・Clinical sequencing using a next-generation sequencing-based multiplex gene assay in patients with advanced solid tumors.
Kou T, Kanai M, Yamamoto Y, Kamada M, Nakatsui M, Sakuma T, Mochizuki H, Hiroshima A, Sugiyama A, Nakamura E, Miyake H, Minamiguchi S, Takaori K, Matsumoto S, Haga H, Seno H, Kosugi S, Okuno Y, Muto M.
Cancer Sci. 2017 Jul;108(7):1440-1446. doi: 10.1111/cas.13265. Epub 2017 May 22.
・Genome-wide DNA methylation analysis during non-alcoholic steatohepatitis-related multistage hepatocarcinogenesis: comparison with hepatitis virus-related carcinogenesis.
Kuramoto J, Arai E, Tian Y, Funahashi N, Hiramoto M, Nammo T, Nozaki Y, Takahashi Y, Ito N, Shibuya A, Ojima H, Sukeda A, Seki Y, Kasama K, Yasuda K, Kanai Y.
Carcinogenesis. 2017 Mar 1;38(3):261-270. doi: 10.1093/carcin/bgx005.
・Genes involved in development and differentiation are commonly methylated in cancers derived from multiple organs: a single-institutional methylome analysis using 1007 tissue specimens.
Ohara K, Arai E, Takahashi Y, Ito N, Shibuya A, Tsuta K, Kushima R, Tsuda H, Ojima H, Fujimoto H, Watanabe SI, Katai H, Kinoshita T, Shibata T, Kohno T, Kanai Y.
Carcinogenesis. 2017 Mar 1;38(3):241-251. doi: 10.1093/carcin/bgw209.
・The Effect of Conformational Flexibility on Binding Free Energy Estimation between Kinases and Their Inhibitors
Mitsugu Araki, Narutoshi Kamiya, Miwa Sato, Masahiko Nakatsui, Takatsugu Hirokawa, Yasushi Okuno
J. Chem. Inf. Model., 2016, 56 (12), pp 2445–2456. doi: 10.1021/acs.jcim.6b00398
・M-path: a compass for navigating potential metabolic pathways.
Araki M, Cox RS 3rd, Makiguchi H, Ogawa T, Taniguchi T, Miyaoku K, Nakatsui M, Hara KY, Kondo A.
Bioinformatics. 2015 Mar 15;31(6):905-11. doi: 10.1093/bioinformatics/btu750. Epub 2014 Nov 13.
・Alternative mammalian target of rapamycin (mTOR) signal activation in sorafenib-resistant hepatocellular carcinoma cells revealed by array-based pathway profiling.
Masuda M, Chen WY, Miyanaga A, Nakamura Y, Kawasaki K, Sakuma T, Ono M, Chen CL, Honda K, Yamada T.
Mol Cell Proteomics. 2014 Jun;13(6):1429-38. doi: 10.1074/mcp.M113.033845. Epub 2014 Mar 18.
・MicroRNA expression and functional profiles of osteosarcoma.
Kobayashi E, Satow R, Ono M, Masuda M, Honda K, Sakuma T, Kawai A, Morioka H, Toyama Y, Yamada T.
Oncology. 2014;86(2):94-103. doi: 10.1159/000357408. Epub 2014 Jan 18.
・Molecular architecture of the active mitochondrial protein gate.
Takuya Shiota, Kenichiro Imai, Jian Qiu, Victoria L. Hewitt, Khershing Tan, Hsin-Hui Shen, Noriyuki Sakiyama, Yoshinori Fukasawa, Sikander Hayat, Megumi Kamiya, Arne Elofsson, Kentaro Tomii, Paul Horton, Nils Wiedemann, Nikolaus Pfanner, Trevor Lithgow, Toshiya Endo., Science. (2015)
・PDGFR-β Plays a Key Role in the Ectopic Migration of Neuroblasts in Cerebral Stroke.
Sato H, Ishii Y, Yamamoto S, Azuma E, Takahashi Y, Hamashima T, Umezawa A, Mori H, Kuroda S, Endo S, Sasahara M., Stem Cells. (2015)
・Alterations of the spindle checkpoint pathway in clinicopathologically aggressive CpG island methylator phenotype clear cell renal cell carcinomas.
Arai E, Gotoh M, Tian Y, Sakamoto H, Ono M, Matsuda A, Takahashi Y, Miyata S, Totsuka H, Chiku S, Komiyama M, Fujimoto H, Matsumoto K, Yamada T, Yoshida T, Kanai Y., Int J Cancer. (2015)
・Epigenetic clustering of gastric carcinomas based on DNA methylation profiles at the precancerous stage: its correlation with tumor aggressiveness and patient outcome.
Yamanoi K, Arai E, Tian Y, Takahashi Y, Miyata S, Sasaki H, Chiwaki F, Ichikawa H, Sakamoto H, Kushima R, Katai H, Yoshida T, Sakamoto M, Kanai Y., Carcinogenesis. (2015)
・Epigenetic clustering of lung adenocarcinomas based on DNA methylation profiles in adjacent lung tissue: Its correlation with smoking history and chronic obstructive pulmonary disease.
Sato T, Arai E, Kohno T, Takahashi Y, Miyata S, Tsuta K, Watanabe S, Soejima K, Betsuyaku T, Kanai Y., Int J Cancer. (2014)
・M-path: A Compass for Navigating Potential Metabolic Pathways.
Araki M, Cox RS 3rd, Makiguchi H, Ogawa T, Taniguchi T, Miyaoku K, Nakatsui M, Hara KY, Kondo A. Bioinformatics (2014)
・Rapid identification of fatty acids and (O-acyl)-ω-hydroxy fatty acids in human meibum by liquid chromatography/high-resolution mass spectrometry.
Mori N, Fukano Y, Arita R, Shirakawa R, Kawazu K, Nakamura M, Amano S. J Chromatogr A (2014)

・Development of a lipid profiling system using reverse-phase liquid chromatography coupled to high-resolution mass spectrometry with rapid polarity switching and an automated lipid identification software.
Yamada T, Uchikata T, Sakamoto S, Yokoi Y, Fukusaki E, Bamba T. J Chromatogr A (2013)

・Diagnostic and Prognostic Significance of the Alternatively Spliced ACTN4 Variant in High-grade Neuroendocrine Pulmonary Tumours.
A Miyanaga, K Honda, K Tsuta, M Masuda, U Yamaguchi, G Fujii, A Miyamoto, S Shinagawa, N Miura, H Tsuda, T Sakuma, H Asamura, A Gemma, and T Yamada. Annals of Oncology (2013)
・Distinct outcome of stage I lung adenocarcinoma with ACTN4 cell motility gene amplification.
Noro R, Honda K, Tsuta K, Ishii G, Maeshima AM, Miura N, Furuta K, Shibata T, Tsuda H, Ochiai A, Sakuma T, Nishijima N, Gemma A, Asamura H, Nagai K, Yamada T. Annals of Oncology (2013)
・Protein Experimental Information Management System (PREIMS) Based on Ontology: Development and Applications.
Sato J, Kozaki K, Handa S, Ikeda T, Saka R, Tomizuka K, Nishiyama Y, Okumura T, Hirai S, Ohno T, Ohta M, Date S, Nakamura H. IPSJ Transactions on Bioinformatics (2013)
・Supercritical fluid chromatography/Orbitrap mass spectrometry based lipidomics platform coupled with automated lipid identification software for accurate lipid profiling.
Yamada T, Uchikata T, Sakamoto S, Yokoi Y, Nishiumi S, Yoshida M, Fukusaki E, Bamba T. J Chromatogr A. (2013)


・Use of Quantitative Shotgun Proteomics to Identify Fibronectin 1 as a Potential Plasma Biomarker for Clear Cell Carcinoma of the Kidney.
Akira Yokomizo, Michiko Takakura, Yae Kanai, Tomohiro Sakuma, Junichi Matsubara, Kazufumi Honda, Seiji Naito, Tesshi Yamada, and Masaya Ono. Cancer Biomarkers (2013)
・Altered Plasma Apolipoprotein Modifications in Patients with Pancreatic Cancer: Protein Characterization and Multi-institutional Validation.
Kazufumi Honda, Takuji Okusaka, Klaus Felix, Shoji Nakamori, Naohiro Sata, Hideo Nagai, Tatsuya Ioka, Akihiko Tsuchida, Takeshi Shimahara, Masashi Shimahara, Yohichi Yasunami, Hideya Kuwabara, Tomohiro Sakuma, Yoshihiko Otsuka, Norihito Ota, Miki Shitashige, Tomoo Kosuge, Markus W B?chler, and Tesshi Yamada. PloS One (2012)
・Biomarker Discovery of Pancreatic and Gastrointestinal Cancer by 2DICAL: 2-Dimensional Image-Converted Analysis of Liquid Chromatography and Mass Spectrometry.
Masaya Ono, Masahiro Kamita, Yusuke Murakoshi, Junichi Matsubara, Kazufumi Honda, Banno Miho, Tomohiro Sakuma, and Tesshi Yamada. International Journal of Proteomics (2012)

・Carbonic Anhydrase I as a New Plasma Biomarker for Prostate Cancer.
Michiko Takakura, Akira Yokomizo, Yoshinori Tanaka, Michimoto Kobayashi, Giman Jung, Miho Banno, Tomohiro Sakuma, Kenjiro Imada, Yoshinao Oda, Masahiro Kamita, Kazufumi Honda, Tesshi Yamada, Seiji Naito, and Masaya Ono. ISRN Oncology (2012)
・Combined Functional Genome Survey of Therapeutic Targets for Clear Cell Carcinoma of the Kidney.
Hideaki Ito, Kazufumi Honda, Reiko Satow, Eri Arai, Miki Shitashige, Masaya Ono, Tomohiro Sakuma, Shigeru Sakano, Katsusuke Naito, Hideyasu Matsuyama, and Tesshi Yamada. Japanese Journal of Clinical Oncology (2011)
・Identification of Adipophilin as a Potential Plasma Biomarker for Colorectal Cancer Using Label-free Quantitative Mass Spectrometry and Protein Microarray.
Junichi Matsubara, Kazufumi Honda, Masaya Ono, Shigeki Sekine, Yoshinori Tanaka, Michimoto Kobayashi, Giman Jung, Tomohiro Sakuma, Shoji Nakamori, Naohiro Sata, Hideo Nagai, Tatsuya Ioka, Takuji Okusaka, Tomoo Kosuge, Akihiko Tsuchida, Masashi Shimahara, Yohichi Yasunami, Tsutomu Chiba, and Tesshi Yamada. Cancer Epidemiology, Biomarkers & Prevention (2011)

・Plasma Biomarker Discovery and Validation for Colorectal Cancer by Quantitative Shotgun Mass Spectrometry and Protein Microarray.
Yusuke Murakoshi, Kazufumi Honda, Shizuka Sasazuki, Masaya Ono, Ayako Negishi, Junichi Matsubara, Tomohiro Sakuma, Hideya Kuwabara, Shoji Nakamori, Naohiro Sata, Hideo Nagai, Tatsuya Ioka, Takuji Okusaka, Tomoo Kosuge, Masashi Shimahara, Yohichi Yasunami, Yoshinori Ino, Akihiko Tsuchida, Tatsuya Aoki, Shoichiro Tsugane, and Tesshi Yamada. Cancer Science (2011)

・Reduced Plasma Level of CXC Chemokine Ligand 7 in Patients with Pancreatic Cancer.
Junichi Matsubara, Kazufumi Honda, Masaya Ono, Yoshinori Tanaka, Michimoto Kobayashi, Giman Jung, Koji Yanagisawa, Tomohiro Sakuma, Shoji Nakamori, Naohiro Sata, Hideo Nagai, Tatsuya Ioka, Takuji Okusaka, Tomoo Kosuge, Akihiko Tsuchida, Masashi Shimahara, Yohichi Yasunami, Tsutomu Chiba, Setsuo Hirohashi, and Tesshi Yamada. Cancer Epidemiology, Biomarkers & Prevention (2011)

・SAHG, a comprehensive database of predicted structures of all human proteins.
Motono C, Nakata J, Koike R, Shimizu K, Shirota M, Amemiya T, Tomii K, Nagano N, Sakaya N, Misoo K, Sato M, Kidera A, Hiroaki H, Shirai T, Kinoshita K, Noguchi T, Ota M. Nucleic Acids Res. (2011)
・Genome-wide germline analyses on cancer susceptibility and GeMDBJ database: Gastric cancer as an example.
Yoshida T, Ono H, Kuchiba A, Saeki N, Sakamoto H. Cancer Sci (2010)
・Payao: a community platform for SBML pathway model curation.
Matsuoka Y, Ghosh S, Kikuchi N, Kitano H. Bioinformatics (2010)
・Reduced Argininosuccinate Synthetase Is a Predictive Biomarker for the Development of Pulmonary Metastasis in Patients with Osteosarcoma.
Kobayashi E, Masuda M, Nakayama R, Ichikawa H, Satow R, Shitashige M, Honda K, Yamaguchi U, Shoji A, Tochigi N, Morioka H, Toyama Y, Hirohashi S, Kawai A, Yamada T. Mol Cancer Ther (2010)
・Survival Prediction for Pancreatic Cancer Patients Receiving Gemcitabine Treatment.
Junichi Matsubara, Masaya Ono, Kazufumi Honda, Ayako Negishi, Hideki Ueno, Takuji Okusaka, Junji Furuse, Koh Furuta, Emiko Sugiyama, Yoshiro Saito, Nahoko Kaniwa, Junichi Sawada, Ayako Shoji, Tomohiro Sakuma, Tsutomu Chiba, Nagahiro Saijo, Setsuo Hirohashi, and Tesshi Yamada. Molecular & Cellular Proteomics (2010)

・GEM-TREND: a web tool for gene expression data mining toward relevant network discovery.
Feng C, Araki M, Kunimoto R, Tamon A, Makiguchi H, Niijima S, Tsujimoto G, Okuno Y. BMC Genomics (2009)
・Identification of a predictive biomarker for hematologic toxicities of gemcitabine.
Matsubara J, Ono M, Negishi A, Ueno H, Okusaka T, Furuse J, Furuta K, Sugiyama E, Saito Y, Kaniwa N, Sawada J, Honda K, Sakuma T, Chiba T, Saijo N, Hirohashi S, Yamada T. J Clin Oncol (2009)

・Large-scale quantitative clinical proteomics by label-free liquid chromatography and mass spectrometry.
Negishi A, Ono M, Handa Y, Kato H, Yamashita K, Honda K, Shitashige M, Satow R, Sakuma T, Kuwabara H, Omura K, Hirohashi S, Yamada T. Cancer Sci (2009)

・Development of a Data-mining System for Differential Profiling of Cell Glycoproteins Based on Lectin Microarray.
Kuno A, Itakura Y, Toyoda M, Takahashi Y, Yamada M, Umezawa A, Hirabayashi J. Journal of Proteomics & Bioinformatics (2008)
・Use of a library of mutated Maackia amurensis hemagglutinin for profiling the cell lineage and differentiation.
Maenuma K, Yim M, Komatsu K, Hoshino M, Takahashi Y, Bovin N, Irimura T. Proteomics (2008)
・Genetic variation in PSCA is associated with susceptibility to diffuse-type gastric cancer.
Study Group of Millennium Genome Project for Cancer Nat Genet (2008)
・CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks.
Funahashi A, Matsuoka Y, Jouraku A, Morohashi M, Kikuchi N, Kitano H. Proceedings of the IEEE (2008)
・The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts.
"Genome Information Integration Project And H-Invitational 2,Yamasaki C, et al." Nucleic Acids Res, Database issue (2008)
・Distinct gene expression-defined classes of gastrointestinal stromal tumor.
Yamaguchi U, Nakayama R, Honda K, Ichikawa H, Hasegawa T, Shitashige M, Ono M, Shoji A, Sakuma T, Kuwabara H, Shimada Y, Sasako M, Shimoda T, Kawai A, Hirohashi S, Yamada T. J Clin Oncol (2008)
・“CellDesigner: A Modeling Tool for Biochemical Networks.”, IEEE Special Issue on Computational
Funahashi A, Jouraku A, Matsuoka Y, Morohashi M, Kikuchi N, Tanimura N, and Kitano H. Systems Biology (2007)
・Melina II: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions
Okumura T, Makiguchi H, Makita Y, Yamashita R, Nakai K. Nucleic Acids Res. (2007)
・Hyaline cartilage formation and enchondral ossification modeled with KUM5 and OP9 chondroblasts.
Sugiki T, Uyama T, Toyoda M, Morioka H, Kume S, Miyado K, Matsumoto K, Saito H, Tsumaki N, Takahashi Y, Toyama Y, Umezawa A. J Cell Biochem (2007)
・Strategy for simulation of CID spectra of N-linked oligosaccharides toward glycomics.
Kameyama A, Nakaya S, Ito H, Kikuchi N, Angata T, Nakamura M, Ishida HK, Narimatsu H. J Proteome Res (2006)
・Molecular cloning and characterization of a novel human beta1,3-glucosyltransferase, which is localized at the endoplasmic reticulum and glucosylates O-linked fucosylglycan on thrombospondin type 1 repeat domain.
Sato T, Sato M, Kiyohara K, Sogabe M, Shikanai T, Kikuchi N, Togayachi A, Ishida H, Ito H, Kameyama A, Gotoh M, Narimatsu H. Glycobiology (2006)
・Label-free quantitative proteomics using large peptide data sets generated by nanoflow liquid chromatography and mass spectrometry.
"Ono M, Shitashige M, Honda K, Isobe T, Kuwabara H, Matsuzuki H, Hirohashi S, Yamada T." Mol Cell Proteomics (2006)

・A strategy for identification of oligosaccharide structures using observational multistage mass spectral library.
Kameyama A, Kikuchi N, Nakaya S, Ito H, Sato T, Shikanai T, Takahashi Y, Takahashi K, Narimatsu H. Anal Chem (2005)
・The carbohydrate sequence markup language (CabosML): an XML description of carbohydrate structures.
Kikuchi N, Kameyama A, Nakaya S, Ito H, Sato T, Shikanai T, Takahashi Y, Narimatsu H. Bioinformatics (2005)
・Estimating immunoregulatory gene networks in human herpesvirus type 6-infected T cells.
Takaku T, Ohyashiki JH, Zhang Y, Ohyashiki K. Biochem Biophys Res Commun (2005)
・Global analysis of the regulatory network structure of gene expression in Saccharomyces cerevisiae.
Gunji W, Kai T, Takahashi Y, Maki Y, Kurihara W, Utsugi T, Fujimori F, Murakami Y. DNA Res (2004)
・An integrated comprehensive workbench for inferring genetic networks: voyagene.
Maki Y, Takahashi Y, Arikawa Y, Watanabe S, Aoshima K, Eguchi Y, Ueda T, Aburatani S, Kuhara S, Okamoto M. J Bioinform Comput Biol (2004)
・Molecular cloning and characterization ofbeta1,4-N-acetylgalactosaminyltransferases IV synthesizing N,N'-diacetyllactosediamine.
Gotoh M, Sato T, Kiyohara K, Kameyama A, Kikuchi N, Kwon YD, Ishizuka Y, Iwai T, Nakanishi H, Narimatsu H. FEBS Lett (2004)
・A novel human b1,3-N-acetylgalactosaminyltransferase which synthesizes a unique carbohydrate structure, GalNAcb1-3GlcNAc.
Hiruma T, Togayachi A, Okamura K, Sato T, Kikuchi N, Kwon YD, Nakamura A, Fujimura K, Gotoh M, Tachibana K, Ishizuka Y, Noce T, Nakamura H, Narimatsu H. J Biol Chem (2004)
・Molecular cloning and characterization of a human multisubstrate specific nucleotide-sugar transporter homologous to Drosophila fringe connection.
Suda T, Kamiyama S, Suzuki M, Kikuchi N, Nakayama K, Narimatsu H, Jigami Y, Aoki T, Nishihara S. J Biol Chem (2004)
・Discovery of Novel Transcription Control Relationships with Gene Regulatory Networks Generated from Multiple-disruption Full Genome Expression Libraries.
Aburatani S, Tashiro K, Savoie CJ, Nishizawa M, Hayashi K, Ito Y, Muta S, Yamamoto K, Ogawa M, Enomoto A, Masaki M, Watanabe S, Maki Y, Takahashi Y, Eguchi Y, Sakaki Y, Kuhara S. DNA Res (2003)
・Initiation of O-glycan synthesis in IgA1 hinge region is determined by a single enzyme, UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2.
Iwasaki H, Zhang Y, Tachibana K, Gotoh M, Kikuchi N, Kwon YD, Togayachi A, Kudo T, Kubota T, Narimatsu H. J Biol Chem (2003)
・Cloning and characterization of a novel UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase, pp-GalNAc-T14.
Wang H, Tachibana K, Zhang Y, Iwasaki H, Kameyama A, Cheng L, Guo J, Hiruma T, Togayachi A, Kudo T, Kikuchi N, Narimatsu H. Biochem Biophys Res Commun (2003)
・Molecular cloning and identification of 3'-phosphoadenosine 5'-phosphosulfate transporter.
Kamiyama S, Suda T, Ueda R, Suzuki M, Okubo R, Kikuchi N, Chiba Y, Goto S, Toyoda H, Saigo K, Watanabe M, Narimatsu H, Jigami Y, Nishihara S. J Biol Chem (2003)
・Characterization of a heparan sulfate 3-O-sulfotransferase-5, an enzyme synthesizing a tetrasulfated disaccharide.
Mochizuki H, Yoshida K, Gotoh M, Sugioka S, Kikuchi N, Kwon YD, Tawada A, Maeyama K, Inaba N, Hiruma T, Kimata K, Narimatsu H. J Biol Chem (2003)
・Chondroitin sulfate synthase-2. Molecular cloning and characterization of a novel human glycosyltransferase homologous to chondroitin sulfate glucuronyltransferase, which has dual enzymatic activities.
Yada T, Gotoh M, Sato T, Shionyu M, Go M, Kaseyama H, Iwasaki H, Kikuchi N, KwonYD, Togayachi A, Kudo T, Watanabe H, Narimatsu H, Kimata K. J Biol Chem (2003)
・Chondroitin sulfate synthase-3. Molecular cloning and characterization.
Yada T, Sato T, Kaseyama H, Gotoh M, Iwasaki H, Kikuchi N, Kwon YD, Togayachi A, Kudo T, Watanabe H, Narimatsu H, Kimata K. J Biol Chem (2003)
・Comparison of glycosyltransferase families using the profile hidden Markov model.
Kikuchi N, Kwon YD, Gotoh M, Narimatsu H. Biochem Biophys Res Commun (2003)
・Molecular cloning and characterization of a novel human beta 1,4-N-acetylgalactosaminyltransferase, beta 4GalNAc-T3, responsible for the synthesis of N,N'-diacetyllactosediamine, galNAc beta 1-4GlcNAc.
Sato T, Gotoh M, Kiyohara K, Kameyama A, Kubota T, Kikuchi N, Ishizuka Y, Iwasaki H, Togayachi A, Kudo T, Ohkura T, Nakanishi H, Narimatsu H. J Biol Chem (2003)
・Enzymatic synthesis of chondroitin with a novel chondroitin sulfate N-acetylgalactosaminyltransferase that transfers N-acetylgalactosamine to glucuronic acid in initiation and elongation of chondroitin sulfate synthesis.
Gotoh M, Sato T, Akashima T, Iwasaki H, Kameyama A, Mochizuki H, Yada T, Inaba N, Zhang Y, Kikuchi N, Kwon YD, Togayachi A, Kudo T, Nishihara S, Watanabe H, Kimata K, Narimatsu H. J Biol Chem (2002)
・Development of a System for the Inference of Large Scale Genetic Networks.
Maki Y, Tominaga D, Okamoto M, Watanabe S, Eguchi Y. Pac Symp Biocomput (2001)
・Cross Talk of Prolyl Isomerases, Pin1/Ess1 and Cyclophilin A.
Fujimori F, Gunji W, Kikuchi J, Mogi T, Ohashi Y, Makino T, Oyama A, Okuhara K, Uchida T, Murakami Y. BBRC (2001)