Full List of Publications

Research Articles:

1. Kim AK, Wu HD, Inoue T. “Synthetic design of farnesyl-electrostatic peptides for development of a protein kinase A membrane translocation switch” Scientific Reports (Accepted, 2021) PDF

2. Nihongaki Y, Matsubayashi HT, Inoue T. “A molecular trap inside microtubules probes luminal access by soluble proteins” Nature Chemical Biology (In Press) PDF

3. Deb Roy A, Gross EG, Pillai GS, Seetharaman S, Etienne-Manneville S, Inoue T. “A phospho-regulated ensemble signal motif of α-TAT1 drives dynamic microtubule acetylation” bioRxiv 2020.09.23.310235 PDF
Note: Highlights in preLights

4. Nakamura H., Rho E., Deng D., Razavi S., Matsubayashi HM., Inoue T. “ActuAtor, a molecular tool for generating force in living cells: Controlled deformation of intracellular structures” bioRxiv 2020.03.30.016360 PDF
Note: Highlights in preLights

5. Wu HD, Kikuchi M, Dagliyan O, Aragaki AK, Nakamura H, Dokholyan NV, Umehara T, Inoue T. “Rational design and implementation of a chemically inducible hetero-trimerization system” Nature Methods 17, 928-936 (2020) PDF
Note: Highlights in Nature Chemical Biology (October 2020)

6. Kim AK, Wu HD, Inoue T. “Rational Design of a Protein Kinase A Nuclear-cytosol Translocation Reporter” Scientific Reports 10, 9365 (2020) PDF

7. Georgess D, Padmanaban V, Sirka O, Coutinho K, Choi A, Frid G, Neumann N, Inoue T, and Ewald A. “Twist1-induced epithelial dissemination requires Prkd1 signaling” Cancer Research 80, 204 (2020) PDF

8. Kremer L, Hennes E, Brause A, Ursu A, Robke L, Matsubayashi HY, Nihongaki Y, Mejdrová I, Eickhoff J, Baumann M, Nencka R, Janning P, Kordes S, Schöler HE, Sterneckert J, Inoue T, Ziegler S, Waldmann H. “Discovery of the Hedgehog Pathway Inhibitor Pipinib that Targets PI4KIIIß” Angewandte Chemie 58, 16617 (2019) PDF

9. Miao YC, Bhattacharya S, Banerjee T, Abubaker-Sharif, B, Long, Y, Inoue T, Devreotes PN, Iglesias PA “Wave patterns organize cellular protrusions and control cortical dynamics” Molecular Systems Biology 15, e8585 (2019) PDF

10. Niu J, Yang W, Yue DT, Inoue T, Ben-Johny M. "Duplex signaling by CaM and Stac3 enhances CaV1.1 function and provides insights into congenital myopathy" J. Gen. Phys. 150, 1145 (2018) PDF

11. Niu J, Dick IE, Yang W, Yue DT, Tomaselli GF, Inoue T, Ben-Johny M. “Allosteric regulators selectively prevent Ca2+-feedback of CaV and NaV channels” eLife 7, e35222a (2018) PDF

10. Takada N, Naito T, Inoue T, Nakayama K, Takatsu H, Shin HW. “Enhanced phospholipid flipping by P4-ATPase promotes membrane deformation” EMBO Reports 37, e97705 (2018) PDF
Note: Press release, “Flipping lipids for cell transport-tubules”

11. Hong S.R., Wang C.L., Chang Y.C., Chang Y.C., Lin C.Y., Hsu N., Cheng H.C., Chiang Y.C., Huang W.E., Shaner NC, Rohatgi R, Inoue T, Lin YC. “Spatiotemporal manipulation of ciliary glutamylation reveals its roles in intraciliary trafficking and Hedgehog signaling” Nature Communications 9, 1732, 1 (2018) PDF
Note: Press release “Scientists Develop Method to Tweak Tiny ‘Antenna’ on Cells”

12. Nakamura H, Lee AA, Afshar AS, Lin YC, Tanigawa M, Suarez A, Razavi S, DeRose R, Bobb D, Hong W, Gabelli SB, Goutsias J, Inoue T. “Intracellular production of hydrogels and synthetic RNA granules by multivalent enhancers.” Nature Materials 17, 79-89 (2018)

13. Phua SC, Chiba S, Suzuki M, Su E, Roberson EC, Pusapati GV, Setou M, Rohatgi R, Reiter JF, Ikegami K, Inoue T. “Dynamic Remodeling of Membrane Composition Drives Cell Cycle through Primary Cilia Excision.” Cell 168, 264-279 (2017) PDF
Note: “Some Cells Need a ‘Haircut’ Before Duplicating” Press release, “Study Shows How and Why Hairlike Structures on Cells are Lost” PKD News Blog, Slider Art

14. Miao YC, Bhattacharya S, Edwards M, Cai HQ, Inoue T, Iglesias PA, Devreotes PN “Altering the threshold of an excitable signal transduction network changes cell migratory modes.” Nature Cell Biology 19, 329-340 (2017) PDF

15. Meier EL, Razavi S, Inoue T, Goley ED. “A novel membrane anchor for FtsZ is linked to cell wall hydrolysis in Caulobacter crescentus.” Mol Microbiol. 101(2), 265-80 (2016) PDF
Note: Cover Art

16. AK, Mullee L, Wang Y, Comartin D, Inoue T, Pelletier L, Morrison CG. “Opposing effects of pericentrin and microcephalin on the pericentriolar material regulate CHK1 activation in the DNA damage response.” Oncogene 30, 2003-2010 (2016)

17. Garcia-Gonzalo FR, Phua SC, Roberson EC, Galo Garcia III, Abedin M, Schurmans S, Inoue T, Reiter JF. “Ciliary Phosphoinositides Modulate Hedgehog Signaling.” Developmental Cell 34, 400-409 (2015) PDF
Note: “Phosphoinositide Code for Primary Cilia” Preview by Developmental Cell, “Ciliary phosphoinositides regulate Hedgehog signaling” Highlight by Nature Reviews Molecular Cell Biology

18. Nguyen HN, Miyamoto T, Yang JM, Inoue T, Sesaki H, Devreotes PN, Iijima M. “Opening the conformation is a master switch for the dual localization and phosphatase activity of PTEN.” Scientific Reports. 5, 12600 (2015) PDF

19. Miyamoto T, Rho E, Sample V, Akano H, Magari M, Ueno T, Chen M, Tokumitsu H, Zhang J, and Inoue T. “Compartmentalized AMPK Signaling Illuminated by Genetically Encoded Molecular Sensors and Actuators” Cell Reports 11, 657-670 (2015) PDF
Note: Press release: “Molecular spies sabotage a protein’s activities in specific cellular compartments”

20. Lin B, Yin T, Wu YI, Inoue T. and Levchenko A. “Interplay between chemotaxis and contact inhibition of locomotion determines exploratory cell migration” Nature Communications 6, 6619 (2015) PDF
Note: Press release: “A digital field guide to cancer cells”

21. Razavi S., Su S. and Inoue T. “Cellular Signaling Circuits Interfaced with Synthetic, Post-Translational, Negating Boolean Logic Devices” ACS Synthetic Biology 3 (9), 676-685 (2014) PDF
Note: “Introducing Authors” ACS Synthetic Biology

22. Onuma H., Komatsu T., Arita M., Hanaoka K., Ueno T., Terai T., Nagano T., and Inoue T. "Synthetically rerouting phagocytosis by rapidly turning inert cells into “Eat you” mode" Science Signaling 7, rs4, 1-7 (2014) PDF
Note: Cover Article

23. Suarez A., Ueno T., Huebner R., McCaffery J.M., and Inoue T. “Bin/Amphiphysin/Rvs (BAR) family members bend membranes in cells” Scientific Reports 4, (4693) 1-6 (2014) PDF

24. Kobayashi T, Kim S, Lin YC, Inoue T, and Dynlacht BD. “CP110-interacting proteins, Talpid3 and Cep290, play overlapping and distinct roles in cilia assembly” Journal of Cell Biology 204, 215-229 (2014) PDF

25. Su S Phua SC, DeRose R, Chiba S, Narita K, Kalugin PN, Katada T, Kontani K, Takeda S and Inoue T. “Genetically encoded calcium indicator illuminates calcium dynamics in cilia” Nature Methods 10, 1105-1107 (2013) PDF
Note: “Author File” Nature Methods

26. Thevathasan, JV, Tan E, Hui Z, Lin YC, Li Y, Inoue T. and Fivaz M. “The small GTPase HRas shapes local PI3K signals through positive feedback and regulates persistent membrane extension in migrating fibroblasts” Molecular Biology of the Cell 24, 2228-2237 (2013) PDF
Note: “Self-Perpetuating Signaling Circuit in Cells May Drive Cancer Spread” Press release

27. Lin YC, Liu T-Y, Razavi S. and Inoue T. “Rapidly Reversible Manipulation of Molecular Activities Using Dual Chemical Dimerizers” Angewandte Chemie 52, 6450-6454 (2013) PDF
Note: “Tandem Orthogonal Chemically Induced Dimerization” Highlights in ChemBioChem (DOI: 10.1002/cbic.201300446)

28. Lin Y.C., Niewiadomski P., Lin B., Nakamura H., Phua S.C., Jiao J., Levchenko A., Inoue T., Rohatgi T., and Inoue T. “Chemically-inducible diffusion trap reveals molecular sieve-like barrier at primary cilia“ Nature Chemical Biology 9, 437-443 (2013) PDF
Note: “Research on cilia heats up: Implications for hearing vision loss and kidney disease” Press release, Featured in “ChemBioVault”, “New cilia research could have implications for kidney disease” (American Society of Nephrology, In The Loop), “New clues about molecular composition of cilia” MIGMS Latest News, “Cilia Admit Large Cytosolic Proteins”, Kidney News, “Signaling: Shifting at Ciliary Base” News & Views, Nature Chemical Biology

29. Lin B., Wang J., Ueno T., Harwell A., Inoue T. and Levchenko A. “Synthetic spatially graded Rac activation drives directed cell polarization and locomotion“ PNAS 109, E3668-E3677 (2012) PDF
Note: “Origin of Disease” Interview by TV science program (NHK Japanese broadcasting company, May 2013 on air), “Rac Gets Cells on Track” Introductory article by Cell Migration Gateway, News and Views by “Biofutur”, Press release “Microchoreography: Researchers use synthetic molecule to guide cellular dance”

30. Sample V, Ni Q, Inoue T and Zhang J. “Controlling Enzymatic Action in Living Cells with a Kinase-dependent Bimolecular Switch” ACS Chemical Biology 8, 116-21 (2013) PDF

31. Phua S.C, Pohlmeyer C., and Inoue T. “Rapidly Relocating Molecules Between Organelles to Manipulate Small GTPase Activity” ACS Chemical Biology 7, 1950-1955 (2012) PDF
Note: “Podcast”, (ACS Chemical Biology), F1000

32. Miyamoto T., DeRose R., Suarez A., Ueno T., Chen M., Sun T.-p., Wolfgang M.J., Mukherjee C., Meyers D. and Inoue T. “Rapid and Orthogonal Logic Gating with a Gibberellin-induced Dimerization System” Nature Chemical Biology 8, 465-470 (2012) PDF
Note: “Tools in Brief”, (Nature Methods, 9, 534 (2012), “Rapamycin’s Sister”), “Interview” by TV Science Channel, Karga7 Pictures, “This Changes Everything” (2012), Press Release: “Researchers Turn Living Cells Into Logic Gates, Moving Toward Cell Circuits“ (“TRENDING”, at SLATE) Video

33. DeRose R., Pohlmeyer C., Umeda N., Ueno T., Nagano T., Kuo S., and Inoue T. Journal of Visualized Experiments, e3794 (2012) “Moving molecules by light; Spatio-temporal manipulation of small GTPase activity at subcellular level and on timescale of seconds in living cells” PDF, Video

34. Ueno T, Falkenburger BH, Pohlmeyer C, and Inoue T. “Triggering Actin Comets Versus Membrane Ruffles: Distinctive Effects of Phosphoinositides on Actin Reorganization” Science Signaling 4(203), ra87 (2011) PDF
Note: “Perspective”, (Science Signaling, 5, pe7 (2012), “How Actin Gets the PIP”), “Editorial Guides” (Science Signaling, 5, eg3 (2012), “A Sense of Direction”), Press release: ”Rearranging the Cell's Skeleton” (Biochemist e-VOLUTION” at Biochemical Society), Featured in F1000, Cover Article

35. Komatsu T, Johnsson K, Okuno H, Bito H, Inoue T, Nagano T and Urano Y. “Real-time measurements of protein dynamics using fluorescence activation-coupled protein labeling (FAPL) method” Journal of American Chemical Society 133(17), 6745-6751 (2011) PDF

36. Umeda N., Ueno T., Pohlmeyer C., Nagano T. and Inoue T. “A photocleavable rapamycin conjugate for spatiotemporal control of small GTPase activity” Journal of American Chemical Society 133(1), 12-14 (2011) (PMID: 21142151) PDF
Note: Press release: “Scientists Use Light to Move Molecules Within Living Cells”

37. Komatsu T, Kukelyansky I, McCaffery JM, Ueno T, Varela LC and Inoue T. “Organelle-Specific, Rapid Induction of Molecular Activities and Membrane Tethering” Nature Methods 7, 206-208 (2010) (PMID: 20154678) PDF
Note: “Breaking News” (Genetic Engineering and Biotechnology News “Hopkins researchers put proteins right where they want them”), Selected for 2013 calendar by ibidi

38. Rahdar M, Inoue T, Meyer T, Zhang J, Vazquez F, and Devreotes PN. “A phosphorylation-dependent intramolecular interaction regulates the membrane association and activity of the tumor suppressor PTEN” Proc. Natl. Acad. Sci. 106(2):480-485 (2009) (PMID: 19114656) PDF

39. Inoue T and Meyer T. “Synthetic activation of endogenous PI3K and Rac identifies an AND-gate switch for cell polarization and migration” PLoS ONE 3(8), e3068 (2008) (PMID: 18728784) PDF

40. Abe N, Klein L, Inoue T, Galvez T, and Meyer T. “Dissecting the role of PI(4,5)P2 in transferrin receptor endocytosis and recycling” J. Cell Sci. 121, 1488-1494 (2008) (PMID: 18411250) PDF

41. Fivaz M, Bandara S, Inoue T and Meyer T. "Robust neuronal symmetry breaking by Ras-triggered local positive feedback" Current Biology 18, 44-50 (2008) PDF

42. Yogo T, Urano Y, Mizushima A, Sunahara H, Inoue T, Hirose K, Iino M, Kikuchi K, and Nagano T., "Selective photoinactivation of protein function through environment-sensitive switching of singlet oxygen generation by photosensitizer" Proc. Natl. Acad. Sci., 105, 28-32 (2008) PDF

43. Aoki. K, Nakamura T, Inoue T, Meyer T, and Matsuda M. “An essential role for the SHIP2-dependent negative feedback loop in neuritogenesis of nerve growth factor–stimulated PC12 cells” J. Cell Biol. 177, 817-827 (2007) PDF

44. Liou J, Fivaz M, Inoue T, and Meyer T. “Live-cell imaging reveals sequential oligomerization and local PM targeting of STIM1 following Ca2+ store depletion” Proc. Natl. Acad. Sci. 104, 9301-9306 (2007) PDF
Note: “Research Roundup” (J. Cell Biol. 177 (6), (2007))

45. Suh BC, Inoue T, Meyer T, and Hille B. “Rapid chemically-induced changes of PtdIns(4,5)P2 gate KCNQ ion channels” Science 314, 1454-1457 (2006) PDF
Note: “Perspectives” (Science 314, 1402-1403 (2006)), “Editor’s Choice” (Science STKE 364, tw410 (2006)), “Spotlight” (ACS Chem. Biol. 1, 608 (2006)), “Research Highlights” (Nature Methods 4, 7 (2007))

46. Heo WD, Inoue T, Park WS, Kim ML, Park BO, Wandless TJ, and Meyer T. “PI(3,4,5)P3 and PI(4,5)P2 lipids target Ras, Rho, Arf and Rab GTPases to the plasma membrane” Science 314, 1458-1461 (2006) PDF

47. Inoue T, Heo WD, Grimley JS, Wandless TJ, and Meyer T. “Inducible translocation strategies to rapidly activate and inhibit small GTPase signaling pathways” Nature Methods 2, 415-418 (2005) PDF

48. Yogo T, Kikuchi K, Inoue T, Hirose K, Iino M, and Nagano T. “Modification of intracellular Ca2+ dynamics by laser inactivation of inositol 1,4,5-trisphosphate receptor using membrane-permeant probes.” Chem. Biol. 11, 1053-1058 (2004) PDF

49. Inoue T, Kikuchi K, Hirose K, Iino M, and Nagano T. “Spatiotemporal Laser Inactivation of Inositol 1,4,5-Trisphosphate Receptors Using Synthetic Small-molecule Probes” Chem. Biol. 10, 503-509 (2003) PDF
Note: Cover Art

50. Nakanishi W, Kikuchi K, Inoue T, Hirose K, Iino M, and Nagano T. “Hydrophobic modifications at 1-phosphate of inositol 1,4,5-trisphosphate analogues enhance receptor binding” Bioorg. Med. Chem. Lett. 12, 911-913 (2002) PDF

51. Inoue T, Kikuchi K, Hirose K, Iino M, and Nagano T. “Small molecule-based laser inactivation of inositol 1,4,5-trisphosphate receptor” Chem. Biol. 8, 9-15 (2001) PDF

52. Inoue T, Kikuchi K, Hirose K, Iino M, and Nagano T. “Synthesis and evaluation of 1-position-modified inositol 1,4,5-trisphosphate analogs” Bioorg. Med. Chem. Lett. 9, 1697-1702 (1999) PDF

Review Articles (Peer-Reviewed):

1. Nakamura H, DeRose R, Inoue T. “Harnessing biomolecular condensates in living cells” Journal of Biochemistry 2019; 166 (1): 13-27 PDF
Note: Cover Art

2. Phua SC, Nihongaki Y., Inoue T. “Autonomy declared by primary cilia through compartmentalization of membrane phosphoinositides” Current Opinion in Cell Biology 2018;50:72-78 PDF

3. Kim AK, DeRose R, Ueno T, Lin B, Komatsu T, Nakamura H, Inoue T. “Toward total synthesis of cell function: Reconstituting cell dynamics with synthetic biology.” Science Signaling. 2016;9:414, re1, 1-7. PDF
Note: Cover Art

4. Coutinho K, Inoue T. “Deconstructing and constructing innate immune functions using molecular sensors and actuators" Proc. SPIE 9871, Sensing and Analysis Technologies for Biomedical and Cognitive Applications 2016, 987102 (May 19, 2016); doi:10.1117/12.2225185 PDF

5. Niu J, Johny MB, Dick IE, Inoue T. “Following Optogenetic Dimerizers and Quantitative Prospects“ Biophysical Journal. 2016;111(6):1132–1140 PDF

6. Phua SC, Lin YC, Inoue T. “An Intelligent Nano-Antenna: Primary cilium harnesses TRP channels to decode polymodal stimuli.” Cell Calcium. 2015;5:415-422. PDF

7. Miyamoto T, Razavi S, DeRose R, Inoue T. “Synthesizing Biomolecule-based Boolean Logic Gates.” ACS Synthetic Biology. 2013;2(2):72-82. PDF
Note: “Podcast” (ACS Synthetic Biology), “Introducing Authors” ACS Synthetic Biology

8. DeRose R, Miyamoto T, Inoue T. “Manipulating signaling at will: chemically-inducible dimerization (CID) techniques resolve problems in cell biology.” Pflügers Archiv 2013;465:409-417. PDF

9. Lin YC, Su S, Inoue T. “Visualizing Molecular Diffusion through Passive Permeability Barriers in Cells: Conventional and Novel Approaches.” Current Opinion in Chemical Biology. 2013;17:663-671. PDF

Invited Review Articles

1. Chiba S, Inoue T. “How to Image Calcium Inside Cellular Compartments“ Jikken Igaku*, 32 (9) 1275-1280 (2014) (*Japanese monthly journal on general life science)

2. Inoue T. “Unraveling molecular mechanism of cell migration using novel perturbation tools” Yakugaku Zasshi* 134 (5), 647-654 (2014) (*Japanese Review of Pharmaceutical Sciences) PDF

3. Miyamoto T, Inoue T. (2012) Life Science Review* 4376. “Synthetic Generation of Intracellular Boolean Logic Gates” (*Japanese online review on latest high profile papers)

4. Inoue T, Kazuya K, Nagano T. (2002) Pharmacia* 38, 131-134. “Spatiotemporal regulation of protein inactivation” (*Japanese Review of Pharmaceutical Sciences)


1. Inoue T. “Primary Cilia”, Jikken Igaku* 2018 (*Japanese monthly journal on general life science)

2. Nakamura H, and Inoue T. “Japanese Scientists in Science Signaling 2016”, Science Signaling 2017

3. Gaus K., Inoue T. “New Biological Frontiers Illuminated by Molecular Sensors and Actuators” Biophysical Journal. 2016;111(6):E01–E02 PDF

4. Miyamoto T, Rho E, Inoue T. “Deconvoluting AMPK Signaling.” Oncotarget. 2015;6:30431-30432. PDF

5. Komatsu T, and Inoue T. “Japanese Scientists in Science Signaling 2014”, Science Signaling 2015

Book Chapters and Science Essays

1. Miyamoto T., Rho E., Kim A., Inoue T. “Cellular application of genetically-encoded sensors and impeders of AMPK Authors” Methods in Molecular Biology (MMB) by Human Press 2018;1732:255-272 PDF

2. Komatsu T, Inoue T. Vol. 1174, 1231-245, 2014 “Organelle specific induction of molecular activities and membrane tethering” Methods in Molecular Biology (MMB) by Humana Press, “Exocytosis and Endocytosis II” PDF

3. Inoue T. “Toward Total Synthesis of Cell Functions” Gendai Kagaku*, 518, 25-30 (2014) (*Japanese monthly magazine of general chemistry)

4. Inoue T. Yakuji Nippo*, Vol. 11254, 2013 (*Japanese daily newspaper on Pharmaceutical Sciences)

5. Inoue T. Jikken Igaku*, Vol. 31, Dec. 2013 (*Japanese monthly journal on general life science)

6. Inoue T. Biology and Physics* 52, (3), 164-165 (2012). “Letter from abroad - One ordinary day of young investigator in US” (*Japanese Society Proceedings in Biophysics)