論文·学会発表

2025年

Rewired chromatin structure and epigenetic gene dysregulation during HTLV-1 infection to leukemogenesis.
Mizuike J, Suzuki K, Tosaka S, Kuze Y, Kobayashi S, Nakashima M, Jimbo K, Nannya Y, Suzuki Y, Uchimaru K, Yamagishi M
Cancer Sci. 2025 Feb;116:513-523.
DOI: 10.1111/cas.16388. PMID: 39561277

Cardiac Reprogramming and Gata4 Overexpression Reduce Fibrosis and Improve Diastolic Dysfunction in Heart Failure With Preserved Ejection Fraction.
Yamada Y, Sadahiro T, Nakano K, Honda S, Abe Y, Akiyama T, Fujita R, Nakamura M, Maeda T, Kuze Y, Onishi M, Seki M, Suzuki Y, Takeuchi C, Iwasaki YW, Murano K, Sakata-Yanagimoto M, Chiba S, Kato H, Sakamoto H, Hiramatsu Y, Ieda M
Circulation. 2025 Feb;151:379-395.
DOI: 10.1161/CIRCULATIONAHA.123.067504. PMID: 39673349

Direct reprogramming of mouse fibroblasts into self-renewable alveolar epithelial-like cells.
Morita A, Ishii M, Asakura T, Yotsukura M, Hegab AE, Kusumoto T, Namkoong H, Ogawa T, Nakatake Y, Oda M, Saito F, Kamata H, Hamamoto J, Okamori S, Ebisudani T, Yasuda H, Sugimoto S, Kuze Y, Seki M, Suzuki Y, Hasegawa N, Asamura H, Watanabe H, Ko M, Sato T, Ieda M, Fukunaga K
NPJ Regen Med. 2025 Jun;10:30.
DOI: 10.1038/s41536-025-00411-4. PMID: 40550799

MBGD: Microbial Genome Database for Comparative Analysis Featuring Enhanced Functionality to Characterize Gene and Genome Functions Through Large-scale Orthology Analysis.
Uchiyama I, Mihara M, Nishide H, Chiba H, Takayanagi M, Kawai M, Takami H
J Mol Biol. 2025 Aug;437:168957.
DOI: 10.1016/j.jmb.2025.168957. PMID: 39826711

小児アレルギー疾患における多項目アレルギー検査ドロップスクリーンの活用に関する検討
“伊藤嘉浩、秋元淳、大竹直人、小布施聖、小川佑人, 三浦順一郎, 藤宮仁、佐藤さくら、海老澤元宏”
Japanese Journal of Allergology. 2025 Apr;第74巻第2号:63-72.
DOI: 10.15036/arerugi.74.63.

2024年

Mechanisms of action and resistance in histone methylation-targeted therapy.
Yamagishi M, Kuze Y, Kobayashi S, Nakashima M, Morishima S, Kawamata T, Makiyama J, Suzuki K, Seki M, Abe K, Imamura K, Watanabe E, Tsuchiya K, Yasumatsu I, Takayama G, Hizukuri Y, Ito K, Taira Y, Nannya Y, Tojo A, Watanabe T, Tsutsumi S, Suzuki Y, Uchimaru K
Nature. 2024 Mar;627:221-228.
DOI: 10.1038/s41586-024-07103-x. PMID: 38383791

Potential utility of pretreatment serum miRNAs for optimal treatment selection in advanced high-grade serous ovarian cancer.
Uehara T, Matsuzaki J, Yoshida H, Ogawa Y, Miura J, Fujimiya H, Yamamoto Y, Kawauchi J, Takizawa S, Yonemori K, Sakamoto H, Kato K, Ishikawa M, Ochiya T
Jpn J Clin Oncol. 2024 Aug;54:917-925.
DOI: 10.1093/jjco/hyae051. PMID: 38651188

Predictive biomarkers of COVID-19 prognosis identified in Bangladesh patients and validated in Japanese cohorts.
Uno K, Hasan A, Nakayama EE, Rahim R, Harada H, Kaneko M, Hashimoto S, Tanaka T, Matsumoto H, Fujimiya H, Shioda T, Rahman M, Yoshizaki K
Sci Rep. 2024 Jun;14:12713.
DOI: 10.1038/s41598-024-63184-8. PMID: 38830928

Spatially resolved gene expression profiling of tumor microenvironment reveals key steps of lung adenocarcinoma development.
Takano Y, Suzuki J, Nomura K, Fujii G, Zenkoh J, Kawai H, Kuze Y, Kashima Y, Nagasawa S, Nakamura Y, Kojima M, Tsuchihara K, Seki M, Kanai A, Matsubara D, Kohno T, Noguchi M, Nakaya A, Tsuboi M, Ishii G, Suzuki Y, Suzuki A
Nat Commun. 2024 Dec;15:10637.
DOI: 10.1038/s41467-024-54671-7. PMID: 39639005

An improved method for the highly specific detection of transcription start sites.
Seki M, Kuze Y, Zhang X, Kurotani KI, Notaguchi M, Nishio H, Kudoh H, Suzaki T, Yoshida S, Sugano S, Matsushita T, Suzuki Y
Nucleic Acids Res. 2024 Jan;52:e7.
DOI: 10.1093/nar/gkad1116. PMID: 37994784

Spatial and single-cell colocalisation analysis reveals MDK-mediated immunosuppressive environment with regulatory T cells in colorectal carcinogenesis.
Hashimoto M, Kojima Y, Sakamoto T, Ozato Y, Nakano Y, Abe T, Hosoda K, Saito H, Higuchi S, Hisamatsu Y, Toshima T, Yonemura Y, Masuda T, Hata T, Nagayama S, Kagawa K, Goto Y, Utou M, Gamachi A, Imamura K, Kuze Y, Zenkoh J, Suzuki A, Takahashi K, Niida A, Hirose H, Hayashi S, Koseki J, Fukuchi S, Murakami K, Yoshizumi T, Kadomatsu K, Tobo T, Oda Y, Uemura M, Eguchi H, Doki Y, Mori M, Oshima M, Shibata T, Suzuki Y, Shimamura T, Mimori K
EBioMedicine. 2024 May;103:105102.
DOI: 10.1016/j.ebiom.2024.105102. PMID: 38614865

2023年

Prediction and association analyses of skin phenotypes in Japanese females using genetic, environmental, and physical features.
Amano S, Yoshikawa T, Ito C, Mabuchi I, Kikuchi K, Ooguri M, Yasuda C
Skin Res Technol. 2023 Jan;29:e13231.
DOI: 10.1111/srt.13231. PMID: 36437544

Direct Reprogramming Improves Cardiac Function and Reverses Fibrosis in Chronic Myocardial Infarction.
Tani H, Sadahiro T, Yamada Y, Isomi M, Yamakawa H, Fujita R, Abe Y, Akiyama T, Nakano K, Kuze Y, Seki M, Suzuki Y, Fujisawa M, Sakata-Yanagimoto M, Chiba S, Fukuda K, Ieda M
Circulation. 2023 Jan;147:223-238.
DOI: 10.1161/CIRCULATIONAHA.121.058655. PMID: 36503256

Establishment of experimental salivary gland cancer models using organoid culture and patient-derived xenografting.
Aizawa Y, Takada K, Aoyama J, Sano D, Yamanaka S, Seki M, Kuze Y, Ramilowski JA, Okuda R, Ueno Y, Nojima Y, Inayama Y, Hatakeyama H, Hatano T, Takahashi H, Nishimura G, Fujii S, Suzuki Y, Taniguchi H, Oridate N
Cell Oncol (Dordr). 2023 Apr;46:409-421.
DOI: 10.1007/s13402-022-00758-6. PMID: 36538240

Spatial and single-cell transcriptomics decipher the cellular environment containing HLA-G+ cancer cells and SPP1+ macrophages in colorectal cancer.
Ozato Y, Kojima Y, Kobayashi Y, Hisamatsu Y, Toshima T, Yonemura Y, Masuda T, Kagawa K, Goto Y, Utou M, Fukunaga M, Gamachi A, Imamura K, Kuze Y, Zenkoh J, Suzuki A, Niida A, Hirose H, Hayashi S, Koseki J, Oki E, Fukuchi S, Murakami K, Tobo T, Nagayama S, Uemura M, Sakamoto T, Oshima M, Doki Y, Eguchi H, Mori M, Iwasaki T, Oda Y, Shibata T, Suzuki Y, Shimamura T, Mimori K
Cell Rep. 2023 Jan;42:111929.
DOI: 10.1016/j.celrep.2022.111929. PMID: 36656712

2022年

VsN, a Reliability-index of Shear-wave Measurement in Sonoelastography, Is Useful for the Diagnosis of Thyroid Tumor Malignancy.
Jikuzono T, Ishibashi O, Kure S, Itoh C, Yamada T, Sugitani I
In Vivo. 2022 Jan;36:264-273.
DOI: 10.21873/invivo.12700. PMID: 34972724

Identification of Galectin-7 as a crucial metastatic enhancer of squamous cell carcinoma associated with immunosuppression.
An J, Nagaki Y, Motoyama S, Kuze Y, Hoshizaki M, Kemuriyama K, Yamaguchi T, Ebihara T, Minamiya Y, Suzuki Y, Imai Y, Kuba K
Oncogene. 2022 Dec;41:5319-5330.
DOI: 10.1038/s41388-022-02525-1. PMID: 36335283

2021年

Genomic profiling reveals heterogeneous populations of ductal carcinoma in situ of the breast.
Nagasawa S, Kuze Y, Maeda I, Kojima Y, Motoyoshi A, Onishi T, Iwatani T, Yokoe T, Koike J, Chosokabe M, Kubota M, Seino H, Suzuki A, Seki M, Tsuchihara K, Inoue E, Tsugawa K, Ohta T, Suzuki Y
Commun Biol. 2021 Apr;4:438.
DOI: 10.1038/s42003-021-01959-9. PMID: 33795819

Chronological genome and single-cell transcriptome integration characterizes the evolutionary process of adult T cell leukemia-lymphoma.
Yamagishi M, Kubokawa M, Kuze Y, Suzuki A, Yokomizo A, Kobayashi S, Nakashima M, Makiyama J, Iwanaga M, Fukuda T, Watanabe T, Suzuki Y, Uchimaru K
Nat Commun. 2021 Aug;12:4821.
DOI: 10.1038/s41467-021-25101-9. PMID: 34376672

Comparative Analysis of Patient-Matched PDOs Revealed a Reduction in OLFM4-Associated Clusters in Metastatic Lesions in Colorectal Cancer.
Okamoto T, duVerle D, Yaginuma K, Natsume Y, Yamanaka H, Kusama D, Fukuda M, Yamamoto M, Perraudeau F, Srivastava U, Kashima Y, Suzuki A, Kuze Y, Takahashi Y, Ueno M, Sakai Y, Noda T, Tsuda K, Suzuki Y, Nagayama S, Yao R
Stem Cell Reports. 2021 Apr;16:954-967.
DOI: 10.1016/j.stemcr.2021.02.012. PMID: 33711267

Complete genome sequence and bioinformatics analysis of nine Egyptian females with clinical information from different geographic regions in Egypt.
ElHefnawi M, Hegazy E, Elfiky A, Jeon Y, Jeon S, Bhak J, Mohamed Metwally F, Sugano S, Horiuchi T, Kazumi A, Blazyte A
Gene. 2021 Feb;769:145237.
DOI: 10.1016/j.gene.2020.145237. PMID: 33127537

2020年

Identification of serum microRNAs predicting the response of esophageal squamous-cell carcinoma to nivolumab.
Sudo K, Kato K, Matsuzaki J, Takizawa S, Aoki Y, Shoji H, Iwasa S, Honma Y, Takashima A, Sakamoto H, Naka T, Sekine S, Boku N, Ochiya T
Jpn J Clin Oncol. 2020 Feb;50:114-121.
DOI: 10.1093/jjco/hyz146. PMID: 31612917

TASUKE+: a web-based platform for exploring GWAS results and large-scale resequencing data.
Kumagai M, Nishikawa D, Kawahara Y, Wakimoto H, Itoh R, Tabei N, Tanaka T, Itoh T
DNA Res. 2020 Feb;27.
DOI: 10.1093/dnares/dsaa002. PMID: 32105308

Association of colitis with gut-microbiota dysbiosis in clathrin adapter AP-1B knockout mice.
Jangid A, Fukuda S, Seki M, Horiuchi T, Suzuki Y, Taylor TD, Ohno H, Prakash T
PLoS One. 2020 Mar;15:e0228358.
DOI: 10.1371/journal.pone.0228358. PMID: 32208434

2019年

Circulating miRNA panels for specific and early detection in bladder cancer.
Usuba W, Urabe F, Yamamoto Y, Matsuzaki J, Sasaki H, Ichikawa M, Takizawa S, Aoki Y, Niida S, Kato K, Egawa S, Chikaraishi T, Fujimoto H, Ochiya T
Cancer Sci. 2019 Jan;110:408-419.
DOI: 10.1111/cas.13856. PMID: 30382619

Serum miRNA-based Prediction of Axillary Lymph Node Metastasis in Breast Cancer.
Shiino S, Matsuzaki J, Shimomura A, Kawauchi J, Takizawa S, Sakamoto H, Aoki Y, Yoshida M, Tamura K, Kato K, Kinoshita T, Kitagawa Y, Ochiya T
Clin Cancer Res. 2019 Mar;25:1817-1827.
DOI: 10.1158/1078-0432.CCR-18-1414. PMID: 30482779

A serum microRNA classifier for the diagnosis of sarcomas of various histological subtypes.
Asano N, Matsuzaki J, Ichikawa M, Kawauchi J, Takizawa S, Aoki Y, Sakamoto H, Yoshida A, Kobayashi E, Tanzawa Y, Nakayama R, Morioka H, Matsumoto M, Nakamura M, Kondo T, Kato K, Tsuchiya N, Kawai A, Ochiya T
Nat Commun. 2019 Mar;10:1299.
DOI: 10.1038/s41467-019-09143-8. PMID: 30898996

Large-scale Circulating microRNA Profiling for the Liquid Biopsy of Prostate Cancer.
Urabe F, Matsuzaki J, Yamamoto Y, Kimura T, Hara T, Ichikawa M, Takizawa S, Aoki Y, Niida S, Sakamoto H, Kato K, Egawa S, Fujimoto H, Ochiya T
Clin Cancer Res. 2019 May;25:3016-3025.
DOI: 10.1158/1078-0432.CCR-18-2849. PMID: 30808771

Development and Validation of an Esophageal Squamous Cell Carcinoma Detection Model by Large-Scale MicroRNA Profiling.
Sudo K, Kato K, Matsuzaki J, Boku N, Abe S, Saito Y, Daiko H, Takizawa S, Aoki Y, Sakamoto H, Niida S, Takeshita F, Fukuda T, Ochiya T
JAMA Netw Open. 2019 May;2:e194573.
DOI: 10.1001/jamanetworkopen.2019.4573. PMID: 31125107

Serum MicroRNA-Based Risk Prediction for Stroke.
Sonoda T, Matsuzaki J, Yamamoto Y, Sakurai T, Aoki Y, Takizawa S, Niida S, Ochiya T
Stroke. 2019 Jun;50:1510-1518.
DOI: 10.1161/STROKEAHA.118.023648. PMID: 31136284

Serum microRNA-based prediction of responsiveness to eribulin in metastatic breast cancer.
Satomi-Tsushita N, Shimomura A, Matsuzaki J, Yamamoto Y, Kawauchi J, Takizawa S, Aoki Y, Sakamoto H, Kato K, Shimizu C, Ochiya T, Tamura K
PLoS One. 2019 Sep;14:e0222024.
DOI: 10.1371/journal.pone.0222024. PMID: 31483849

Serum microRNA profile enables preoperative diagnosis of uterine leiomyosarcoma.
Yokoi A, Matsuzaki J, Yamamoto Y, Tate K, Yoneoka Y, Shimizu H, Uehara T, Ishikawa M, Takizawa S, Aoki Y, Kato K, Kato T, Ochiya T
Cancer Sci. 2019 Dec;110:3718-3726.
DOI: 10.1111/cas.14215. PMID: 31599471

MBGD update 2018: microbial genome database based on hierarchical orthology relations covering closely related and distantly related comparisons.
Uchiyama I, Mihara M, Nishide H, Chiba H, Kato M
Nucleic Acids Res. 2019 Jan;47:D382-D389.
DOI: 10.1093/nar/gky1054. PMID: 30462302

TASUKE+: a web-based platform for exploring genome-wide association studies results and large-scale resequencing data.
Kumagai M, Nishikawa D, Kawahara Y, Wakimoto H, Itoh R, Tabei N, Tanaka T, Itoh T
DNA Res. 2019 Dec;26:445-452.
DOI: 10.1093/dnares/dsz022. PMID: 31539030

2018年

Integrated extracellular microRNA profiling for ovarian cancer screening.
Yokoi A, Matsuzaki J, Yamamoto Y, Yoneoka Y, Takahashi K, Shimizu H, Uehara T, Ishikawa M, Ikeda SI, Sonoda T, Kawauchi J, Takizawa S, Aoki Y, Niida S, Sakamoto H, Kato K, Kato T, Ochiya T
Nat Commun. 2018 Oct;9:4319.
DOI: 10.1038/s41467-018-06434-4. PMID: 30333487

2016年

Analysis on Gene Expression Profile in Oncospheres and Early Stage Metacestodes from Echinococcus multilocularis.
Huang F, Dang Z, Suzuki Y, Horiuchi T, Yagi K, Kouguchi H, Irie T, Kim K, Oku Y
PLoS Negl Trop Dis. 2016 Apr;10:e0004634.
DOI: 10.1371/journal.pntd.0004634. PMID: 27092774

Fluorescence-Activated Cell Sorting and Gene Expression Profiling of GFP-Positive Cells from Transgenic Zebrafish Lines.
Tanabe H, Seki M, Itoh M, Deepak A, Lal P, Horiuchi T, Suzuki Y, Kawakami K
Methods Mol Biol. 2016 Jan;1451:93-106.
DOI: 10.1007/978-1-4939-3771-4_7. PMID: 27464803

2015年

Detection of plant viruses in natural environments by using RNA-Seq.
Nagano AJ, Honjo MN, Mihara M, Sato M, Kudoh H
Methods Mol Biol. 2015 Jan;1236:89-98.
DOI: 10.1007/978-1-4939-1743-3_8. PMID: 25287498

MBGD update 2015: microbial genome database for flexible ortholog analysis utilizing a diverse set of genomic data.
Uchiyama I, Mihara M, Nishide H, Chiba H
Nucleic Acids Res. 2015 Jan;43:D270-6.
DOI: 10.1093/nar/gku1152. PMID: 25398900

2013年

MBGD update 2013: the microbial genome database for exploring the diversity of microbial world.
Uchiyama I, Mihara M, Nishide H, Chiba H
Nucleic Acids Res. 2013 Jan;41:D631-5.
DOI: 10.1093/nar/gks1006. PMID: 23118485

The ancestor of extant Japanese fancy mice contributed to the mosaic genomes of classical inbred strains.
Takada T, Ebata T, Noguchi H, Keane TM, Adams DJ, Narita T, Shin-I T, Fujisawa H, Toyoda A, Abe K, Obata Y, Sakaki Y, Moriwaki K, Fujiyama A, Kohara Y, Shiroishi T
Genome Res. 2013 Aug;23:1329-38.
DOI: 10.1101/gr.156497.113. PMID: 23604024

TASUKE: a web-based visualization program for large-scale resequencing data.
Kumagai M, Kim J, Itoh R, Itoh T
Bioinformatics. 2013 Jul;29:1806-8.
DOI: 10.1093/bioinformatics/btt295. PMID: 23749962

2012年

Deciphering and prediction of transcriptome dynamics under fluctuating field conditions.
Nagano AJ, Sato Y, Mihara M, Antonio BA, Motoyama R, Itoh H, Nagamura Y, Izawa T
Cell. 2012 Dec;151:1358-69.
DOI: 10.1016/j.cell.2012.10.048. PMID: 23217716

Sagace: a web-based search engine for biomedical databases in Japan.
Morita M, Igarashi Y, Ito M, Chen YA, Nagao C, Sakaguchi Y, Sakate R, Masui T, Mizuguchi K
BMC Res Notes. 2012 Oct;5:604.
DOI: 10.1186/1756-0500-5-604. PMID: 23110816

2011年

Os-GIGANTEA confers robust diurnal rhythms on the global transcriptome of rice in the field.
Izawa T, Mihara M, Suzuki Y, Gupta M, Itoh H, Nagano AJ, Motoyama R, Sawada Y, Yano M, Hirai MY, Makino A, Nagamura Y
Plant Cell. 2011 May;23:1741-55.
DOI: 10.1105/tpc.111.083238. PMID: 21571948

Development and External Validation of a Nomogram Predicting the Probability of Significant Gleason Sum Upgrading among Japanese Patients with Localized Prostate Cancer.
Imamoto T, Utsumi T, Takano M, Komaru A, Fukasawa S, Suyama T, Kawamura K, Kamiya N, Miura J, Suzuki H, Ueda T, Ichikawa T
Prostate Cancer. 2011 Jan;2011:754382.
DOI: 10.1155/2011/754382. PMID: 22110999

2010年

SALAD database: a motif-based database of protein annotations for plant comparative genomics.
Mihara M, Itoh T, Izawa T
Nucleic Acids Res. 2010 Jan;38:D835-42.
DOI: 10.1093/nar/gkp831. PMID: 19854933

H-InvDB in 2009: extended database and data mining resources for human genes and transcripts.
Yamasaki C, Murakami K, Takeda J, Sato Y, Noda A, Sakate R, Habara T, Nakaoka H, Todokoro F, Matsuya A, Imanishi T, Gojobori T
Nucleic Acids Res. 2010 Jan;38:D626-32.
DOI: 10.1093/nar/gkp1020. PMID: 19933760

2009年

SNP HiTLink: a high-throughput linkage analysis system employing dense SNP data.
Fukuda Y, Nakahara Y, Date H, Takahashi Y, Goto J, Miyashita A, Kuwano R, Adachi H, Nakamura E, Tsuji S
BMC Bioinformatics. 2009 Apr;10:121.
DOI: 10.1186/1471-2105-10-121. PMID: 19393044

External validation and head-to-head comparison of Japanese and Western prostate biopsy nomograms using Japanese data sets.
Utsumi T, Kawamura K, Suzuki H, Kamiya N, Imamoto T, Miura J, Ueda T, Maruoka M, Sekita N, Mikami K, Ichikawa T
Int J Urol. 2009 Apr;16:416-9.
DOI: 10.1111/j.1442-2042.2009.02254.x. PMID: 19226358

2008年

Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees.
Matsuya A, Sakate R, Kawahara Y, Koyanagi KO, Sato Y, Fujii Y, Yamasaki C, Habara T, Nakaoka H, Todokoro F, Yamaguchi K, Endo T, Oota S, Makalowski W, Ikeo K, Suzuki Y, Hanada K, Hashimoto K, Hirai M, Iwama H, Saitou N, Hiraki AT, Jin L, Kaneko Y, Kanno M, Murakami K, Noda AO, Saichi N, Sanbonmatsu R, Suzuki M, Takeda J, Tanaka M, Gojobori T, Imanishi T, Itoh T
Nucleic Acids Res. 2008 Jan;36:D787-92.
PMID: 17982176

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, Murakami K, Fujii Y, Sato Y, Harada E, Takeda J, Taniya T, Sakate R, Kikugawa S, Shimada M, Tanino M, Koyanagi KO, Barrero RA, Gough C, Chun HW, Habara T, Hanaoka H, Hayakawa Y, Hilton PB, Kaneko Y, Kanno M, Kawahara Y, Kawamura T, Matsuya A, Nagata N, Nishikata K, Noda AO, Nurimoto S, Saichi N, Sakai H, Sanbonmatsu R, Shiba R, Suzuki M, Takabayashi K, Takahashi A, Tamura T, Tanaka M, Tanaka S, Todokoro F, Yamaguchi K, Yamamoto N, Okido T, Mashima J, Hashizume A, Jin L, Lee KB, Lin YC, Nozaki A, Sakai K, Tada M, Miyazaki S, Makino T, Ohyanagi H, Osato N, Tanaka N, Suzuki Y, Ikeo K, Saitou N, Sugawara H, O’Donovan C, Kulikova T, Whitfield E, Halligan B, Shimoyama M, Twigger S, Yura K, Kimura K, Yasuda T, Nishikawa T, Akiyama Y, Motono C, Mukai Y, Nagasaki H, Suwa M, Horton P, Kikuno R, Ohara O, Lancet D, Eveno E, Graudens E, Imbeaud S, Debily MA, Hayashizaki Y, Amid C, Han M, Osanger A, Endo T, Thomas MA, Hirakawa M, Makalowski W, Nakao M, Kim NS, Yoo HS, De Souza SJ, Bonaldo Mde F, Niimura Y, Kuryshev V, Schupp I, Wiemann S, Bellgard M, Shionyu M, Jia L, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Zhang Q, Go M, Minoshima S, Ohtsubo M, Hanada K, Tonellato P, Isogai T, Zhang J, Lenhard B, Kim S, Chen Z, Hinz U, Estreicher A, Nakai K, Makalowska I, Hide W, Tiffin N, Wilming L, Chakraborty R, Soares MB, Chiusano ML, Suzuki Y, Auffray C, Yamaguchi-Kabata Y, Itoh T, Hishiki T, Fukuchi S, Nishikawa K, Sugano S, Nomura N, Tateno Y, Imanishi T, Gojobori T
Nucleic Acids Res. 2008 Jan;36:D793-9.
PMID: 18089548

The Rice Annotation Project Database (RAP-DB): 2008 update.
Rice Annotation Project, Tanaka T, Antonio BA, Kikuchi S, Matsumoto T, Nagamura Y, Numa H, Sakai H, Wu J, Itoh T, Sasaki T, Aono R, Fujii Y, Habara T, Harada E, Kanno M, Kawahara Y, Kawashima H, Kubooka H, Matsuya A, Nakaoka H, Saichi N, Sanbonmatsu R, Sato Y, Shinso Y, Suzuki M, Takeda J, Tanino M, Todokoro F, Yamaguchi K, Yamamoto N, Yamasaki C, Imanishi T, Okido T, Tada M, Ikeo K, Tateno Y, Gojobori T, Lin YC, Wei FJ, Hsing YI, Zhao Q, Han B, Kramer MR, McCombie RW, Lonsdale D, O’Donovan CC, Whitfield EJ, Apweiler R, Koyanagi KO, Khurana JP, Raghuvanshi S, Singh NK, Tyagi AK, Haberer G, Fujisawa M, Hosokawa S, Ito Y, Ikawa H, Shibata M, Yamamoto M, Bruskiewich RM, Hoen DR, Bureau TE, Namiki N, Ohyanagi H, Sakai Y, Nobushima S, Sakata K, Barrero RA, Sato Y, Souvorov A, Smith-White B, Tatusova T, An S, An G, OOta S, Fuks G, Fuks G, Messing J, Christie KR, Lieberherr D, Kim H, Zuccolo A, Wing RA, Nobuta K, Green PJ, Lu C, Meyers BC, Chaparro C, Piegu B, Panaud O, Echeverria M
Nucleic Acids Res. 2008 Jan;36:D1028-33.
PMID: 18089549

Development of a new nomogram for predicting the probability of a positive initial prostate biopsy in Japanese patients with serum PSA levels less than 10 ng/mL.
Kawamura K, Suzuki H, Kamiya N, Imamoto T, Yano M, Miura J, Shimbo M, Suzuki N, Nakatsu H, Ichikawa T
Int J Urol. 2008 Jul;15:598-603.
DOI: 10.1111/j.1442-2042.2008.02058.x. PMID: 18462353

In silico identification of short nucleotide sequences associated with gene expression of pollen development in rice.
Mihara M, Itoh T, Izawa T
Plant Cell Physiol. 2008 Oct;49:1451-64.
DOI: 10.1093/pcp/pcn129. PMID: 18835840

Gene-L’EXPO: a tool to extract knowledge From transcriptomes and find ‘Literature-Sparse’ relationships between genes and tissues.
Hishiki T, Tamada I, Okubo K
AMIA Annu Symp Proc. 2008 Nov;2008:313-7.
PMID: 18999036

2007年

Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana.
Rice Annotation Project, Itoh T, Tanaka T, Barrero RA, Yamasaki C, Fujii Y, Hilton PB, Antonio BA, Aono H, Apweiler R, Bruskiewich R, Bureau T, Burr F, Costa de Oliveira A, Fuks G, Habara T, Haberer G, Han B, Harada E, Hiraki AT, Hirochika H, Hoen D, Hokari H, Hosokawa S, Hsing YI, Ikawa H, Ikeo K, Imanishi T, Ito Y, Jaiswal P, Kanno M, Kawahara Y, Kawamura T, Kawashima H, Khurana JP, Kikuchi S, Komatsu S, Koyanagi KO, Kubooka H, Lieberherr D, Lin YC, Lonsdale D, Matsumoto T, Matsuya A, McCombie WR, Messing J, Miyao A, Mulder N, Nagamura Y, Nam J, Namiki N, Numa H, Nurimoto S, O’Donovan C, Ohyanagi H, Okido T, Oota S, Osato N, Palmer LE, Quetier F, Raghuvanshi S, Saichi N, Sakai H, Sakai Y, Sakata K, Sakurai T, Sato F, Sato Y, Schoof H, Seki M, Shibata M, Shimizu Y, Shinozaki K, Shinso Y, Singh NK, Smith-White B, Takeda J, Tanino M, Tatusova T, Thongjuea S, Todokoro F, Tsugane M, Tyagi AK, Vanavichit A, Wang A, Wing RA, Yamaguchi K, Yamamoto M, Yamamoto N, Yu Y, Zhang H, Zhao Q, Higo K, Burr B, Gojobori T, Sasaki T
Genome Res. 2007 Feb;17:175-83.
PMID: 17210932

Linking the clinical vocabulary of diseases to the genes by mapping UMLS to OMIM allelic variant fields.
Hishiki T, Tamada I
AMIA Annu Symp Proc. 2007 Oct;976.
PMID: 18694076

2006年

Development of a nomogram to predict probability of positive initial prostate biopsy among Japanese patients.
Suzuki H, Komiya A, Kamiya N, Imamoto T, Kawamura K, Miura J, Suzuki N, Nakatsu H, Hata A, Ichikawa T
Urology. 2006 Jan;67:131-6.
PMID: 16413348

TACT: Transcriptome Auto-annotation Conducting Tool of H-InvDB.
Yamasaki C, Kawashima H, Todokoro F, Imamizu Y, Ogawa M, Tanino M, Itoh T, Gojobori T, Imanishi T
Nucleic Acids Res. 2006 Jul;34:W345-9.
PMID: 16845023

2003年

Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice.
Rice Full-Length cDNA Consortium, National Institute of Agrobiological Sciences Rice Full-Length cDNA Project Team, Kikuchi S, Satoh K, Nagata T, Kawagashira N, Doi K, Kishimoto N, Yazaki J, Ishikawa M, Yamada H, Ooka H, Hotta I, Kojima K, Namiki T, Ohneda E, Yahagi W, Suzuki K, Li CJ, Ohtsuki K, Shishiki T, Foundation of Advancement of International Science Genome Sequencing & Analysis Group, Otomo Y, Murakami K, Iida Y, Sugano S, Fujimura T, Suzuki Y, Tsunoda Y, Kurosaki T, Kodama T, Masuda H, Kobayashi M, Xie Q, Lu M, Narikawa R, Sugiyama A, Mizuno K, Yokomizo S, Niikura J, Ikeda R, Ishibiki J, Kawamata M, Yoshimura A, Miura J, Kusumegi T, Oka M, Ryu R, Ueda M, Matsubara K, RIKEN, Kawai J, Carninci P, Adachi J, Aizawa K, Arakawa T, Fukuda S, Hara A, Hashizume W, Hayatsu N, Imotani K, Ishii Y, Itoh M, Kagawa I, Kondo S, Konno H, Miyazaki A, Osato N, Ota Y, Saito R, Sasaki D, Sato K, Shibata K, Shinagawa A, Shiraki T, Yoshino M, Hayashizaki Y, Yasunishi A
Science. 2003 Jul;301:376-9.
PMID: 12869764

2002年

Akaike’s information criterion for a measure of linkage disequilibrium.
Shimo-onoda K, Tanaka T, Furushima K, Nakajima T, Toh S, Harata S, Yone K, Komiya S, Adachi H, Nakamura E, Fujimiya H, Inoue I
J Hum Genet. 2002 Jan;47:649-55.
PMID: 12522686

Identification of candidate genes for Sjögren’s syndrome using MRL/lpr mouse model of Sjögren’s syndrome and cDNA microarray analysis.
Azuma T, Takei M, Yoshikawa T, Nagasugi Y, Kato M, Otsuka M, Shiraiwa H, Sugano S, Mitamura K, Sawada S, Masuho Y, Seki N
Immunol Lett. 2002 May;81:171-6.
PMID: 11947921

2000年

Isolation of novel mouse genes differentially expressed in brain using cDNA microarray.
Yoshikawa T, Nagasugi Y, Azuma T, Kato M, Sugano S, Hashimoto K, Masuho Y, Muramatsu M, Seki N
Biochem Biophys Res Commun. 2000 Aug;275:532-7.
PMID: 10964698