博士（工学）, Tokyo University

A large-scale targeted proteomics of plasma extracellular vesicles shows utility for prognosis prediction subtyping in colorectal cancer.
Kasahara, K., Narumi, R., Nagayama, S., Masuda, K., Esaki, T., Obama, K., *Tomonaga, T., Sakai, Y., *Shimizu, Y., *Adachi, J.
Cancer Med., 12, 7616-7626, 2023

ePURE_JSBML: A tool for constructing a deterministic model of a reconstituted Escherichia coli protein translation system with a user-specified nucleic acid sequence.
*Shimizu, Y., Tanimura, N., Matsuura, T.
Adv. Biol., 7, e2200177-e2200177, 2023

Ebola virus-like particles reprogram cellular metabolism.
Tang, H., Abouleila, Y., Saris, A., Shimizu, Y., Ottenhoff, T. H. M., *Mashaghi, A.
J. Mol. Med., 101, 557-568, 2023

Versatile and multiplexed mass spectrometry-based absolute quantification with cell-free-synthesized internal standard peptides.
Masuda, K., Kasahara, K., Narumi, R., Shimojo, M., *Shimizu, Y.
J. Proteomics, 251, 104393, 2022

In vitro reconstitution of the Escherichia coli 70S ribosome with a full set of recombinant ribosomal proteins.
Aoyama, R., Masuda, K., Shimojo, M., Kanamori, T., Ueda, T., *Shimizu, Y.
J. Biochem., 171, 227-237, 2022

Efficient and precise protein synthesis in a cell-free system using a set of in vitro transcribed tRNAs with nucleotide modifications.
Amikura, K., Hibi, K., *Shimizu, Y.
Methods Mol., 2433, 151-168, 2022

Cell-Free Synthesis of Human Endothelin Receptors and Its Application to Ribosome Display.
Nakai, H., Isshiki, K., Hattori, M., Maehira, H., Yamaguchi, T., Masuda, K., Shimizu, Y., Watanabe, T., Hohsaka, T., Shihoya, W., Nureki, O., Kato, Y., Watanabe, H., *Matsuura, T.
Anal. Chem., (94), 3831-3839, 2022

Tracking metabolites at single-cell resolution reveals metabolic dynamics during plant mitosis.
Okubo-Kurihara, E., Ali, A., Hiramoto, M., Kurihara, Y., Abouleila, Y., Abdelazem, E. M., Kawai, T., Makita, Y., Kawashima, M., Esaki, T., Shimada, H., Mori, T., Hirai, M. Y., Higaki, T., Hasezawa, S., Shimizu, Y., Masujima, T., *Matsui, M.
Plant Physiol., 189, 459-464, 2022

Capillary microsampling-based single-cell metabolomics by mass spectrometry and its applications in medicine and drug discovery.
Abouleila Y., Ali, A., Masuda, K., Mashaghi, A., *Shimizu, Y.
Cancer Biomark., 33, 437-447, 2022

A red light-responsive photoswitch for deep tissue optogenetics.
Kuwasaki, Y., Suzuki, K., Yu, G., Yamamoto, S., Otabe, T., Kakihara, Y., Nishiwaki, M., Miyake, K., Fushimi, K., Bekdash, R., Shimizu, Y., Narikawa, R., Nakajima, T., Yazawa, M., *Sato, M.
Nat. Biotechnol., 40, 1672-1679, 2022

Transfer RNA Synthesis-Coupled Translation and DNA Replication in a Reconstituted Transcription/Translation System.
Miyachi, R., Shimizu, Y., *Ichihashi, N.
ACS Synth. Biol., 11, 2791-2799, 2022

Direct infusion nano-electrospray ionization mass spectrometry for therapeutic drug monitoring of ciprofloxacin and its metabolites in human saliva.
Demeiry, M. E., Ali, A., Abouleila, Y., Zarad, W., El-Gendy, H, Salam, R. A., Hadad, G., Shimizu, Y., Masujima, T., *Emara, S.
J. Pharm. Biomed. Anal., 195(113866), 2021

Boundary-Free Ribosome Compartmentalization by Gene Expression on a Surface.
Levy, M., Falkovich, R., Vonshak, O., Bracha, D., Tayar, A. M., Shimizu, Y., Daube, S. S., *Bar-Ziv, R. H.
ACS Synth. Biol., 10, 609-619, 2021

Antisense Oligonucleotide Modified with Disulfide Units Induces Efficient Exon Skipping in mdx Myotubes through Enhanced Membrane Permeability and Nucleus Internalization.
Hiraoka, H., Shu, Z., Tri Le, B., Masuda, K., Nakamoto, K., Fangjie, L., Abe, N., Hashiya, F., Kimura, Y., Shimizu, Y., Veedu, R. N., *Abe, H.
ChemBioChem, 22, 3437-3442, 2021

Quantification and targeted detection of ciprofloxacin in dosage form and human urine by direct injection nano-electrospray ionization multi-stage mass spectrometry.
Demeiry, M. E., Ali, A., Abouleila, Y., Shimizu, Y., Masujima, T., Salam, R. A., Hadad, G., *Emara, S.
Microchem. J., 153, 104534, 2020

In vitro reconstitution of functional small ribosomal subunit assembly for comprehensive analysis of ribosomal elements in E. coli.
Shimojo, M., Amikura, K., Masuda, K., Kanamori, T., Ueda, T., *Shimizu, Y.
Commun. Biol., 3, 142, 2020

Versatile whole-organ/body staining and imaging based on electrolyte-gel properties of biological tissues.
*Susaki, E. A., Shimizu, C., Kuno, A., Tainaka, K., Li, X., Nishi, K., Morishima, K., Ono, H., Ode, K. L., Saeki, Y., Miyamichi, K., Isa, K., Yokoyama, C., Kitaura, H., Ikemura, M., Ushiku, T., Shimizu, Y., Saito, T., Saido, T. C., Fukayama, M., Onoe, H., Touhara, K., Isa, T., Kakita, A., Shibayama, M., *Ueda, H. R.
Nat. Commun., 11, 1982, 2020

Chemically synthesized circular RNAs with phosphoramidate linkages enable rolling circle translation.
Nakamoto, K., Abe, N., Tsuji, G., Kimura, Y., Tomoike, F., Shimizu, Y., *Abe, H.
Chem. Commun., 56, 6217-6220, 2020

Prospects for Comprehensive Analyses of Circulating Tumor Cells in Tumor Biology.
Aoki, M., Shoji, H., Kashiro, A., Takeuchi, K., Shimizu, Y., *Honda, K.
CANCERS, 12, 1135, 2020

Mass spectrometry-based absolute quantification of amyloid proteins in pathology tissue specimens: Merits and limitations.
Ogawa, M., Shintani-Domoto, Y., Nagashima, Y., Ode, K. L., Sato, A., Shimizu, Y., Ohashi, K., Roehrl, M. H. A., Ushiku, T., Ueda, H. R., *Fukayama, M.
PLOS ONE, 15, e0235143, 2020

Reconstituted cell-free protein synthesis using in vitro transcribed tRNAs.
Hibi, K., Amikura, K., Sugiura, N., Masuda, K., Ohno, S., Yokogawa, T., Ueda, T., *Shimizu, Y.
Commun. Biol., 3, 350, 2020

Phosphorothioate Modification of mRNA Accelerates the Rate of Translation Initiation to Provide More Efficient Protein Synthesis.
Kawaguchi, D., Kodama, A., Abe, N., Takebuchi, K., Hashiya, F., Tomoike, F., Nakamoto, K., Kimura, Y., *Shimizu, Y., *Abe, H.
Angew. Chem. Int. Ed. Engl., 59, 17403-17407, 2020

Live single cell mass spectrometry reveals cancer-specific metabolic profiles of circulating tumor cells.
Abouleila, Y., Onidani, K., Ali, A., Shoji, H., Kawai, T., Lim, C. T., Kumar, V., Okaya, S., Kato, K., Hiyama, E., Yanagida, T., Masujima, T., *Shimizu, Y., *Honda, K.
Cancer Sci., 110, 697-706, 2019

High-resolution crystal structure of peptidyl-tRNA hydrolase from Thermus thermophilus.
Matsumoto, A., Uehara, Y., Shimizu, Y., Ueda, T., Uchiumi, T., *Ito, K.
Proteins, 87, 226-235, 2019

Single-cell screening of tamoxifen abundance and effect using mass spectrometry and Raman-spectroscopy.
Ali, A., Abouleila, Y., Shimizu, Y., Hiyama, E., Watanabe, T. M., Yanagida, T., *Germond, A.
Anal. Chem., 91, 2710-2718, 2019

Phosphorogenic and spontaneous formation of tris(bipyridine)ruthenium in peptide scaffolds.
Karimiavargania, M., Tada, S., Minagawa, N., Shimizu, Y., Hirose, T., Ito, Y., *Uzawa, T.
J. Pept. Sci., 25, e3158, 2019

Single-cell metabolomics by mass spectrometry: Advances, challenges, and future applications.
Ali, A., Abouleila, Y., Shimizu, Y., Hiyama, E., Emara, S., *Mashaghi, A., *Hankemeier, T.
Trends Analyt. Chem., 120, 115436, 2019

A three-dimensional single-cell-resolution whole-brain atlas using CUBIC-X expansion microscopy and tissue clearing.
Murakami, T. C., Mano, T., Saikawa, S., Horiguchi, S. A., Shigeta, D., Baba, K., Sekiya, H., Shimizu, Y., Tanaka, K. F., Kiyonari, H., Iino, M., Mochizuki, H., Tainaka, K., *Ueda, H. R.
Nat. Neurosci., 21, 625-637, 2018

Quantitative Characterization of Translational Riboregulators Using an in Vitro Transcription-Translation System.
Senoussi, A., Lee Tin Wah, J., Shimizu, Y., Robert, J., Jaramillo, A., Findeiss, S., Axmann, I. M., *Estevez-Torres, A.
ACS Synth. Biol., 7, 1269-1278, 2018

Cell-free synthesis of stable isotope-labeled internal standards for targeted quantitative proteomics.
Narumi, R., Masuda, K., Tomonaga, T., Adachi, J., Ueda, H. R., *Shimizu, Y.
Synth. Syst. Biotechnol., 3, 97-104, 2018

Robustness of a reconstituted Escherichia coli protein translation system analyzed by computational modeling.
*Matsuura, T., Hosoda, K., Shimizu, Y.
ACS Synth. Biol., 7, 1964-1972, 2018

Chemical Landscape for Tissue Clearing Based on Hydrophilic Reagents.
Tainaka, K., Murakami, T. C., Susaki, E. A., Shimizu, C., Saito, R., Takahashi, K., Hayashi-Takagi, A., Sekiya, H., Arima, Y., Nojima, S., Ikemura, M., Ushiku, T., Shimizu, Y., Murakami, M., Tanaka, K. F., Iino, M., Kasai, H., Sasaoka, T., Kobayashi, K., Miyazono, K., Morii, E., Isa, T., Fukayama, M., Kakita, A., *Ueda, H. R.
Cell Rep., 24, 2196-2210. e9, 2018

Reconstitution of 30S ribosomal subunits in vitro using ribosome biogenesis factors.
Tamaru, D., *Amikura, K., Shimizu, Y., Nierhaus, K. H., Ueda, T.
RNA, 24, 1512-1519, 2018

G-Protein Coupled Receptor Protein Synthesis on a Lipid Bilayer Using a Reconstituted Cell-Free Protein Synthesis System.
Gessesse, B., Nagaike, T., Nagata, K., Shimizu, Y., *Ueda, T.
Life (Basel), 8, e54, 2018

Reaction dynamics analysis of a reconstituted Escherichia coli protein translation system by computational modeling.
*Matsuura, T., Tanimura, N., Hosoda, K., Yomo, T., *Shimizu, Y.
Proc. Natl. Acad. Sci. U. S. A., 114, E1336-E1344, 2017
Corresponding

Mass spectrometry-based absolute quantification reveals rhythmic variation of mouse circadian clock proteins.
#Narumi, R., #*Shimizu, Y., Ukai-Tadenuma, M., Ode, K. L., Kanda, G. N., Shinohara, Y., Sato, A., Matsumoto, K., *Ueda, H. R.
Proc. Natl. Acad. Sci. U. S. A., 113, E3461-E3467, 2016
Lead

Mammalian Reverse Genetics without Crossing Reveals Nr3a as a Short-Sleeper Gene.
Sunagawa, G. A., Sumiyama, K., Ukai-Tadenuma, M., Perrin, D., Fujishima, H., Ukai, H., Nishimura, O., Shi, S., Ohno, R., Narumi, R., Shimizu, Y., Tone, D., Ode, K. L., Kuraku, S., *Ueda, H. R.
Cell Rep., 14, 662-677, 2016

Integration of a reconstituted cell-free protein-synthesis system on a glass microchip.
#*Tanaka, Y. #*Shimizu, Y.
Anal. Sci., 31, 67-71, 2015
Lead, Corresponding

The PURE System for Protein Production.
Shimizu, Y., Kuruma, Y., Kanamori, T., *Ueda, T.
Methods Mol. Biol., 1118, 275-284, 2014

Biochemical aspects of bacterial strategies for handling the incomplete translation processes.
*Shimizu, Y.
Front. Microbiol., 5, 170, 2014

Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis.
Susaki, E. A., Tainaka, K., Perrin, D., Kishino, F., Tawara, T., Watanabe, T. M., Yokoyama, C., Onoe, H., Eguchi, M., Yamaguchi, S., Abe, T., Kiyonari, H., Shimizu, Y., Miyawaki, A., Yokota, H., *Ueda, H. R.
Cell, 157, 726-739, 2014

Crystallization and preliminary X-ray analysis of peptidyl-tRNA hydrolase from Thermus thermophilus HB8.
Matsumoto, A., Shimizu, Y., Takemoto, C., Ueda, T., Uchiumi, T., *Ito, K.
Acta. Crystallogr. Sect. F. Struct. Biol. Cryst. Commun., 69, 332-335, 2013

Structural basis for the substrate recognition and catalysis of peptidyl-tRNA hydrolase.
*Ito, K., Murakami, R., Mochizuki, M., Qi, H., Shimizu, Y., Miura, K. I., Ueda, T., Uchiumi, T.
Nucleic Acids Res., 40, 10521-10531, 2012

ArfA recruits RF2 into stalled ribosomes.
*Shimizu, Y.
J. Mol. Biol., 423, 624-631, 2012

Crystal structure analysis of the translation factor RF3 (release factor 3).
Kihira, K. Shimizu, Y., Shomura, Y., Shibata, N., Kitamura, M., Nakagawa, A, Ueda, T., Ochi, K., *Higuchi, Y.
FEBS Lett., 586, 3705-3709, 2012

Robust in vitro affinity maturation strategy based on interface-focused high-throughtput mutational scanning.
*Fujino, Y., Fujita, R., Wada K., Fujishige, K., Kanamori, T., Hunt, L., Shimizu, Y., *Ueda, T.
Biochem. Biophys. Res. Commun., 428, 395-400, 2012

Single molecule imaging of the trans-translation entry process via anchoring of the tagged ribosome.
Zhou Z. P., Shimizu, Y., *Tadakuma, T., Taguchi, H., Ito, K., Ueda, T.
J. Biochem., 149, 609-618, 2011

Application of micro-reactor chip technique for millisecond quenching of deuterium incorporation into 70S ribosomal protein complex.
Yamamoto, T., Shimizu, Y., Ueda, T., Shiro, Y., *Suematsu, M.
Int. J. Mass Spectrom., 302, 132-138, 2011

Crystallization and preliminary X-ray analysis of peptidyl-tRNA hydrolase from Escherichia coli in complex with the acceptor-TYC domain of tRNA.
*Ito, K., Qi, H., Shimizu, Y., Murakami, R., Miura, K. I., Ueda, T., Uchiumi, T.
Acta. Crystallogr. Sect. F. Struct. Biol. Cryst. Commun., 67, 1566-1569, 2011

Mg2+ dependence of 70 S ribosomal protein flexibility revealed by hydrogen/deuterium exchange and mass spectrometry.
Yamamoto, T., Shimizu, Y., Ueda, T., *Shiro, Y.
J. Biol. Chem., 285, 5646-5652, 2010

PURE technology.
Shimizu, Y., *Ueda, T.
Methods Mol. Biol., 607, 11-21, 2010

A highly controllable reconstituted cell-free system -- a breakthrough in protein synthesis research.
Ohashi, H., Kanamori, T., Shimizu, Y., *Ueda, T.
Curr. Pharm. Biotechnol., 11, 267-271, 2010

Epitope mapping using ribosome display in a reconstituted cell-free protein synthesis system.
Osada, E., *Shimizu, Y., Akbar, B. K., Kanamori, T., Ueda, T.
J. Biochem., 145, 593-700, 2009

Real-time monitoring of cell-free translation on a quartz-crystal microbalance.
Takahashi, S., Iida, M., Furusawa, H., Shimizu, Y., Ueda, T., *Okahata, Y.
J. Am. Chem. Soc., 131, 9326-9332, 2009

70S ribosomes bind to Shine-Dalgarno sequences without required dissociations.
Takahashi, S., Akita, R., Matsuno, H., Furusawa, H., Shimizu, Y., Ueda, T., *Okahata, Y.
ChemBioChem, 9, 870-873, 2008

Single molecule imaging of full protein synthesis by immobilized ribosomes.
Uemura, S., Iizuka, R., Ueno, T., Shimizu, Y., Taguchi, H., Ueda, T., Puglisi, J. D., *Funatsu, T.
Nucleic Acids Res., 36, e70, 2008

Efficient protein selection based on ribosome display system with purified components.
Ohashi, H., *Shimizu, Y., Ying, B. W., Ueda, T.
Biochem. Biophys. Res. Commun., 352, 270-276, 2007
Corresponding

Ribosomal protein S1 is not essential for the trans-translation machinery.
Qi, H., *Shimizu, Y., Ueda, T.
J. Mol. Biol., 386, 845-852, 2007
Corresponding

Protein-based peptide-bond formation by aminoacyl-tRNA protein transferase.
Watanabe, K., Toh, Y., Suto, K., Shimizu, Y., Oka, N., Wada, T., *Tomita, K.
Nature, 449, 867-871, 2007

EF-Tu mutants expand amino acid tolerance of protein biosynthesis system.
Doi, Y., *Ohtsuki, T., Shimizu, Y., Ueda, T., *Sisido, M.
J. Am. Chem. Soc., 129, 14458-14462, 2007

Kinetic analysis of the effects of translation enhancers in translation initiation.
Takahashi, S., Furusawa, H., Shimizu, Y., Ueda, T., *Okahata, Y.
Nucleic Acids Symp. Ser. (Oxf)., 51, 45-46, 2007

Crystal structures of leucyl/phenylalanyl-tRNA-protein transferase and its complex with an aminoacyl-tRNA analog.
#Suto, K., #Shimizu, Y., Watanabe, K., Ueda, T., Fukai, S., Nureki, O. *Tomita, K.
EMBO J., 25(5942), 5950, 2006
Lead

SmpB triggers GTP hydrolysis of elongation factor Tu on ribosomes by compensating for the lack of codon-anticodon interaction during trans-translation initiation.
Shimizu, Y., *Ueda, T.
J. Biol. Chem., 281, 15987-15996, 2006

Cell-free translation systems for protein engineering.
Shimizu, Y., Kuruma, Y., Ying, B. W., Umekage, S., *Ueda, T.
FEBS J., 273, 4133-4140, 2006

Kinetic analysis of ribosome binding process onto mRNA using a quartz-crystal microbalance.
Takahashi, S., Akita, R., Furusawa, H., Shimizu, Y., Ueda, T., *Okahata, Y.
Nucleic Acids Symp. Ser., 50, 49-50, 2006

Esterification of Escherichia coli tRNAs with D-histidine and D-lysine by aminoacyl-tRNA synthetases.
Takayama, T., Ogawa, T., Hidaka, M., Shimizu, Y., Ueda, T., *Masaki, H.
Biosci. Biotechnol. Biochem., 69, 1040-1041, 2005

Protein synthesis by pure translation systems.
Shimizu, Y., Kanamori, T., *Ueda, T.
Methods, 36, 299-304, 2005

Development of a minimal cell-free translation system for the synthesis of presecretory and integral membrane proteins.
Kuruma, Y., Nishiyama, K., Shimizu, Y., Muller, M., *Ueda, T.
Biotechnol. Prog., 21, 1243-1251, 2005

Evidence for the translation initiation of leaderless mRNAs by the intact 70 S ribosome without its dissociation into subunits in eubacteria.
Udagawa, T., Shimizu, Y., *Ueda, T.
J. Biol. Chem., 279, 8539-8546, 2004

A point mutation in ribosomal protein L7/L12 reduces its ability to form a compact dimer structure and to assemble into the GTPase center.
Nomura, T., Mochizuki, R., Dabbs, E. R., Shimizu, Y., Ueda, T., Hachimori, A., *Uchiumi, T.
Biochemistry, 42, 4691-4698, 2003

A novel screening system for self-mRNA targeting proteins.
Ying, B. W., Suzuki, T., Shimizu, Y., *Ueda, T.
J. Biochem., 133, 485-491, 2003

The role of SmpB protein in trans-translation.
Shimizu, Y., *Ueda, T.
FEBS Lett., 514, 74-77, 2002
Lead

Cell-free translation reconstituted with purified components.
Shimizu, Y., Inoue, A., Tomari, Y., Suzuki, T., Yokogawa, T., Nishikawa, K., *Ueda, T.
Nat. Biotechnol., 19, 751-755, 2001
Lead