Sara Illodo, Hyeong-ku Kim, Je-Kyung Ryu*. Atomic Force Microscopy Analysis of Bridging-Induced Phase Separation Mediated by SMC Proteins. In SMC Proteins (eds Murayama, Y., Kakui, Y.) Methods in Molecular Biology 2991, 69-82 (Humana, New York, 2026).

Andrea Bonato#*, Jae-Won Jang, Do-Gyun Kim, Kyoung-Wook Moon, Davide Michieletto*, Je-Kyung Ryu*.Spontaneously directed loop extrusion in SMC complexes emerges from broken detailed balance and anisotropic DNA search. Nucleic Acids Research 53(14), gkaf725 (2025).

Hanbyeol Kim#, Do-Gyun Kim#, Seongyun Ha, Jun-Young Jang, Francisca N. de L. Vitorino, Joanna M. Gongora, Woochul Kim, Yoonji Oh, Gyeongsik Park, Hyeji Kang, Soo-Hyun Im, Chan Kwon Jung, Seon-Young Kim, Inkyung Jung, Jae-Kyung Won, Benjamin A. Garcia, Su-Jin Kim, Kyu Eun Lee, Je-Kyung Ryu*, Chul-Hwan Lee*. EZH1 Q571R-mediated chromatin compaction and its oncogenic potential in thyroid cancer. bioRxiv (2025).

Winnie Tan#, Jeong Veen Park, Hariprasad Venugopal, Jie Qiong Lou, Prabavi Shayana Dias, Pedro L. Baldoni, Toby Dite, Kyoung-Wook Moon, Christine R. Keenan, Alexandra D. Gurzau, Andrew Leis, Jumana Yousef, Vineet Vaibhav, Laura F. Dagley, Ching-Seng Ang, Laura Corso, Chen Davidovich, Stephin J. Vervoort, Gordon K. Smyth, Marnie E. Blewitt, Rhys S. Allan, Elizabeth Hinde, Sheena D'Arcy, Je-Kyung Ryu*, Shabih Shakeel*. MORC2 is a phosphorylation-dependent DNA compaction machine. Nature Communications 16, 5606 (2025).

Lucy Brennan#, Hyeong-Ku Kim, Serafin Colmenares, Tatum Ego, Amit Kumar, Sam Safran, Je-Kyung Ryu, Gary Karpen*. HP1a promotes chromatin liquidity and drives spontaneous heterochromatin compartmentalization. bioRxiv (2024).

Kyoung-Wook Moon#, Do-Gyun Kim, Je-Kyung Ryu*. Anisotropic scrunching of SMC with a baton-pass mechanism. Commun. Biol 7, 881 (2024).

Jeong Veen Park#, Jeong Jun Kim & Je-Kyung Ryu*. Mechanism of phase condensation for chromosome architecture and function. Exp. Mol. Med. 56, 809-819 (2024).

Wanki Yoo#, Yi Wei Song, Jihyun Kim, Jihye Ahn, Jaehoon Kim, Yongdae Shin, Je-Kyung Ryu, Kyeong Kyu Kim*. Molecular basis for SOX2-dependent regulation of super-enhancer activity. Nucleic Acids Research 51(22), 11999-12019 (2023).

Kyoung-Wook Moon#, Je-Kyung Ryu*. Current working models of SMC-driven DNA-loop extrusion. Biochem. Soc. Trans 51(5), 1801-1810 (2023).

Houda Yasmine Ali Moussa, Kyung Chul Shin, Janarthanan Ponraj, Soo Jin Kim, Je-Kyung Ryu, Said Mansour, Yongsoo Park. Requirement of Cholesterol for Calcium-Dependent Vesicle Fusion by Strengthening Synaptotagmin-1-Induced Membrane Bending. Advanced Science 10(15), 2206823 (2023).

Je-Kyung Ryu#, Sang-Hyun Rah#, Richard Janissen#, Jacob W. Karppenmakers#, and Cees Dekker*. Condensin extrudes DNA loops in steps upto hundreds of base pairs that are generated by ATP binding events. Nucleic Acids Research 50(2), 820-832 (2022).

Biswajit Pradhan#, Roman Barth, Eugene Kim, Iain F. Davidson, Benedikt Bauer, Theo van Laar, Wayne Wang, Je-Kyung Ryu, Jaco van der Torre, Jan-Michael Peters, and Cees Dekker*. SMC complexes can traverse physical roadblocks bigger than their ring size. Cell Reports 41(3), 111491 (2022).

Je-Kyung Ryu#*, Da-Eun Hwang, and Jeong-Mo Choi*. Current understandings of molecular phase separation in chromosome, Int. J. Mol. Sci. 22(19), 10736 (2021).

Changwon Kim#, Min Ju Shon#, Sung Hyun Kim, Gee Sung Eun, Je-Kyung Ryu, Changbong Hyeon, ReinhardJahn and Tae-Young Yoon*.Extreme parsimony in ATP consumption by 20S complexes in the global disassembly of single SNARE complexes. Nature Communications 12, 3206 (2021).

Hansol Lee#, Haemin Noh, and Je-Kyung Ryu*. Structure-function relationships of SMC proteins for DNA loop extrusion. Biodesign 9(1), 1-13 (2021).

Je-Kyung Ryu#, Celine Bouchoux, Hon Wing Liu, Eugene Kim, Masashi Minamino, Ralph de Groot, AllardKatan, Andrea Bonato, Davide Marenduzzo, Davide Michieletto, Frank Uhlmann*, and Cees Dekker*. Bridging-induced phase separation induced by cohesin SMC protein complexes. Science Advances 7(7), abe5905 (2021).

Je-Kyung Ryu#, Allard Katan, Eli van der Sluis, Thomas Wisse, Jaco van der Torre, Ralph de Groot, Christian Haering, and Cees Dekker*. The condensin holocomplex cycles dynamically between open and collapsed states. Nature Structural & Molecular Biology 27, 1134-1141 (2020).

Yongsoo Park* and Je-Kyung Ryu*. Models of synaptotagmin-1 to trigger Ca2+-dependent vesicle fusion. FEBS Letters 592(21), 3480-3492 (2018).

Je-Kyung Ryu#, Soo Jin Kim#, Sang-Hyun Rah, Ji In Kang, Hi Eun Jung, Heung-Kyu Lee, Jie-Oh Lee, Beom Seok Park, Tae-Young Yoon*, and Ho Min Kim*. Reconstruction of LPS transfer cascade reveals structural determinants within LBP, CD14 and TLR4-MD2 for efficient LPS recognition and transfer. Immunity 46(1), 38-50 (2017).

Je-Kyung Ryu#, Reinhard Jahn*and Tae-Young Yoon*. Progresses in understanding N-ethylmaleimide sensitive factor (NSF) mediated disassembly of SNARE complexes. Biopolymers 105(8), 518-531 (2016).

Je-Kyung Ryu#, Duyoung Min#, Sang-Hyun Rah#, Soo Jin Kim, Yongsoo Park, Haesoo Kim, Changbong Hyeon, Ho Min Kim, Reinhard Jahn &Tae-Young Yoon. Spring-loaded unraveling of a single SNARE complex by NSF inone round of ATP turnover. Science 347(6229), 1485-1489 (2015).

Wooli Bae#, Kipom Kim#, Duyoung Min, Je-Kyung Ryu, Changbong Hyeon& Tae-Young Yoon. Programmed folding of DNA origami structures through single-molecule force control. Nature Communications 5, 5654 (2014).