Publications

Original papers｜ Review articles ｜ Book chapters

Original papers

2020

"Analysis of the stability of 70 housekeeping genes during iPS reprogramming."
Yulia Panina, Arno Germond, Tomonobu M. Watanabe
Scientific Reports 10, 21711, doi: 10.1038/s41598-020-78863-5 (Dec 2020)

"Following Embryonic Stem Cells, Their Differentiated Progeny, and Cell-State Changes During iPS Reprogramming by Raman Spectroscopy."
Arno Germond, Yulia Panina, Mikio Shiga, Hirohiko Niioka, Tomonobu M. Watanabe
Analytical Chemistry 92(22), 14915–14923, doi: 10.1021/acs.analchem.0c01800 (Oct 2020)

"Multiplexed 129Xe HyperCEST MRI Detection of Genetically Reconstituted Bacterial Protein Nanoparticles in Human Cancer Cells."
Ryota Mizushima, Kanako Inoue, Hideaki Fujiwara, Atsuko H. Iwane, Tomonobu M. Watanabe, Atsuomi Kimura
Contrast Media & Molecular Imaging 2020, 5425934. doi: 10.1155/2020/5425934 (Mar. 2020)

"An improved fluorescent protein-based expression reporter system that utilizes bioluminescence resonance energy transfer and peptide-assisted complementation."
Taishi Kakizuka, Akira Takai, Keiko Yoshizawa, Yasushi Okada, Tomonobu M Watanabe
Chemical Communications 56, 3625-3628. doi: 10.1039/c9cc08664a (Mar. 2020)

2019

"Advanced CUBIC tissue clearing for whole-organ cell profiling."
Katsuhiko Matsumoto, Tomoki T. Mitani, Shuhei A. Horiguchi, Junichi Kaneshiro, Tatsuya C. Murakami, Tomoyuki Mano, Hiroshi Fujishima, Ayumu Konno, Tomonobu M. Watanabe, Hirokazu Hirai, Hiroki R. Ueda
Nature Protocols 14, 3506-3537. doi: 10.1038/s41596-019-0240-9 (Dec. 2019)

"Linking substrate and nucleus via actin cytoskeleton in pluripotency maintenance of mouse embryonic stem cells."
Brit Gracy　David, Hideaki Fujita, Kyota Yasuda, Kazuko Okamoto, Yulia Panina, Junya Ichinose, Osamu Sato, Masanobu Horie, Taro Ichimura, Yasushi Okada, Tomonobu M Watanabe
Stem Cell Research 41, 101614, doi: 10.1016/j.scr.2019.101614 (Dec. 2019)

"Second harmonic generation polarization microscopy as a tool for protein structure analysis."
Junichi Kaneshiro, Yasushi Okada, Tomohiro Shima, Mika Tsujii, Katsumi Imada, Taro Ichimura, Tomonobu M. Watanabe
Biophysics and Physicobiology 16, 147-157, doi: 10.2142/biophysico.16.0_147 (Sep. 2019)

"Pairwise efficiency: a new mathematical approach to qPCR data analysis increases the precision of the calibration curve assay."
Yulia Panina, Arno Germond, Brit G. David, Tomonobu M. Watanabe
BMC Bioinformatics 201920, 295, doi:10.1186/s12859-019-2911-5 (May. 2019)

"Theoretical modeling reveals that regulatory T cells increase T cell-interaction with antigen-presenting cells for stable immune-tolerance."
Tomoyuki Yamaguchi, Shunsuke Teraguchi, Chikara Furusawa, Hiroaki Machiyama, Tomonobu M Watanabe, Hideaki Fujita, Shimon Sakaguchi, Toshio Yanagida
International Immunology, dxz043, doi:10.1093/intimm/dxz043 (May. 2019)

"Single-Cell Screening of Tamoxifen Abundance and Effect Using Mass Spectrometry and Raman-Spectroscopy."
Ahmed Ali, Yasmine Abouleila, Yoshihiro Shimizu, Eiso Hiyama, Tomonobu M. Watanabe, Toshio Yanagida, Arno Germond
Analtical Chemistry 91(4) 2710-2718, doi:10.1021/acs.analchem.8b04393 (Jan. 2019)

2018

"Kinesin-binding-triggered conformation switching of microtubules contributes to polarized transport."
Tomohiro Shima, Manatsu Morikawa, Junichi Kaneshiro, Taketoshi Kambara, Shinji Kamimura, Toshiki Yagi, Hiroyuki Iwamoto, Sotaro Uemura, Hideki Shigematsu, Mikako Shirouzu, Taro Ichimura, Tomonobu M. Watanabe, Ryo Nitta, Yasushi Okada, Nobutaka Hirokawa
Jounal of Cell Biology 217(12), 4164-4183, doi:10.1083/jcb.201711178 (Dec. 2018)

"Single cell analysis reveals a biophysical aspect of collective cell-state transition in embryonic stem cell differentiation"
Kazuko Okamoto, Arno Germond, Hideaki Fujita, Chikara Furusawa, Yasushi Okada, Tomonobu M. Watanabe
Scientific Reports 8, doi:10.1038/s41598-018-30461-2 (Aug. 2018)

"Cell type discrimination based on image features of molecular component distribution"
Arno Germond, Taro Ichimura, Liang-da Chiu, Katsumasa Fujita, Tomonobu M. Watanabe, Hideaki Fujita
Scientific Reports 8, doi:10.1038/s41598-018-30276-1 (Aug. 2018)

"Raman spectral signature reflects transcriptomic features of antibiotic resistance in Escherichia coli"
Arno Germond, Taro Ichimura, Takaaki Horinouchi, Hideaki Fujita, Chikara Furusawa, Tomonobu M. Watanabe
Communication Biology, doi:10.1038/s42003-018-0093-8 (Jul. 2018)

"Validation of Common Housekeeping Genes as Reference for qPCR Gene Expression Analysis During iPS Reprogramming Process"
Yulia Panina, Arno Germond, Tomonobu M. Watanabe
Scientific Reports 8, Article number: 8716, doi:10.1038/s41598-018-26707-8 (Jun. 2018)

2017

"Myosin X is recruited to nascent focal adhesions at the leading edge and induces multi-cycle filopodial elongation"
Kangmin He, Tsuyoshi Sakai, Yoshikazu Tsukasaki, Tomonobu M. Watanabe & Mitsuo Ikebe
Scientific Reports 7, Article number: 13685, doi:10.1038/s41598-017-06147-6 (Oct. 2017)

"The use of a genetically encoded molecular crowding sensor in various biological phenomena"
Hiroaki Machiyama, Takamitsu J. Morikawa, Kazuko Okamoto, Tomonobu M. Watanabe and Hideaki Fujita
Biophysics and Physicobiology, doi: 10.2142/biophysico.14.0_119 (Aug. 2017)

"In vivo analysis of protein crowding within the nuclear pore complex in interphase and mitosis"
Hide A. Konishi, Suguru Asai, Tomonobu M. Watanabe & Shige H. Yoshimura
Scientific Reports 7, Article number: 5709, doi:10.1038/s41598-017-05959-w (Jul. 2017)

"Raman spectroscopy as a tool for ecology and evolution"
Germond A, Kumar V, Ichimura T, Moreau J, Furusawa C, Fujita H, Watanabe TM.
J. R. Soc. Interface, doi:10.1098/rsif.2017.0174. (Jun. 2017)

"A novel c-Src recruitment pathway from the cytosol to focal adhesions"
Machiyama H, Yamaguchi T, Watanabe TM, Fujita H.
FEBS Lett., doi:10.1002/1873-3468.12696 (May. 2017)

"Human Myosin VIIa Is a Very Slow Processive Motor Protein on Various Cellular Actin Structures"
Sato O, Komatsu S, Sakai T, Tsukasaki Y,
Tanaka R, Mizutani T, Watanabe TM, Ikebe R, Ikebe M.
J Biol Chem., doi:10.1038/srep43569 (May. 2017)

"Activated full-length myosin-X moves processively on filopodia with large steps toward diverse two-dimensional directions"
Sato O, Jung HS, Komatsu S, Tsukasaki Y, Watanabe TM, Homma K, Ikebe M.
Scientific Reports 7, Article number: 44237, doi: 10.1038/srep44237 (Mar. 2017)

"Protein expression guided chemical profiling of living cells by the simultaneous observation of Raman scattering and anti-Stokes fluorescence emission"
Liang-da Chiu, Taro Ichimura, Takumasa Sekiya, Hiroaki Machiyama, Tomonobu Watanabe, Hideaki Fujita, Takeaki Ozawa & Katsumasa Fujita
Scientific Reports 7, Article number: 43569, doi:10.1038/srep43569 (Mar. 2017)

2016

"Non-label immune cell state prediction using Raman spectroscopy"
Taro Ichimura, Liang-da Chiu, Katsumasa Fujita, Hiroaki Machiyama, 
Tomoyuki Yamaguchi, Tomonobu M. Watanabe & Hideaki Fujita
Scientific Reports 6, Article number: 37562, doi:10.1038/srep37562 (Nov. 2016)

"Simultaneous nano-tracking of multiple motor proteins via spectral discrimination of quantum dots"
Taishi Kakizuka, Keigo Ikezaki, Junichi Kaneshiro, Hideaki Fujita, Tomonobu M. Watanabe, Taro Ichimura
Biomedical Optics Express,Vol. 7, No. 7, pp. 2475-2493, doi: 10.1364/BOE.7.002475 (Jun. 2016)

"Dependence of fluorescent protein brightness on protein concentration in solution and enhancement of it"
Takamitsu J. Morikawa, Hideaki Fujita, Akira Kitamura, Takashi Horio, Johtaro Yamamoto, Masataka Kinjo, Akira Sasaki, Hiroaki Machiyama, Keiko Yosizawa, Taro Ichimura, Katsumi Imada, Takeharu Nagai, Tomonobu M. Watanabe
Scientific Reports 6, Article number: 22342, doi:10.1038/srep22342 (Mar. 2016)

"Full control of polarization state with a pair of electro-optic modulators for polarization-resolved optical microscopy"
Junichi Kaneshiro, Tomonobu. M. Watanabe, Hideaki Fujita, Taro Ichimura
Applied Optics, 55(5), 1082-1089, doi:10.1364/AO.55.001082 (Jan. 2016)

2015

"SH3 domain of c-Src governs its dynamics at focal adhesions and the cell membrane"
Hiroaki Machiyama, Tomoyuki Yamaguchi, Yasuhiro Sawada, Tomonobu M. Watanabe, Hideaki Fujita
FEBS Journal, 282(20), 4034-4055, doi:10.1111/febs.13404 (Sep. 2015)

"Predictive diagnosis of the risk of breast cancer recurrence after surgery by single-particle quantum dot imaging"
Kohsuke Gonda, Minoru Miyashita, Hideo Higuchi, Hiroshi Tada, Tomonobu M. Watanabe, Mika Watanabe, Takanori Ishida, Noriaki Ohuchi
Scientific Reports 5, Article number: 14322, doi:10.1038/srep14322 (Sep. 2015)

"Visualizing the appearance and disappearance of the attractor of differentiation using Raman spectral imaging"
Taro Ichimura, Liang-da Chiu, Katsumasa Fujita, Hiroaki Machiyama, Satoshi Kawata, Tomonobu M. Watanabe, Hideaki Fujita
Scientific Reports, 5, Article number: 11358, doi:10.1038/srep11358 (Jun. 2015)

"Particle Simulation of Oxidation Induced Band 3 Clustering in Human Erythrocytes"
Hanae Shimo, Satya Nanda Vel Arjunan, Hiroaki Machiyama, Taiko Nishino, Makoto Suematsu, Hideaki Fujita, Masaru Tomita, Koichi Takahashi
PLoS Comput. Biol., 11(6): e1004210. doi:10.1371 (Jun. 2015)

"Gene dynamics of core transcription factors for pluripotency in embryonic stem cells"
Brit G. David, Kazuko Okamoto, Taishi Kakizuka, Taro Ichimura, Tomonobu M. Watanabe, Hideaki Fujita
J. Biosci. Bioeng., 119(4), 406-409. (Apr. 2015)

"Comprehensive chemical secretory measurement of single cells trapped in a micro-droplet array with mass spectrometry"
Hideaki Fujita, Tsuyoshi Esaki, Tsutomu Masujima, Akitsu Hotta, Soo Hyeon Kim, Hiroyuki Noji, Tomonobu M. Watanabe
RSC Adv., 5, 16968-16971. (Jan. 2015)

"Fluid driving system for a micropump by differentiating iPS cells into cardiomyocytes on a tent-like structure"
Yo Tanaka, Hideaki Fujita
Sensors and Actuators B: Chemical, 210, 267-272. (Jan. 2015)

2014

"Displacement of p130Cas from focal adhesions links actomyosin contraction to cell migration"
Hiroaki Machiyama, Hiroaki Hirata, Xia Kun Loh, Madhu Mathi Kanchi, Hideaki Fujita, Song Hui Tan, Keiko Kawauchi, Yasuhiro Sawada
J. Cell. Sci., 127 (16), 3440-3450. (Jun. 2014)

"Culturing of mouse and human cells on soft substrates promote the expression of stem cell markers"
Sayaka Higuchi, Tomonobu M. Watanabe, Keiko Kawauchi, Taro Ichimura, Hideaki Fujita
J Biosci Bioeng., 117(6), 749-755 (Jun. 2014)

"Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis"
Etsuo A. Susaki, Kazuki Tainaka, Dimitri Perrin, Fumiaki Kishino, Takehiro Tawara, Tomonobu M. Watanabe, Chihiro Yokoyama, Hirotaka Onoe, Megumi Eguchi, Shun Yamaguchi, Takaya Abe, Hiroshi Kiyonari, Yoshihiro Shimizu, Atsushi Miyawaki, Hideo Yokota, Hiroki R. Ueda
Cell, 157(3), 726-739 (Apr. 2014)

"Induction of functional tissue-engineered skeletal muscle constructs by defined electrical stimulation"
Akira Ito, Yasunori Yamamoto, Masanori Sato, Kazushi Ikeda, Masahiro Yamamoto, Hideaki Fujita, Eiji Nagamori, Yoshinori Kawabe, Masamichi Kamihira
Scientific Reports, 4:4781. doi:10.1038/srep04781 (Apr. 2014)

"Direct evidence of polar nature of ferroelastic twin boundaries in CaTiO3 obtained by second harmonic generation microscope"
Hiroko Yokota, H. Usami, R. Haumont, P. Hicher, Junichi Kaneshiro, E. K. H. Salje, Yoshiaki Uesu
Phys. Rev., B 89(14), 144109 (Apr. 2014)

"Visualizing Cell State Transition Using Raman Spectroscopy"
Taro Ichimura, Liang-da Chiu, Katsumasa Fujita, Satoshi Kawata, Tomonobu M. Watanabe, Toshio Yanagida, Hideaki Fujita
PLoS One, 9(1), e84478 (Jan. 2014)

2013

"Tip-enhanced nano-Raman analytical imaging of locally induced strain distribution in carbon nanotubes"
Taka-aki Yano, Taro Ichimura, Shota Kuwahara, Fekhra H’Dhili, Kazumasa Uetsuki, Yoshito Okuno, Prabhat Verma, and Satoshi Kawata
Nature Communications 4, 2592 (Oct. 2013)

"Metabolic flux analysis of genetically engineered Saccharomyces cerevisiae that produces lactate under micro-aerobic conditions"
Eiji Nagamori, Kazunori Shimizu, Hideaki Fujita, Kenro Tokuhiro, Nobuhiro Ishida, Haruo Takahashi
Bioprocess Biosyst Eng., 36(9), 1261-1265 (Sep. 2013)

"Glycine Insertion Makes Yellow Fluorescent Protein Sensitive to Hydrostatic Pressure"
Tomonobu M. Watanabe, Katsumi Imada, Keiko Yoshizawa, Masayoshi Nishijima, Chiaki Kato, Fumiyoshi Abe, Takamitsu J. Morikawa, Miki Kinoshita, Hideaki Fujita, Toshio Yanagida
PLoS ONE, 8(8), e73212 (Aug. 2013)

"Four-Dimensional Spatial Nanometry of Single Particles in Living Cells Using Polarized Quantum Rods"
Tomonobu M. Watanabe, Fumihiko Fujii, Takashi Jin, Eiji Umemoto, Masayuki Miyasaka, Hideaki Fujita, Toshio Yanagida
Biophysical Journal, 105(3), 555-564 (Aug. 2013)

"Rab6a releases LIS1 from a dynein idling complex and activates dynein for retrograde movement"
Masami Yamada, Kanako Kumamoto, Shintaro Mikuni, Yoshiyuki Arai, Masataka Kinjo, Takeharu Nagai, Yoshikazu Tsukasaki, Tomonobu M Watanabe, Mitsuru Fukui, Mingyue Jin, Shiori Toba, Shinji Hirotsune
Nature Communications 4, 2033 (Jun. 2013)

"Far-field free tapping-mode tip-enhanced Raman microscopy"
Jun Yu, Yuika Saito, Taro Ichimura, Satoshi Kawata, Prabhat Verma
Applied Physics Letters, 102(12), 123110 (Mar. 2013)

"Heart extracellular matrix supports cardiomyocyte differentiation of mouse embryonic stem cells"
Sayaka Higuchi, Qingsong Lin, Jigang Wang, Teck Kwang Lim,Shashikant B. Joshi, Ganesh Srinivasan Anand, Maxey C.M. Chung, Michael P. Sheetz, Hideaki Fujita
J Biosci Bioeng, 115(3), 320-325 (Mar. 2013)

"Improving spinning disk confocal microscopy by preventing pinhole cross-talk for intravital imaging"
Togo Shimozawa, Kazuo Yamagata, Takefumi Kondo, Shigeo Hayashi, Atsunori Shitamukai, Daijiro Konno, Fumio Matsuzaki, Jun Takayama, Shuichi Onami, Hiroshi Nakayama, Yasuhito Kosugi, Tomonobu M. Watanabe, Katsumasa Fujita, Yuko Mimori-Kiyosue
PNAS, 110(9), 3399-3404 (Feb. 2013)

"Fed-batch system for cultivating genetically engineered yeast that produces lactic acid via the fermentative promoter"
Eiji Nagamori, Hideaki Fujita, Kazunori Shimizu, Kenro Tokuhiro, Nobuhiro Ishida, Haruo Takahashi
J Biosci Bioeng, 115(2), 193-195 (Feb. 2013)

2012

"Multilayered, core/shell nanoprobes based on magnetic ferric oxide particles and quantum dots for multimodality imaging of breast cancer tumors"
Qiang Ma, Yuko Nakane, Yuki Mori, Miyuki Hasegawa, Yoshichika Yoshioka, Tomonobu M.Watanabe, Kohsuke Gonda, Noriaki Ohuchi, Takashi Jin
Biomaterials, 33(33), 8486-8494 (Nov. 2012)

"Distinct modulated pupil function system for real-time imaging of living cells"
Tomonobu M.Watanabe, Yoshikazu Tsukasaki, Hideaki Fujita, Taro Ichimura, Tatsuya Saitoh, Shizuo Akira, Toshio Yanagida
PLoS One, 7(9), e44028 (Sep. 2012)

"Engineering strain-sensitive yellow fluorescent protein"
Taro Ichimura, Hideaki Fujita, Keiko Yoshizawa, Tomonobu M.Watanabe
Chemical Communications, 48(63), 7871-7873 (Aug. 2012)

"p130Cas-dependent actin remodelling regulates myogenic differentiation"
Keiko Kawauchi, Wee Wee Tan, Keigo Araki, Farhana Binte Abu Bakar, Minsoo Kim, Hideaki Fujita, Hiroaki Hirata, Yasuhiro Sawada
Biochem J., 445(3), 323-332 (Aug. 2012)

"Atg9 vesicles are an important membrane source during early steps of autophagosome formation"
Hayashi Yamamoto, Soichiro Kakuta, Tomonobu M.Watanabe, Akira Kitamura, Takayuki Sekito, Chika Kondo-Kakuta, Rie Ichikawa, Masataka Kinjo, Yoshinori Ohsumi
Journal of Cell Biology, 198(2), 219-233 (Jul. 2012)

"Subnanometric stabilization of plasmon-enhanced optical microscopy"
Taka-aki Yano, Taro Ichimura, Shota Kuwahara, Prabhat Verma, Satoshi Kawata
Nanotechnology, 23(20), 205503 (May, 2012)

"Chromatin plasticity as a differentiation index during muscle differentiation of C2C12 myoblasts"
Tomonobu M.Watanabe, Sayaka Higuchi, Keiko Kawauchi, Yoshikazu Tsukasaki, Taro Ichimura, Hideaki Fujita
Biochem. Biophys. Res. Commun., 418(4), 742-747 (Feb. 2012)

Review articles

Book chapters