Preprint

  1. Nakamoto C*, Goto Y*, Tomizawa Y, Fukata Y, Fukata M, Harpsoe K, Gloriam D.E., Aoki K**Takeuchi T**. (*equal contribution, **Corresponding author)
    A genetically encoded red fluorescence dopamine biosensor enables dual imaging of dopamine and norepinephrine.
    bioRxiv
    , 2020. doi: https://doi.org/10.1101/2020.05.25.115162
  2. Goto YAoki K
    Development of optogenetic tools to manipulate cell cycle checkpoints
    bioRxiv, 2020. doi: https://doi.org/10.1101/2020.06.22.166264
  3. Ashida K, Aoki K, Ito S.
    Experimental evaluation of thermodynamic cost and speed limit in living cells via information geometry.
    bioRxiv, 2020. doi:10.1101/2020.11.29.403097
  4. Hatano Y, Suzuki S, Nakamura A, Yoshii T, Atsuta-Tsunoda K, Aoki K, Tsukiji S.
    A chemogenetic platform for controlling plasma membrane signaling and synthetic signal oscillation.
    bioRxiv, 2021. doi:10.1101/2021.03.16.435568
  5. Yamamoto K, Miura H, Ishida M, Sawai S, Kondo Y, Aoki K.
    Optogenetic relaxation of actomyosin contractility uncovers mechanistic roles of cortical tension during cytokinesis.
    bioRxiv. 2021. doi:10.1101/2021.04.19.440549
  6. Sakai K, Kondo Y, Fujioka H, Kamiya M, Aoki K, Goto Y.
    Near-infrared imaging in fission yeast by genetically encoded biosynthesis of phycocyanobilin.
    bioRxiv. 2021. doi:10.1101/2021.05.19.444883
  7. Yagi-Utsumi M, Aoki K, Watanabe H, Song C, Nishimura S, Satoh T, Yanaka S, Ganser C, Tanaka S, Schnapka V, Goh EW, Furutani Y, Murata K, Uchihashi T, Arakawa K, Kato K.
    Desiccation-induced fibrous condensation of CAHS protein from an anhydrobiotic tardigrade.
    bioRxiv. 2021. doi:10.1101/2021.06.22.449423
  8. Tany R, Goto Y, Kondo Y, Aoki K.
    Multiplexed fluorescence imaging of GPCR downstream signaling dynamics at the single-cell level.
    bioRxiv. 2021. doi:10.1101/2021.08.22.457285
  9. Hu X, Roy SR, Jin C, Li G, Zhang Q, Natsuko A, Asahina S, Kajiwara T, Feng B, Aoki K, Takahara A, Zhang Y.
    Control Cell Migration by Engineering Integrin Ligand Assembly.
    bioRxiv. 2021. p. 2021.09.14.460227. doi:10.1101/2021.09.14.460227

2021

  1. Goto YKondo YAoki K.
    Visualization and Manipulation of Intracellular Signaling.
    Adv Exp Med Biol. 2021;1293:225-234. doi: 10.1007/978-981-15-8763-4_13
  2. Yano T, Tsukita K, Kanoh H, Nakayama S, Kashihara H, Mizuno T, Tanaka H, Matsui T, Goto Y, Komatsubara A, Aoki K, Takahashi R, Tamura A, Tsukita S.
    A microtubule‐LUZP1 association around tight junction promotes epithelial cell apical constriction.
    The EMBO Journal. 2021;40. https://doi.org/10.15252/embj.2020104712
  3. Kajiwara K, Yamano S, Aoki K, Okuzaki D, Matsumoto K, Okada M.
    CDCP1 promotes compensatory renal growth by integrating Src and Met signaling.
    Life Sci Alliance. 2021;4. doi:10.26508/lsa.202000832
  4. Asakura Y, Kondo Y, Aoki K, Naoki H.
    Hierarchical modeling of mechano-chemical dynamics of epithelial sheets across cells and tissue.
    Sci Rep. 2021;11: 4069. doi:10.1038/s41598-021-83396-6
  5. Farahani PE, Reed EH, Underhill EJ, Aoki K, Toettcher JE.
    Signaling, Deconstructed: Using Optogenetics to Dissect and Direct Information Flow in Biological Systems.
    Annu Rev Biomed Eng. 2021. doi:10.1146/annurev-bioeng-083120-111648
  6. Ito REOneyama CAoki K.
    Oncogenic mutation or overexpression of oncogenic KRAS or BRAF is not sufficient to confer oncogene addiction.

    PLoS One. 2021 Apr 1;16(4):e0249388. doi: 10.1371/journal.pone.0249388. eCollection 2021.
  7. Wen C, Miura T, Voleti V, Yamaguchi K, Tsutsumi M, Yamamoto K, Otomo K, Fujie Y, Teramoto T, Ishihara T, Aoki K, Nemoto T, Hillman EM, Kimura KD.
    3DeeCellTracker, a deep learning-based pipeline for segmenting and tracking cells in 3D time lapse images.
    Elife. 2021;10: e59187. doi:10.7554/eLife.59187
  8. Nakamura AGoto YKondo YAoki K.
    Shedding light on developmental ERK signaling with genetically encoded biosensors.
    Development. 2021;148. doi:10.1242/dev.199767
  9. Verma A, Jena SG, Isakov DR, Aoki K, Toettcher JE, Engelhardt BE.
    A self-exciting point process to study multicellular spatial signaling patterns.
    Proc Natl Acad Sci U S A. 2021;118. doi:10.1073/pnas.2026123118
  10. Matsui K, Okamoto K, Hasegawa T, Ohtsuka H, Shimasaki T, Ihara K, Goto Y, Aoki K, Aiba H.
    Identification of ksg1 mutation showing long-lived phenotype in fission yeast.
    Genes Cells. 2021. doi:10.1111/gtc.12897
  11. Lin S, Hirayama D, Maryu G, Matsuda K, Hino N, Deguchi E, Aoki K, Iwamoto R, Terai K, Matsuda M.
    Redundant roles of EGFR ligands in the ERK activation waves during collective cell migration.
    Life Sci Alliance. 2022;5: e202101206. doi:10.26508/lsa.202101206

2020

  1. Nakamura A, Oki C, Kato K, Fujinuma S, Maryu G, Kuwata K, Yoshii T, Matsuda M, Aoki K, Tsukiji S
    Engineering orthogonal, plasma membrane-specific SLIPT systems for multiplexed chemical control of signaling pathways in living single cells
    ACS Chemical Biology, 2020, 15; 1004-1015.  doi: 10.1021/acschembio.0c00024
  2. Yagi H, Yagi-Utsumi M, Honda R, Ohta Y, Saito T, Nishio M, Ninagawa S, Suzuki K, Anzai T, Kamiya Y, Aoki K, Nakanishi M, Satoh T, Kato K
    Improved secretion of glycoproteins using an N-glycan-restricted passport sequence tag recognized by cargo receptor
    Nature Communications, 2020, 11; 1368.  doi: 10.1038/s41467-020-15192-1
  3. Hino N, Rossetti L, Marin-Llaurado A, Aoki K, Trepat X, Matsuda M, Hirashima T
    ERK-mediated mechanochemical waves direct collective cell polarization
    Developmental Cell, Volume 53, Issue 6, 22 June 2020, Pages 646-660.e8
  4. Akiyama S, Aoki K, Kubo Y
    Biophysical research in Okazaki, Japan.
    Biophysical Reviews, 15 Feb 2020, 12(2):237-243
    DOI: 10.1007/s12551-020-00633-4 PMID: 32062838 PMCID: PMC7242583
  5. Uda Y, Miura H, Goto Y, Yamamoto K, Mii Y, Kondo Y, Takada S, Aoki K
    Improvement of Phycocyanobilin Synthesis for Genetically Encoded Phytochrome-Based Optogenetics
    ACS Chemical Biology, November 9, 2020 https://doi.org/10.1021/acschembio.0c00477

2019

  1. Komatsubara A*, Goto Y*, Kondo Y, Matsuda M, Aoki K** (*equal contribution, **Corresponding Author)
    Single-cell quantification of the concentrations and dissociation constants of endogeneous proteins
    Journal of Biological Chemistry, 2019, 294; 6062-6072.  doi: 10.1074/jbc.RA119.007685

2018

  1. Oda S, Uda Y, Goto Y, Miura H, Aoki K (Corresponding Author)
    Optogenetic Tools for Quantitative Biology: The Genetically Encoded PhyB–PIF Light-inducible Dimerization System and Its Application for Controlling Signal Transduction
    Optogenetics, 2018; 137-148.  doi: 10.1016/j.celrep.2018.08.020
  2. Miura H, Kondo Y, Matsuda M, Aoki K (Corresponding Author)
    Cell-to-cell heterogeneity in p38-mediated cross-inhibition of JNK causes stochastic cell death
    Cell Reports, 2018, 24; 2658-2668.  doi: 10.1016/j.celrep.2018.08.020
  3. Muta Y, Fujita Y, Sumiyama K, Sakurai A, Taketo MM, Chiba T, Seno H, Aoki K, Matsuda M, Imajo M.
    Composite regulation of ERK activity dynamics underlying tumour-specific traits in the intestine
    Nature Communications, 2018, 9; 2174.  doi: 10.1038/s41467-018-04527-8
  4. Maryu G*, Miura H*, Uda Y, Komatsubara AT, Matsuda M, Aoki K (Corresponding Author)(* Equal contribution)
    Live-cell imaging with genetically encoded protein kinase activity reporters
    Cell Structure and Function, 2018, 43; 61-74.  doi: 10.1247/csf.18003
  5. Kondo Y (Corresponding Author), Aoki K, Ishii S
    Inverse tissue mechanics of cell monolayer expansion
    PLoS Computational Biology, 2018, 14; e1006029.  doi: 10.1371/journal.pcbi.1006029

2017

  1. Aoki K (Corresponding Author), Kondo Y, Naoki H, Hiratsuka T, Itoh RE, Matsuda M. Access the recommendation on F1000Prime
    Propagating Wave of ERK Activation Orients Collective Cell Migration.
    Developmental Cell,
    2017, 43; 305–317.  doi: 10.1016/j.devcel.2017.10.016
  2. Uda Y, Goto Y, Oda S, Kohchi T, Matsuda M, Aoki K (Corresponding Author)
    Efficient synthesis of phycocyanobilin in mammalian cells for optogenetic control of cell signaling
    Proc. Natl. Acad. Sci. U.S.A., 2017, 114; 11962-11967.  doi: 10.1073/pnas.1707190114
    *Some plasmids used in this study are deposited in Addgene

2016

  1. Yamao M, Aoki K, Yukinawa N, Ishii S, Matsuda M, Naoki H
    Two New FRET Imaging Measures: Linearly Proportional to and Highly Contrasting the Fraction of Active Molecules.
    PLoS One. 2016, 11; e0164254.  doi: 10.1371/journal.pone.0164254
  2. Kamezaki A, Sato F, Aoki K, Asakawa K, Kawakami K, Matsuzaki F, Sehara-Fujiwara A
    Visualization of Neuregulin 1 ectodomain shedding reveals its local processing in vitro and in vivo
    Scientific Reports, 2016, 6; 28873.  doi: 10.1038/srep28873
  3. Maryu G, Matsuda M, Aoki K (Corresponding Author)
    Multiplexed fluorescence imaging of ERK and Akt activities and cell-cycle progression
    Cell Structure and Function, 2016, 41; 81-92.  doi: 10.1247/csf.16007.  CSF Award!
  4. Inaba K, Oda K, Aoki K, Sone K, Ikeda Y, Miyasaka A, Kashiyama T, Fukuda T, Makii C, Arimoto T, Wada-Hiraike O, Kawana K, Yano T, Osuga Y, Fujii T.
    Synergistic antitumor effects of combination of PI3K/mTOR and MEK inhibition (SAR245409 and pimasertib) in mucinous ovarian carcinoma cells by fluorescence resonance energy transfer imaging
    Oncotarget
    , 2016, 7; 29577-29591.  doi: 10.18632/oncotarget.8807

2015

  1. Nagata Y, Kontani K, Enami T, Kataoka K, Ishii R, Totoki Y, Kataoka TR, Hirata M, Aoki K, Nakano K, Kitanaka A, Sakata-Yanagimoto M, Egami S, Shiraishi Y, Chiba K, Tanaka H, Shiozawa Y, Yoshizato T, Suzuki H, Kon A, Yoshida K, Sato Y, Sato-Otsubo A, Sanada M, Munakata W, Nakamura H, Hama N, Miyano S, Nureki O, Shibat T, Haga H, Shimoda K, Katada T, Chiba S, Watanabe T, Ogawa S
    Variegated RHOA mutations in adult T-cell leukemia/lymphoma
    Blood, 2015, 127; 596-604.  doi: 10.1182/blood-2015-06-644948
  2. Yamao M, Naoki H, Kunida K, Aoki K, Matsuda M, Ishii S
    Distinct predictive performance of Rac1 and Cdc42 in cell migration
    Scientific Reports, 2015, 5; 17527.  doi:10.1038/srep17527
  3. Aoki K (Corresponding Author)
    Visualization of Intracellular Signaling with Fluorescence Resonance Energy Transfer-Based Biosensors
    Protein Modifications in Pathogenic Dysregulation of Signaling, 2015; 31-41.  doi: 10.1007/978-4-431-55561-2
  4. Komatsubara AT, Matsuda M, Aoki K (Corresponding Author)
    Quantitative analysis of recombination between YFP and CFP genes of FRET biosensors introduced by lentiviral or retroviral gene transfer
    Scientific Reports, 2015, 5; 13283.  doi:10.1038/srep13283
  5. Komatsu N, Fujita Y, Matsuda M, Aoki K (Corresponding Author)
    mTORC1 upregulation via ERK-dependent gene expression change confers intrinsic resistance to MEK inhibitors in oncogeneic KRas-mutant cancer cells
    Oncogene, 2015, 34; 5607-5616.  doi:10.1038/onc.2015.16
  6. Hiratsuka T, Fujita Y, Naoki H, Aoki K, Kamioka Y, Matsuda M
    Intercellular propagation of extracellular signal-regulated kinase activation revealed by in vivo imaging of mouse epidermis
    eLife, 2015, 4; e05178.  doi: 10.7554/eLife.05178.001

2014

  1. Sadaie W, Harada Y, Matsuda M, Aoki K (Corresponding Author)
    Quantitative in vivo fluorescence cross-correlation analyses highlight the importance of competitive effect in the regulation of protein-protein interactions
    Molecular and Cellular Biology, 2014, 34; 3272-3290.  doi: 10.1128/MCB.00087-14
  2. Access the recommendation on F1000PrimeFujita Y, Komatsu N, Matsuda M, Aoki K (Corresponding Author)
    FRET-based quantitative analysis of feedforward and feedback loops in EGFR signaling and the sensitivity to molecular targeting drugs
    FEBS Journal, 2014, 281; 3177-3192.  doi: 10.1111/febs.12852
  3. Miura H, Matsuda M, Aoki K (Corresponding Author)
    Development of a FRET biosensor with high specificity for Akt
    Cell Structure and Function
    , 2014, 39; 9-20.  doi: http://doi.org/10.1247/csf.13018.  CSF Award!

2013

  1. Access the recommendation on F1000PrimeAoki K (Corresponding Author), Kumagai Y, Sakurai A, Komatsu N, Fujita Y, Shionyu C, Matsuda M
    Stochastic ERK activation induced by noise and cell-cell propagation regulates cell density-dependent proliferation
    Molecular Cell
    , 2013, 52; 529-40.  doi: 10.1016/j.molcel.2013.09.015
  2. Aoki K (Corresponding Author), Takahashi K, Kaizu K, Matsuda M
    A Quantitative Model of ERK MAP Kinase Phosphorylation in Crowded Media
    Scientific Reports, 2013, 3; 1541.  doi: 10.1038/srep01541
  3. Aoki K (Corresponding Author), Kamioka Y, Matsuda M
    Fluorescence resonance energy transfer imaging of cell signaling from in vitro to in vivo: Basis of biosensor construction, live imaging, and image processing
    Development, Growth and Differentiation
    , 2013, 55; 515-522.  doi: 10.1111/dgd.12039

2012

  1. Kunida K, Matsuda M, Aoki K (Corresponding Author)
    FRET imaging and statistical signalprocessing reveal positive and negative feedback loops regulating themorphology of randomly migrating HT-1080 cells
    Journal of Cell Science, 2012, 125; 2381-2192. doi:
  2. Aoki K, Komatsu N, Hirata E, Kamioka Y, Matsuda M
    Stable expression of FRET biosensors: A new light in cancer research
    Cancer Science, 2012, 103; 614-619. doi: 10.1111/j.1349-7006.2011.02196.x
  3. Aoki K, Komatsu N, Goto A, Matsuda M
    Visualization of Protein Kinase Activities in Living Cells
    Protein Kinase Technologies, 2012, 3-12. doi: 10.1007/978-1-61779-824-5_1

2011

  1. Access the recommendation on F1000PrimeKomatsu N, Aoki K (Corresponding Author) , Yamada M, Yukinaga H, Fujita Y, Kamioka Y, Matsuda M
    Development of an optimized backbone of FRET biosensors for kinases and GTPases
    Molecular Biology of the Cell, 2011, 22; 4647-4656.  doi: 10.1091/mbc.e11-01-0072
  2. Aoki K (Corresponding Author), Yamada M, Kunida K, Yasuda S, Matsuda M
    Processive phosphorylation of ERK MAP kinase in mammalian cells
    Proc Natl. Acad. Sci. U.S.A., 2011, 108; 12675-12680.  doi:
  3. Access the recommendation on F1000PrimeParrini MC, Sadou-Dubourgnoux A, Aoki K, Kunida K, Biondini M, Hatzoglou A, Poullet P, Formstecher E, Yeaman C, Matsuda M, Rossé C, Camonis J
    SH3BP1, an exocyst-associated RhoGAP, inactivates Rac1 at the front to drive cell motility
    Molecular Cell, 2011, 42; 650-661.  doi: 10.1016/j.molcel.2011.03.032
  4. Kiyokawa E, Aoki K, Nakamura T, Matsuda M
    Spatiotemporal regulation of small GTPases as revealed by probes based on the principle of Forster Resonance Energy Transfer (FRET): Implications for signaling and pharmacology
    Annual Review of Pharmacology and Toxicology, 2011, 51; 337-358.  doi: 10.1146/annurev-pharmtox-010510-100234

2010

  1. Mitsushima M, Aoki K, Ebisuya M, Matsumura S, Yamamoto T, Matsuda M, Toyoshima F, Nishida EAccess the recommendation on F1000Prime
    Revolving movement of a dynamic cluster of actin filaments during mitosis
    Journal of Cell Biology, 2010, 191; 453-462.  doi: 10.1083/jcb.201007136
  2. Kamioka Y, Yasuda S, Fujita Y, Aoki K, Matsuda M
    Access the recommendation on F1000PrimeMultiple decisive phosphorylation sites for the negative feedback regulation of SOS1 via ERK
    Journal of Biological Chemistry,
    2010, 285; 33540-33548.  doi:
  3. Yoshiki S, Matsunaga-Udagawa R, Aoki K, Kamioka Y, Kiyokawa E, Matsuda M
    Ras and Calcium Signaling Pathways Converge at Raf1 via the Shoc2 Scaffold Protein
    Molecular Biology of the Cell, 2010, 21; 1088-1096.  doi: 10.1091/mbc.e09-06-0455
  4. Matsunaga-Udagawa R, Fujita Y, Yoshiki S, Terai K, Kamioka Y, Kiyokawa E, Yugi K, Aoki K (Corresponding Author), Matsuda M
    The scaffold protein Shoc2/SUR-8accelerates the interaction of Ras and Raf
    Journal of Biological Chemistry, 2010, 285; 7818-7826.  doi:

2009

  1. Aoki K, Matsuda M
    Visualization of small GTPase activity with fluorescence resonance energy transfer-based biosensors
    Nature Protocols, 2009, 4; 1623-1631. doi: 10.1038/nprot.2009.175

2008

  1. Tsukada Y, Aoki K, Nakamura T, Sakumura Y, Matsuda M, Ishii S
    Quantification of local morphodynamics and local GTPase activity by edge evolution tracking
    PLoS Computational Biology, 2008, 4; e1000223.  doi: 10.1371/journal.pcbi.1000223
  2. Nakamura T, Aoki K, Matsuda M
    FRET imaging and in silico simulation: analysis of the signaling network of nerve growth factor-induced neuritogenesis
    Brain Cell Biology, 2008, 36; 19-30.  doi: 10.1007/s11068-008-9028-5
  3. Aoki K, Kiyokawa E, Nakamura T, Matsuda M
    Visualization of growth signal transduction cascades in living cells with genetically encoded probes based on Forster resonance energy transfer
    Philosophical Transactions of The Royal Society B Biological Sciences, 2008, 363; 2143-2151.  doi: 10.1098/rstb.2008.2267
  4. Nishioka T, Aoki K, Hikake K, Yoshizaki H, Kiyokawa E, Matsuda M
    Rapid Turnover Rate of Phosphoinositides at the Front of Migrating MDCK Cells
    Molecular Biology of the Cell, 2008, 19; 4213-4223.  doi: 10.1091/mbc.e08-03-0315
  5. Itoh RE, Kiyokawa E, Aoki K, Nishioka T, Akiyama T, Matsuda M
    Phosphorylation and activation of the Rac1 and Cdc42 GEF Asef in A431 cells stimulated by EGF
    Journal of Cell Science, 2008, 121; 2635-2642.  doi:

2007

  1. Aoki K, Nakamura T, Inoue T, Meyer T, Matsuda M
    An essential role for the SHIP2-dependentnegative feedback loop in neuritogenesis of NGF-stimulated PC12 cells
    Journal of Cell Biology, 2007, 177; 817-827.  doi: 10.1083/jcb.200609017
  2. Hisata S, Sakisaka T, Baba T, Yamada T, Aoki K, Matsuda M, Takai Y
    Rap1-PDZ-GEF1 interacts with a neurotrophin receptor at late endosomes, leading to sustained activation of Rap1 and ERK and neurite outgrowth
    Journal of Cell Biology, 2007, 178; 843-860.  doi: 10.1083/jcb.200610073

2006

  1. Access the recommendation on F1000PrimeKawase K, Nakamura T, Takaya A, Aoki K, Namikawa K, Kiyama H, Inagaki S, Takemoto H, Saltiel AR, Matsuda M
    GTP Hydrolysis of a Rho-family GTPase TC10 promotes exocytic vesicle fusion
    Developmental Cell, 2006, 11; 411-421.  doi: 10.1016/j.devcel.2006.07.008
  2. Fujioka A, Terai K, Itoh RE, Aoki K, Nakamura T, Kuroda S, Nishida E, Matsuda M
    Dynamics of the RAS/ERK map kinase cascade as monitored by fluorescence probes
    Journal of Biological Chemistry, 2006, 281; 8917-8926.  doi:
  3. Yoshizaki H, Aoki K, Nakamura T, Matsuda M
    Regulation of RalA GTPase by phosphatidylinositol 3-kinase as visualized by FRET probes
    Biochemical Society Transactions, 2006, 34; 851-854.  doi: 10.1042/BST0340851

2005

  1. Nakamura T, Aoki K, Matsuda M
    Monitoring spatio-temporal regulation of Ras and Rho GTPases with GFP-based FRET probes
    Methods, 2005, 37; 146-153.  doi: 10.1016/j.ymeth.2005.05.021
  2. Nakamura T, Aoki K, Matsuda M
    FRET imaging in nerve growth cones reveals a high level of RhoA activity within the peripheral domain
    Molecular Brain Research, 2005, 139; 277-287.  doi: 10.1016/j.molbrainres.2005.05.030
  3. Aoki K, Nakamura T, Fujikawa K, Matsuda M
    Local PIP3 Accumulation Recruits Vav2 and Vav3 to Activate Rac1/Cdc42 and Initiate Neurite Outgrowth in Nerve Growth Factor-stimulated PC12 Cells
    Molecular Biology of the Cell, 2005, 16; 2207-2017.  doi: 10.1091/mbc.e04-10-0904

2004

  1. Access the recommendation on F1000PrimeAoki K, Nakamura T, Matsuda M
    Spatio-temporal regulation of Rac1 andCdc42 activity during nerve growth factor-induced neurite outgrowth in PC12 cells
    Journal of Biological Chemistry, 2004, 279; 713-719.  doi: 10.1074/jbc.M306382200