2014 Taoka M, Morofuji N, Yamauchi Y, Ojima H, Kubota D, Terukina G, Nobe Y, Nakayama H, Takahashi N, Kosuge T, Isobe T, Kondo T. Global PROTOMAP Profiling to Search for Biomarkers of Early-Recurrent Hepatocellular Carcinoma. J Proteome Res. 2014 Jul 7. 石川英明、中山　洋、田岡万悟、高橋信弘、礒辺俊明質量分析法を利用したRNA代謝異常症のリボヌクレオプロテオミクス解析実験医学　増刊　Vol.32-No.10 1478-1485 Miyazawa N, Yoshikawa H, Magae S, Ishikawa H, Izumikawa K, Terukina G, Suzuki A, Nakamura-Fujiyama S, Miura Y, Hayano T, Komatsu W, Isobe T, Takahashi N. Human cell growth regulator Ly-1 antibody reactive homologue accelerates processing of preribosomal RNA. Genes Cells. 2014 Apr;19(4):273-86. doi: 10.1111/gtc.12129. Epub 2014 Feb 4. Ishikawa H, Nobe Y, Izumikawa K, Yoshikawa H, Miyazawa N, Terukina G, Kurokawa N, Taoka M, Yamauchi Y, Nakayama H, Isobe T, Takahashi N. Identification of truncated forms of U1 snRNA reveals a novel RNA degradation pathway during snRNP biogenesis. Nucleic Acids Res. 2014 Feb 1;42(4):2708-24. doi: 10.1093/nar/gkt1271. Epub 2013 Dec 5. 2013 Izumikawa K, Ishikawa H, Yoshikawa H, Terukina G, Miyazawa N, Nakayama H, Nobe Y, Taoka M, Yamauchi Y, Phillipsen S, Isobe T, Takahashi N. Friend of Prmt1, FOP is a Novel Component of the Nuclear SMN Complex Isolated Using Biotin Affinity Purification Izumikawa et al., J Proteomics Bioinform 2013, S7 吉川治孝・泉川桂一・石川英明・高橋信弘（Yoshikawa H, Izumikawa K, Ishikawa H, Takahashi N.）リボソームサブユニットの生合成の調節　[The regulatory mechanism underlying ribosomal subunit synthesis]. 生化学　第85巻第10号　861-870　（Seikagaku. 2013 Oct;85(10):861-70. ） Yamauchi Y, Taoka M, Nobe Y, Izumikawa K, Takahashi N, Nakayama H, Isobe T. Denaturing reversed phase liquid chromatographic separation of non-coding ribonucleic acids on macro-porous polystyrene-divinylbenzene resins. J Chromatogr A. 2013 Oct 18;1312:87-92. doi: 10.1016/j.chroma.2013.09.021. Epub 2013 Sep 9. 2012 Kaji H, Shikanai T, Sasaki-Sawa A, Wen H, Fujita M, Suzuki Y, Sugahara D, Sawaki H, Yamauchi Y, Shinkawa T, Taoka M, Takahashi N, Isobe T, Narimatsu H. Large-scale identification of N-glycosylated proteins of mouse tissues and construction of a glycoprotein database, GlycoProtDB. J Proteome Res. 2012 Sep 7;11(9):4553-66. doi: 10.1021/pr300346c. Epub 2012 Aug 13. 2011 Yoshikawa H, Komatsu W, Hayano T, Miura Y, Homma K, Izumikawa K, Ishikawa H, Miyazawa N, Tachikawa H, Yamauchi Y, Isobe T, Takahashi N. Splicing Factor 2-Associated Protein p32 Participates in Ribosome Biogenesis by Regulating the Binding of Nop52 and Fibrillarin to Preribosome Particles. Mol Cell Proteomics. 2011 Aug;10(8):M110.006148.Epub 2011 May 2. Nakayama H, Takahashi N, Isobe T. Informatics for mass spectrometry-based RNA analysis. Mass Spectrom Rev. 2011 Feb 16. doi: 10.1002/mas.20325. Terukina G, Yoshida Y, Takahashi N. Peptidyl-prolyl cis-trans isomerase xFKBP1B induces ectopic secondary axis and is involved in eye formation during Xenopus embryogenesis. Dev Growth Differ. 2011 Jan;53(1):55-68. doi: 10.1111/j.1440-169X.2010.01227.x. 2010 Takahashi N. The study of ribonucleoproteomics using mass spectrometry (ms)-based technologies: Forming the firm basis of genome wide-RNA analysis. Mass Spectrom Rev. 2010 Dec 22. Taoka M, Ikumi M, Nakayama H, Masaki S, Matsuda R, Nobe Y, Yamauchi Y, Takeda J, Takahashi N, Isobe T. In-gel digestion for mass spectrometric characterization of RNA from fluorescently stained polyacrylamide gels. Anal Chem. 2010 Sep 15;82(18):7795-803. 2009 Taoka M, Yamauchi Y, Nobe Y, Masaki S, Nakayama H, Ishikawa H, Takahashi N, Isobe T. An analytical platform for mass spectrometry-based identification and chemical analysis of RNA in ribonucleoprotein complexes. Nucleic Acids Res. 2009 Nov;37(21):e140. Fujiyama-Nakamura S, Yoshikawa H, Homma K, Hayano T, Tsujimura-Takahashi T, Izumikawa K, Ishikawa H, Miyazawa N, Yanagida M, Miura Y, Shinkawa T, Yamauchi Y, Isobe T, Takahashi N. Parvulin (Par14), a peptidyl-prolyl cis-trans isomerase, is a novel rRNA processing factor that evolved in the metazoan lineage. Mol Cell Proteomics. 2009 Jul;8(7):1552-65. Epub 2009 Apr 14. Nakayama H, Akiyama M, Taoka M, Yamauchi Y, Nobe Y, Ishikawa H, Takahashi N, Isobe T. Ariadne: a database search engine for identification and chemical analysis of RNA using tandem mass spectrometry data. Nucleic Acids Res. 2009 Apr;37(6):e47. Epub 2009 Mar 6. 2008 Hayano T, Yamauchi Y, Asano K, Tsujimura T, Hashimoto S, Isobe T, Takahashi N. Automated SPR-LC-MS/MS system for protein interaction analysis. J Proteome Res. 2008 Sep;7(9):4183-90. Epub 2008 Jul 25. Kurosawa G, Akahori Y, Morita M, Sumitomo M, Sato N, Muramatsu C, Eguchi K, Matsuda K, Takasaki A, Tanaka M, Iba Y, Hamada-Tsutsumi S, Ukai Y, Shiraishi M, Suzuki K, Kurosawa M, Fujiyama S, Takahashi N, Kato R, Mizoguchi Y, Shamoto M, Tsuda H, Sugiura M, Hattori Y, Miyakawa S, Shiroki R, Hoshinaga K, Hayashi N, Sugioka A, Kurosawa Y. Comprehensive screening for antigens overexpressed on carcinomas via isolation of human mAbs that may be therapeutic. Proc Natl Acad Sci U S A. 2008 May 20;105(20):7287-92. Epub 2008 May 12. Kimura T, Horibe T, Sakamoto C, Shitara Y, Fujiwara F, Komiya T, Yamamoto A, Hayano T, Takahashi N, Kikuchi M. Evidence for mitochondrial localization of P5, a member of the protein disulphide isomerase family. J Biochem. 2008 Aug;144(2):187-96. Epub 2008 Apr 19. Izumikawa K, Yanagida M, Hayano T, Tachikawa H, Komatsu W, Shimamoto A, Futami K, Furuichi Y, Shinkawa T, Yamauchi Y, Isobe T, Takahashi N. Association of human DNA helicase RecQ5beta with RNA polymerase II and its possible role in transcription. Biochem J. 2008 Aug 1;413(3):505-16. 2007 Kaji H, Kamiie J, Kawakami H, Kido K, Yamauchi Y, Shinkawa T, Taoka M, Takahashi N, Isobe T. Proteomics reveals N-linked glycoprotein diversity in Caenorhabditis elegans and suggests an atypical translocation mechanism for integral membrane proteins. Mol Cell Proteomics. 2007 Dec;6(12):2100-9. Epub 2007 Aug 30. Oda T, Hayano T, Miyaso H, Takahashi N, Yamashita T. Hsp90 regulates the Fanconi anemia DNA damage response pathway. Blood. 2007 Jun 1;109(11):5016-26. Epub 2007 Feb 27. 2006 Sekiguchi T, Hayano T, Yanagida M, Takahashi N, Nishimoto T. NOP132 is required for proper nucleolus localization of DEAD-box RNA helicase DDX47. Nucleic Acids Res. 2006;34(16):4593-608. Epub 2006 Sep 8. Ishikawa H, Tachikawa H, Miura Y, Takahashi N. TRIM11 binds to and destabilizes a key component of the activator-mediated cofactor complex (ARC105) through the ubiquitin-proteasome system. FEBS Lett. 2006 Sep 4;580(20):4784-92. Epub 2006 Aug 4. Stavreva DA*, Kawasaki M*, Dundr M, Koberna K, Müller WG, Tsujimura-Takahashi T, Komatsu W, Hayano T, Isobe T, Raska I, Misteli T, Takahashi N, McNally JG. (*Equally Contribution) Potential roles for ubiquitin and the proteasome during ribosome biogenesis. Mol Cell Biol. 2006 Jul;26(13):5131-45. Erratum in: Mol Cell Biol. 2006 Aug;26(16):6308. Nagano K, Itagaki C, Izumi T, Nunomura K, Soda Y, Tani K, Takahashi N, Takenawa T, Isobe T. Rb plays a role in survival of Abl-dependent human tumor cells as a downstream effector of Abl tyrosine kinase. Oncogene. 2006 Jan 26;25(4):493-502. Kaji H, Yamauchi Y, Takahashi N, Isobe T. Mass spectrometric identification of N-linked glycopeptides using lectin-mediated affinity capture and glycosylation site-specific stable isotope tagging. Nat Protoc. 2006;1(6):3019-27. 2005 Nunomura K, Nagano K, Itagaki C, Taoka M, Okamura N, Yamauchi Y, Sugano S, Takahashi N, Izumi T, Isobe T. Cell surface labeling and mass spectrometry reveal diversity of cell surface markers and signaling molecules expressed in undifferentiated mouse embryonic stem cells. Mol Cell Proteomics. 2005 Dec;4(12):1968-76. Epub 2005 Sep 20. Shinkawa T, Taoka M, Yamauchi Y, Ichimura T, Kaji H, Takahashi N, Isobe T. STEM: a software tool for large-scale proteomic data analyses. J Proteome Res. 2005 Sep-Oct;4(5):1826-31. Kimura T, Imaishi K, Hagiwara Y, Horibe T, Hayano T, Takahashi N, Urade R, Kato K, Kikuchi M. ERp57 binds competitively to protein disulfide isomerase and calreticulin. Biochem Biophys Res Commun. 2005 May 27;331(1):224-30. Nagano K, Taoka M, Yamauchi Y, Itagaki C, Shinkawa T, Nunomura K, Okamura N, Takahashi N, Izumi T, Isobe T. Large-scale identification of proteins expressed in mouse embryonic stem cells. Proteomics. 2005 Apr;5(5):1346-61. Ichimura T, Yamamura H, Sasamoto K, Tominaga Y, Taoka M, Kakiuchi K, Shinkawa T, Takahashi N, Shimada S, Isobe T. 14-3-3 proteins modulate the expression of epithelial Na+ channels by phosphorylation-dependent interaction with Nedd4-2 ubiquitin ligase. J Biol Chem. 2005 Apr 1;280(13):13187-94. Epub 2005 Jan 26. 2004 Taoka M, Yamauchi Y, Shinkawa T, Kaji H, Motohashi W, Nakayama H, Takahashi N, Isobe T. Only a small subset of the horizontally transferred chromosomal genes in Escherichia coli are translated into proteins. Mol Cell Proteomics. 2004 Aug;3(8):780-7. Epub 2004 Apr 28. Yoshimura Y, Yamauchi Y, Shinkawa T, Taoka M, Donai H, Takahashi N, Isobe T, Yamauchi T. Molecular constituents of the postsynaptic density fraction revealed by proteomic analysis using multidimensional liquid chromatography-tandem mass spectrometry. J Neurochem. 2004 Feb;88(3):759-68. Yoshida Y, Kim S, Chiba K, Kawai S, Tachikawa H, Takahashi N. Calcineurin inhibitors block dorsal-side signaling that affect late-stage development of the heart, kidney, liver, gut and somitic tissue during Xenopus embryogenesis. Dev Growth Differ. 2004 Apr;46(2):139-52. Yanagida M, Hayano T, Yamauchi Y, Shinkawa T, Natsume T, Isobe T, Takahashi N. Human fibrillarin forms a sub-complex with splicing factor 2-associated p32, protein arginine methyltransferases, and tubulins alpha 3 and beta 1 that is independent of its association with preribosomal ribonucleoprotein complexes. J Biol Chem. 2004 Jan 16;279(3):1607-14. Epub 2003 Oct 28. 2003 Hayano T, Yanagida M, Yamauchi Y, Shinkawa T, Isobe T, Takahashi N. Proteomic analysis of human Nop56p-associated pre-ribosomal ribonucleoprotein complexes. Possible link between Nop56p and the nucleolar protein treacle responsible for Treacher Collins syndrome. J Biol Chem. 2003 Sep 5;278(36):34309-19. Epub 2003 May 30. Takahashi N, Yanagida M, Fujiyama S, Hayano T, Isobe T. Proteomic snapshot analyses of preribosomal ribonucleoprotein complexes formed at various stages of ribosome biogenesis in yeast and mammalian cells. Mass Spectrom Rev. 2003 Sep-Oct;22(5):287-317. Review. Suda Y, Tachikawa H, Yokota A, Nakanishi H, Yamashita N, Miura Y, Takahashi N. Saccharomyces cerevisiae QNS1 codes for NAD(+) synthetase that is functionally conserved in mammals. Yeast. 2003 Aug;20(11):995-1005. Takahashi N, Kaji H, Yanagida M, Hayano T, Isobe T. Proteomics: advanced technology for the analysis of cellular function. J Nutr. 2003 Jun;133(6 Suppl 1):2090S-2096S. Kaji H, Saito H, Yamauchi Y, Shinkawa T, Taoka M, Hirabayashi J, Kasai K, Takahashi N, Isobe T. Lectin affinity capture, isotope-coded tagging and mass spectrometry to identify N-linked glycoproteins. Nat Biotechnol. 2003 Jun;21(6):667-72. Epub 2003 May 18. Mawuenyega KG, Kaji H, Yamuchi Y, Shinkawa T, Saito H, Taoka M, Takahashi N, Isobe T. Large-scale identification of Caenorhabditis elegans proteins by multidimensional liquid chromatography-tandem mass spectrometry. J Proteome Res. 2003 Jan-Feb;2(1):23-35. 2002 Natsume T, Yamauchi Y, Nakayama H, Shinkawa T, Yanagida M, Takahashi N, Isobe T. A direct nanoflow liquid chromatography-tandem mass spectrometry system for interaction proteomics. Anal Chem. 2002 Sep 15;74(18):4725-33. Fujiyama S, Yanagida M, Hayano T, Miura Y, Isobe T, Fujimori F, Uchida T, Takahashi N. Isolation and proteomic characterization of human Parvulin-associating preribosomal ribonucleoprotein complexes. J Biol Chem. 2002 Jun 28;277(26):23773-80. Epub 2002 Apr 17. Yanagisawa J, Kitagawa H, Yanagida M, Wada O, Ogawa S, Nakagomi M, Oishi H, Yamamoto Y, Nagasawa H, McMahon SB, Cole MD, Tora L, Takahashi N, Kato S. Nuclear receptor function requires a TFTC-type histone acetyl transferase complex. Mol Cell. 2002 Mar;9(3):553-62. 2001 Yanagida M, Shimamoto A, Nishikawa K, Furuichi Y, Isobe T, Takahashi N. Isolation and proteomic characterization of the major proteins of the nucleolin-binding ribonucleoprotein complexes. Proteomics. 2001 Nov;1(11):1390-404. Nakanishi H, Nakayama K, Yokota A, Tachikawa H, Takahashi N, Jigami Y. Hut1 proteins identified in Saccharomyces cerevisiae and Schizosaccharomyces pombe are functional homologues involved in the protein-folding process at the endoplasmic reticulum. Yeast. 2001 Apr;18(6):543-54. 2000 Yanagida M, Miura Y, Yagasaki K, Taoka M, Isobe T, Takahashi N. Matrix assisted laser desorption/ionization-time of flight-mass spectrometry analysis of proteins detected by anti-phosphotyrosine antibody on two-dimensional-gels of fibrolast cell lysates after tumor necrosis factor-alpha stimulation. Electrophoresis. 2000 May;21(9):1890-8. Lee S, Takeda Y, Kawano H, Hosoya H, Nomoto M, Fujimoto D, Takahashi N, Watanabe K. Expression and regulation of a gene encoding neural recognition molecule NB-3 of the contactin/F3 subgroup in mouse brain. Gene. 2000 Mar 21;245(2):253-66. Ikura T, Hayano T, Takahashi N, Kuwajima K. Fast folding of Escherichia coli cyclophilin A: a hypothesis of a unique hydrophobic core with a phenylalanine cluster. J Mol Biol. 2000 Mar 31;297(3):791-802. ~1999 主要論文 Matsuoka K., Taoka M., Satozawa N., Nakayama N., Ichimura T., Takahashi N., Yamakuni T., Song S. -Y., & Isobe T., (1994) "A nuclear factor containing the leucine-rich repeats expressed in murine cerebellar neurons." Proc. Natl. Acad. Sci. USA, 91, 9670-9674. Noboru Maki, Fumiko Sekiguchi, Junichi Nishimaki, Keiko Miwa, Toshiya Hayano, Nobuhiro Takahashi*, and Masanori Suzuki (1990) "Complementary DNA encoding the human T-cell FK506-binding protein, a peptidyl prolyl cis-trans isomerase distinct from cyclophilin" Proc. Natl. Acad. Sci. USA 87, 5440-5443. (*Corresponding author) Nobuhiro Takahashi, Toshiya Hayano, and Masanori Suzuki (1989) "Peptidyl-prolyl cis-trans isomerase is the cyclosporin A-binding protein cyclophilin." Nature, 336, 473-475. Tohru Ichimura, Toshiaki Isobe, Tsuneo Okuyama, Nobuhiro Takahashi, Kazuaki Araki, Ryozo Kuwano, and Yasuo Takahashi (1988) "Moleculer cloning of cDNA coding for brain-specific 14-3-3 protein, a protein kinase-dependent activator of tyrosin and tryptophan hydroxylases "Proc. Natl. Acad. Sci. USA, 85, 7084-7088. Karen Hass, Jeanne Madison, Noriaki Ishioka, Nobuhiro Takahashi, Kunio Arai, and Frank W. Putnam (1988) "The same substitution, glutamic acid -> lysine at position 501, occurs in three alloalbumins of asiatic origin: Albumin Vancouver, Birmingham, and Adana" Proc. Natl. Acad. Sci. USA, 85, 6692-6696. Nobuhiro Takahashi, Yoko Takahashi, Toshiaki Isobe, Frank W. Putnam, Mikio Fujita, Chiyoko Satoh, and James V. Neel (1987) "Amino acid substitutions in inherited albumin variants from Amerindian and Japanese populations" Proc. Natl. Acad. Sci. USA, 84, 8001-8005. Nobuhiro Takahashi, Yoko Takahashi, Baruch S. Blumberg, and Frank W. Putnam (1987) "Amino acid substitutions in genetic variants of human serum albumin and in sequences inferred from molecular cloning" Proc. Natl. Acad. Sci. USA, 84, 4413-4417. Nobuhiro Takahashi, Yoko Takahashi, and Frank W. Putnam (1987) "Structural changes and metal binding by proalbumins and other amino-terminal genetic variants of human serum albumiln." Proc. Natl. Acad. Sci. USA, 84, 7403- 7407. Noriaki Ishioka, Nobuhiro Takahashi, and Frank W. Putnam (1986) "Amino acid sequence of human plasma a-1-B glycoprotein: Homology to the immunoglobulin supergene family" Proc. Natl. Acad. Sci. USA, 83, 2363-2367. Nobuhiro Takahashi, Yoko Takahashi, and Frank W. Putnam (1986) "Primary structure of blood coagulation factor XIIIa (fibrinoligase, transglutaminase)from human placenta" Proc. Natl. Acad. Sci. USA, 83, 8019-8023. Noriaki Ishioka, Nobuhiro Takahashi, and Frank W. Putnam (1986) "Analysis of the mechanism, rate, and site of proteolytic cleavage of human immunoglobulin D by high-pressure liquid chromatography." Proc. Natl. Acad. Sci. USA, 83, 61-65. Nobuhiro Takahashi, Yoko Takahashi, and Frank W. Putnam (1985) "Complete amino acid sequence of human hemopexin, the heme-binding protein of serum" Proc. Natl. Acad. Sci. USA, 82, 73-77. Nobuhiro Takahashi, Yoko Takahashi, and Frank W. Putnam (1985) "Periodicity of leucine and tandem repetition of a 24-amino acid segment in the primary structure of leucine-rich a-2-glycoprotein of human serum." Proc. Natl. Acad. Sci. USA, 82, 1906-1910. Nobuhiro Takahashi, Thomas L. Ortel, and Frank W. Putnam (1984) "Single-chain structure of human ceruloplasmin: The complete amino acid sequence of the whole molecule" Proc. Natl. Acad. Sci. USA, 81, 390-394. Nobuhilro Takahashi, Yoko Takahashi, and Frank W. Putnam (1984) "Structure of human hemopexin: O-glycosyl sites and unusual clustering of tryptophan residues" Proc. Natl. Acad. Sci. USA, 81, 2021-2025. Jay N. Lozier, Nobuhiro Takahashi, and Frank W. Putnam (1984) "Complete amino acid sequence of human plasma b-2-glycoprotein I." Proc. Natl. Acad. Sci. USA, 81, 3640-3644. Thomas L Ortel, Nobuhiro Takahashi, and Frank W. Putnam (1984) "Structural model of human ceruloplasmin based on internal triplication, hydrophilic/hydrophobic character, and secondary structure of domains." Proc. Natl. Acad. Sci. USA, 81, 4761-4765. Nobuhiro Takahashi, Rachel A. Bauman, Thomas L. Ortel, Francis E. Dwulet, Chi-Chi Wang, and Frank W. Putnam (1983) "Internal triplication in the structure of human ceruloplasmin" Proc. Natl. Acad. Sci. USA, 80, 115-119. Yoko Takahashi, Nobuhiro Takahashi, Daniel Tetaert, and Frank W. Putnam (1983) "Complete covalent structure of a human IgD: Sequence of the lambda light chain" Proc. Natl. Acad. Sci. USA, 80, 3686-3690. Nobuhiro Takahashi, Daniel Tetaert, Debuire Brigitte, Lin Lien-Ching, and Frank W. Putnamn (1982) "Complete amino acid sequence of the delta heavy chain of human immunoglobulin D" Proc. Natl. Acad. Sci. USA, 79, 2850-2854. Frank W. Putnam, Nobuhiro Takahashi, Daniel Tetaert, Debuire Brigitte, and Lin Lien-Ching (1981) "Amino acid sequence of the first constant region domain and the hinge region of the delta-heavy chain of human IgD" Proc. Natl. Acad. Sci. USA, 78, 6168-6172. Tomotaka Shinoda, Nobuhiro Takahashi, Tatsunori Takayasu,Tsuneo Okuyama, and Akira Shimizu (1981) "Complete amino acid sequence of the Fc region of a human delta-chain" Proc. Natl. Acad. Sci. USA, 78, 785-789.

2014

Taoka M, Morofuji N, Yamauchi Y, Ojima H, Kubota D, Terukina G, Nobe Y, Nakayama H, Takahashi N, Kosuge T, Isobe T, Kondo T.

Global PROTOMAP Profiling to Search for Biomarkers of Early-Recurrent Hepatocellular Carcinoma.

J Proteome Res. 2014 Jul 7.

石川英明、中山　洋、田岡万悟、高橋信弘、礒辺俊明

質量分析法を利用したRNA代謝異常症のリボヌクレオプロテオミクス解析

実験医学　増刊　Vol.32-No.10 1478-1485

Miyazawa N, Yoshikawa H, Magae S, Ishikawa H, Izumikawa K, Terukina G, Suzuki A, Nakamura-Fujiyama S, Miura Y, Hayano T, Komatsu W, Isobe T, Takahashi N.

Human cell growth regulator Ly-1 antibody reactive homologue accelerates processing of preribosomal RNA.

Genes Cells. 2014 Apr;19(4):273-86. doi: 10.1111/gtc.12129. Epub 2014 Feb 4.

Ishikawa H, Nobe Y, Izumikawa K, Yoshikawa H, Miyazawa N, Terukina G, Kurokawa N, Taoka M, Yamauchi Y, Nakayama H, Isobe T, Takahashi N.

Identification of truncated forms of U1 snRNA reveals a novel RNA degradation pathway during snRNP biogenesis.

Nucleic Acids Res. 2014 Feb 1;42(4):2708-24. doi: 10.1093/nar/gkt1271. Epub 2013 Dec 5.

2013

Izumikawa K, Ishikawa H, Yoshikawa H, Terukina G, Miyazawa N, Nakayama H, Nobe Y, Taoka M, Yamauchi Y, Phillipsen S, Isobe T, Takahashi N.

Friend of Prmt1, FOP is a Novel Component of the Nuclear SMN Complex Isolated Using Biotin Affinity Purification

Izumikawa et al., J Proteomics Bioinform 2013, S7

吉川治孝・泉川桂一・石川英明・高橋信弘（Yoshikawa H, Izumikawa K, Ishikawa H, Takahashi N.）

リボソームサブユニットの生合成の調節　 [The regulatory mechanism underlying ribosomal subunit synthesis].

生化学　第85巻第10号　861-870　（Seikagaku. 2013 Oct;85(10):861-70. ）

Yamauchi Y, Taoka M, Nobe Y, Izumikawa K, Takahashi N, Nakayama H, Isobe T.

Denaturing reversed phase liquid chromatographic separation of non-coding ribonucleic acids on macro-porous polystyrene-divinylbenzene resins.

J Chromatogr A. 2013 Oct 18;1312:87-92. doi: 10.1016/j.chroma.2013.09.021. Epub 2013 Sep 9.

2012

Kaji H, Shikanai T, Sasaki-Sawa A, Wen H, Fujita M, Suzuki Y, Sugahara D, Sawaki H, Yamauchi Y, Shinkawa T, Taoka M, Takahashi N, Isobe T, Narimatsu H.

Large-scale identification of N-glycosylated proteins of mouse tissues and construction of a glycoprotein database, GlycoProtDB.

J Proteome Res. 2012 Sep 7;11(9):4553-66. doi: 10.1021/pr300346c. Epub 2012 Aug 13.

2011

Yoshikawa H, Komatsu W, Hayano T, Miura Y, Homma K, Izumikawa K, Ishikawa H, Miyazawa N, Tachikawa H, Yamauchi Y, Isobe T, Takahashi N.

Splicing Factor 2-Associated Protein p32 Participates in Ribosome Biogenesis by Regulating the Binding of Nop52 and Fibrillarin to Preribosome Particles.

Mol Cell Proteomics. 2011 Aug;10(8):M110.006148.Epub 2011 May 2.

Nakayama H, Takahashi N, Isobe T.

Informatics for mass spectrometry-based RNA analysis.

Mass Spectrom Rev. 2011 Feb 16. doi: 10.1002/mas.20325.

Terukina G, Yoshida Y, Takahashi N.

Peptidyl-prolyl cis-trans isomerase xFKBP1B induces ectopic secondary axis and is involved in eye formation during Xenopus embryogenesis.

Dev Growth Differ. 2011 Jan;53(1):55-68. doi: 10.1111/j.1440-169X.2010.01227.x.

2010

Takahashi N.

The study of ribonucleoproteomics using mass spectrometry (ms)-based technologies: Forming the firm basis of genome wide-RNA analysis.

Mass Spectrom Rev. 2010 Dec 22.

Taoka M, Ikumi M, Nakayama H, Masaki S, Matsuda R, Nobe Y, Yamauchi Y, Takeda J, Takahashi N, Isobe T.

In-gel digestion for mass spectrometric characterization of RNA from fluorescently stained polyacrylamide gels.

Anal Chem. 2010 Sep 15;82(18):7795-803.

2009

Taoka M, Yamauchi Y, Nobe Y, Masaki S, Nakayama H, Ishikawa H, Takahashi N, Isobe T.

An analytical platform for mass spectrometry-based identification and chemical analysis of RNA in ribonucleoprotein complexes.

Nucleic Acids Res. 2009 Nov;37(21):e140.

Fujiyama-Nakamura S, Yoshikawa H, Homma K, Hayano T, Tsujimura-Takahashi T, Izumikawa K, Ishikawa H, Miyazawa N, Yanagida M, Miura Y, Shinkawa T, Yamauchi Y, Isobe T, Takahashi N.

Parvulin (Par14), a peptidyl-prolyl cis-trans isomerase, is a novel rRNA processing factor that evolved in the metazoan lineage.

Mol Cell Proteomics. 2009 Jul;8(7):1552-65. Epub 2009 Apr 14.

Nakayama H, Akiyama M, Taoka M, Yamauchi Y, Nobe Y, Ishikawa H, Takahashi N, Isobe T.

Ariadne: a database search engine for identification and chemical analysis of RNA using tandem mass spectrometry data.

Nucleic Acids Res. 2009 Apr;37(6):e47. Epub 2009 Mar 6.

2008

Hayano T, Yamauchi Y, Asano K, Tsujimura T, Hashimoto S, Isobe T, Takahashi N.

Automated SPR-LC-MS/MS system for protein interaction analysis.

J Proteome Res. 2008 Sep;7(9):4183-90. Epub 2008 Jul 25.

Kurosawa G, Akahori Y, Morita M, Sumitomo M, Sato N, Muramatsu C, Eguchi K, Matsuda K, Takasaki A, Tanaka M, Iba Y, Hamada-Tsutsumi S, Ukai Y, Shiraishi M, Suzuki K, Kurosawa M, Fujiyama S, Takahashi N, Kato R, Mizoguchi Y, Shamoto M, Tsuda H, Sugiura M, Hattori Y, Miyakawa S, Shiroki R, Hoshinaga K, Hayashi N, Sugioka A, Kurosawa Y.

Comprehensive screening for antigens overexpressed on carcinomas via isolation of human mAbs that may be therapeutic.

Proc Natl Acad Sci U S A. 2008 May 20;105(20):7287-92. Epub 2008 May 12.

Kimura T, Horibe T, Sakamoto C, Shitara Y, Fujiwara F, Komiya T, Yamamoto A, Hayano T, Takahashi N, Kikuchi M.

Evidence for mitochondrial localization of P5, a member of the protein disulphide isomerase family.

J Biochem. 2008 Aug;144(2):187-96. Epub 2008 Apr 19.

Izumikawa K, Yanagida M, Hayano T, Tachikawa H, Komatsu W, Shimamoto A, Futami K, Furuichi Y, Shinkawa T, Yamauchi Y, Isobe T, Takahashi N.

Association of human DNA helicase RecQ5beta with RNA polymerase II and its possible role in transcription.

Biochem J. 2008 Aug 1;413(3):505-16.

2007

Kaji H, Kamiie J, Kawakami H, Kido K, Yamauchi Y, Shinkawa T, Taoka M, Takahashi N, Isobe T.

Proteomics reveals N-linked glycoprotein diversity in Caenorhabditis elegans and suggests an atypical translocation mechanism for integral membrane proteins.

Mol Cell Proteomics. 2007 Dec;6(12):2100-9. Epub 2007 Aug 30.

Oda T, Hayano T, Miyaso H, Takahashi N, Yamashita T.

Hsp90 regulates the Fanconi anemia DNA damage response pathway.

Blood. 2007 Jun 1;109(11):5016-26. Epub 2007 Feb 27.

2006

Sekiguchi T, Hayano T, Yanagida M, Takahashi N, Nishimoto T.

NOP132 is required for proper nucleolus localization of DEAD-box RNA helicase DDX47.

Nucleic Acids Res. 2006;34(16):4593-608. Epub 2006 Sep 8.

Ishikawa H, Tachikawa H, Miura Y, Takahashi N.

TRIM11 binds to and destabilizes a key component of the activator-mediated cofactor complex (ARC105) through the ubiquitin-proteasome system.

FEBS Lett. 2006 Sep 4;580(20):4784-92. Epub 2006 Aug 4.

Stavreva DA*, Kawasaki M*, Dundr M, Koberna K, Müller WG, Tsujimura-Takahashi T, Komatsu W, Hayano T, Isobe T, Raska I, Misteli T, Takahashi N, McNally JG. (*Equally Contribution)

Potential roles for ubiquitin and the proteasome during ribosome biogenesis.

Mol Cell Biol. 2006 Jul;26(13):5131-45. Erratum in: Mol Cell Biol. 2006 Aug;26(16):6308.

Nagano K, Itagaki C, Izumi T, Nunomura K, Soda Y, Tani K, Takahashi N, Takenawa T, Isobe T.

Rb plays a role in survival of Abl-dependent human tumor cells as a downstream effector of Abl tyrosine kinase.

Oncogene. 2006 Jan 26;25(4):493-502.

Kaji H, Yamauchi Y, Takahashi N, Isobe T.

Mass spectrometric identification of N-linked glycopeptides using lectin-mediated affinity capture and glycosylation site-specific stable isotope tagging.

Nat Protoc. 2006;1(6):3019-27.

2005

Nunomura K, Nagano K, Itagaki C, Taoka M, Okamura N, Yamauchi Y, Sugano S, Takahashi N, Izumi T, Isobe T.

Cell surface labeling and mass spectrometry reveal diversity of cell surface markers and signaling molecules expressed in undifferentiated mouse embryonic stem cells.

Mol Cell Proteomics. 2005 Dec;4(12):1968-76. Epub 2005 Sep 20.

Shinkawa T, Taoka M, Yamauchi Y, Ichimura T, Kaji H, Takahashi N, Isobe T.

STEM: a software tool for large-scale proteomic data analyses.

J Proteome Res. 2005 Sep-Oct;4(5):1826-31.

Kimura T, Imaishi K, Hagiwara Y, Horibe T, Hayano T, Takahashi N, Urade R, Kato K, Kikuchi M.

ERp57 binds competitively to protein disulfide isomerase and calreticulin.

Biochem Biophys Res Commun. 2005 May 27;331(1):224-30.

Nagano K, Taoka M, Yamauchi Y, Itagaki C, Shinkawa T, Nunomura K, Okamura N, Takahashi N, Izumi T, Isobe T.

Large-scale identification of proteins expressed in mouse embryonic stem cells.

Proteomics. 2005 Apr;5(5):1346-61.

Ichimura T, Yamamura H, Sasamoto K, Tominaga Y, Taoka M, Kakiuchi K, Shinkawa T, Takahashi N, Shimada S, Isobe T.

14-3-3 proteins modulate the expression of epithelial Na+ channels by phosphorylation-dependent interaction with Nedd4-2 ubiquitin ligase.

J Biol Chem. 2005 Apr 1;280(13):13187-94. Epub 2005 Jan 26.

2004

Taoka M, Yamauchi Y, Shinkawa T, Kaji H, Motohashi W, Nakayama H, Takahashi N, Isobe T.

Only a small subset of the horizontally transferred chromosomal genes in Escherichia coli are translated into proteins.

Mol Cell Proteomics. 2004 Aug;3(8):780-7. Epub 2004 Apr 28.

Yoshimura Y, Yamauchi Y, Shinkawa T, Taoka M, Donai H, Takahashi N, Isobe T, Yamauchi T.

Molecular constituents of the postsynaptic density fraction revealed by proteomic analysis using multidimensional liquid chromatography-tandem mass spectrometry.

J Neurochem. 2004 Feb;88(3):759-68.

Yoshida Y, Kim S, Chiba K, Kawai S, Tachikawa H, Takahashi N.

Calcineurin inhibitors block dorsal-side signaling that affect late-stage development of the heart, kidney, liver, gut and somitic tissue during Xenopus embryogenesis.

Dev Growth Differ. 2004 Apr;46(2):139-52.

Yanagida M, Hayano T, Yamauchi Y, Shinkawa T, Natsume T, Isobe T, Takahashi N.

Human fibrillarin forms a sub-complex with splicing factor 2-associated p32, protein arginine methyltransferases, and tubulins alpha 3 and beta 1 that is independent of its association with preribosomal ribonucleoprotein complexes.

J Biol Chem. 2004 Jan 16;279(3):1607-14. Epub 2003 Oct 28.

2003

Hayano T, Yanagida M, Yamauchi Y, Shinkawa T, Isobe T, Takahashi N.

Proteomic analysis of human Nop56p-associated pre-ribosomal ribonucleoprotein complexes. Possible link between Nop56p and the nucleolar protein treacle responsible for Treacher Collins syndrome.

J Biol Chem. 2003 Sep 5;278(36):34309-19. Epub 2003 May 30.

Takahashi N, Yanagida M, Fujiyama S, Hayano T, Isobe T.

Proteomic snapshot analyses of preribosomal ribonucleoprotein complexes formed at various stages of ribosome biogenesis in yeast and mammalian cells.

Mass Spectrom Rev. 2003 Sep-Oct;22(5):287-317. Review.

Suda Y, Tachikawa H, Yokota A, Nakanishi H, Yamashita N, Miura Y, Takahashi N.

Saccharomyces cerevisiae QNS1 codes for NAD(+) synthetase that is functionally conserved in mammals.

Yeast. 2003 Aug;20(11):995-1005.

Takahashi N, Kaji H, Yanagida M, Hayano T, Isobe T.

Proteomics: advanced technology for the analysis of cellular function.

J Nutr. 2003 Jun;133(6 Suppl 1):2090S-2096S.

Kaji H, Saito H, Yamauchi Y, Shinkawa T, Taoka M, Hirabayashi J, Kasai K, Takahashi N, Isobe T.

Lectin affinity capture, isotope-coded tagging and mass spectrometry to identify N-linked glycoproteins.

Nat Biotechnol. 2003 Jun;21(6):667-72. Epub 2003 May 18.

Mawuenyega KG, Kaji H, Yamuchi Y, Shinkawa T, Saito H, Taoka M, Takahashi N, Isobe T.

Large-scale identification of Caenorhabditis elegans proteins by multidimensional liquid chromatography-tandem mass spectrometry.

J Proteome Res. 2003 Jan-Feb;2(1):23-35.

2002

Natsume T, Yamauchi Y, Nakayama H, Shinkawa T, Yanagida M, Takahashi N, Isobe T.

A direct nanoflow liquid chromatography-tandem mass spectrometry system for interaction proteomics.

Anal Chem. 2002 Sep 15;74(18):4725-33.

Fujiyama S, Yanagida M, Hayano T, Miura Y, Isobe T, Fujimori F, Uchida T, Takahashi N.

Isolation and proteomic characterization of human Parvulin-associating preribosomal ribonucleoprotein complexes.

J Biol Chem. 2002 Jun 28;277(26):23773-80. Epub 2002 Apr 17.

Yanagisawa J, Kitagawa H, Yanagida M, Wada O, Ogawa S, Nakagomi M, Oishi H, Yamamoto Y, Nagasawa H, McMahon SB, Cole MD, Tora L, Takahashi N, Kato S.

Nuclear receptor function requires a TFTC-type histone acetyl transferase complex.

Mol Cell. 2002 Mar;9(3):553-62.

2001

Yanagida M, Shimamoto A, Nishikawa K, Furuichi Y, Isobe T, Takahashi N.

Isolation and proteomic characterization of the major proteins of the nucleolin-binding ribonucleoprotein complexes.

Proteomics. 2001 Nov;1(11):1390-404.

Nakanishi H, Nakayama K, Yokota A, Tachikawa H, Takahashi N, Jigami Y.

Hut1 proteins identified in Saccharomyces cerevisiae and Schizosaccharomyces pombe are functional homologues involved in the protein-folding process at the endoplasmic reticulum.

Yeast. 2001 Apr;18(6):543-54.

2000

Yanagida M, Miura Y, Yagasaki K, Taoka M, Isobe T, Takahashi N.

Matrix assisted laser desorption/ionization-time of flight-mass spectrometry analysis of proteins detected by anti-phosphotyrosine antibody on two-dimensional-gels of fibrolast cell lysates after tumor necrosis factor-alpha stimulation.

Electrophoresis. 2000 May;21(9):1890-8.

Lee S, Takeda Y, Kawano H, Hosoya H, Nomoto M, Fujimoto D, Takahashi N, Watanabe K.

Expression and regulation of a gene encoding neural recognition molecule NB-3 of the contactin/F3 subgroup in mouse brain.

Gene. 2000 Mar 21;245(2):253-66.

Ikura T, Hayano T, Takahashi N, Kuwajima K.

Fast folding of Escherichia coli cyclophilin A: a hypothesis of a unique hydrophobic core with a phenylalanine cluster.

J Mol Biol. 2000 Mar 31;297(3):791-802.

~1999 主要論文

Matsuoka K., Taoka M., Satozawa N., Nakayama N., Ichimura T., Takahashi N., Yamakuni T., Song S. -Y., & Isobe T., (1994)

"A nuclear factor containing the leucine-rich repeats expressed in murine cerebellar neurons."

Proc. Natl. Acad. Sci. USA, 91, 9670-9674.

Noboru Maki, Fumiko Sekiguchi, Junichi Nishimaki, Keiko Miwa, Toshiya Hayano, Nobuhiro Takahashi*, and Masanori Suzuki (1990)

"Complementary DNA encoding the human T-cell FK506-binding protein, a peptidyl prolyl cis-trans isomerase distinct from cyclophilin"

Proc. Natl. Acad. Sci. USA 87, 5440-5443. (*Corresponding author)

Nobuhiro Takahashi, Toshiya Hayano, and Masanori Suzuki (1989)

"Peptidyl-prolyl cis-trans isomerase is the cyclosporin A-binding protein cyclophilin."

Nature, 336, 473-475.

Tohru Ichimura, Toshiaki Isobe, Tsuneo Okuyama, Nobuhiro Takahashi, Kazuaki Araki, Ryozo Kuwano, and Yasuo Takahashi (1988)

"Moleculer cloning of cDNA coding for brain-specific 14-3-3 protein, a protein kinase-dependent activator of tyrosin and tryptophan hydroxylases

"Proc. Natl. Acad. Sci. USA, 85, 7084-7088.

Karen Hass, Jeanne Madison, Noriaki Ishioka, Nobuhiro Takahashi, Kunio Arai, and Frank W. Putnam (1988)

"The same substitution, glutamic acid -> lysine at position 501, occurs in three alloalbumins of asiatic origin: Albumin Vancouver, Birmingham, and Adana"

Proc. Natl. Acad. Sci. USA, 85, 6692-6696.

Nobuhiro Takahashi, Yoko Takahashi, Toshiaki Isobe, Frank W. Putnam, Mikio Fujita, Chiyoko Satoh, and James V. Neel (1987)

"Amino acid substitutions in inherited albumin variants from Amerindian and Japanese populations"

Proc. Natl. Acad. Sci. USA, 84, 8001-8005.

Nobuhiro Takahashi, Yoko Takahashi, Baruch S. Blumberg, and Frank W. Putnam (1987)

"Amino acid substitutions in genetic variants of human serum albumin and in sequences inferred from molecular cloning"

Proc. Natl. Acad. Sci. USA, 84, 4413-4417.

Nobuhiro Takahashi, Yoko Takahashi, and Frank W. Putnam (1987)

"Structural changes and metal binding by proalbumins and other amino-terminal genetic variants of human serum albumiln."

Proc. Natl. Acad. Sci. USA, 84, 7403- 7407.

Noriaki Ishioka, Nobuhiro Takahashi, and Frank W. Putnam (1986)

"Amino acid sequence of human plasma a-1-B glycoprotein: Homology to the immunoglobulin supergene family"

Proc. Natl. Acad. Sci. USA, 83, 2363-2367.

Nobuhiro Takahashi, Yoko Takahashi, and Frank W. Putnam (1986)

"Primary structure of blood coagulation factor XIIIa (fibrinoligase, transglutaminase)from human placenta"

Proc. Natl. Acad. Sci. USA, 83, 8019-8023.

Noriaki Ishioka, Nobuhiro Takahashi, and Frank W. Putnam (1986)

"Analysis of the mechanism, rate, and site of proteolytic cleavage of human immunoglobulin D by high-pressure liquid chromatography."

Proc. Natl. Acad. Sci. USA, 83, 61-65.

Nobuhiro Takahashi, Yoko Takahashi, and Frank W. Putnam (1985)

"Complete amino acid sequence of human hemopexin, the heme-binding protein of serum"

Proc. Natl. Acad. Sci. USA, 82, 73-77.

Nobuhiro Takahashi, Yoko Takahashi, and Frank W. Putnam (1985)

"Periodicity of leucine and tandem repetition of a 24-amino acid segment in the primary structure of leucine-rich a-2-glycoprotein of human serum."

Proc. Natl. Acad. Sci. USA, 82, 1906-1910.

Nobuhiro Takahashi, Thomas L. Ortel, and Frank W. Putnam (1984)

"Single-chain structure of human ceruloplasmin: The complete amino acid sequence of the whole molecule"

Proc. Natl. Acad. Sci. USA, 81, 390-394.

Nobuhilro Takahashi, Yoko Takahashi, and Frank W. Putnam (1984)

"Structure of human hemopexin: O-glycosyl sites and unusual clustering of tryptophan residues"

Proc. Natl. Acad. Sci. USA, 81, 2021-2025.

Jay N. Lozier, Nobuhiro Takahashi, and Frank W. Putnam (1984)

"Complete amino acid sequence of human plasma b-2-glycoprotein I."

Proc. Natl. Acad. Sci. USA, 81, 3640-3644.

Thomas L Ortel, Nobuhiro Takahashi, and Frank W. Putnam (1984)

"Structural model of human ceruloplasmin based on internal triplication, hydrophilic/hydrophobic character, and secondary structure of domains."

Proc. Natl. Acad. Sci. USA, 81, 4761-4765.

Nobuhiro Takahashi, Rachel A. Bauman, Thomas L. Ortel, Francis E. Dwulet, Chi-Chi Wang, and Frank W. Putnam (1983)

"Internal triplication in the structure of human ceruloplasmin"

Proc. Natl. Acad. Sci. USA, 80, 115-119.

Yoko Takahashi, Nobuhiro Takahashi, Daniel Tetaert, and Frank W. Putnam (1983)

"Complete covalent structure of a human IgD: Sequence of the lambda light chain"

Proc. Natl. Acad. Sci. USA, 80, 3686-3690.

Nobuhiro Takahashi, Daniel Tetaert, Debuire Brigitte, Lin Lien-Ching, and Frank W. Putnamn (1982)

"Complete amino acid sequence of the delta heavy chain of human immunoglobulin D"

Proc. Natl. Acad. Sci. USA, 79, 2850-2854.

Frank W. Putnam, Nobuhiro Takahashi, Daniel Tetaert, Debuire Brigitte, and Lin Lien-Ching (1981)

"Amino acid sequence of the first constant region domain and the hinge region of the delta-heavy chain of human IgD"

Proc. Natl. Acad. Sci. USA, 78, 6168-6172.

Tomotaka Shinoda, Nobuhiro Takahashi, Tatsunori Takayasu,Tsuneo Okuyama, and Akira Shimizu (1981)

"Complete amino acid sequence of the Fc region of a human delta-chain"

Proc. Natl. Acad. Sci. USA, 78, 785-789.