Publications

2021

• ”Microscopic temperature control reveals cooperative regulation of actin–myosin interaction by drebrin E.”
  Hiroaki Kubota, Hiroyuki Ogawa, Makito Miyazaki, Shuya Ishii, Kotaro Oyama, Yuki Kawamura, Shin'ichi Ishiwata and Madoka Suzuki (2021) Nano Lett. doi: https://doi.org/10.1021/acs.nanolett.1c02955 [Link]. 

• "Synchrony of sarcomeric movement regulates left ventricular pump function in the in vivo beating mouse heart."
  Fuyu Kobirumaki-Shimozawa, Togo Shimozawa, Kotaro Oyama, Shunsuke Baba, Jia Li, Tomohiro Nakanishi, Takako Terui, William E. Louch, Shin’ichi Ishiwata and Norio Fukuda (2021)
  J. Gen. Physiol. 153 (11): e202012860 [Link].

• "Recent advances on myocardium physiology.”
  Norio Fukuda, Henk Granzier, Shin'ichi Ishiwata and Sachio Morimoto (2021) Frontiers in Physiol. 12: 697852. doi: 10.3389/fphys.2021.697852 [Link].

• "Nanoscopic changes in the lattice structure of striated muscle sarcomeres involved in the mechanism of spontaneous oscillatory contraction (SPOC)."
  Kono, F., Kawai, S., Shimamoto, Y. and Ishiwata, S. (2020)
  Sci. Rep. 10, 16372 [Link].

• "Tug-of-war between actomyosin-driven antagonistic forces determines the positioning symmetry in cell-sized confinement."
  Ryota Sakamoto, Masatoshi Tanabe, Tetsuya Hiraiwa, Kazuya Suzuki, Shin’ichi Ishiwata, Yusuke T. Maeda and Makito Miyazaki (2020).
  Nature Commun. 11:3063 [Link].

• "Research Exchange with Cris: From Fluorescence Spectroscopy to Human Myocardium."
  Shin'ichi Ishiwata (2020)
  Biophys. Rev. 12, 773-775. doi: 10.1007/s12551-020-00706-4 [Link].

• "Single-cell temperature mapping with fluorescent thermometer nanosheets."
  Kotaro Oyama, Mizuho Gotoh, Yuji Hosaka, Tomoko G. Oyama, Aya Kubonoya, Yuma Suzuki, Tomomi Arai, Seiichi Tsukamoto, Yuki Kawamura, Hideki Itoh, Seine A. Shintani, Toshiko Yamazawa, Mitsumasa Taguchi, Shin’ichi Ishiwata, and Norio Fukuda (2020).
  J. Gen. Physiol. 152(8): e201912469. [Article], [Commentary]

• "Thermal activation of thin filaments in striated muscle."
  Shuya Ishii, Kotaro Oyama, Seine A. Shintani, Fuyu Kobirumaki-Shimozawa, Shin'ichi Ishiwata and Norio Fukuda (2020).
  Frontiers in Physiology, 11:278. doi: 10.3389/fphys.2020.00278 [Link].

• "Real-time in vivo imaging of mouse left ventricle reveals fluctuating movements of the intercalated discs."
  Fuyu Kobirumaki-Shimozawa, Tomohiro Nakanishi, Togo Shimozawa,Takako Terui, Kotaro Oyama, Jia Li, William Louch, Shin'ichi Ishiwata and Norio Fukuda (2020).
  Nanomaterials, 10, 532; doi:10.3390/nano10030532 [Link].

• "On the on-line journal "Biophysics and Physicobiology (BPPB)"."
  Shin'ichi Ishiwata (2020)
  Biophys. Rev. 12, 217-219 [Link]. 

• "Microscopic heat pulses activate cardiac thin filaments."
  Shuya Ishii, Kotaro Oyama, Tomomi Arai, Hideki Itoh, Seine A. Shintani, Madoka Suzuki, Fuyu Kobirumaki-Shimozawa, Takako Terui, Norio Fukuda, Shin’ichi Ishiwata (2019)
  J. Gen. Physiol., DOI: 10.1085/jgp.201812243 [Link].

• "Functional significance of HCM mutants of tropomyosin, V95A and D175N, studied with in vitro motility assays"
  Shuya Ishii, Madoka Suzuki, Shin’ichi Ishiwata, and Masataka Kawai (2019)
  Biophys. Physicobiol., Volume 16 Pages 28-40 [Link]. 

• "Processive Nanostepping of Formin mDia1 Loosely Coupled with Actin Polymerization"
  Hiroaki Kubota, Makito Miyazaki, Taisaku Ogawa, Togo Shimozawa, Kazuhiko Kinosita, Jr., and Shin’ichi Ishiwata (2018)
  Nano Lett., 18(10):6617-6624, DOI: 10.1021/acs.nanolett.8b03277, Epub 2018 Sep 27 [Link].

• "Optimization of fluorescent labeling for in vivo nano-imaging of sarcomeres in the mouse heart"
  Fuyu Kobirumaki-Shimozawa, Togo Shimozawa, Kotaro Oyama, Yasuharu Kushida, Takako Terui, Shin'ichi Ishiwata, and Norio Fukuda (2018)
  BioMed. Res. International, Volume 2018, Article ID 4349170, 8 pages [aritcle].

• "Sarcomeric auto-oscillations in single myofibrils from the heart of patients with dilated cardiomyopathy"
  Tatsuya Kagemoto, Kotaro Oyama, Mitsunori Yamane, Seiichi Tsukamoto, Fuyu Kobirumaki-Shimozawa, Amy Li, Cristobal dos Remedios, Norio Fukuda, and Shin’ichi Ishiwata (2018)
  Circulation: Heart Failure, 2018;11:e004333, DOI: 10.1161/CIRCHEARTFAILURE.117.004333 [Link].

• "Estimation of actomyosin active force maintained by tropomyosin and troponin complex under vertical forces in the in vitro motility assay system"
  Shuya Ishii, Masataka Kawai, Shin'ichi Ishiwata, and Madoka Suzuki (2018)
  PLOS One, 13(2), e0192558, 1–16 [Link]. 

• "Radial stiffness characteristics of the overlap regions of sarcomeres in isolated skeletal myofibrils in pre-force generating state"
  Daisuke Miyashiro, Misato Ohtsuki, Yuta Shimamoto, Jun’ichi Wakayama, Yuki Kunioka, Takakazu Kobayashi, Shin’ichi Ishiwata, and Takenori Yamada (2017)
  Biophys. Physicobiol. 14, 207-220 [Link].

• "Biphasic effect of profilin impacts the formin mDia1 force-sensing mechanism in actin polymerization"
  Hiroaki Kubota, Makito Miyazaki, Taisaku Ogawa, Togo Shimozawa, Kazuhiko Kinosita Jr., and Shin’ichi Ishiwata (2017)
  Biophys. J. 113, 461-471 [Link].

• "Dynamic properties of bio-motile systems as a liquid-crystalline structure"
  Shin’ichi Ishiwata, Makito Miyazaki, Katsuhiko Sato, Koutaro Nakagome, Seine A. Shintani, Fuyu Kobirumaki-Shimozawa, Norio Fukuda, Kazuya Suzuki, Jun Takagi, Yuta Shimamoto, and Takeshi Itabashi (2017)
  Mol. Cryst. Liq. Cryst. 647, 127-150 [Link].

• "Optical visualisation of thermogenesis in stimulated single-cell brown adipocytes”
  Rókus Kriszt, Satoshi Arai, Hideki Itoh, Michelle H. Lee, Anna G. Goralczyk, Xiu Min Ang, Aaron M. Cypess, Andrew P. White, Farnaz Shamsi, Ruidan Xue, Jung Yeol Lee, Sung-Chan Lee, Yanyan Hou, Tetsuya Kitaguchi, Thankiah Sudhaharan, Shin'ichi Ishiwata, E. Birgitte Lane, Young-Tae Chang, Yu-Hua Tseng, Madoka Suzuki, and Michael Raghunath (2017)
  Sci. Rep. 7, 1383 [Link].

• "Spatial confinement of active microtubule networks induces large-scale rotational cytoplasmic flow"
  Kazuya Suzuki, Makito Miyazaki, Jun Takagi, Takeshi Itabashi, and Shin’ichi Ishiwata (2017)
  Proc. Natl. Acad. Sci. USA 114, 2922-2927 [Link].

• "Mechanical properties of spindle poles are symmetrically balanced"
  Kazuya Suzuki, Takeshi Itabashi, and Shin’ichi Ishiwata (2017)
  Biophys. Physicobiol. 14, 1-11 [Link]. 

• "In vivo cardiac nano-imaging: A new technology for high-precision analyses of sarcomere dynamics in the heart"
  Togo Shimozawa, Erisa Hirokawa, Fuyu Kobirumaki-Shimozawa, Kotaro Oyama, Seine A. Shintani, Takako Terui, Yasuharu Kushida, Seiichi Tsukamoto, Teruyuki Fujii, Shin'ichi Ishiwata, and Norio Fukuda (2017)
  Prog. Biophys. Mol. Biol. 124, 31-40 [Link]. 

• "Facilely-fabricated luminescent nanoparticle thermosensor for real-time microthermography in living animals"
  Ferdinandus, Satoshi Arai, Shinji Takeoka, Shin'ichi Ishiwata, Madoka Suzuki, and Hirotaka Sato (2016)
  ACS Sens. 1, 1222-1227 [Link].

• "Simultaneous imaging of local calcium and single sarcomere length in rat neonatal cardiomyocytes using yellow Cameleon-Nano140"
  Seiichi Tsukamoto*, Teruyuki Fujii*, Kotaro Oyama*, Seine A. Shintani, Togo Shimozawa, Fuyu Kobirumaki-Shimozawa, Shin’ichi Ishiwata, and Norio Fukuda (2016) *equal contribution
  J. Gen. Physiol. 148, 341-355 [Link] (Selected as the cover photo) .

• "A beetle flight muscle displays leg muscle microstructure"
  Toshiki Shimomura, Hiroyuki Iwamoto, Tat Thang Vo Doan, Shin’ichi Ishiwata, Hirotaka Sato, and Madoka Suzuki (2016)
  Biophys. J. 111, 1295-1303 [Link].

• "Model simulation of the SPOC wave in a bundle of striated myofibrils"
  Koutaro Nakagome, Katsuhiko Sato, Seine A. Shintani, and Shin’ichi Ishiwata (2016)
  Biophys. Physicobiol. 13, 217-226 [Link].

• "A model for measured traveling waves at end-diastole in human heart wall by ultrasonic imaging method"
  Naoaki Bekki, Seine A. Shintani, Shin'ichi Ishiwata, and Hiroshi Kanai
  J. Phys. Soc. Jpn. 85, 044802 [Link].

• "Direct organelle thermometry with fluorescence lifetime imaging microscopy in single myotubes"
  Hideki Itoh, Satoshi Arai, Thankiah Sudhaharan, Sung-Chan Lee, Young-Tae Chang, Shin’ichi Ishiwata, Madoka Suzuki, and E. Birgitte Lane (2016)
  Chem. Comm. 52, 4458-4461 [Link]. 

• "Nano-imaging of the beating mouse heart in vivo: importance of sarcomere dynamics, as opposed to sarcomere length per se, in the regulation of cardiac function"
  Fuyu Kobirumaki-Shimozawa*, Kotaro Oyama*, Togo Shimozawa*, Akari Mizuno, Takashi Ohki, Takako Terui, Susumu Minamisawa, Shin’ichi Ishiwata, and Norio Fukuda (2016)
  *equal contribution
  J. Gen. Physiol. 147, 53-62 [Link]. 

• "Triggering of high-speed neurite outgrowth using an optical microheater"
  Kotaro Oyama*, Vadim Zeeb*, Yuki Kawamura, Tomomi Arai, Mizuho Gotoh, Hideki Itoh, Takeshi Itabashi, Madoka Suzuki, and Shin’ichi Ishiwata (2015)
  *equal contribution
  Sci. Rep. 5, 16611 [Link].

• "The 105 gap issue between calculation and measurement in single-cell thermometry"
  Madoka Suzuki, Vadim Zeeb, Satoshi Arai, Kotaro Oyama, and Shin’ichi Ishiwata (2015)
  Nat. Methods 10, 802-803 [Link].

• "Micro-thermography in millimeter-scale animals by orally-dosed fluorescent nanoparticle thermosensors"
  Satoshi Arai, Ferdinandus, Shinji Takeoka, Shin'ichi Ishiwata, Hirotaka Sato, and Madoka Suzuki (2015)
  Analyst 140, 7534-7539 [Link].

• "Directional bleb formation in spherical cells under temperature gradient"
  Kotaro Oyama*, Tomomi Arai*, Akira Isaka*, Taku Sekiguchi, Hideki Itoh, Yusuke Seto, Makito Miyazaki, Takeshi Itabashi, Takashi Ohki, Madoka Suzuki, and Shin'ichi Ishiwata (2015)
  *equal contribution
  Biophys. J. 109, 355-364 [Link].

• "Cell-sized spherical confinement induces the spontaneous formation of contractile actomyosin rings in vitro"
  Makito Miyazaki, Masataka Chiba, Hiroki Eguchi, Takashi Ohki, and Shin'ichi Ishiwata (2015)
  Nat. Cell Biol. 17, 480-489 [Link].

• "Preparation of cell-sized water-in-oil droplets for in vitro reconstitution of biological processes in cellular compartments"
  Makito Miyazaki, Masataka Chiba, and Shin'ichi Ishiwata (2015)
  Protoc. Exch. doi:10.1038/protex.2015.029 [Link].

• "Luminescent nanothermometers for biological applications"
  Madoka Suzuki, Satoshi Arai, Kotaro Oyama, and Shin’ichi Ishiwata (2015)
  CRC Concise Encyclopedia of Nanotechnology (ed. by B.I. Kharisov, O.V. Kharissova and U.O. Mendez, Taylor and Francis/CRC Press, 2015), 851-859.

• "High-frequency sarcomeric auto-oscillations induced by heating in living neonatal cardiomyocytes of the rat"
  Seine A. Shintani, Kotaro Oyama, Norio Fukuda, and Shin'ichi Ishiwata (2015)
  Biochem. Biophys. Res. Commun. 457, 165-170 [Link].

• "Spontaneous oscillatory contraction (SPOC) in cardiomyocytes"
  Tatsuya Kagemoto, Amy Li, Cris dos Remedios, and Shin’ichi Ishiwata (2015)
  Biophys. Rev. 7, 15-24 [Link].

• "Oral dosing of chemical indicators for in vivo monitoring of Ca2+ dynamics in insect muscle"
  Ferdinandus, Satoshi Arai, Shin'ichi Ishiwata, Madoka Suzuki, and Hirotaka Sato (2015)
  PLOS ONE 10, e0116655 [Link].

• "Microscopic heat pulse-induced calcium dynamics in single WI-38 fibroblasts"
  Hideki Itoh, Kotaro Oyama, Madoka Suzuki, and Shin'ichi Ishiwata (2014)
  BIOPHYSICS 10, 109-119 [Link].

• "Quantitative analysis of the lamellarity of giant liposomes prepared by the inverted emulsion method"
  Masataka Chiba*, Makito Miyazaki*, and Shin'ichi Ishiwata (2014) *equal contribution
  Biophys. J. 107, 346-354 [Link].

• "Cardiac thin filament regulation and the Frank-Starling mechanism"
  Fuyu Kobirumaki-Shimozawa, Takahiro Inoue, Seine A. Shintani, Kotaro Oyama, Takako Terui, Susumu Minamisawa, Shin’ichi Ishiwata, and Norio Fukuda (2014)
  J. Physiol. Sci. 64, 221–232 [Link].

• "Characterization of Olig2 expression during cerebellar development"
  Yusuke Seto, Shin'ichi Ishiwata, and Mikio Hoshino (2014)
  Gene Expr. Patterns 15, 1-7 [Link].

• "Temporal identity transition from Purkinje cell progenitors to GABAergic interneuron progenitors in the cerebellum"
  Yusuke Seto, Tomoya Nakatani, Norihisa Masuyama, Shinichiro Taya, Minoru Kumai, Yasuko Minaki, Akiko Hamaguchi, Yukiko U. Inoue, Takayoshi Inoue, Satoshi Miyashita, Tomoyuki Fujiyama, Mayumi Yamada, Heather Chapman, Kenneth J. Campbell, Mark A. Magnuson, Christopher V. Wright, Yoshiya Kawaguchi, Kazuhiro Ikenaka, Hirohide Takebayashi, Shin’ichi Ishiwata, Yuichi Ono, and Mikio Hoshino (2014)
  Nat. Commun. 5, 3337 [Link].

• "Sarcomere length nanometry in rat neonatal cardiomyocytes expressed with α-actinin-AcGFP in Z-discs"
  Seine A. Shintani, Kotaro Oyama, Fuyu Kobirumaki-Shimozawa, Takashi Ohki, Shin'ichi Ishiwata, and Norio Fukuda (2014)
  J. Gen. Physiol. 143, 513-524 [Link]. 

• "Micromechanics of the vertebrate meiotic spindle examined by stretching along the pole-to-pole axis"
  Jun Takagi, Takeshi Itabashi, Kazuya Suzuki, Yuta Shimamoto, Tarun M. Kapoor, and Shin'ichi Ishiwata (2014)
  Biophys. J. 106, 735-740 [Link]. 

• "A nanoparticle-based ratiometric and self-calibrated fluorescent thermometer for single living cells"
  Yoshiaki Takei, Satoshi Arai, Atsushi Murata, Masao Takabayashi, Kotaro Oyama, Shin'ichi Ishiwata, Shinji Takeoka, and Madoka Suzuki (2013)
  ACS Nano 8, 198-206 [Link].

• "Using micromanipulation to analyze control of vertebrate meiotic spindle size"
  Jun Takagi, Takeshi Itabashi, Kazuya Suzuki, Tarun M. Kapoor, Yuta Shimamoto, and Shin’ichi Ishiwata (2013)
  Cell Rep. 5, 44-50 [Link].

• "Chromosome position at the spindle equator is regulated by chromokinesin and a bipolar microtubule array"
  Jun Takagi*, Takeshi Itabashi*, Kazuya Suzuki, and Shin'ichi Ishiwata (2013) *equal contribution
  Sci. Rep. 3, 2808 [Link].

• "Locally and globally coupled oscillators in muscle"
  Katsuhiko Sato, Yoshiki Kuramoto, Masako Ohtaki, Yuta Shimamoto, and Shin'ichi Ishiwata (2013)
  Phys. Rev. Lett. 111, 108104 [Link].

• "NF-κB-dependent and -independent pathways in the protective effects of activated protein C in hippocampal and cortical neurons at excitotoxicity"
  Lubov Gorbacheva, Svetlana Strukova, Vsevolod Pinelis, Shin’ichi Ishiwata, Rolf Stricker, and Georg Reiser (2013)
  Neurochem. Intl. 63, 101-111 [Link].

• "Responses of chromosome segregation machinery to mechanical perturbations"
  Takeshi Itabashi, Jun Takagi, Kazuya Suzuki, and Shin'ichi Ishiwata (2013)
  BIOPHYSICS 9, 73-78 [Link]. 

• "Protein-protein interactions in solution and their interplay with protein specific functions"
  Takaaki Sato, Toshiko Fukasawa, Togo Shimozawa, Teruyuki Komatsu, Hiromi Sakai, and Shin'ichi Ishiwata (2012)
  J. Phys. Soc. Jpn. 81, SA00.

• "Improvement of the yields of recombinant actin and myosin V-HMM in the insect cell/baculovirus system by the addition of nutrients to the high-density cell culture"
  Takashi Ohki, Sergey V. Mikhailenko, Tomomi Arai, Shuya Ishii, and Shin'ichi Ishiwata (2012)
  J. Muscle Res. Cell Motil. 33(5), 351–358 [Link].

• "Mass spectrometric screening of ligands with lower off-rate from a clicked-based pooled library"
  Satoshi Arai, Shota Hirosawa, Yusuke Oguchi, Madoka Suzuki, Atsushi Murata, Shin'ichi Ishiwata, and Shinji Takeoka (2012)
  ACS Comb. Sci. 14(8), 451–455 [Link].

• "Mechanical impulses can control metaphase progression in a mammalian cell"
  Takeshi Itabashi, Yasuhiko Terada, Kenta Kuwana, Tetsuo Kan, Isao Shimoyama, and Shin'ichi Ishiwata (2012)
  Proc. Natl. Acad. Sci. USA 109(19), 7320-7325 [Link].

• "Walking nanothermometers: Spatiotemporal temperature measurement of transported acidic organelles in single living cells"
  Kotaro Oyama, Masao Takabayashi, Yoshiaki Takei, Satoshi Arai, Shinji Takeoka, Shin'ichi Ishiwata, and Madoka Suzuki (2012)
  Lab Chip 12(9), 1591-1593 [Link].

• "Sarcomere imaging by quantum dots for the study of cardiac muscle physiology"
  Fuyu Kobirumaki-Shimozawa, Kotaro Oyama, Takahiro Serizawa, Akari Mizuno, Tatsuya Kagemoto, Togo Shimozawa, Shin'ichi Ishiwata, Satoshi Kurihara, and Norio Fukuda (2012)
  J. Biomed. Biotech. 2012, 313814 [Link]. 

• "Microscopic heat pulses induce contraction of cardiomyocytes without calcium transients"
  Kotaro Oyama, Akari Mizuno, Seine A. Shintani, Hideki Itoh, Takahiro Serizawa, Norio Fukuda, Madoka Suzuki, and Shin'ichi Ishiwata (2012)
  Biochem. Biophys. Res. Commun. 417, 607-612 [Link]. 

• "Quasiperiodic distribution of rigor cross-bridges along a reconstituted thin filament in a skeletal myofibril"
  Madoka Suzuki and Shin'ichi Ishiwata (2011)
  Biophys. J. 101, 2740-2748 [Link].

• "The role of tropomyosin domains in cooperative activation of the actin-myosin interaction"
  Yusuke Oguchi, Junji Ishizuka, Sarah E Hitchcock-DeGregori, Shin'ichi Ishiwata, and Masataka Kawai (2011)
  J. Mol. Biol. 414, 667-680 [Link].

• "Sarcomere length-dependent Ca2+ activation in skinned rabbit psoas muscle fibers: coordinated regulation of thin filament cooperative activation and passive force"
  Norio Fukuda, Takahiro Inoue, Mitsunori Yamane, Takako Terui, Fuyu Kobirumaki, Iwao Ohtsuki, Shin'ichi Ishiwata, and Satoshi Kurihara (2011)
  J. Physiol. Sci. 61(6), 515-523 [Link].

• "Real-time measurement of the length of a single sarcomere in rat ventricular myocytes: a novel analysis with quantum dots"
  Takahiro Serizawa, Takako Terui, Tatsuya Kagemoto, Akari Mizuno, Togo Shimozawa, Fuyu Kobirumaki, Shin'ichi Ishiwata, Satoshi Kurihara, and Norio Fukuda (2011)
  Am. J. Physiol. Cell Physiol. 301(5), C1116-C1127 [Link].

• "Depressed contractile performance and reduced fatigue resistance insingle skinned fibers of soleus muscle after long-term disuse in rats"
  Jun Udaka, Takako Terui, Iwao Ohtsuki, Keishi Marumo, Shin'ichi Ishiwata, Satoshi Kurihara, and Norio Fukuda (2011)
  J. Appl. Physiol. 111(4), 1080-1087 [Link].

• "Insights into the micro-mechanical properties of the metaphase spindle"
  Yuta Shimamoto, Yusuke T. Maeda, Shin'ichi Ishiwata, Albert J. Libchaber, and Tarun M. Kapoor (2011)
  Cell 145, 1062-1074 [Link].

• "The bidirectional depolymerizer MCAK generates force by disassembling both microtubule ends"
  Yusuke Oguchi, Seiichi Uchimura, Takashi Ohki, Sergey V. Mikhailenko, and Shin'ichi Ishiwata (2011)
  Nat. Cell Biol. 13, 846-852 [Link].

• "SPontaneous Oscillatory Contraction (SPOC): auto-oscillations observed in striated muscle at partial activation"
  James Erle Wolfe, Shin'ichi Ishiwata, Filip Braet, Renee Whan, Yingying Su, Sean Lal, and Cristobal G. dos Remedios (2011)
  Biophys. Rev. 3, 53-62 [Link].

• "A theory on auto-oscillation and contraction in striated muscle"
  Katsuhiko Sato, Masako Ohtaki, Yuta Shimamoto, and Shin'ichi Ishiwata (2011)
  Prog. Biophys. Mol. Biol. 105, 199-207 [Link].

• "Contractile system of muscle as an auto-oscillator"
  Shin'ichi Ishiwata, Yuta Shimamoto*, and Norio Fukuda* (2011) *equal contribution
  Prog. Biophys. Mol. Biol. 105, 187-198 [Link].

• "Two-dimensional periodic texture of actin filaments formed upon drying"
  Hajime Honda and Shin'ichi Ishiwata (2011)
  BIOPHYSICS 7, 11-19 [Link | PDF (2,070 KB)]. 

• "Regulatory mechanism of length-dependent activation in skinned porcineventricular muscle: role of thin filament cooperative activation in the Frank-Starling relation"
  Takako Terui*, Yuta Shimamoto*, Mitsunori Yamane, Fuyu Kobirumaki, Iwao Ohtsuki, Shin'ichi Ishiwata, Satoshi Kurihara, and Norio Fukuda (2010) *equal contribution
  J. Gen. Physiol. 136, 469-482 [Link].

• "Modulation of the mechano-chemical properties of myosin V by drebrin-E"
  Hiroaki Kubota, Ryoki Ishikawa, Takashi Ohki, Junji Ishizuka, Sergey V. Mikhailenko, and Shin'ichi Ishiwata (2010)
  Biochem. Biophys. Res. Commun. 400(4), 643-648 [Link].

• "Molecular motors as an auto-oscillator"
  Shin'ichi Ishiwata, Yuta Shimamoto, and Madoka Suzuki (2010)
  HFSP J. 4(3), 100-104 [Link | PDF (215 KB)].

• "A Potential Role of Actin Filament Polymerization/Depolymerization in Smooth Muscle Contraction"
  Masaru Watanabe, Shin'ichi Ishiwata, and Ying-Ming Liou (2010)
  Adapt. Med. 2(1), 23-28.

• "Insights into the mechanisms of myosin and kinesin molecular motors from the single-molecule unbinding force measurements"
  Sergey V. Mikhailenko, Yusuke Oguchi, and Shin'ichi Ishiwata (2010)
  J Royal Soc. Interface. 7, S295-S306 [Link].

• "Robust processivity of myosin V under off-axis loads"
  Yusuke Oguchi, Sergey V. Mikhailenko, Takashi Ohki, Adrian O. Olivares, Enrique M. De La Cruz, and Shin'ichi Ishiwata (2010)
  Nat. Chem. Biol. 6(4), 300-305 [Link].

• "Key residues on microtubule responsible for activation of kinesin ATPase"
  Seiichi Uchimura*, Yusuke Oguchi*, You Hachikubo, Shin'ichi Ishiwata, and Etsuko Muto (2010) *equal contribution
  EMBO J. 29, 1167-1175 [Link].

• "Titin-based regulations of diastolic and systolic functions ofmammalian cardiac muscle"
  Norio Fukuda, Takako Terui, Shin'ichi Ishiwata, and Satoshi Kurihara (2010)
  J. Mol. Cell. Cardiol. 48(5), 876-881 [Link].

• "Activated protein C prevents glutamate- and thrombin-induced activation of nuclear factor-κB in cultured hippocampal neurons"
  L. Gorbacheva, V. Pinelis, S. Ishiwata, S. Strukova, and G. Reiser (2010)
  Neurosci. 165(4), 1138-1146 [Link]. 

• 興味の赴くままに（リレーエッセイ：私が影響を受けた論文（8））」
  石渡信一(2021)
  生物物理 61(2), 119-20.

• 「1分子計測の躍進」
  石渡信一 (2019)
  日本物理学会誌 74, 386-38.

• 「動物運動を解き明かす創発的物理」（翻訳）
  石渡信一 (2018)
  パリティ 33(No.09), 23-3.

• 「生体分子マシンの歴史と未来」
  石渡信一、板橋岳志 (2017)
  「分子マシンの科学（日本化学会編）」化学同人 pp.37-4.

• 「生物分子機械」
  石渡信一、会誌編集委員会 (2017)
  日本物理学会誌 72.

• 「In vitro再構成による収縮環の形成機構の解明」
  宮崎牧人、石渡信一 (2016)
  生物物理 56(3), 174-17.

• 「細胞に働く力とエネルギー論」（翻訳）
  宮崎牧人、石渡信一 (2016)
  パリティ 31(No.2), 32-4.

• 「30年を振り返って」
  石渡信一 (2015)
  パリティ 30(No.9), 67-6.

• 「横紋筋のメカノバイオフィジックス：マクロからミクロへ」
  石渡信一、島本勇太、福田紀男 (2015)
  「メカノバイオロジー（曽我部正博編）」化学同人 pp.159-17.

• 「心筋収縮系にみる自励振動現象SPOC」
  石渡信一、佐藤勝彦 (2015)
  日本物理学会誌 70, 519-529.

• 「INTERVIEW: 細胞研究への新たなアプローチ」
  石渡信一 (2015)
  新鐘（早稲田大学） 81, 15-1.

• 「生物運動の物理」
  石渡信一 (2015)
  パリティ 30(No.4), 30-3.

• 原田慶恵・石渡信一 編「１分子生物学」化学同人

「１分子生物学の展開」石渡信一 (2014)「１分子生物学」化学同人 pp.1-7
「キネシン分子の単頭・双頭結合変換」石渡信一 (2014)「１分子生物学」化学同人 pp.61-62

• 「歩くナノ温度計」
  鈴木団、大山廣太郎、石渡信一 (2013)
  生物物理 53(3), 158-15.

• 「染色体分配装置の構造と機能の力学応答」
  板橋岳志、石渡信一 (2013)
  実験医学 31(2)増刊, 193-198 [Link].

• 「普通でない“普通の学会”」
  石渡信一 (2012)
  生物物理 52(2), 068-06.

• 「F-アクチン溶液の２次元乾燥パターン」
  本多元、石渡信一 (2011)
  生物物理 51(2), 9.

• 「BIOPHYSICSの活性化に向けて」
  石渡信一 (2011)
  生物物理 51(1), 44-4.

• 「創立50周年に想う」
  石渡信一 (2010)
  生物物理 50.

• 「自己組織化とは—生物」
  石渡信一 (2010)
  自己組織化ハンドブック（国武豊喜監修）、エヌ・ティー・エス、 第１章 第５節, 19-2.