RIKEN Center for Biosystems Dynamics Research (BDR)

Kanaya T., Jinnohara T., Sakakibara S., Tachibana N., Sasaki T., Kato T., Riemann M., Jin J., Shiroguchi K., Kawakami E., Ohno H.
"RelB and C/EBPα critically regulate the development of Peyer’s patch mononuclear phagocytes"
Mucosal Immunology, in press.     web / pdf

Nakai-Futatsugi Y., Jin J., Ogawa T., Sakai N., Maeda A., Hironaka K., Fukuda M., Danno H., Tanaka Y., Hori S., Shiroguchi K., Takahashi M.
"Pigmentation level of human iPSC-derived retinal pigment epithelium cell does not indicate a specific gene expression profile"
eLife 12 RP92510 (2024).     web / pdf
    featured in   Digest

Takahashi S., Ochiai S., Jin J., Takahashi N., Toshima S., Ishigame H., Kabashima K., Kubo M., Nakayama M., Shiroguchi K., Okada T.
“Sensory neuronal STAT3 is critical for IL-31 receptor expression and inflammatory itch”
Cell Reports 42 (12) 113433 (2023).     web / pdf    プレスリリース
    featured in   Tii生命科学

Jin J., Yamamoto R., Shiroguchi K.
“High-throughput identification and quantification of bacterial cells in the microbiota based on 16S rRNA sequencing with single-base accuracy using BarBIQ”
Nature Protocols 19, 207 (2024).     web / pdf    プレスリリース
    featured in   X-MOL,   Tii生命科学

Cui G., Shimba A., Jin J., Hojo N., Asahi T., Abe S., Ejima A., Okada S., Ohira K., Kato R., Tani-ichi S., Yamada R., Ebihara T., Shiroguchi K., Ikuta K.
“CD45 Alleviates Airway Inflammation and Lung Fibrosis by Limiting Expansion and Activation of ILC2s”
Proc. Natl. Acad. Sci. USA. 120 (36) e2215941120 (2023).     web / pdf    プレスリリース
    featured in Tii生命科学,   医療NEWS

Fujimura T., Enomoto Y., Katsura H., Ogawa T., Baba S., Ogata A., Yamaoka A., Shiroguchi K., Morimoto M.
“Identifying a Lung Stem Cell Subpopulation by Combining Single-Cell Morphometrics, Organoid Culture, and Transcriptomics”
Stem Cells, sxad044 (2023).     web / pdf    プレスリリース

Jin J.^§, Ogawa T.^§, Hojo N., Kryukov K., Shimizu K., Ikawa T., Imanishi T., Okazaki T., Shiroguchi K. (^§equally contributed)
“Robotic data acquisition with deep learning enables cell image-based prediction of transcriptomic phenotypes”
Proc. Natl. Acad. Sci. USA. 120 (1) e2210283120 (2023).     web / pdf    プレスリリース
    featured in 日刊工業新聞,   RNA-Seq Blog,   OPTRONICS ONLINE,   客観日本,   科学新聞,   Science Japan.

Cui G, Shimba A, Jin J, Ogawa T, Muramoto Y, Miyachi H, Abe S, Asahi T, Tani-Ichi S, Dijkstra JM, Iwamoto Y, Kryukov K, Zhu Y, Takami D, Hara T, Kitano S, Xu Y, Morita H, Zhang M, Zreka L, Miyata K, Kanaya T, Okumura S, Ito T, Hatano E, Takahashi Y, Watarai H, Oike Y, Imanishi T, Ohno H, Ohteki T, Minato N, Kubo M, Hollander GA, Ueno H, Noda T, Shiroguchi K, Ikuta K.
“A circulating subset of iNKT cells mediates antitumor and antiviral immunity”
Sci. Immunol. 7, eabj8760 (2022).     web / pdf    プレスリリース     
    featured in Nature immunology, Science Japan  

Jin J., Yamamoto R., Takeuchi T., Cui G., Miyauchi E., Hojo N., Ikuta K., Ohno H., Shiroguchi K.
“High-throughput identification and quantification of single bacterial cells in the microbiota”
Nat. Commun. 13, 863 (2022).     web / pdf    プレスリリース     
    featured in Sciworthy,   客観日本,   日本経済新聞 電子版,   日経産業新聞,   Research Highlight (RIKEN)

Ogawa T., Ochiai K., Iwata T., Ikawa T., Tsuzuki T., Shiroguchi K.,Takahashi T.
“Different cell imaging methods did not significantly improve immune cell image classification performance”
PLOS ONE 7(1): e0262397 (2022).     web / pdf

Zhang B., Vogelzang A., Miyajima M., Sugiura Y., Wu Y., Chamoto K., Nakano R., Hatae R., Menzies R.J., Sonomura K., Hojo N., Ogawa T., Kobayashi W., Tsutsui Y., Yamamoto S., Maruya M., Narushima S., Suzuki K., Sugiya H., Murakami K., Hashimoto M., Ueno H., Kobayashi T., Ito K., Hirano T., Shiroguchi K., Matsuda F., Suematsu M., Honjo T., Fagarasan S.
“B cell-derived GABA elicits IL-10+ macrophages to limit anti-tumour immunity”
Nature 599, 471-476 (2021).     web / pdf     Press Release    プレスリリース     

Nishida M., Yamashita N., Ogawa T., Koseki K., Warabi E., Ohue T., Komatsu M., Matsushita H., Kakimi K., Kawakami E., Shiroguchi K., Udono H.
“Mitochondrial reactive oxygen species trigger metformin-dependent antitumor immunity via activation of Nrf2/mTORC1/p62 axis in tumor-infiltrating CD8T lymphocytes”
J. for ImmunoTherapy of Cancer 2021;9:e00295 (2021).     web / pdf

Aso H., Nagaoka S., Kawakami E., Ito J., Islam S., Tan B J.Y., Nakaoka S., Ashizaki K., Shiroguchi K., Suzuki Y., Satou Y., Koyanagi Y., Sato K.
“Multiomics investigation revealing the characteristics 1 of HIV-1-infected cells”
Cell Reports 32, 107887 (2020).     web / pdf

Kimura S., Nakamura Y., Kobayashi N., Shiroguchi K., Kawakami E., Mutoh M., Takahashi-Iwanaga H., Yamada T., Hisamoto M., Nakamura M., Udagawa N., Sato S., Kaisho T., Iwanaga T., Hase K.
"Osteoprotegerin-dependent M cell self-regulation balances gut infection and immunity"
Nat. Commun. 11, 234 (2020).     web / pdf

Yazaki J., Kawashima Y., Ogawa T., Kobayashi A., Okoshi M., Watanabe T., Yoshida S., Kii I., Egami S., Amagai M., Hosoya T., Shiroguchi K.,Ohara O.
"HaloTag-based conjugation of proteins to barcoding-oligonucleotides"
Nucleic Acids Research, gkz1086 (2019).     web / pdf     Press Release    プレスリリース      featured by newspapers,   e.g.,   日経バイオテク

Miyamoto C., Kojo S., Yamashita M., Moro K., Lacaud G., Shiroguchi K, Taniuchi I., Ebihara T.
"Runx/Cbfβ complexes protect group 2 innate lymphoid cells from exhausted-like hyporesponsiveness during allergic airway inflammation"
Nat. Commun. 10, 447, 1-13 (2019).     web / pdf

Ise W., Fujii K., Shiroguchi K., Ito A, Kometani K., Takeda K., Kawakami E., Yamashita K., Suzuki K., Okada T., Kurosaki T.
"T follicular helper cell-germinal center B cell interaction strength regulates entry into plasma cell or recycling GC cell fate"
Immunity 48, 702-715 (2018).     web / pdf     Press Release    プレスリリース

Tenno M., Kojo S., Lawir D.-F., Hess I., Shiroguchi K., Ebihara T., Endo T.A., Muroi S., Satoh R., Kawamoto H., Boehm T., Taniuchi I.
"Cbfβ2 controls differentiation of and confers homing capacity to prethymic progenitors"
J. Exp. Med. 215, 595-610 (2018).     web / pdf     プレスリリース

Ogawa T.^§, Kryukov K.^§, Imanishi T., Shiroguchi K. (^§equally contributed)
"The efficacy and further functional advantages of random-base molecular barcodes for absolute and digital quantification of nucleic acid molecules"
Sci.Rep. 7, 13576 (2017).     web / pdf     プレスリリース      featured by newspapers,   e.g.,   産経新聞    日本経済新聞

Tenno M., Shiroguchi K., Muroi S., Kawakami E., Koseki K., Kryukov K., Imanishi T., Ginhoux F., Taniuchi I.
"Cbfβ2 deficiency preserves Langerhans cell precursors by lack of selective TGFβ receptor signaling"
J. Exp. Med. 214, 2933-2946 (2017).     web / pdf     プレスリリース

Suzuki H., Mitsuno K., Shiroguchi K., Tsugane M., Okano T., Dohi T., Tsuji T.
"One-step Micromolding of Complex 3D Microchambers for Single-Cell Analysis"
Lab. Chip. 17, 647-652 (2017).     web / pdf

Sumitomo J, Emori C, Matsuno Y, Ueno M, Kawasaki K, Endo TA, Shiroguchi K., Fujii W, Naito K, Sugiura K.
“Mouse oocytes suppress mir-322-5p expression in ovarian granulosa cells”
J. Reprod. Dev. 393-399 (2016).     web / pdf

Chen H.^§, Shiroguchi K.^§, Ge H., Xie X.S. (^§equally contributed)
“Genome-wide study of mRNA degradation and transcript elongation in Escherichia coli”
Molecular Systems Biology 11, 781 (2015).     web / pdf

Chiwata R., Kohori A., Kawakami T., Shiroguchi K., Furuike S., Adachi K., Sutoh K., Yoshida M., Kinosita Jr. K.
“None of the Rotor Residues of F1-ATPase Are Essential for Torque Generation”
Biophys. J. 106, 2166-2174 (2014).     web / pdf

Miyazaki M., Kinosita Jr. K., Shiroguchi K.
“Accurate polarity control and parallel alignment of actin filaments for myosin-powered transport systems”
RSC Adv. 3, 8728-8733 (2013).     web / pdf

Shiroguchi K., Jia T.Z., Sims P.A., Xie X.S.
“Digital RNA Sequencing Minimizes Sequence-Dependent Bias and Amplification Noise with Optimized Single Molecule Barcodes”
Proc. Natl. Acad. Sci. USA, 109, 1347-1352 (2012).     web / pdf
         Recommended by Faculty of 1000

Shiroguchi K.*, Chin H.F., Hannemann D.E., Muneyuki E., De La Cruz E.M.*, Kinosita Jr. K. (* corresponding authors)
“Direct Observation of the Myosin Va Recovery Stroke That Contributes to Unidirectional Stepping along Actin”
PLoS Biol. 9: e1001031 (2011).     web / pdf
         Featured in the article "The Next Step for Motor Proteins" in PLoS Biology

Kohori A., Chiwata R., Hossain M.D., Furuike S., Shiroguchi K., Adachi K., Yoshida M., Kinosita Jr. K.
“Torque Generation in F1-ATPase Devoid of the Entire Amino-Terminal Helix of the Rotor That Fills Half of the Stator Orifice”
Biophysical J. 101, 188-195 (2011).     web / pdf

Shiroguchi K., Kinosita Jr. K.
“Myosin V walks by lever action and Brownian motion”
Science, 316, 1208-1212 (2007).     web / pdf

Kobayashi T., Shiroguchi K., Edamatsu M., Toyoshima Y.Y.
“Microtubule-binding properties of dynactin p150 expedient for dynein motility”
Biochem. Biophys. Res. Comm. 340, 23-28 (2006).     web / pdf

Nishiura M., Kon T., Shiroguchi K., Ohkura R., Toyoshima Y.Y., Sutoh K.
“A single-headed recombinant fragment of Dictyostelium cytoplasmic dynein can drive the robust sliding of microtubules”
J. Biol. Chem. 279, 22799-22802 (2004).     web / pdf

Toba S., Gibson T.M., Shiroguchi K., Toyoshima Y.Y., Asai D.J.
“Properties of the full-length heavy chains of Tetrahymena ciliary outer arm dynein separated by urea treatment”
Cell Motil. Cytoskel. 58, 30-38 (2004).     web / pdf

Shiroguchi K., Ohsugi M., Edamatsu M., Yamamoto T., Toyoshima Y.Y.
“The second microtubule-binding site of monomeric Kid enhances the microtubule affinity”
J. Biol. Chem. 278, 22460-22465 (2003).     web / pdf

Ohsugi M., Tokai-Nishizumi N., Shiroguchi K., Inoue J., Toyoshima Y.Y., Yamamoto T.
“Cdc2-mediated phosphorylation of chromokinesin Kid controls its distribution to spindle and chromosomes”
EMBO J. 22, 2091-2103 (2003).     web / pdf

Shiroguchi K., Toyoshima Y.Y.
“Regulation of monomeric dynein activity by ATP and ADP concentrations”
Cell Motil. Cytoskel. 49, 189-199 (2001).     web / pdf

Suzuki H., Mitsuno K., Shiroguchi K., Okano T., Dohi T., Tsuji T.
"One-Step PDMS Micromolding Process for Tapered Three-Dimensional Structures"
APCOT, Kanazawa Japan (2016).

Mitsuno K., Ikeda H., Tsugane M., Okano T., Shiroguchi K., Suzuki H.
"3D-shaped microchamber for the Single-cell Analysis"
Proc. μTAS 2015, p522-524, Gyeongju, Korea (2015).

Jin J., Liu X,. Shiroguchi K.
"Long journey of 16S rRNA-amplicon sequencing toward cell-based functional bacterial microbiota characterization"
iMetaOmics (2024).     web / pdf

Suzuki M., Shiroguchi K.
BSJ 2019 “Single-cell PRESTO” session     web / pdf
Biophysical Reviews (2020) Springer.

Shiroguchi K.
Distinguishing and Searching for Minority Cells: Small in Number, But Large in Effect     web / pdf
Minorities and Small Numbers from Molecules to Organisms in Biology (Springer) p39-44.

Shiroguchi K.
“A rod probe reveals gait of myosin V”
Physics of Self-Organization Systems, World Scientific Singapore, 37-46 (2008).     web / pdf

Kinosita Jr. K., Shiroguchi K., Ali M.Y., Adachi K., Itoh H.
“On the walking mechanism of linear molecular motors”
Adv. Exp. Med. Biol. 592, 369-384 (2007).     web / pdf

Kinosita Jr. K., Shiroguchi K., Okamoto T., Adachi K., Onoue Y., Itoh H.
“Is your video camera linear?”
Seibutsu Butsuri (Biophysics) 45, 216-218 (2005).     web / pdf

Kinosita Jr. K., Ali M.Y., Adachi K., Shiroguchi K., Itoh H.
“How two-foot molecular motors may walk”
Adv. Exp. Med. Biol. 565, 205-219 (2005).     web / pdf

城口克之
個々の細胞の画像から遺伝子発現状態を推定する
生物物理 64(1) 35-37 (2024).     web / pdf

城口克之
細胞の明視野画像から細胞種や状態を読み取る基盤技術
光アライアンス (日本工業出版) Vol.34 No.8 p1-3 (2023).     web / pdf

城口克之
BarBIQ法：１つの細胞を見分けて正確に細菌の種類と数を計測する新規細菌叢解析法
細胞 (ニューサイエンス社) Vol.55 No.3 p20-23 (p152-155) (2023).     web / pdf

城口克之
細胞1つの種類を見分けて計数する新規細菌叢解析法
B&I (BIOSCIENCE and INDUSTRY) Vol.80 No.5 p412-413 (2022).     web / pdf

城口克之、小川泰策
DNA分子バーコード法とその新機能
バイオイノベーションに向けて　〜バイテクノロジーの新技術からの新しい視点〜（シーエムシー出版）p1-6     web / pdf

城口克之
１細胞、１分子における核酸配列決定・定量技術の現状と展望
臨床免疫・アレルギー科（科学評論社）Vol.70 No.5 p526-531 (2018)     web / pdf

城口克之
少数細胞を見分ける・探し出す　〜少数だけど影響力がある細胞に注目してみよう〜     web / pdf
少数性生物学（永井健治、冨樫祐一 編、日本評論社）p43-50

城口克之
デジタルRNAシークエンシング　ゲノムワイドな１分子定量法     web / pdf
化学と生物（日本農芸化学会）　Vol.54 No.11 p787-788 (2016)

城口克之、小川泰策
次世代シークエンサーを用いたDNA, RNAの網羅的デジタル計測     web / pdf
現代化学　2016年9月号（No. 546) p47-50

城口克之
Editor「１細胞解析」
記事 "Digital RNA Sequencing"     web / pdf
日本免疫学会　JSI Newsletter Vol.24, No.24-2, p21 (2016)

城口克之
３章　非筋ミオシン     web / pdf
１分子生物学　　原田慶恵・石渡信一 編　化学同人

城口克之
３章　リニアモーター：ミオシン     web / pdf
1分子ナノバイオ計測　分子から生命システムを探る革新的技術　野地博行編　化学同人

城口克之
"RNA シークエンシング"
生物物理 vol.53 p290-294 (2013).     web / pdf

城口克之、陸　思嘉    (K. Shiroguchi and S. Lu)
“１細胞全ゲノムシークエンシングの“夜明け””    (Dawn of the Single Cell Whole Genome Sequencing)
ゲノム医学・生命科学研究　総集編     ポストゲノムの１０年は何をもたらしたか
実験医学増刊　vol.31 No.15 (2013).     web / pdf

城口克之
2本足モーター，ミオシンVの脚の動きを見る
生物物理、49(1) 27-29 (2009).     web / pdf

K. Shiroguchi
“Myosin V walks by lever action and Brownian motion”
Japanese Scientists in Science p17 (2008).     web / pdf

Katsuyuki Shiroguchi, Others
A patent application filed on a device for nucleic acid amplification
Granted

Nozomi Hojo, Katsuyuki Shiroguchi
A patent application filed on cell manipulation

Jianshi Jin, Katsuyuki Shiroguchi, Reiko Yamamoto
A patent application filed on the identification and quantification of bacteria
Granted

Taisaku Ogawa, Katsuyuki Shiroguchi, Others
A patent application filed on a cell picking system
Granted

Katsuyuki Shiroguchi
A patent application filed on a sequencing technology
Granted

Katsuyuki Shiroguchi
"One-step reverse transcription template-switching PCR"
JP6924496

Xie X.S., Shiroguchi K., Sims P.A., Jia T.Z.
A patent application filed on a sequencing technology
Harvard University
Granted

中谷賞奨励賞
公益財団法人 中谷医工計測技術振興財団 (2020)
Nakatani Award Incentive Prize
Nakatani Foundation for advancement of measuring technologies in biomedical engineering

1st Place Poster Award
Gordon Research Conference: Single Molecule Approaches to Biology
New London, NH, USA (2006)

Early Research in Biophysics Award
The Biophysical Society of Japan (2005)

城口克之
海外だより　from Harvard University, Boston
生物物理 50(1) 50-51 (2010).     web / pdf

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