Original papers


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

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. "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

Proceedings (reviewed)


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).

Reviews and Books


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

Reviews and Books in Japanese


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

Patents


小川泰策、城口克之、他
A patent application filed on a single-cell picking system

城口克之
"METHOD FOR SEQUENCING AND ANALYSIS OF NUCLEIC ACID"
理化学研究所 PCT/JP2018/023778

城口克之
A patent application filed on nucleic acid amplification

城口克之、他
A patent application filed

城口克之、鈴木宏明、岡野太治
"マイクロウェルプレート、マイクロウェル装置、細胞解析方法及びマイクロウェルプレートの製造方法"
理化学研究所、中央大学 特願2015-44934 (2015).

Xie X.S., Shiroguchi K., Sims P.A., Jia T.Z.
“Single Cell Nucleic Acid Detection and Analysis”
Harvard University, US9260753.

Awards


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

2005     Early Research in Biophysics Award
            The Biophysical Society of Japan

Others


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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