Publications

Peer-reviewed journals

41. Youngmin Jo^*, Donghyun Yim^*, Chan E Park, Insung Yong, Jongbeom Lee, Wonjin Cho, Kwang Ho Ahn, Chanhee Yang, Jae-Byum Chang, Young-Gyun Park, Taek-Soo Kim, Taeyoon Kim^§, and Pilnam Kim^§, "Bi-directional crosstalk between cells and extracellular matrix leads to network morphogenesis in multi-layered tissues," under review

40. Kyohei Matsuda^*, Wonyeong Jung^*, Takuya Kobayashi, Mitsuhiro Sugawa, Masahiko Yamagishi, Yoko Y. Toyoshima, Taeyoon Kim^§, and Junichiro Yajima^§, "Myosin-driven F-actin fragmentation facilitates contraction of actin networks," Cytoskeleton (2024) online first, DOI: 10.1002/cm.21848, PMID: 38456577 (link)

39. Laura Pulido-Cifuentes, Ahmad Athamneh, Yuri Efremov, Arvind Raman, Taeyoon Kim, and Daniel Suter^§, "A modified motor-clutch model reveals that neuronal growth cones respond faster to soft substrates," Molecular Biology of the Cell (2024) 35(ar47): 1-12, DOI: 10.1091/mbc.E23-09-0364, PMID: 38354034 (link)

38. Shihang Ding, Shinji Deguchi, Taeyoon Kim^§, "Unraveling a key molecular player governing pulmonary alveolar development," American Journal of Respiratory Cell and Molecular Biology (2024) online first, DOI: 10.1165/rcmb.2024-0025ED, PMID: 38301261 (link) (commentary)

37. Weiguo Fan, Kolade Adebowale, Yuan Li, Md Foysal Rabbi, Lorand Vancza, Dongning Chen, Koshi Kunimoto, Gergely Mozes, Yisi Li, Junyan Tao, Satdarshan P.S. Monga, Gregory W. Charville, Rebecca G. Wells, Renumathy Dhanasekaran, Taeyoon Kim, Ovijit Chaudhuri, and Natalie J. Török^§, "Matrix viscoelasticity promotes liver cancer progression in the pre-cirrhotic liver," Nature (2024) 626: 635-642, DOI: 10.1038/s41586-023-06991-9, PMID: 38297127 (link)

36. Brandon Slater^*, Wonyeong Jung^*, and Taeyoon Kim^§, "Emergence of diverse patterns driven by molecular motors in the motility assay," Cytoskeleton (2023) online first, DOI: 10.1002/cm.21808, PMID: 37947256 (link)

35. Jing Li, Daniel Szymanski^§, and Taeyoon Kim^§, "Probing stress-regulated ordering of the plant cortical microtubule array via a computational approach," BMC Plant Biology (2023) 23: 308, DOI: 10.1186/s12870-023-04252-5, PMID: 37291489 (link)

34. Devin B. Mair, Ceylin Elmasli, June H. Kim, Amanda D. Barreto, Supeng Ding, Luo Gu, Seth H. Weinberg, Taeyoon Kim, Deok-Ho Kim^§, and Rong Li^§, "The Arp2/3 complex enhances cell migration on elastic substrates," Molecular Biology of the Cell (2023) 34(7): 1-10, DOI: 10.1091/mbc.E22-06-0243, PMID: 36989030 (link)

33. Camelia G. Muresan^*, Zachary G. Sun^*, Vikrant Yadav, A. Pasha Tabatabai, Laura Lanier, June Hyung Kim, Taeyoon Kim, and Michael P. Murrell^§, "F-actin architecture determines constraints on myosin thick filament motion," Nature Communications, (2022) 13: 7008, DOI: 10.1038/s41467-022-34715-6, PMID: 36385016 (link)

32. Hang Zhou, Wonyeong Jung, Tamanna Ishrat Farhana, Kazuya Fujimoto, Taeyoon Kim, and Ryuji Yokokawa^§, "Durability of aligned microtubules dependent on persistence length determines phase transition and pattern formation in collective motion," ACS Nano (2022) 16(9): 14765-14778, DOI: 10.1021/acsnano.2c05593, PMID: 36098647 (link)

31. Yuval Mulla, Mario J. Avellaneda, Antoine Roland, Lucia Baldauf, Wonyeong Jung, Taeyoon Kim^§, Sander J. Tans^§, and Gijsje H. Koenderink^§, "Weak catch bonds make strong networks," Nature Materials (2022) 21: 1019-1023, DOI: 10.1038/s41563-022-01288-0, PMID: 36008604 (link)

30. Qilin Yu, Taeyoon Kim^§, and Vijay Rajagopal^§, "Role of actin filaments and cis binding in cadherin clustering and patterning," PLOS Computational Biology (2022) 18(7): e1010257, DOI: 10.1371/journal.pcbi.1010257, PMID: 35802763 (link)

29. Vlad Costache^*, Séréna P. Garcia^*, Camille Plancke, Jing Li, Simon Begnaud, Shashi Kumar Suman, Anne-Cécile Reymann, Taeyoon Kim^§, and Francois B. Robin^§, "Rapid assembly of a polar network architecture drives efficient actomyosin contractility," Cell Reports (2022) 39(9): 110868, DOI: 10.1016/j.celrep.2022.110868, PMID: 35649363 (link)

28. Brandon Slater^*, Jing Li^*, Dhiraj Indana^*, Yihao Xie, Ovijit Chaudhuri^§, and Taeyoon Kim^§, "Transient mechanical interactions between cells and viscoelastic extracellular matrix," Soft Matter (2021) 17: 10274-10285, DOI: 10.1039/D0SM01911A, PMID: 34137758 (link)

27. Vivek Gupta, Sungmin Nam, Donghyun Yim, Jaclyn Camuglia, Judy Martin, Erin N. Sanders, Lucy E. O'Brien, Adam C. Martin, Taeyoon Kim, and Ovijit Chaudhuri^§, "The nature of cell division forces in epithelial monolayers," Journal of Cell Biology (2021) 220(8): e202011106, DOI: 10.1083/jcb.202011106, PMID: 34132746 (link)

26. Sungmin Nam, Yung-Hao Lin, Taeyoon Kim^§, and Ovijit Chaudhuri^§, "Cellular pushing forces during mitosis drive mitotic elongation in collagen gel," Advanced Science (2021) 8(4): 2000403, DOI: 10.1002/advs.202000403, PMID: 33643782 (link)

25. Wonyeong Jung^*, Jing Li^*, Ovijit Chaudhuri, and Taeyoon Kim^§, “Nonlinear elastic and inelastic properties of cells,” Journal of Biomechanical Engineering (2020) 142(10): 100806, DOI: 10.1115/1.4046863, PMID: 32253428 (link)

24. Katrina M. Wisdom, Dhiraj Indana, Pei-En Chou, Rajiv Desai, Taeyoon Kim^§, and Ovijit Chaudhuri^§, “Covalent cross-linking of basement membrane-like matrices physically restricts invasive protrusions in breast cancer cells,” Matrix Biology (2020) 85-86: 94-111, DOI: 10.1016/j.matbio.2019.05.006, PMID: 31163245 (link)

23. Wonyeong Jung^*, Luke Fillenwarth^*, Atsushi Matsuda, Jing Li, Yasuhiro Inoue^§, and Taeyoon Kim^§, "Collective and contractile filament motions in the myosin motility assay," Soft Matter (2020) 16: 1548-1559, DOI: 10.1039/C9SM02082A, PMID: 31942899 (link)

22. Wonyeong Jung, A. Pasha Tabatabai, Jacob Thomas, S. M. Ali Tabei, Michael Murrell, and Taeyoon Kim^§, “Dynamic motions of molecular motors in the actin cytoskeleton,” Cytoskeleton (2019) 76(11-12): 517-531, DOI: 10.1002/cm.21582, PMID: 31758841 (link)

21. Vikrant Yadav, Deb S. Banerjee, A. Pasha Tabatabai, David R. Kovar, Taeyoon Kim, Shiladitya Banerjee, and Michael Murrell^§, "Filament nucleation tunes mechanical memory in active polymer networks," Advanced Functional Materials (2019) 29: 1905243, DOI: 10.1002/adfm.201905243, PMID: 32523502 (link)

20. Atsushi Matsuda^*, Jing Li^*, Peter Brumm, Taiji Adachi, Yasuhiro Inoue^§, and Taeyoon Kim^§, “Mobility of molecular motors regulates contractile behaviors of actin networks,” Biophysical Journal (2019) 116: 2161-2171, DOI: 10.1016/j.bpj.2019.04.018, PMID: 31103238 (link)

19. Abdel-Rahman Hassan, Thomas Biel, and Taeyoon Kim^§, “Mechanical model for durotactic cell migration,” ACS Biomaterials Science & Engineering (2019) 5(8): 3954-3963, DOI: 10.1021/acsbiomaterials.8b01365, PMID: 32676537 (link)

18. Abdel-Rahman Hassan, Thomas Biel, David M. Umulis, and Taeyoon Kim^§ , “Interplay between the persistent random walk and the contact inhibition of locomotion leads to collective cell behaviors,” Bulletin of Mathematical Biology (2019) 81(8): 3301-3321, DOI: 10.1007/s11538-019-00585-1, PMID: 30788690 (link)

17. Jing Li, Taeyoon Kim, and Daniel B. Szymanski^§, “Multi-scale regulation of cell branching: Modeling morphogenesis,” Developmental Biology (2019) 451(1): 40-52, DOI: 10.1016/j.ydbio.2018.12.004, PMID: 30529250 (link)

16. Qilin Yu^*, Jing Li^*, Michael P. Murrell, and Taeyoon Kim^§ , “Balance between force generation and relaxation leads to pulsed contraction of actomyosin networks,” Biophysical Journal (2018) 115(10): 2003-2013, DOI: 10.1016/j.bpj.2018.10.008, PMID: 30389091 (link)

15. Jing Li^*, Thomas Biel^*, Pranith Lomada^*, Qilin Yu, and Taeyoon Kim^§, “Buckling-induced F-actin fragmentation modulates the contraction of active cytoskeletal networks,” Soft Matter (2017) 13: 3213-3220, DOI: 10.1039/c6sm02703b, PMID: 28398452 (link)

14. Tamara C. Bidone^*, Wonyeong Jung^*, Daniel Maruri, Carlos Borau, Roger D. Kamm^§, and Taeyoon Kim^§, “Morphological transformation and force generation of active cytoskeletal networks,” PLOS Computational Biology (2017) 13(1): e1005277, DOI: 10.1371/journal.pcbi.1005277, PMID: 28114384 (link)

13. Ian Linsmeier, Shiladitya Banerjee, Patrick Oakes, Wonyeong Jung, Taeyoon Kim, and Michael P. Murrell^§, “Disordered actomyosin networks are sufficient to produce cooperative and telescopic contractility,” Nature Communications (2016) 7: 12615, DOI: 10.1038/ncomms12615, PMID: 27558758 (link)

12. Wonyeong Jung, Michael P. Murrell, and Taeyoon Kim^§, “F-actin fragmentation induces distinct mechanisms of stress relaxation in the actin cytoskeleton,” ACS Macro Letters (2016) 5(6): 641-645, DOI: 10.1021/acsmacrolett.6b00232 (link)

11. Michael Mak, Muhammad Zaman^§, Roger D. Kamm^§, and Taeyoon Kim^§, “Interplay of active processes modulates tension and drives phase transition in self-renewing, motor-driven cytoskeletal networks,” Nature Communications (2016) 7: 10323, DOI: 10.1038/ncomms10323, PMID: 26744226 (link)

10. Wonyeong Jung, Michael P. Murrell, and Taeyoon Kim^§, “F-actin cross-linking enhances the stability of force generation in disordered actomyosin networks,” Computational Particle Mechanics (2015) 2(4): 317-327, DOI: 10.1007/s40571-015-0052-9  (link)

9. Michael Mak, Taeyoon Kim, Muhammad Zaman^§, and Roger D. Kamm^§, “Multiscale mechanobiology: Computational models for integrating molecules to multicellular systems,” Integrative Biology (2015) 7(10): 1093-1108, DOI: 10.1039/c5ib00043b, PMID: 26019013 (link)

8. Tamara C. Bidone, Taeyoon Kim, Marco A. Deriu, Umberto Morbiducci, and Roger D. Kamm^§, “Multiscale impact of nucleotides and cations on the conformational equilibrium, elasticity and rheology of actin filaments and crosslinked networks,” Biomechanics and Modeling in Mechanobiology (2015) 14(5): 1143-1155, DOI: 10.1007/s10237-015-0660-6, PMID: 25708806 (link)

7. Taeyoon Kim^§, “Determinants of contractile forces generated in disorganized actomyosin bundles,”Biomechanics and Modeling in Mechanobiology (2015) 14(2): 345-355, DOI: 10.1007/s10237-014-0608-2, PMID: 25103419 (link)

6. Taeyoon Kim, Margaret L. Gardel^§,and Ed Munro^§, “Determinants of fluidlike behavior and effective viscosity in cross-linked actin networks,” Biophysical Journal (2014) 106(3): 526-534, DOI: 10.1016/j.bpj.2013.12.031, PMID: 24507593 (link)

5. Carlos Borau^*, Taeyoon Kim^*,Tamara C. Bidone, José Manuel García-Aznar, and Roger D. Kamm^§, “Dynamic mechanisms of cell rigidity sensing: Insights from a computational model of actomyosin networks,” PLOS One (2012) 7(11): e49174, DOI: 10.1371/journal.pone.0049174, PMID: 23139838 (link)

4. Taeyoon Kim, Wonmuk Hwang,and Roger D. Kamm^§, “Dynamic role of cross-linking proteins in actin rheology,” Biophysical Journal (2011) 101(7): 1597-1603, DOI: 10.1016/j.bpj.2011.08.033, PMID: 21961585 link)

3. Hyungsuk Lee, Benjamin Pelz, Jorge M. Ferrer, Taeyoon Kim, Matthew J. Lang, and Roger D. Kamm^§, “Cytoskeletal deformation at high strains and the role of cross-link unfolding or unbinding,” Cellular and Molecular Bioengineering (2009) 2(1): 28-38, DOI: 10.1007/s12195-009-0048-8 (link)

2. Taeyoon Kim, Wonmuk Hwang,Hyungsuk Lee, and Roger D. Kamm^§, “Computational analysis of viscoelastic properties of crosslinked actin networks,” PLOS Computational Biology (2009) 5(7): e1000439, DOI: 10.1371/journal.pcbi.1000439, PMID: 19609348 (link)

1. Taeyoon Kim, Wonmuk Hwang, and Roger D. Kamm^§, “Computational analysis of a cross-linked actin-like network,” Experimental Mechanics (2009) 49(1): 91-104, DOI: 10.1007/s11340-007-9091-3  (link)

Conference proceedings

1. Taeyoon Kim, Wonmuk Hwang, and Roger D. Kamm^§, “Computational investigation of dynamic properties of actin networks with crosslinking proteins,” ASME 2010 First Global Congress on NanoEngineering for Medicine and Biology (2010) Houston, TX, USA, NEMB2010-13156, 343-344, DOI: 10.1115/NEMB2010-13156 (link)

Book chapters

2. Jing Li*, Wonyeong Jung*, Sungmin Nam, Ovijit Chaudhuri, and Taeyoon Kim^§, “Roles of interactions between cells and extracellular matrices for cell migration and matrix remodeling” in Multi-Scale Extracellular Matrix Mechanics and Mechanobiology (2019) Springer, ISBN: 978-3-030-20182-1 (link)

1. Roger D. Kamm^§, Taeyoon Kim, and Wonmuk Hwang, “Ch. 13: Analysis of the models for cytoskeletal rheology” in Tributes to Yuan-Cheng Fung on His 90th Birthday: Biomechanics: From Molecules to Man (2009) World Scientific (link)

* indicates equal contribution.
§ indicates corresponding author(s).