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Items: 1 to 50 of 95

1.

Noncanonical STAT1 phosphorylation expands its transcriptional activity into promoting LPS-induced IL-6 and IL-12p40 production.

Metwally H, Tanaka T, Li S, Parajuli G, Kang S, Hanieh H, Hashimoto S, Chalise JP, Gemechu Y, Standley DM, Kishimoto T.

Sci Signal. 2020 Mar 24;13(624). pii: eaay0574. doi: 10.1126/scisignal.aay0574.

PMID:
32209697
2.

Dysregulated Expression of the Nuclear Exosome Targeting Complex Component Rbm7 in Nonhematopoietic Cells Licenses the Development of Fibrosis.

Fukushima K, Satoh T, Sugihara F, Sato Y, Okamoto T, Mitsui Y, Yoshio S, Li S, Nojima S, Motooka D, Nakamura S, Kida H, Standley DM, Morii E, Kanto T, Yanagita M, Matsuura Y, Nagasawa T, Kumanogoh A, Akira S.

Immunity. 2020 Mar 17;52(3):542-556.e13. doi: 10.1016/j.immuni.2020.02.007.

PMID:
32187520
3.

Impact and relevance of alcohol dehydrogenase enantioselectivities on biotechnological applications.

Koesoema AA, Standley DM, Senda T, Matsuda T.

Appl Microbiol Biotechnol. 2020 Apr;104(7):2897-2909. doi: 10.1007/s00253-020-10440-2. Epub 2020 Feb 15. Review.

PMID:
32060695
4.

Initial phospholipid-dependent Irgb6 targeting to Toxoplasma gondii vacuoles mediates host defense.

Lee Y, Yamada H, Pradipta A, Ma JS, Okamoto M, Nagaoka H, Takashima E, Standley DM, Sasai M, Takei K, Yamamoto M.

Life Sci Alliance. 2019 Dec 18;3(1). pii: e201900549. doi: 10.26508/lsa.201900549. Print 2020 Jan.

5.

Correction to: Structural basis for a highly (S)-enantioselective reductase towards aliphatic ketones with only one carbon difference between side chain.

Koesoema AA, Sugiyama Y, Xu Z, Standley DM, Senda M, Senda T, Matsuda T.

Appl Microbiol Biotechnol. 2019 Dec;103(23-24):9555. doi: 10.1007/s00253-019-10138-0.

PMID:
31728584
6.

Reversible control of enantioselectivity by the length of ketone substituent in biocatalytic reduction.

Koesoema AA, Sugiyama Y, Sriwong KT, Xu Z, Verina S, Standley DM, Senda M, Senda T, Matsuda T.

Appl Microbiol Biotechnol. 2019 Dec;103(23-24):9529-9541. doi: 10.1007/s00253-019-10206-5. Epub 2019 Nov 13.

PMID:
31720775
7.

Structural basis for a highly (S)-enantioselective reductase towards aliphatic ketones with only one carbon difference between side chain.

Koesoema AA, Sugiyama Y, Xu Z, Standley DM, Senda M, Senda T, Matsuda T.

Appl Microbiol Biotechnol. 2019 Dec;103(23-24):9543-9553. doi: 10.1007/s00253-019-10093-w. Epub 2019 Nov 15. Erratum in: Appl Microbiol Biotechnol. 2019 Nov 15;:.

PMID:
31482280
8.

Structural Modeling of Lymphocyte Receptors and Their Antigens.

Li S, Wilamowski J, Teraguchi S, van Eerden FJ, Rozewicki J, Davila A, Xu Z, Katoh K, Standley DM.

Methods Mol Biol. 2019;2048:207-229. doi: 10.1007/978-1-4939-9728-2_17.

PMID:
31396940
9.

Translation-dependent unwinding of stem-loops by UPF1 licenses Regnase-1 to degrade inflammatory mRNAs.

Mino T, Iwai N, Endo M, Inoue K, Akaki K, Hia F, Uehata T, Emura T, Hidaka K, Suzuki Y, Standley DM, Okada-Hatakeyama M, Ohno S, Sugiyama H, Yamashita A, Takeuchi O.

Nucleic Acids Res. 2019 Sep 19;47(16):8838-8859. doi: 10.1093/nar/gkz628.

PMID:
31329944
10.

Structural Determinants of the APOBEC3G N-Terminal Domain for HIV-1 RNA Association.

Fukuda H, Li S, Sardo L, Smith JL, Yamashita K, Sarca AD, Shirakawa K, Standley DM, Takaori-Kondo A, Izumi T.

Front Cell Infect Microbiol. 2019 May 21;9:129. doi: 10.3389/fcimb.2019.00129. eCollection 2019.

11.

N4BP1 restricts HIV-1 and its inactivation by MALT1 promotes viral reactivation.

Yamasoba D, Sato K, Ichinose T, Imamura T, Koepke L, Joas S, Reith E, Hotter D, Misawa N, Akaki K, Uehata T, Mino T, Miyamoto S, Noda T, Yamashita A, Standley DM, Kirchhoff F, Sauter D, Koyanagi Y, Takeuchi O.

Nat Microbiol. 2019 Sep;4(9):1532-1544. doi: 10.1038/s41564-019-0460-3. Epub 2019 May 27.

PMID:
31133753
12.

MAFFT-DASH: integrated protein sequence and structural alignment.

Rozewicki J, Li S, Amada KM, Standley DM, Katoh K.

Nucleic Acids Res. 2019 Jul 2;47(W1):W5-W10. doi: 10.1093/nar/gkz342.

13.

Allergic conversion of protective mucosal immunity against nasal bacteria in patients with chronic rhinosinusitis with nasal polyposis.

Takeda K, Sakakibara S, Yamashita K, Motooka D, Nakamura S, El Hussien MA, Katayama J, Maeda Y, Nakata M, Hamada S, Standley DM, Hayama M, Shikina T, Inohara H, Kikutani H.

J Allergy Clin Immunol. 2019 Mar;143(3):1163-1175.e15. doi: 10.1016/j.jaci.2018.07.006. Epub 2018 Jul 25.

PMID:
30053529
14.

Arid5a stabilizes OX40 mRNA in murine CD4+ T cells by recognizing a stem-loop structure in its 3'UTR.

Hanieh H, Masuda K, Metwally H, Chalise JP, Mohamed M, Nyati KK, Standley DM, Li S, Higa M, Zaman MM, Kishimoto T.

Eur J Immunol. 2018 Apr;48(4):593-604. doi: 10.1002/eji.201747109. Epub 2018 Feb 5.

15.

Characterization of SPP inhibitors suppressing propagation of HCV and protozoa.

Hirano J, Okamoto T, Sugiyama Y, Suzuki T, Kusakabe S, Tokunaga M, Fukuhara T, Sasai M, Tougan T, Matsunaga Y, Yamashita K, Sakai Y, Yamamoto M, Horii T, Standley DM, Moriishi K, Moriya K, Koike K, Matsuura Y.

Proc Natl Acad Sci U S A. 2017 Dec 12;114(50):E10782-E10791. doi: 10.1073/pnas.1712484114. Epub 2017 Nov 29.

16.

Clonal evolution and antigen recognition of anti-nuclear antibodies in acute systemic lupus erythematosus.

Sakakibara S, Arimori T, Yamashita K, Jinzai H, Motooka D, Nakamura S, Li S, Takeda K, Katayama J, El Hussien MA, Narazaki M, Tanaka T, Standley DM, Takagi J, Kikutani H.

Sci Rep. 2017 Nov 27;7(1):16428. doi: 10.1038/s41598-017-16681-y.

17.

Structural basis for the assembly of the Ragulator-Rag GTPase complex.

Yonehara R, Nada S, Nakai T, Nakai M, Kitamura A, Ogawa A, Nakatsumi H, Nakayama KI, Li S, Standley DM, Yamashita E, Nakagawa A, Okada M.

Nat Commun. 2017 Nov 20;8(1):1625. doi: 10.1038/s41467-017-01762-3.

18.

Essential role for GABARAP autophagy proteins in interferon-inducible GTPase-mediated host defense.

Sasai M, Sakaguchi N, Ma JS, Nakamura S, Kawabata T, Bando H, Lee Y, Saitoh T, Akira S, Iwasaki A, Standley DM, Yoshimori T, Yamamoto M.

Nat Immunol. 2017 Aug;18(8):899-910. doi: 10.1038/ni.3767. Epub 2017 Jun 12.

PMID:
28604719
19.

Mapping circulating serum miRNAs to their immune-related target mRNAs.

Nosirov B, Billaud J, Vandenbon A, Diez D, Wijaya E, Ishii KJ, Teraguchi S, Standley DM.

Adv Appl Bioinform Chem. 2017 Feb 2;10:1-9. doi: 10.2147/AABC.S121598. eCollection 2017.

20.

TLR4-induced NF-κB and MAPK signaling regulate the IL-6 mRNA stabilizing protein Arid5a.

Nyati KK, Masuda K, Zaman MM, Dubey PK, Millrine D, Chalise JP, Higa M, Li S, Standley DM, Saito K, Hanieh H, Kishimoto T.

Nucleic Acids Res. 2017 Mar 17;45(5):2687-2703. doi: 10.1093/nar/gkx064.

21.

Advax, a Delta Inulin Microparticle, Potentiates In-built Adjuvant Property of Co-administered Vaccines.

Hayashi M, Aoshi T, Haseda Y, Kobiyama K, Wijaya E, Nakatsu N, Igarashi Y, Standley DM, Yamada H, Honda-Okubo Y, Hara H, Saito T, Takai T, Coban C, Petrovsky N, Ishii KJ.

EBioMedicine. 2017 Feb;15:127-136. doi: 10.1016/j.ebiom.2016.11.015. Epub 2016 Dec 1.

22.

A simple method to control over-alignment in the MAFFT multiple sequence alignment program.

Katoh K, Standley DM.

Bioinformatics. 2016 Jul 1;32(13):1933-42. doi: 10.1093/bioinformatics/btw108. Epub 2016 Feb 26.

23.

Arid5a regulates naive CD4+ T cell fate through selective stabilization of Stat3 mRNA.

Masuda K, Ripley B, Nyati KK, Dubey PK, Zaman MM, Hanieh H, Higa M, Yamashita K, Standley DM, Mashima T, Katahira M, Okamoto T, Matsuura Y, Takeuchi O, Kishimoto T.

J Exp Med. 2016 Apr 4;213(4):605-19. doi: 10.1084/jem.20151289. Epub 2016 Mar 28.

24.

Structural basis for the regulation of enzymatic activity of Regnase-1 by domain-domain interactions.

Yokogawa M, Tsushima T, Noda NN, Kumeta H, Enokizono Y, Yamashita K, Standley DM, Takeuchi O, Akira S, Inagaki F.

Sci Rep. 2016 Mar 1;6:22324. doi: 10.1038/srep22324.

25.

Hepatocyte Factor JMJD5 Regulates Hepatitis B Virus Replication through Interaction with HBx.

Kouwaki T, Okamoto T, Ito A, Sugiyama Y, Yamashita K, Suzuki T, Kusakabe S, Hirano J, Fukuhara T, Yamashita A, Saito K, Okuzaki D, Watashi K, Sugiyama M, Yoshio S, Standley DM, Kanto T, Mizokami M, Moriishi K, Matsuura Y.

J Virol. 2016 Jan 20;90(7):3530-42. doi: 10.1128/JVI.02776-15.

26.

Design of a protein tag and fluorogenic probe with modular structure for live-cell imaging of intracellular proteins.

Kamikawa Y, Hori Y, Yamashita K, Jin L, Hirayama S, Standley DM, Kikuchi K.

Chem Sci. 2016 Jan 1;7(1):308-314. doi: 10.1039/c5sc02351c. Epub 2015 Sep 30.

27.

RabGDIα is a negative regulator of interferon-γ-inducible GTPase-dependent cell-autonomous immunity to Toxoplasma gondii.

Ohshima J, Sasai M, Liu J, Yamashita K, Ma JS, Lee Y, Bando H, Howard JC, Ebisu S, Hayashi M, Takeda K, Standley DM, Frickel EM, Yamamoto M.

Proc Natl Acad Sci U S A. 2015 Aug 18;112(33):E4581-90. doi: 10.1073/pnas.1510031112. Epub 2015 Aug 3.

28.

Regnase-1 and Roquin Regulate a Common Element in Inflammatory mRNAs by Spatiotemporally Distinct Mechanisms.

Mino T, Murakawa Y, Fukao A, Vandenbon A, Wessels HH, Ori D, Uehata T, Tartey S, Akira S, Suzuki Y, Vinuesa CG, Ohler U, Standley DM, Landthaler M, Fujiwara T, Takeuchi O.

Cell. 2015 May 21;161(5):1058-1073. doi: 10.1016/j.cell.2015.04.029.

29.

Hydroxypropyl-β-cyclodextrin spikes local inflammation that induces Th2 cell and T follicular helper cell responses to the coadministered antigen.

Onishi M, Ozasa K, Kobiyama K, Ohata K, Kitano M, Taniguchi K, Homma T, Kobayashi M, Sato A, Katakai Y, Yasutomi Y, Wijaya E, Igarashi Y, Nakatsu N, Ise W, Inoue T, Yamada H, Vandenbon A, Standley DM, Kurosaki T, Coban C, Aoshi T, Kuroda E, Ishii KJ.

J Immunol. 2015 Mar 15;194(6):2673-82. doi: 10.4049/jimmunol.1402027. Epub 2015 Feb 13.

30.

Dynamics of enhancers in myeloid antigen presenting cells upon LPS stimulation.

Vandenbon A, Teraguchi S, Takeuchi O, Suzuki Y, Standley DM.

BMC Genomics. 2014;15 Suppl 10:S4. doi: 10.1186/1471-2164-15-S10-S4. Epub 2014 Dec 12.

31.

RNA-LIM: a novel procedure for analyzing protein/single-stranded RNA propensity data with concomitant estimation of interface structure.

Hall D, Li S, Yamashita K, Azuma R, Carver JA, Standley DM.

Anal Biochem. 2015 Mar 1;472:52-61. doi: 10.1016/j.ab.2014.11.004. Epub 2014 Dec 3.

PMID:
25479604
32.

Akirin2 is critical for inducing inflammatory genes by bridging IκB-ζ and the SWI/SNF complex.

Tartey S, Matsushita K, Vandenbon A, Ori D, Imamura T, Mino T, Standley DM, Hoffmann JA, Reichhart JM, Akira S, Takeuchi O.

EMBO J. 2014 Oct 16;33(20):2332-48. doi: 10.15252/embj.201488447. Epub 2014 Aug 8.

33.

Kotai Antibody Builder: automated high-resolution structural modeling of antibodies.

Yamashita K, Ikeda K, Amada K, Liang S, Tsuchiya Y, Nakamura H, Shirai H, Standley DM.

Bioinformatics. 2014 Nov 15;30(22):3279-80. doi: 10.1093/bioinformatics/btu510. Epub 2014 Jul 26.

PMID:
25064566
34.

Quantifying sequence and structural features of protein-RNA interactions.

Li S, Yamashita K, Amada KM, Standley DM.

Nucleic Acids Res. 2014 Sep;42(15):10086-98. doi: 10.1093/nar/gku681. Epub 2014 Jul 25.

35.

High-resolution modeling of antibody structures by a combination of bioinformatics, expert knowledge, and molecular simulations.

Shirai H, Ikeda K, Yamashita K, Tsuchiya Y, Sarmiento J, Liang S, Morokata T, Mizuguchi K, Higo J, Standley DM, Nakamura H.

Proteins. 2014 Aug;82(8):1624-35. doi: 10.1002/prot.24591. Epub 2014 May 13.

PMID:
24756852
36.

Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation.

Morikawa H, Ohkura N, Vandenbon A, Itoh M, Nagao-Sato S, Kawaji H, Lassmann T, Carninci P, Hayashizaki Y, Forrest AR, Standley DM, Date H, Sakaguchi S; FANTOM Consortium.

Proc Natl Acad Sci U S A. 2014 Apr 8;111(14):5289-94. doi: 10.1073/pnas.1312717110. Epub 2014 Mar 27.

37.

Intrinsic disorder mediates cooperative signal transduction in STIM1.

Furukawa Y, Teraguchi S, Ikegami T, Dagliyan O, Jin L, Hall D, Dokholyan NV, Namba K, Akira S, Kurosaki T, Baba Y, Standley DM.

J Mol Biol. 2014 May 15;426(10):2082-97. doi: 10.1016/j.jmb.2014.03.006. Epub 2014 Mar 17.

38.

Blockade of TLR3 protects mice from lethal radiation-induced gastrointestinal syndrome.

Takemura N, Kawasaki T, Kunisawa J, Sato S, Lamichhane A, Kobiyama K, Aoshi T, Ito J, Mizuguchi K, Karuppuchamy T, Matsunaga K, Miyatake S, Mori N, Tsujimura T, Satoh T, Kumagai Y, Kawai T, Standley DM, Ishii KJ, Kiyono H, Akira S, Uematsu S.

Nat Commun. 2014 Mar 18;5:3492. doi: 10.1038/ncomms4492.

39.

A novel protein distance matrix based on the minimum arc-length between two amino-acid residues on the surface of a globular protein.

Hall D, Li S, Yamashita K, Azuma R, Carver JA, Standley DM.

Biophys Chem. 2014 Jun;190-191:50-5. doi: 10.1016/j.bpc.2014.01.005. Epub 2014 Feb 13.

PMID:
24589301
40.

Structures and interface mapping of the TIR domain-containing adaptor molecules involved in interferon signaling.

Enokizono Y, Kumeta H, Funami K, Horiuchi M, Sarmiento J, Yamashita K, Standley DM, Matsumoto M, Seya T, Inagaki F.

Proc Natl Acad Sci U S A. 2013 Dec 3;110(49):19908-13. doi: 10.1073/pnas.1222811110. Epub 2013 Nov 19.

41.

MAFFT: iterative refinement and additional methods.

Katoh K, Standley DM.

Methods Mol Biol. 2014;1079:131-46. doi: 10.1007/978-1-62703-646-7_8.

PMID:
24170399
42.

Blind prediction of interfacial water positions in CAPRI.

Lensink MF, Moal IH, Bates PA, Kastritis PL, Melquiond AS, Karaca E, Schmitz C, van Dijk M, Bonvin AM, Eisenstein M, Jiménez-García B, Grosdidier S, Solernou A, Pérez-Cano L, Pallara C, Fernández-Recio J, Xu J, Muthu P, Praneeth Kilambi K, Gray JJ, Grudinin S, Derevyanko G, Mitchell JC, Wieting J, Kanamori E, Tsuchiya Y, Murakami Y, Sarmiento J, Standley DM, Shirota M, Kinoshita K, Nakamura H, Chavent M, Ritchie DW, Park H, Ko J, Lee H, Seok C, Shen Y, Kozakov D, Vajda S, Kundrotas PJ, Vakser IA, Pierce BG, Hwang H, Vreven T, Weng Z, Buch I, Farkash E, Wolfson HJ, Zacharias M, Qin S, Zhou HX, Huang SY, Zou X, Wojdyla JA, Kleanthous C, Wodak SJ.

Proteins. 2014 Apr;82(4):620-32. doi: 10.1002/prot.24439. Epub 2013 Nov 23.

43.

The second messenger phosphatidylinositol-5-phosphate facilitates antiviral innate immune signaling.

Kawasaki T, Takemura N, Standley DM, Akira S, Kawai T.

Cell Host Microbe. 2013 Aug 14;14(2):148-58. doi: 10.1016/j.chom.2013.07.011.

44.

A novel function prediction approach using protein overlap networks.

Liang S, Zheng D, Standley DM, Guo H, Zhang C.

BMC Syst Biol. 2013 Jul 17;7:61. doi: 10.1186/1752-0509-7-61.

45.

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions.

Moretti R, Fleishman SJ, Agius R, Torchala M, Bates PA, Kastritis PL, Rodrigues JP, Trellet M, Bonvin AM, Cui M, Rooman M, Gillis D, Dehouck Y, Moal I, Romero-Durana M, Perez-Cano L, Pallara C, Jimenez B, Fernandez-Recio J, Flores S, Pacella M, Praneeth Kilambi K, Gray JJ, Popov P, Grudinin S, Esquivel-Rodríguez J, Kihara D, Zhao N, Korkin D, Zhu X, Demerdash ON, Mitchell JC, Kanamori E, Tsuchiya Y, Nakamura H, Lee H, Park H, Seok C, Sarmiento J, Liang S, Teraguchi S, Standley DM, Shimoyama H, Terashi G, Takeda-Shitaka M, Iwadate M, Umeyama H, Beglov D, Hall DR, Kozakov D, Vajda S, Pierce BG, Hwang H, Vreven T, Weng Z, Huang Y, Li H, Yang X, Ji X, Liu S, Xiao Y, Zacharias M, Qin S, Zhou HX, Huang SY, Zou X, Velankar S, Janin J, Wodak SJ, Baker D.

Proteins. 2013 Nov;81(11):1980-7. doi: 10.1002/prot.24356. Epub 2013 Aug 23.

46.

Deconstructing RNA: optical measurement of composition and structure.

Hobro AJ, Standley DM, Ahmad S, Smith NI.

Phys Chem Chem Phys. 2013 Aug 21;15(31):13199-208. doi: 10.1039/c3cp52406j.

PMID:
23824161
47.

Malt1-induced cleavage of regnase-1 in CD4(+) helper T cells regulates immune activation.

Uehata T, Iwasaki H, Vandenbon A, Matsushita K, Hernandez-Cuellar E, Kuniyoshi K, Satoh T, Mino T, Suzuki Y, Standley DM, Tsujimura T, Rakugi H, Isaka Y, Takeuchi O, Akira S.

Cell. 2013 May 23;153(5):1036-49. doi: 10.1016/j.cell.2013.04.034.

48.

A Parzen window-based approach for the detection of locally enriched transcription factor binding sites.

Vandenbon A, Kumagai Y, Teraguchi S, Amada KM, Akira S, Standley DM.

BMC Bioinformatics. 2013 Jan 21;14:26. doi: 10.1186/1471-2105-14-26.

49.

MAFFT multiple sequence alignment software version 7: improvements in performance and usability.

Katoh K, Standley DM.

Mol Biol Evol. 2013 Apr;30(4):772-80. doi: 10.1093/molbev/mst010. Epub 2013 Jan 16.

50.

A novel unbiased measure for motif co-occurrence predicts combinatorial regulation of transcription.

Vandenbon A, Kumagai Y, Akira S, Standley DM.

BMC Genomics. 2012;13 Suppl 7:S11. doi: 10.1186/1471-2164-13-S7-S11. Epub 2012 Dec 13.

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