Naoto Hori

Nottingham Research Fellow at School of Pharamacy, University of Nottingham

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Research interests

• RNA folding, structures and functions
• Macromolecular assembly (RNA-protein complexes, in particular)
• Translation system in the cell
• Computational methods and algorithms
• Palatability, functions and recipes of Natto

Publications

17. Condensates in RNA repeat sequences are heterogeneously organized and exhibit reptation dynamics
    Nguyen HT ; Hori N ; Thirumalai D
    Nat. Chem. (2022) 10.1038/s41557-022-00934-z    [bioRxiv]
    
16. Shape changes and cooperativity in the folding of the central domain of the 16S ribosomal RNA
    Hori N ; Denesyuk NA ; Thirumalai D
    Proc. Natl. Acad. Sci. U.S.A. (2021) 118: e2020837118 10.1073/pnas.2020837118    [bioRxiv]
    
15. Theory and simulations for RNA folding in mixtures of monovalent and divalent cations
    Nguyen HT ; Hori N ; Thirumalai D
    Proc. Natl. Acad. Sci. U.S.A. (2019) 116(42): 21022-21030 10.1073/pnas.1911632116    [PDF]
14. Ion Condensation onto Ribozyme is Site-Specific and Fold-Dependent
    Hori N ; Denesyuk NA ; Thirumalai D
    Biophys. J. (2019) 116(12): 2400-2410 10.1016/j.bpj.2019.04.037    [PDF]
    ---> Featured in New and Notable: "Site-Specific Binding of Non-Site-Specific Ions"
13. Molecular Simulations of Ion Effects on the Thermodynamics of RNA Folding
    Denesyuk NA ; Hori N ; Thirumalai D
    J. Phys. Chem. B (2018) 122(50): 11860-11867 10.1021/acs.jpcb.8b08142   
12. Frictional Effects on RNA Folding: Speed Limit and Kramers Turnover
    Hori N ; Denesyuk NA ; Thirumalai D
    J. Phys. Chem. B (2018) 122(49): 11279-11288 10.1021/acs.jpcb.8b07129    [arXiv]
11. Sequence-dependent Three Interaction Site (TIS) Model for Single and Double-stranded DNA
    Chakraborty D ; Hori N ; Thirumalai D
    J. Chem. Theory Comput. (2018) 14(7): 3763-3779 10.1021/acs.jctc.8b00091    [bioRxiv] [arXiv]
10. Monovalent ions modulate the flux through multiple folding pathways of an RNA pseudoknot
    Roca J ; Hori N ; Baral S ; Velmurugu Y ; Narayanan R ; Narayanan P ; Thirumalai D ; Ansari A
    Proc. Natl. Acad. Sci. U.S.A. (2018) 115(31) E7313-E7322 10.1073/pnas.1717582115    [PDF]

9. Protein Collapse is Encoded in the Folded State Architecture
   Samanta HS ; Zhuravlev PI ; Hinczewski M ; Hori N ; Chakrabarti S ; Thirumalai D
   Soft Matter (2017) 13(19): 3622-3638 10.1039/C7SM00074J    [arXiv]
8. Recognize Online Handwritten Bangla Characters Using Hausdorff Distance-Based Feature
   Sen S ; Sarkar R ; Roy K ; Hori N
   Proceedings of the 5th International Conference on Frontiers in Intelligent Computing (2017) 515: 541-549 Springer 10.1007/978-981-10-3153-3_54
7. Handwritten Devanagari numerals recognition using grid based Hausdorff distance
   Bhowmik S ; Sen S ; Hori N ; Sarkar R ; Nasipuri M
   Computer, Communication and Electrical Technology (2017) 15-18 CRC Press ISBN 9781315400624
6. Salt Effects on the Thermodynamics of a Frameshifting RNA Pseudoknot under Tension
   Hori N ; Denesyuk NA ; Thirumalai D
   J. Mol. Biol. (2016) 428(14): 2847-2859 10.1016/j.jmb.2016.06.002    [arXiv]
5. How co-translational folding of multi-domain protein is affected by elongation schedule: Molecular simulations
   Tanaka T ; Hori N ; Takada S
   PLOS Comput. Biol. (2015) 11(7): e1004356 10.1371/journal.pcbi.1004356    [PDF]
4. Coarse-grained structure-based model for RNA-protein complexes developed by fluctuation matching
   Hori N ; Takada S
   J. Chem. Theory Comput. (2012) 8(9): 3384-3394 10.1021/ct300361j
3. CafeMol: A coarse-grained biomolecular simulator for simulating proteins at work
   Kenzaki H ; Koga N ; Hori N ; Kanada R ; Li W ; Okazaki K ; Yao XQ ; Takada S
   J. Chem. Theory Comput. (2011) 7(6): 1979-1989 10.1021/ct2001045
2. Multiscale methods for protein folding simulations
   Li W ; Yoshii H ; Hori N ; Kameda T ; Takada S
   Methods (2010) 52: 106-114 10.1016/j.ymeth.2010.04.014
1. Folding energy landscape and network dynamics of small globular proteins
   Hori N ; Chikenji G ; Berry RS ; Takada S
   Proc. Natl. Acad. Sci. U.S.A. (2009) 106(1): 73-78 10.1073/pnas.0811560106     [PDF]

Presentations

See here

Academic & Professional Experience

• Mar 2020 - Present, Nottingham Research Fellow, University of Nottingham
• Jan 2016 - Mar 2020, Postdoctoral Fellow, University of Texas at Austin (Prof. Thirumalai's lab)
• Feb 2014 - Dec 2015, Research Associate, University of Maryland (Prof. Thirumalai's lab)
• Apr 2013 - Dec 2013, Postdoctoral Fellow, Kyoto University (Prof. Takada's lab.)
• Apr 2010 - Mar 2013, JSPS Research Fellow (DC1) (Prof. Takada's lab.)
• Apr 2009 - Mar 2010, Research Associate, Kyoto University (Prof. Takada's lab.)
• Apr 2008 - Mar 2009, Software Engineer, Kozo Keikaku Engineering Inc.

Education

• Apr 2010 - Mar 2013, Ph.D. in Biophysics, Kyoto University (Prof. Takada's lab.)
• Apr 2006 - Mar 2008, M.Sc. in Chemistry, Kobe University
• Apr 2002 - Mar 2006, B.Sc. in Chemistry, Kobe University