Naoto Hori

Contact

• workRoom B27 Boots Science Building
  University Park
  Nottingham
  NG7 2RD
  UK
• work0115 74 87627
• Naoto.Hori@nottingham.ac.uk
• https://hori-lab.github.io

Biography

Academic & Professional Experience

• 2023 - Present, Assistant Professor, University of Nottingham
• 2020 - 2023, Nottingham Research Fellow, University of Nottingham
• 2016 - 2019, Postdoctoral Fellow, University of Texas at Austin (Prof. Thirumalai's lab)
• 2014 - 2015, Research Associate, University of Maryland (Prof. Thirumalai's lab)
• 2010 - 2013, JSPS Research Fellow (DC1) (Prof. Takada's lab.)
• 2009 - 2010, Research Associate, Kyoto University (Prof. Takada's lab.)
• 2008 - 2009, Software Engineer, Kozo Keikaku Engineering Inc.

Education

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

Recent Publications

• BALAKA MONDAL, DEBAYAN CHAKRABORTY, NAOTO HORI, HUNG T. NGUYEN and D. THIRUMALAI, 2024. Competition between stacking and divalent cation-mediated electrostatic interactions determines the conformations of short DNA sequences Journal of Chemical Theory and Computation. 20(7), 2934-2946
• HIRANMAY MAITY, HUNG T. NGUYEN, NAOTO HORI and D. THIRUMALAI, 2024. Salt-dependent self-association of trinucleotide repeat RNA sequences The Journal of Physical Chemistry Letters. 15(14), 3820-3827
• HIRANMAY MAITY, HUNG T. NGUYEN, NAOTO HORI and D. THIRUMALAI, 2023. Odd-even disparity in the population of slipped hairpins in RNA repeat sequences with implications for phase separation Proceedings of the National Academy of Sciences of the United States of America. 120(24), e2301409120
• NAOTO HORI and D. THIRUMALAI, 2023. Watching ion-driven kinetics of folding and misfolding caused by energetic and topological frustration one molecule at a time Nucleic Acids Research. 51(19), 10737–10751

• View all publications

• BALAKA MONDAL, DEBAYAN CHAKRABORTY, NAOTO HORI, HUNG T. NGUYEN and D. THIRUMALAI, 2024. Competition between stacking and divalent cation-mediated electrostatic interactions determines the conformations of short DNA sequences Journal of Chemical Theory and Computation. 20(7), 2934-2946
• HIRANMAY MAITY, HUNG T. NGUYEN, NAOTO HORI and D. THIRUMALAI, 2024. Salt-dependent self-association of trinucleotide repeat RNA sequences The Journal of Physical Chemistry Letters. 15(14), 3820-3827
• HIRANMAY MAITY, HUNG T. NGUYEN, NAOTO HORI and D. THIRUMALAI, 2023. Odd-even disparity in the population of slipped hairpins in RNA repeat sequences with implications for phase separation Proceedings of the National Academy of Sciences of the United States of America. 120(24), e2301409120
• NAOTO HORI and D. THIRUMALAI, 2023. Watching ion-driven kinetics of folding and misfolding caused by energetic and topological frustration one molecule at a time Nucleic Acids Research. 51(19), 10737–10751
• HUNG T. NGUYEN, NAOTO HORI and D. THIRUMALAI, 2022. Condensates in RNA repeat sequences are heterogeneously organized and exhibit reptation dynamics Nature Chemistry. 14, 775-785
• NAOTO HORI, NATALIA A. DENESYUK and D. THIRUMALAI, 2021. Shape changes and cooperativity in the folding of the central domain of the 16S ribosomal RNA Proceedings of the National Academy of Sciences of the United States of America. 118(10), e2020837118
• NAOTO HORI, NATALIA A. DENESYUK and D. THIRUMALAI, 2019. Ion Condensation onto Ribozyme is Site-Specific and Fold-Dependent Biophysical Journal. 116(12), 2400-2410
• HUNG T. NGUYEN, NAOTO HORI and D. THIRUMALAI, 2019. Theory and simulations for RNA folding in mixtures of monovalent and divalent cations Proceedings of the National Academy of Sciences of the United States of America. 116(42), 21022-21030
• JORJETHE ROCA, NAOTO HORI, SAROJ BARAL, YOGAMBIGAI VELMURUGU, RANJANI NARAYANAN, PRASANTH NARAYANAN, D. THIRUMALAI and ANJUM ANSARI, 2018. Monovalent ions modulate the flux through multiple folding pathways of an RNA pseudoknot Proceedings of the National Academy of Sciences of the United States of America. 115(31), E7313-E7322
• DEBAYAN CHAKRABORTY, NAOTO HORI and D. THIRUMALAI, 2018. Sequence-dependent Three Interaction Site (TIS) Model for Single and Double-stranded DNA Journal of Chemical Theory and Computation. 14(7), 3763-3779
• NAOTO HORI, NATALIA A. DENESYUK and D. THIRUMALAI, 2018. Frictional Effects on RNA Folding: Speed Limit and Kramers Turnover Journal of Physical Chemistry B. 122(49), 11279-11288
• NATALIA A. DENESYUK, NAOTO HORI and D. THIRUMALAI, 2018. Molecular Simulations of Ion Effects on the Thermodynamics of RNA Folding Journal of Physical Chemistry B. 122(50), 11860-11867
• HIMADRI S. SAMANTA, PAVEL I. ZHURAVLEV, MICHAEL HINCZEWSKI, NAOTO HORI, SHAON CHAKRABARTI and D. THIRUMALAI, 2017. Protein Collapse is Encoded in the Folded State Architecture Soft Matter. 13(19), 3622-3638
• SHIBAPRASAD SEN, RAM SARKAR, KAUSHIK ROY and NAOTO HORI, 2017. Recognize Online Handwritten Bangla Characters Using Hausdorff Distance-Based Feature In: Proceedings of the 5th International Conference on Frontiers in Intelligent Computing: Theory and Applications. 515. 541-549
• NAOTO HORI, NATALIA A. DENESYUK and D. THIRUMALAI, 2016. Salt Effects on the Thermodynamics of a Frameshifting RNA Pseudoknot under Tension Journal of Molecular Biology. 428(14), 2847-2859
• TOMOHIRO TANAKA, NAOTO HORI and SHOJI TAKADA, 2015. How co-translational folding of multi-domain protein is affected by elongation schedule: Molecular simulations PLOS Computational Biology. 11(7), e1004356
• HIROO KENZAKI, NOBUYASU KOGA, NAOTO HORI, RYO KANADA, WENFEI LI, KEI-ICHI OKAZAKI, XIN-QIU YAO and SHOJI TAKADA, 2011. CafeMol: A coarse-grained biomolecular simulator for simulating proteins at work Journal of Chemical Theory and Computation. 7(6), 1979-1989
• WENFEI LI, HIROAKI YOSHII, NAOTO HORI, TOMOSHI KAMEDA and SHOJI TAKADA, 2010. Multiscale methods for protein folding simulations Methods. 52(1), 106-114
• NAOTO HORI, GEORGE CHIKENJI, R. STEPHEN BERRY and SHOJI TAKADA, 2009. Folding energy landscape and network dynamics of small globular proteins Proceedings of the National Academy of Sciences of the United States of America. 106(1), 73-78