364 

2.     Seok-Oh Jeong, Jiyoung Kang, Chongwon Pae, Jinseok Eo, Sung Min Park, Junho Son, and Hae-Jeong Park, Empirical Bayes estimation of pairwise maximum entropy model for nonlinear brain state dynamics, Neuroimage, 244, 118618, 2021. doi: 10.1016/j.neuroimage.2021.118618

3.     Jiyoung Kang+, Seok-Oh Jeong+, Chongwon Pae, and Hae-Jeong Park+*, Bayesian estimation of maximum entropy model for individualized energy landscape analysis of brain state dynamics. Hum Brain Mapp. 2021. doi: 10.1002/hbm.25442. 

4.     Hae-Jeong Park+* and Jiyoung Kang+*, A computational framework for controlling the self-restorative brain based on the free energy and degeneracy principles, Front Comput Neurosci, 15, 590019, 2021. doi: 10.3389/fncom.2021.590019 

5.     Jiyoung Kang+, Jinseok Eo, Dong Myeong Lee, and Hae-Jeong Park+, A computational framework for optimal control of a self-adjustive neural system with activity-dependent and homeostatic plasticity, Neuroimage, 230, 117805, 2021.

6.     Ryu-ichiro Terada, Jiyoung Kang, Masaru Tateno, Theoretical Analysis of the Dynamical Effects of the Amino Acid Residue Replacement in the Vicinity of the [4Fe-4S] Proximal Cluster on the O2-Tolerance of the [NiFe]-Hydrogenases, J. Phys. Soc. Jpn., 90, 034804, 2021.

7.     Jiyoung Kang, Kyesam Jung, Jinseok Eo, Junho Son, and Hae-Jeong Park, Dynamic causal modeling of hippocampal activity measured via mesoscopic voltage-sensitive dye imaging, Neuroimage, 213, 116755, 2020.

8.     Mary Miyaji, Ryohei Furuta, Osamu Hosoya, Kuniaki Sano, Norikazu Hara, Ryozo Kuwano, Jiyoung Kang, Masaru Tateno, Kimiko M. Tsutsui, and Ken Tsutsui, Topoisomerase IIβ targets DNA crossovers formed between distant homologous sites to induce chromatin opening. Sci. Rep. 10, 18550, 2020. 

9.     Jiyoung Kang, Chongwon Pae, and Hae-Jeong Park, Graph-theoretical analysis for energy landscape reveals the organization of state transitions in the resting-state human cerebral cortex, PLoS One, 14, e0222161, 2019.

*Editor’s pick (PLOS Complexity Channel): https://channels.plos.org/complexity 

10.  Kyesam Jung+, Jiyoung Kang+, Seungsoo Chung, and Hae-Jeong Park, Dynamic causal modeling for calcium imaging: Exploration of differential effective connectivity for sensory processing in a barrel cortical column, Neuroimage, 201, 116008, 2019.

11.  Kazuhiko Yamasaki, Tomomi Kubota, Tomoko Yamasaki, Izuru Nagashima, Hiroki Shimizu, Ryu-ichiro Terada, Hiroshi Nishigami, Jiyoung Kang, Masaru Tateno, Hiroaki Tateno, Structural basis for specific recognition of core fucosylation in N-glycans by Pholiota squarrosa lectin (PhoSL), Glycobiology, 29, 576–587, 2019.

12.  Hiroshi Nishigami, Jiyoung Kang, Ryu-ichiro Terada, Hiori Kino, Kazuhiko Yamasaki, Masaru Tateno, Is it possible for short peptide composed of positively- and negatively-charged “hydrophilic” amino acid residue-clusters to form metastable “hydrophobic” packing?, Physical Chemistry Chemical Physics, 21, 9683-9693, 2019. (Cover Image)

13.  Hiroshi Nishigami, Jiyoung Kang, Kazuhiko Yamasaki, and Masaru Tateno, Specific Coordination Mode and Electrostatic Ion Atmosphere Effects of Divalent Cations Regulating Spatially Crossing Configurations of DNA Duplexes, J. Phys. Soc. Jpn., 88, 044801, 2019.

14.  Atsushi Nakamura, Jiyoung Kang, Ryu-ichiro Terada, Hiori Kino, Yasufumi Umena, Keisuke Kawakami, Jian-Ren Shen, Nobuo Kamiya, Masaru Tateno, Novel Mechanism of Cl-Dependent Proton Dislocation in Photosystem II (PSII): Hybrid Ab initio Quantum Mechanics/Molecular Mechanics Molecular Dynamics Simulation, J. Phys. Soc. Jpn., 88, 084802, 2019.

15.  Noor Dina Muhd Noor, Hiroaki Matsuura, Koji Nishikawa, Hulin Tai, Shun Hirota, Jaehyun Kim, Jiyoung Kang, Masaru Tateno, Ki-Seok Yoon, Seiji Ogo, Shintaro Kubota, Yasuhito Shomura, and Yoshiki Higuchi, Redox-dependent conformational changes of a proximal [4Fe–4S] cluster in Hyb-type [NiFe]-hydrogenase to protect the active site from O2, Chem. Comm., 54, 12385-12388, 2018. 

16.  Kakeru Sakabe, Jiyoung Kang, Ryu-ichiro Terada, Hiroshi Nishigami, and Masaru Tateno, Possible Transition from Hybrid Ribozyme/Protein Catalyst toward Protein Enzyme to Compensate for Defective Catalytic Activator, J. Phys. Soc. Jpn., 87, 124801, 2018.

17.  Jaehyun Kim, Jiyoung Kang, Hiroshi Nishigami, Hiori Kino, and Tateno, Masaru, Ab Initio Electronic Structure Calculation of [4Fe-3S] Cluster of Hydrogenase as Dihydrogen Dissociation/Production Catalyst, J. Phys. Soc. Jpn., 87, 034804, 2018.

18.  Jiyoung Kang, Chongwon Pae, and Hae-Jeong Park, Energy landscape analysis of the subcortical brain network unravels system properties beneath resting state dynamics, Neuroimage, 149, 153–164, 2017. (Cover Image)

19.  Jiyoung Kang, Kazuhiko Yamasaki, Kuniaki Sano, Ken Tsutsui, Kimiko M. Tsutsui, and Masaru Tateno, Simulated Annealing-Extended Sampling for Multicomponent Decomposition of Spectral Data of DNA Complexed with Peptide, J. Phys. Soc. Jpn., 86, 014802, 2017.

 *Editor’s pick (Biomedical Advances): http://biomedical-advances.org/ep-20179-5/

20.  Jiyoung Kang and Masaru Tateno, Effects of a positive feedback loop upon the stability of bi-connected elementary biochemical reaction cycles, J. Phys. Soc. Jpn, 86, 074802, 2017.

21.  Jiyoung Kang, Hiori Kino, Martin J. Field, and Masaru Tateno: Electronic Structure Rearrangements in Hybrid Ribozyme/Protein Catalysis, J. Phys. Soc. Jpn., 86, 044801, 2017.

22.  Asuka Sugimoto, Jiyoung Kang, Takuya Sumi, and Masaru Tateno, Novel strategy for discrimination of transcription factor binding motifs employing mathematical neural network, J. Phys. Soc. Jpn., 86, 074803, 2017.

23.  Satoru Shimada, Kyoko Shinzawa-Itoh, Junpei Baba, Shimpei Aoe, Atsuhiro Shimada, Eiki Yamashita, Jiyoung Kang, Masaru Tateno, Shinya Yoshikawa and Tomitake Tsukihara, Complex structure of cytochrome c-cytochrome c oxidase reveals a novel protein-protein interaction mode, EMBO J., 86, 291-300, 2017.

24.  Minoru Kubo, Satoru Nakashima, Satoru Yamaguchi, Takashi Ogura, Masao Mochizuki, Jiyoung Kang, Masaru Tateno, Kyoko Shinzawa-Itoh, Koji Kato, and Shinya Yoshikawa, Effective Pumping Proton Collection Facilitated by a Copper Site (CuB) of Bovine Heart Cytochrome c Oxidase, Revealed by a Newly Developed Time-resolved Infrared System: J. Biol. Chem., 228, 30259-69, 2013. 

25.  Hiroaki Saito, Masashi Iwayama, Taku Mizukami, Jiyoung Kang, Masaru Tateno, Hidemi Nagao, Molecular Dynamics Study on Binding Free Energy of Azurin–Cytochrome c551 Complex, Chem. Phys. Lett., 556, 297–302, 2013. 

26.  Ryo Nakaki, Jiyoung Kang, and Masaru Tateno, A novel ab initio identification system of transcriptional regulation motifs in genome DNA sequences based on direct comparison scheme of signal/noise distributions: Nucleic Acids Res., 40, 8835-48, 2012.

27.  Jiyoung Kang, Shigehide Kuroyanagi, Tomohiro Akisada, Yohsuke Hagiwara, and Masaru Tateno, Unidirectional mechanistic valved mechanisms for ammonia transport in GatCAB: J. Chem. Theory Comput., 8, 649-660, 2012.

28.  Jiyoung Kang, Yohsuke Hagiwara, and Masaru Tateno, Biological applications of hybrid quantum mechanics / molecular mechanics calculation, J. Biomed. Biotech., 2012, 236157, 2012, http://dx.doi.org/10.1155/2012/236157 (Review article)

29.  Jiyoung Kang, Hiori Kino, and Masaru Tateno, A theoretical investigation of the functional role of the axial methionine ligand of the CuA site in cytochrome c oxidase, Biochim. Biophys. Acta Bioenerg., 1807, 1314-27, 2011. 

30.  Yohsuke Hagiwara, Jiyoung Kang, and Masaru Tateno, Structural Instability of the Active Site of T1 Lipase Induced by Replacement of Na+ with Water Complexed with the Phenylalanine Aromatic Ring, J. Chem. Theory. Comput., 7, 2593-99, 2011. 

31.  Jiyoung Kang, Takehiro Ohta, Yohsuke Hagiwara, Keigo Nishikawa, Tetsunori Yamamoto, Hidemi Nagao, and Masaru Tateno: Electronic and geometric structures of the blue copper site of azurin investigated by QM/MM hybrid calculations: J. Phys. Cond. Matt., 21, 064235, 2009. 

32.  Mauro Boero, Jiyoung Kang, Shin Tokumoto, and Masaru Tateno: A First-Principle Exploration of Heme a and Heme a3 of the Bovine Cytochrome c Oxidase in Reduced and Oxidized Charge States: J. Comp. Theor. Nanosci., 6, 2640-47, 2009.

33.  Takehiro Ohta, Yohsuke Hagiwara, Jiyoung Kang, Keigo Nishikawa, Tetsunori Yamamoto, Hidemi Nagao, and Masaru Tateno: Evaluation of Electronic and Geometrical Properties of the Blue Copper Site in Fully Solvated Azurin by QM/MM Hybrid Calculations Using a New Interface Program Connecting QM and MM Engine: J. Comp. Theor. Nanosci., 6, 2648-55, 2009.

Japanese article

34.  姜 志姈，萩原陽介，舘野　賢, コンピュータ・シミュレーションによる生体触媒反応機構の研究, 応用物理(2011), 第80券, 第7号,  p.610 –14, 2011. (Japanese review article, 컴퓨터 시뮬레이션에 의한 생체촉매반응매커니즘의 연구, 응용물리)