Biography

I am currently a postdoctoral researcher in the Computational Biophysics Research Team at RIKEN. I have started my current job since May, 2019. My research interests include functional mechanisms of DNA-protein binding, multi-scale organization of the genome, liquid-liquid phase separation in gene expression, and modeling of biomolecules in molecular dynamics (MD) simulations. Besides, I write code for MD softwares GENESIS and CafeMol.

I used to be a free software fanatic (FSF), with up to 10+ years of using various Linux distributions. But now I prefer to use many paid softwares, if available, to save my time and to focus more on truely interesting things.

In order to participate in a sport without any physical contact, I started practicing the Rubik’s cube from 2009, and I broke the national record for the $2\times 2$ cube in a game in 2010. Unfortunately, I stopped practicing since then.

• Nucleosome allostery in pioneer transcription factor binding
  Cheng Tan, Shoji Takada
  Proc. Natl. Acad. Sci., 2020, 117 (34), 20586-20596.

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• A singularity-free torsion angle potential for coarse-grained molecular dynamics simulations
  Cheng Tan, Jaewoon Jung, Chigusa Kobayashi, Yuji Sugita
  J. Chem. Phys., 2020, 153, 044110.

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• Nucleosomes as allosteric scaffolds for genetic regulation
  Shoji Takada, Giovanni B Brandani, Cheng Tan
  Curr. Opin. Struct. Biol., 2020, 62, 93-101.

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• Dynamic and Structural Modeling of the Specificity in Protein-DNA Interactions Guided by Binding Assay and Structure Data
  Cheng Tan, Shoji Takada
  J. Chem. Theory Comput., 2018, 14 (7), 3877-3889.

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• DNA sliding in nucleosomes via twist defect propagation revealed by molecular simulations
  Giovanni B. Brandani, Toru Niina, Cheng Tan, Shoji Takada
  Nucl. Acids Res., 2018, 46 (6), 2788-2801

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• Sequence-dependent nucleosome sliding in rotation-coupled and uncoupled modes revealed by molecular simulations
  Toru Niina, Giovanni B. Brandani, Cheng Tan, Shoji Takada
  PLoS Comp. Biol., 2017, 13 (12), e1005880

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• Dynamic Coupling among Protein Binding, Sliding, and DNA Bending Revealed by Molecular Dynamics
  Cheng Tan, Tsuyoshi Terakawa, Shoji Takada
  J. Am. Chem. Soc., 2016, 138 (27), 8512–8522.

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• Modeling Structural Dynamics of Biomolecular Complexes by Coarse-Grained Molecular Simulations
  Shoji Takada, Ryo Kanada, Cheng Tan, Tsuyoshi Terakawa, Wenfei Li, Hiroo Kenzaki
  Acc. Chem. Res., 2015, 48 (12), 3026–3035.

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• Atomistic Picture for the Folding Pathway of a Hybrid-1 Type Human Telomeric DNA G-quadruplex
  Yunqiang Bian, Cheng Tan, Jun Wang, Yuebiao Sheng, Jian Zhang, Wei Wang
  PLoS Comput. Biol., 2014, 10 (4), e1003562.

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• Localized Frustration and Binding-Induced Conformational Change in Recognition of 5S RNA by TFIIIA Zinc Finger
  Cheng Tan, Wenfei Li, Wei Wang
  J. Phys. Chem. B, 2013, 117 (50), 15917–15925.

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• A singularity-free torsion angle potential for coarse-grained molecular dynamics simulations

  Wed, Sep 16, 2020, The 58th Annual Meeting of the Biophysical Society of Japan

• Allostery of Nucleosomal DNA for Transcription Factor Binding

  Tue, Sep 24, 2019, The 57th Annual Meeting of the Biophysical Society of Japan (Symposium: Integrative approaches towards understanding of gene expression)

• Binding and Diffusion of HMG Proteins on DNA Studied by Molecular Dynamics Simulations

  Fri, Dec 21, 2018, Visit to Prof. Kamagata’s group in Tohoku Univ.

• ctan@c-tan.com
• 81-78-304-5323
• @C_Tan
• Integrated Innovation Building (IIB) N702, 6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, Japan
• Workday 10:00 to 20:00