業績

2019

英語論文
1.Sato K, Niida A, Masuda T, Shimizu D, Tobo T, Kuroda Y, Eguchi H, Nakagawa T, Suzuki Y, Mimori K.
 Multiregion Genomic Analysis of Serially Transplanted Patient-derived Xenograft Tumors.
 Cancer Genomics Proteomics. 2019 Jan-Feb;16(1):21-27. doi: 10.21873/cgp.20109.
2.Takayama KI, Suzuki Y, Yamamoto S, Obinata D, Takahashi S, Inoue S.
 Integrative Genomic Analysis of OCT1 Reveals Coordinated Regulation of Androgen Receptor in Advanced Prostate Cancer.
 Endocrinology. 2019 Feb 1;160(2):463-472. doi: 10.1210/en.2018-00923.
3.Shabardina V, Kischka T, Manske F, Grundmann N, Frith MC, Suzuki Y, Makałowski W.
 NanoPipe-a web server for nanopore MinION sequencing data analysis.
 Gigascience. 2019 Feb 1;8(2). pii: giy169. doi: 10.1093/gigascience/giy169.
4.Ogawa Y, Shiraki T, Asano Y, Muto A, Kawakami K, Suzuki Y, Kojima D, Fukada Y.
 Six6 and Six7 coordinately regulate expression of middle-wavelength opsins in zebrafish.
 Proc Natl Acad Sci U S A. 2019 Feb 14. pii: 201812884. doi: 10.1073/pnas.1812884116.
5.Kurotaki D, Kawase W, Sasaki H, Nakabayashi J, Nishiyama A, Morse HC 3rd, Ozato K, Suzuki Y, Tamura T.
 Epigenetic control of early dendritic cell lineage specification by the transcription factor IRF8 in mice.
 Blood. 2019 Feb 22. pii: blood-2018-06-857789. doi: 10.1182/blood-2018-06-857789. [Epub ahead of print]
6.Kidoya H, Muramatsu F, Shimamura T, Jia W, Satoh T, Hayashi Y, Naito H, Kunisaki Y, Arai F, Seki M,  Suzuki Y, Osawa T, Akira S, Takakura N.
 Regnase-1-mediated post-transcriptional regulation is essential for hematopoietic stem and progenitor cell homeostasis.
 Nat Commun. 2019 Mar 6;10(1):1072. doi: 10.1038/s41467-019-09028-w.
7.Hayashi N, Kuroda Y, Saito T, Tsuruda Y, Niida A, Otsu H, Eguchi H, Masuda T,
 Suzuki Y, Natsugoe S, Mimori K.
 A clinical trial of somatic and germline analyses for healthy longevity in a postoperative cancer patient.
 Surg Today. 2019 Mar 6. doi: 10.1007/s00595-019-01789-7. [Epub ahead of print]
8.Okazaki Y, Takahata S, Hirakawa H, Suzuki Y, Onodera Y.
 Molecular evidence for recent divergence of X- and Y-linked gene pairs in Spinacia oleracea L.
 PLoS One. 2019 Apr 9;14(4):e0214949. doi: 10.1371/journal.pone.0214949. eCollection 2019.
9.Seki M, Suzuki A, Sereewattanawoot S, Suzuki Y.
 Single-Cell DNA-Seq and RNA-Seq in Cancer Using the C1 System.
 Adv Exp Med Biol. 2019;1129:27-50. doi: 10.1007/978-981-13-6037-4_3.
10.Kashima Y, Suzuki A, Suzuki Y.
 An Informative Approach to Single-Cell Sequencing Analysis.
 Adv Exp Med Biol. 2019;1129:81-96. doi: 10.1007/978-981-13-6037-4_6.
11.Runtuwene LR, Tuda JSB, Mongan AE, Suzuki Y.
 On-Site MinION Sequencing.
 Adv Exp Med Biol. 2019;1129:143-150. doi: 10.1007/978-981-13-6037-4_10.

2018

英語論文
1.Rosikiewicz W, Suzuki Y, Makalowska I.
 OverGeneDB: a database of 5' end protein coding overlapping genes in human and mouse genomes.
 Nucleic Acids Res. 2018 Jan 4;46(D1):D186-D193. doi: 10.1093/nar/gkx948.
2.Suzuki A, Kawano S, Mitsuyama T, Suyama M, Kanai Y, Shirahige K, Sasaki H, Tokunaga K, Tsuchihara K, Sugano S, Nakai K,
 Suzuki Y.
 DBTSS/DBKERO for integrated analysis of transcriptional regulation.
 Nucleic Acids Res. 2018 Jan 4;46(D1):D229-D238. doi: 10.1093/nar/gkx1001.
3.Miyai T, Takano J, Endo TA, Kawakami E, Agata Y, Motomura Y, Kubo M, Kashima Y, Suzuki Y,
 Kawamoto H, Ikawa T.
 Three-step transcriptional priming that drives the commitment of multipotent progenitors toward B cells.
 Genes Dev. 2018 Jan 15;32(2):112-126. doi: 10.1101/gad.309575.117. Epub 2018 Feb 9.
4.Katsuma S, Kawamoto M, Shoji K, Aizawa T, Kiuchi T, Izumi N, Ogawa M, Mashiko T, Kawasaki H, Sugano S, Tomari Y,
 Suzuki Y, Iwanaga M.
 Transcriptome profiling reveals infection strategy of an insect maculavirus.
 DNA Res. 2018 Jan 17. doi: 10.1093/dnares/dsx056. [Epub ahead of print]
5.Misawa K, Tarumoto N, Tamura S, Osa M, Hamamoto T, Yuki A, Kouzaki Y, Imai K, Ronald RL, Yamaguchi T, Murakami T, Maesaki S,
 Suzuki Y, Kawana A, Maeda T.
 Single nucleotide polymorphisms in genes encoding penicillin-binding proteins in β-lactamase-negative ampicillin-resistant
 Haemophilus influenzae in Japan.
 BMC Res Notes. 2018 Jan 20;11(1):53. doi: 10.1186/s13104-018-3169-0.
6.Masuda S, Suzuki Y, Fujitani Y, Mitsui R, Nakagawa T, Shintani M, Tani A.
 Lanthanide-Dependent Regulation of Methylotrophy in Methylobacteriumaquaticum Strain 22A.
 mSphere. 2018 Jan 24;3(1). pii: e00462-17. doi: 10.1128/mSphere.00462-17. eCollection 2018 Jan-Feb.
7.Oikawa T, Otsuka Y, Onodera Y, Horikawa M, Handa H, Hashimoto S, Suzuki Y, Sabe H.
 Necessity of p53-binding to the CDH1 locus for its expression defines two epithelial cell types differing in their integrity.
 Sci Rep. 2018 Jan 25;8(1):1595. doi: 10.1038/s41598-018-20043-7.
8.Imai K, Tarumoto N, Amo K, Takahashi M, Sakamoto N, Kosaka A, Kato Y, Mikita K, Sakai J, Murakami T,
 Suzuki Y, Maesaki S, Maeda T.
 Non-invasive diagnosis of cutaneous leishmaniasis by the direct boil loop-mediated isothermal amplification method and MinION™
 nanopore sequencing.
 Parasitol Int. 2018 Feb;67(1):34-37. doi: 10.1016/j.parint.2017.03.001. Epub 2017 Mar 11.
9.Yamaguchi T, Suzuki T, Sato T, Takahashi A, Watanabe H, Kadowaki A, Natsui M, Inagaki H, Arakawa S, Nakaoka S, Koizumi Y, Seki S,
 Adachi S, Fukao A, Fujiwara T, Natsume T, Kimura A, Komatsu M, Shimizu S, Ito H, Suzuki Y, Penninger JM,
 Yamamoto T, Imai Y, Kuba K.
 The CCR4-NOT deadenylase complex controls Atg7-dependent cell death and heart function.
 Sci Signal. 2018 Feb 6;11(516). pii: eaan3638. doi: 10.1126/scisignal.aan3638.
10.Shabardina V, Kischka T, Kmita H, Suzuki Y, Makałowski W.
 Environmental adaptation of Acanthamoeba castellanii and Entamoeba histolytica at genome level as seen
 by comparative genomic analysis.
 Int J Biol Sci. 2018 Feb 12;14(3):306-320. doi: 10.7150/ijbs.23869. eCollection 2018.
11.Takemura N, Kurashima Y, Mori Y, Okada K, Ogino T, Osawa H, Matsuno H, Aayam L, Kaneto S, Park EJ, Sato S,
 Matsunaga K, Tamura Y,Ouchi Y, Kumagai Y, Kobayashi D, Suzuki Y, Yoshioka Y, Nishimura J, Mori M,
 Ishii KJ, Rothenberg ME, Kiyono H, Akira S, Uematsu S.
 Eosinophil depletion suppresses radiation-induced small intestinal fibrosis.
 Sci Transl Med. 2018 Feb 21;10(429). pii: eaan0333. doi: 10.1126/scitranslmed.aan0333.
12.Hanada K, Tezuka A, Nozawa M, Suzuki Y, Sugano S, Nagano AJ, Ito M, Morinaga SI.
 Functional divergence of duplicate genes several million years after gene duplication in Arabidopsis.
 DNA Res. 2018 Feb 21. doi: 10.1093/dnares/dsy005. [Epub ahead of print]
13.Kashima Y, Suzuki A, Liu Y, Hosokawa M, Matsunaga H, Shirai M, Arikawa K, Sugano S, Kohno T, Takeyama H, Tsuchihara K,
 Suzuki Y.
 Combinatory use of distinct single-cell RNA-seq analytical platforms reveals the heterogeneous transcriptome response.
 Sci Rep. 2018 Feb 22;8(1):3482. doi: 10.1038/s41598-018-21161-y.
14.Zhang X, Mizukoshi M, Zhang H, Tan E, Igarashi Y, Suzuki Y, Mitsuyama S, Kinoshita S, Saito K, Watabe S,
 Asakawa S.
 Ultrahigh-Density Linkage Map Construction Using Low-Coverage Whole-Genome Sequencing of a Doubled Haploid Population:
 Case Study of Torafugu (Takifugu rubripes).
 Genes (Basel). 2018 Feb 26;9(3). pii: E120. doi: 10.3390/genes9030120.
15.Mimura I, Hirakawa Y, Kanki Y, Nakaki R, Suzuki Y, Tanaka T, Aburatani H, Nangaku M.
 Genome-wide analysis revealed that DZNep reduces tubulointerstitial fibrosis via down-regulation of pro-fibrotic genes.
 Sci Rep. 2018 Feb 28;8(1):3779. doi: 10.1038/s41598-018-22180-5.
16.Sakai E, Nakayama M, Oshima H, Kouyama Y, Niida A, Fujii S, Ochiai A, Nakayama KI, Mimori K, Suzuki Y,
 Hong CP, Ock CY, Kim SJ, Oshima M.
 Combined Mutation of Apc, Kras, and Tgfbr2 Effectively Drives Metastasis of Intestinal Cancer.
 Cancer Res. 2018 Mar 1;78(5):1334-1346. doi: 10.1158/0008-5472.CAN-17-3303. Epub 2017 Dec 27.
17.Kurotaki D, Nakabayashi J, Nishiyama A, Sasaki H, Kawase W, Kaneko N, Ochiai K, Igarashi K, Ozato K,
 Suzuki Y, Tamura T.
 Transcription Factor IRF8 Governs Enhancer Landscape Dynamics in Mononuclear Phagocyte Progenitors.
 Cell Rep. 2018 Mar 6;22(10):2628-2641. doi: 10.1016/j.celrep.2018.02.048.
18.Sereewattanawoot S, Suzuki A, Seki M, Sakamoto Y, Kohno T, Sugano S, Tsuchihara K, Suzuki Y.
 Identification of potential regulatory mutations using multi-omics analysis and haplotyping of lung adenocarcinoma cell lines.
 Sci Rep. 2018 Mar 21;8(1):4926. doi: 10.1038/s41598-018-23342-1.
19.Tano K, Onoguchi-Mizutani R, Yeasmin F, Uchiumi F, Suzuki Y, Yada T, Akimitsu N.
 Identification of Minimal p53 Promoter Region Regulated by MALAT1 in Human Lung Adenocarcinoma Cells.
 Front Genet. 2018 Mar 26;8:208. doi: 10.3389/fgene.2017.00208. eCollection 2017.
20.Ishiura H, Doi K, Mitsui J, Yoshimura J, Matsukawa MK, Fujiyama A, Toyoshima Y, Kakita A, Takahashi H,
 Suzuki Y, Sugano S, Qu W, Ichikawa K, Yurino H, Higasa K, Shibata S, Mitsue A, Tanaka M, Ichikawa Y,
 Takahashi Y, Date H, Matsukawa T, Kanda J, Nakamoto FK, Higashihara M, Abe K, Koike R, Sasagawa M, Kuroha Y, Hasegawa N,
 Kanesawa N, Kondo T, Hitomi T, Tada M, Takano H, Saito Y, Sanpei K, Onodera O, Nishizawa M, Nakamura M, Yasuda T, Sakiyama Y,
 Otsuka M, Ueki A, Kaida KI, Shimizu J, Hanajima R, Hayashi T, Terao Y, Inomata-Terada S, Hamada M, Shirota Y, Kubota A, Ugawa Y,
 Koh K, Takiyama Y, Ohsawa-Yoshida N, Ishiura S, Yamasaki R, Tamaoka A, Akiyama H, Otsuki T, Sano A, Ikeda A, Goto J, Morishita S,
 Tsuji S.
 Expansions of intronic TTTCA and TTTTA repeats in benign adult familial myoclonic epilepsy.
 Nat Genet. 2018 Apr;50(4):581-590. doi: 10.1038/s41588-018-0067-2. Epub 2018 Mar 5.
21.Kudoh T, Takahashi M, Osabe T, Toyoda A, Hirakawa H, Suzuki Y, Ohmido N, Onodera Y.
 Molecular insights into the non-recombining nature of the spinach male-determining region.
 Mol Genet Genomics. 2018 Apr;293(2):557-568. doi: 10.1007/s00438-017-1405-2. Epub 2017 Dec 8.
22.Lanjakornsiripan D, Pior BJ, Kawaguchi D, Furutachi S, Tahara T, Katsuyama Y, Suzuki Y, Fukazawa Y,
 Gotoh Y.
 Layer-specific morphological and molecular differences in neocortical astrocytes and their dependence on neuronal layers.
 Nat Commun. 2018 Apr 24;9(1):1623. doi: 10.1038/s41467-018-03940-3.
23.Klangnurak W, Fukuyo T, Rezanujjaman MD, Seki M, Sugano S, Suzuki Y, Tokumoto T.
 Candidate gene identification of ovulation-inducing genes by RNA sequencing with an in vivo assay in zebrafish.
 PLoS One. 2018 May 1;13(5):e0196544. doi: 10.1371/journal.pone.0196544. eCollection 2018.
24.Enya S, Kawakami K, Suzuki Y, Kawaoka S.
 A novel zebrafish intestinal tumor model reveals a role for cyp7a1-dependent tumor-liver crosstalk in causing adverse effects
 on the host.
 Dis Model Mech. 2018 May 3;11(8). pii: dmm032383. doi: 10.1242/dmm.032383.
25.Runtuwene LR, Tuda JSB, Mongan AE, Makalowski W, Frith MC, Imwong M, Srisutham S, Nguyen Thi LA, Tuan NN, Eshita Y,
 Maeda R, Yamagishi J, Suzuki Y.
 Nanopore sequencing of drug-resistance-associated genes in malaria parasites, Plasmodium falciparum.
 Sci Rep. 2018 May 29;8(1):8286. doi: 10.1038/s41598-018-26334-3.
26.Imai K, Tarumoto N, Runtuwene LR, Sakai J, Hayashida K, Eshita Y, Maeda R, Tuda J, Ohno H, Murakami T, Maesaki S,
 Suzuki Y, Yamagishi J, Maeda T.
 An innovative diagnostic technology for the codon mutation C580Y in kelch13 of Plasmodium falciparum
 with MinION nanopore sequencer.
 Malar J. 2018 May 29;17(1):217. doi: 10.1186/s12936-018-2362-x.
27.Suzuki-Kerr H, Iwagawa T, Sagara H, Mizota A, Suzuki Y, Watanabe S.
 Pivotal roles of Fezf2 in differentiation of cone OFF bipolar cells and functional maturation of cone ON bipolar cells in retina.
 Exp Eye Res. 2018 Jun;171:142-154. doi: 10.1016/j.exer.2018.03.017. Epub 2018 Mar 17.
28.Ueno K, Iwagawa T, Ochiai G, Koso H, Nakauchi H, Nagasaki M, Suzuki Y, Watanabe S.
 Author Correction: Analysis of Müller glia specific genes and their histone modification using Hes1-promoter driven
 EGFP expressing mouse.
 Sci Rep. 2018 Jun 7;8(1):8946. doi: 10.1038/s41598-018-27041-9.
29.Kato M, Nakamura H, Nagai M, Kubo T, Elzawahry A, Totoki Y, Tanabe Y, Furukawa E, Miyamoto J, Sakamoto H, Matsumoto S,
 Sunami K, Arai Y, Suzuki Y, Yoshida T, Tsuchihara K, Tamura K, Yamamoto N, Ichikawa H, Kohno T, Shibata T.
 A computational tool to detect DNA alterations tailored to formalin-fixed paraffin-embedded samples
 in cancer clinical sequencing.
 Genome Med. 2018 Jun 7;10(1):44. doi: 10.1186/s13073-018-0547-0.
30.Nakatsuka Y, Vandenbon A, Mino T, Yoshinaga M, Uehata T, Cui X, Sato A, Tsujimura T, Suzuki Y, Sato A,
 Handa T, Chin K, Sawa T, Hirai T, Takeuchi O.
 Pulmonary Regnase-1 orchestrates the interplay of epithelium and adaptive immune systems to protect against pneumonia.
 Mucosal Immunol. 2018 Jul;11(4):1203-1218. doi: 10.1038/s41385-018-0024-5. Epub 2018 Apr 25.
31.Horikawa Y, Hosomichi K, Enya M, Ishiura H, Suzuki Y, Tsuji S, Sugano S, Inoue I, Takeda J.
 No novel, high penetrant gene might remain to be found in Japanese patients with unknown MODY.
 J Hum Genet. 2018 Jul;63(7):821-829. doi: 10.1038/s10038-018-0449-4. Epub 2018 Apr 18.
32.Arai E, Miura F, Totoki Y, Yamashita S, Tian Y, Gotoh M, Ojima H, Nakagawa H, Takahashi Y, Nakamura H, Hama N, Kato M,
 Kimura H, Suzuki Y, Ito T, Shibata T, Kanai Y.
 Epigenome mapping of human normal purified hepatocytes: personal epigenome variation and genome-epigenome correlation.
 Epigenomics. 2018 Jul;10(7):955-979. doi: 10.2217/epi-2017-0111. Epub 2018 Jul 4.
33.Imamura K, Takaya A, Ishida YI, Fukuoka Y, Taya T, Nakaki R, Kakeda M, Imamachi N, Sato A, Yamada T, Onoguchi-Mizutani R,
 Akizuki G, Tanu T, Tao K, Miyao S, Suzuki Y, Nagahama M, Yamamoto T, Jensen TH, Akimitsu N.
 Diminished nuclear RNA decay upon Salmonella infection upregulates antibacterial noncoding RNAs.
 EMBO J. 2018 Jul 2;37(13). pii: e97723. doi: 10.15252/embj.201797723. Epub 2018 Jun 7.
34.Nishiyama T, Sakayama H, de Vries J, Buschmann H, Saint-Marcoux D, Ullrich KK, Haas FB, Vanderstraeten L, Becker D, Lang D,
 Vosolsobě S, Rombauts S, Wilhelmsson PKI, Janitza P, Kern R, Heyl A, Rümpler F, Villalobos LIAC, Clay JM, Skokan R, Toyoda A,
 Suzuki Y, Kagoshima H, Schijlen E, Tajeshwar N, Catarino B, Hetherington AJ, Saltykova A, Bonnot C,
 Breuninger H, Symeonidi A, Radhakrishnan GV, Van Nieuwerburgh F, Deforce D, Chang C, Karol KG, Hedrich R, Ulvskov P, Glöckner G,
 Delwiche CF, Petrášek J, Van de Peer Y, Friml J, Beilby M, Dolan L, Kohara Y, Sugano S, Fujiyama A, Delaux PM, Quint M, Theißen G,
 Hagemann M, Harholt J, Dunand C, Zachgo S, Langdale J, Maumus F, Van Der Straeten D, Gould SB, Rensing SA.
 The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization.
 Cell. 2018 Jul 12;174(2):448-464.e24. doi: 10.1016/j.cell.2018.06.033.
35.Abe KI, Funaya S, Tsukioka D, Kawamura M, Suzuki Y, Suzuki MG, Schultz RM, Aoki F.
 Minor zygotic gene activation is essential for mouse preimplantation development.
 Proc Natl Acad Sci U S A. 2018 Jul 17;115(29):E6780-E6788. doi: 10.1073/pnas.1804309115. Epub 2018 Jul 2.
36.Saito T, Niida A, Uchi R, Hirata H, Komatsu H, Sakimura S, Hayashi S, Nambara S, Kuroda Y, Ito S, Eguchi H, Masuda T, Sugimachi K,
 Tobo T, Nishida H, Daa T, Chiba K, Shiraishi Y, Yoshizato T, Kodama M, Okimoto T, Mizukami K, Ogawa R, Okamoto K, Shuto M, Fukuda K,
 Matsui Y, Shimamura T, Hasegawa T, Doki Y, Nagayama S, Yamada K, Kato M, Shibata T, Mori M, Aburatani H, Murakami K,
 Suzuki Y, Ogawa S, Miyano S, Mimori K.
 A temporal shift of the evolutionary principle shaping intratumor heterogeneity in colorectal cancer.
 Nat Commun. 2018 Jul 23;9(1):2884. doi: 10.1038/s41467-018-05226-0.
37.Shoji M, Minato H, Ogaki S, Seki M, Suzuki Y, Kume S, Kuzuhara T.
 Different murine-derived feeder cells alter the definitive endoderm differentiation of human induced pluripotent stem cells.
 PLoS One. 2018 Jul 26;13(7):e0201239. doi: 10.1371/journal.pone.0201239. eCollection 2018.
38.Sugimachi K, Sakimura S, Kuramitsu S, Hirata H, Niida A, Iguchi T, Eguchi H, Masuda T, Morita M, Toh Y, Maehara Y,
 Suzuki Y, Mimori K.
 Serial mutational tracking in surgically resected locally advanced colorectal cancer with neoadjuvant chemotherapy.
 Br J Cancer. 2018 Aug;119(4):419-423. doi: 10.1038/s41416-018-0208-5. Epub 2018 Aug 3.
39.Nagano H, Hashimoto N, Nakayama A, Suzuki S, Miyabayashi Y, Yamato A, Higuchi S, Fujimoto M, Sakuma I, Beppu M, Yokoyama M,
 Suzuki Y, Sugano S, Ikeda K, Tatsuno I, Manabe I, Yokote K, Inoue S, Tanaka T.
 p53-inducible DPYSL4 associates with mitochondrial supercomplexes and regulates energy metabolism in adipocytes and cancer cells.
 Proc Natl Acad Sci U S A. 2018 Aug 14;115(33):8370-8375. doi: 10.1073/pnas.1804243115. Epub 2018 Jul 30.
40.Nishikawa Y, Shimoda N, Fereig RM, Moritaka T, Umeda K, Nishimura M, Ihara F, Kobayashi K, Himori Y, Suzuki Y,
 Furuoka H.
 Neospora caninum Dense Granule Protein 7 Regulates the Pathogenesis of Neosporosis by Modulating Host Immune Response.
 Appl Environ Microbiol. 2018 Aug 31;84(18). pii: e01350-18. doi: 10.1128/AEM.01350-18. Print 2018 Sep 15.
41.Vandenbon A, Kumagai Y, Lin M, Suzuki Y, Nakai K.
 Waves of chromatin modifications in mouse dendritic cells in response to LPS stimulation.
 Genome Biol. 2018 Sep 19;19(1):138. doi: 10.1186/s13059-018-1524-z.
42.Ando T, Matsuda T, Goto K, Hara K, Ito A, Hirata J, Yatomi J, Kajitani R, Okuno M, Yamaguchi K, Kobayashi M, Takano T,
 Minakuchi Y, Seki M, Suzuki Y, Yano K, Itoh T, Shigenobu S, Toyoda A, Niimi T.
 Repeated inversions within a pannier intron drive diversification of intraspecific colour patterns of ladybird beetles.
 Nat Commun. 2018 Sep 21;9(1):3843. doi: 10.1038/s41467-018-06116-1.
43.Takahashi T, Nakano Y, Onomoto K, Murakami F, Komori C, Suzuki Y, Yoneyama M, Ui-Tei K.
 LGP2 virus sensor regulates gene expression network mediated by TRBP-bound microRNAs.
 Nucleic Acids Res. 2018 Sep 28;46(17):9134-9147. doi: 10.1093/nar/gky575.
44.Kawata K, Hatano A, Yugi K, Kubota H, Sano T, Fujii M, Tomizawa Y, Kokaji T, Tanaka KY, Uda S, Suzuki Y,
 Matsumoto M, Nakayama KI, Saitoh K, Kato K, Ueno A, Ohishi M, Hirayama A, Soga T, Kuroda S.
 Trans-omic Analysis Reveals Selective Responses to Induced and Basal Insulin across Signaling, Transcriptional,
 and Metabolic Networks.
 iScience. 2018 Sep 28;7:212-229. doi: 10.1016/j.isci.2018.07.022. Epub 2018 Sep 10.
45.Igarashi Y, Zhang H, Tan E, Sekino M, Yoshitake K, Kinoshita S, Mitsuyama S, Yoshinaga T, Chow S, Kurogi H, Shinoda A, Han YS,
 Wakiya R, Mochioka N, Yamamoto T, Kuwada H, Kaji Y, Suzuki Y, Gojobori T, Kobayashi T, Saitoh K, Watabe S,
 Asakawa S.
 Whole-Genome Sequencing of 84 Japanese Eels Reveals Evidence against Panmixia and Support for Sympatric Speciation.
 Genes (Basel). 2018 Sep 28;9(10). pii: E474. doi: 10.3390/genes9100474.
46.Chen Y, Yu H, Pask AJ, Fujiyama A, Suzuki Y, Sugano S, Shaw G, Renfree M.
 Effects of androgen and oestrogen on the IGF pathways controlling phallus growth.
 Reproduction. 2018 Oct 1. pii: REP-18-0416.R1. doi: 10.1530/REP-18-0416. [Epub ahead of print]
47.Hayashida K, Umemiya-Shirafuji R, Sivakumar T, Yamagishi J, Suzuki Y, Sugimoto C, Yokoyama N.
 Establishment of a mouse-tick infection model for Theileria orientalis and analysis of its transcriptome.
 Int J Parasitol. 2018 Oct;48(12):915-924. doi: 10.1016/j.ijpara.2018.05.012. Epub 2018 Aug 31.
48.Kerckhove M, Tanaka K, Umehara T, Okamoto M, Kanematsu S, Hayashi H, Yano H, Nishiura S, Tooyama S, Matsubayashi Y,
 Komatsu T, Park S, Okada Y, Takahashi R, Kawano Y, Hanawa T, Iwasaki K, Nozaki T, Torigoe H, Ikematsu K,
 Suzuki Y, Tanaka K, Martin P, Shimokawa I, Mori R.
 Targeting miR-223 in neutrophils enhances the clearance of Staphylococcus aureus in infected wounds.
 EMBO Mol Med. 2018 Oct;10(10). pii: e9024. doi: 10.15252/emmm.201809024.
49.Takahashi S, Osabe K, Fukushima N, Takuno S, Miyaji N, Shimizu M, Takasaki-Yasuda T, Suzuki Y, Dennis ES,
 Seki M, Fujimoto R.
 Genome-wide characterization of DNA methylation, small RNA expression, and histone H3 lysine nine di-methylation in Brassica rapa L.
 DNA Res. 2018 Oct 1;25(5):511-520. doi: 10.1093/dnares/dsy021.
50.Chen Y, Yu H, Pask AJ, Fujiyama A, Suzuki Y, Sugano S, Shaw G, Renfree MB.
 Hormone-responsive genes in the SHH and WNT/β-catenin signaling pathways influence urethral closure and phallus growth.
 Biol Reprod. 2018 Oct 1;99(4):806-816. doi: 10.1093/biolre/ioy117.
51.Yoshitake K, Igarashi Y, Mizukoshi M, Kinoshita S, Mitsuyama S, Suzuki Y, Saito K, Watabe S, Asakawa S.
 Artificially designed hybrids facilitate efficient generation of high-resolution linkage maps.
 Sci Rep. 2018 Oct 31;8(1):16104. doi: 10.1038/s41598-018-34431-6.
52.Liu R, Wang J, Ukai M, Sewon K, Chen P, Suzuki Y, Wang H, Aihara K, Okada-Hatakeyama M, Chen L.
 Hunt for the tipping point during endocrine resistance process in breast cancer by dynamic network biomarkers.
 J Mol Cell Biol. 2018 Nov 1. doi: 10.1093/jmcb/mjy059. [Epub ahead of print]
53.Chen Y, Takikawa M, Tsutsumi S, Yamaguchi Y, Okabe A, Shimada M, Kawase T, Sada A, Ezawa I, Takano Y, Nagata K,
 Suzuki Y, Semba K, Aburatani H, Ohki R.
 PHLDA1, another PHLDA family protein that inhibits Akt.
 Cancer Sci. 2018 Nov;109(11):3532-3542. doi: 10.1111/cas.13796. Epub 2018 Oct 13.
54.Seki M, Katsumata E, Suzuki A, Sereewattanawoot S, Sakamoto Y, Mizushima-Sugano J, Sugano S, Kohno T, Frith MC, Tsuchihara K,
 Suzuki Y.
 Evaluation and application of RNA-Seq by MinION.
 DNA Res. 2018 Nov 20. doi: 10.1093/dnares/dsy038. [Epub ahead of print]
55.Tomizawa SI, Kobayashi Y, Shirakawa T, Watanabe K, Mizoguchi K, Hoshi I, Nakajima K, Nakabayashi J, Singh S, Dahl A,
 Alexopoulou D, Seki M, Suzuki Y, Royo H, Peters AHFM, Anastassiadis K, Stewart AF, Ohbo K.
 Kmt2b conveys monovalent and bivalent H3K4me3 in mouse spermatogonial stem cells at germline and embryonic promoters.
 Development. 2018 Nov 30;145(23). pii: dev169102. doi: 10.1242/dev.169102.
56.Suzuki H, Nishida H, Kondo H, Yoda R, Iwata T, Nakayama K, Enomoto T, Wu J, Moriya-Ito K, Miyazaki M, Wakabayashi Y, Kishida T,
 Okabe M, Suzuki Y, Ito T, Hirota J, Nikaido M.
 A Single Pheromone Receptor Gene Conserved across 400 My of Vertebrate Evolution.
 Mol Biol Evol. 2018 Dec 1;35(12):2928-2939. doi: 10.1093/molbev/msy186.
57.Nakahama T, Kato Y, Kim JI, Vongpipatana T, Suzuki Y, Walkley CR, Kawahara Y.
 ADAR1-mediated RNA editing is required for thymic self-tolerance and inhibition of autoimmunity.
 EMBO Rep. 2018 Dec;19(12). pii: e46303. doi: 10.15252/embr.201846303. Epub 2018 Oct 25.

2017

英語論文
1.Terajima H, Yoshitane H, Ozaki H, Suzuki Y, Shimba S, Kuroda S, Iwasaki W, Fukada Y.
 ADARB1 catalyzes circadian A-to-I editing and regulates RNA rhythm.
 Nat Genet. 2017 Jan;49(1):146-151. doi: 10.1038/ng.3731. Epub 2016 Nov 28.
2.Sekimoto N, Suzuki A, Suzuki Y, Sugano S.
 Expression of miR?26a exhibits a negative correlation with HMGA1 and regulates cancer progression by targeting HMGA1 in lung
 adenocarcinoma cells.
 Mol Med Rep. 2017 Feb;15(2):534-542. doi: 10.3892/mmr.2016.6053. Epub 2016 Dec 15.
3.Panthee S, Hamamoto H, Suzuki Y, Sekimizu K.
 In silico identification of lysocin biosynthetic gene cluster from Lysobacter sp. RH2180-5.
 J Antibiot (Tokyo). 2017 Feb;70(2):204-207. doi: 10.1038/ja.2016.102. Epub 2016 Aug 24.
4.Takei Y, Wong MK, Pipil S, Ozaki H, Suzuki Y, Iwasaki W, Kusakabe M.
 Molecular mechanisms underlying active desalination and low water permeability in the esophagus of eels acclimated to seawater.
 Am J Physiol Regul Integr Comp Physiol. 2017 Feb 1;312(2):R231-R244. doi: 10.1152/ajpregu.00465.2016. Epub 2016 Dec 21.
5.Galipon J, Ishii R, Suzuki Y, Tomita M, Ui-Tei K.
 Differential Binding of Three Major Human ADAR Isoforms to Coding and Long Non-Coding Transcripts.
 Genes (Basel). 2017 Feb 11;8(2). pii: E68. doi: 10.3390/genes8020068.
6.Zhang Y, Matsuzaka T, Yano H, Furuta Y, Nakano T, Ishikawa K, Fukuyo M, Takahashi N, Suzuki Y, Sugano S, Ide H, Kobayashi I.
 Restriction glycosylases: involvement of endonuclease activities in the restriction process.
 Nucleic Acids Res. 2017 Feb 17;45(3):1392-1403. doi: 10.1093/nar/gkw1250.
7.Hotta K, Kikuchi M, Kitamoto T, Kitamoto A, Ogawa Y, Honda Y, Kessoku T, Kobayashi K, Yoneda M, Imajo K, Tomeno W, Nakaya A,
 Suzuki Y, Saito S, Nakajima A.
 Identification of core gene networks and hub genes associated with progression of non-alcoholic fatty liver disease by RNA sequencing.
 Hepatol Res. 2017 Feb 20. doi: 10.1111/hepr.12877. [Epub ahead of print]
8.Imamachi N, Salam KA, Suzuki Y, Akimitsu N.
 A GC-rich sequence feature in the 3' UTR directs UPF1-dependent mRNA decay in mammalian cells.
 Genome Res. 2017 Mar;27(3):407-418. doi: 10.1101/gr.206060.116. Epub 2016 Dec 9.
9.Misawa A, Takayama KI, Fujimura T, Homma Y, Suzuki Y, Inoue S.
 Androgen-induced lncRNA POTEF-AS1 regulates apoptosis-related pathway to facilitate cell survival in prostate cancer cells.
 Cancer Sci. 2017 Mar;108(3):373-379. doi: 10.1111/cas.13151.
10.Nakaoka T, Iga M, Yamada T, Koujima I, Takeshima M, Zhou X, Suzuki Y, Ogihara MH, Kataoka H.
 Deep sequencing of the prothoracic gland transcriptome reveals new players in insect ecdysteroidogenesis.
 PLoS One. 2017 Mar 3;12(3):e0172951. doi: 10.1371/journal.pone.0172951. eCollection 2017.
11.Imai K, Tarumoto N, Amo K, Takahashi M, Sakamoto N, Kosaka A, Kato Y, Mikita K, Sakai J, Murakami T, Suzuki Y, Maesaki S,
 Maeda T.
 Non-invasive diagnosis of cutaneous leishmaniasis by the direct boil loop-mediated isothermal amplification method and MinION?
 nanopore sequencing.
 Parasitol Int. 2017 Mar 11. pii: S1383-5769(17)30043-0. doi: 10.1016/j.parint.2017.03.001. [Epub ahead of print]
12.Mimura I, Hirakawa Y, Kanki Y, Kushida N, Nakaki R, Suzuki Y, Tanaka T, Aburatani H, Nangaku M.
 Novel lnc RNA regulated by HIF-1 inhibits apoptotic cell death in the renal tubular epithelial cells under hypoxia.
 Physiol Rep. 2017 Apr;5(8). pii: e13203. doi: 10.14814/phy2.13203.
13.Jinda W, Taylor TD, Suzuki Y, Thongnoppakhun W, Limwongse C, Lertrit P, Trinavarat A, Atchaneeyasakul LO.
 Whole Exome Sequencing in Eight Thai Patients With Leber Congenital Amaurosis Reveals Mutations in the CTNNA1 and CYP4V2
 Genes.
 Invest Ophthalmol Vis Sci. 2017 Apr 1;58(4):2413-2420. doi: 10.1167/iovs.16-21322.
14.Karlic R, Ganesh S, Franke V, Svobodova E, Urbanova J, Suzuki Y, Aoki F, Vlahovicek K, Svoboda P.
 Long non-coding RNA exchange during the oocyte-to-embryo transition in mice.
 DNA Res. 2017 Apr 1;24(2):129-141. doi: 10.1093/dnares/dsw058.
15.Reteng P, Vrisca V, Sukarno I, Djarkoni IH, Kalangi JA, Jacobs GE, Runtuwene LR, Eshita Y, Maeda R, Suzuki Y, Mongan AE,
 Warouw SM, Yamagishi J, Tuda J.
 Genetic polymorphisms in Plasmodium falciparum chloroquine resistance genes, pfcrt and pfmdr1, in North Sulawesi, Indonesia.
 BMC Res Notes. 2017 Apr 4;10(1):147. doi: 10.1186/s13104-017-2468-1.
16.Paudel A, Hamamoto H, Panthee S, Kaneko K, Matsunaga S, Kanai M, Suzuki Y, Sekimizu K.
 A Novel Spiro-Heterocyclic Compound Identified by the Silkworm Infection Model Inhibits Transcription in Staphylococcus aureus.
 Front Microbiol. 2017 Apr 25;8:712. doi: 10.3389/fmicb.2017.00712. eCollection 2017.
17.Tokizawa M, Kusunoki K, Koyama H, Kurotani A, Sakurai T, Suzuki Y, Sakamoto T, Kurata T, Yamamoto YY.
 Identification of Arabidopsis genic and non-genic promoters by paired-end sequencing of TSS tags.
 Plant J. 2017 May;90(3):587-605. doi: 10.1111/tpj.13511. Epub 2017 Apr 4.
18.Yoshinaga M, Nakatsuka Y, Vandenbon A, Ori D, Uehata T, Tsujimura T, Suzuki Y, Mino T, Takeuchi O.
 Regnase-1 Maintains Iron Homeostasis via the Degradation of Transferrin Receptor 1 and Prolyl-Hydroxylase-Domain-Containing
 Protein 3 mRNAs.
 Cell Rep. 2017 May 23;19(8):1614-1630. doi: 10.1016/j.celrep.2017.05.009.
19.Fujita T, Yuno M, Suzuki Y, Sugano S, Fujii H.
 Identification of physical interactions between genomic regions by enChIP-Seq.
 Genes Cells. 2017 Jun;22(6):506-520. doi: 10.1111/gtc.12492. Epub 2017 May 5.
20.Fujita T, Kitaura F, Yuno M, Suzuki Y, Sugano S, Fujii H.
 Locus-specific ChIP combined with NGS analysis reveals genomic regulatory regions that physically interact with the Pax5 promoter in
 a chicken B cell line.
 DNA Res. 2017 Jun 6. doi: 10.1093/dnares/dsx023. [Epub ahead of print]
21.Yamagishi J, Runtuwene LR, Hayashida K, Mongan AE, Thi LAN, Thuy LN, Nhat CN, Limkittikul K, Sirivichayakul C,
 Sathirapongsasuti N, Frith M, Makalowski W, Eshita Y, Sugano S, Suzuki Y.
 Serotyping dengue virus with isothermal amplification and a portable sequencer.
 Sci Rep. 2017 Jun 14;7(1):3510. doi: 10.1038/s41598-017-03734-5.
22.Ueno K, Iwagawa T, Ochiai G, Koso H, Nakauchi H, Nagasaki M, Suzuki Y, Watanabe S.
 Analysis of Muller glia specific genes and their histone modification using Hes1-promoter driven EGFP expressing mouse.
 Sci Rep. 2017 Jun 15;7(1):3578. doi: 10.1038/s41598-017-03874-8.
23.Ezura K, Ji-Seong K, Mori K, Suzuki Y, Kuhara S, Ariizumi T, Ezura H.
 Genome-wide identification of pistil-specific genes expressed during fruit set initiation in tomato (Solanum lycopersicum).
 PLoS One. 2017 Jul 6;12(7):e0180003. doi: 10.1371/journal.pone.0180003. eCollection 2017.
24.Liu Y, Irie T, Yada T, Suzuki Y.
 A new computational method to predict transcriptional activity of a DNA sequence from diverse datasets of massively parallel reporter
 assays.
 Nucleic Acids Res. 2017 Jul 27;45(13):e124. doi: 10.1093/nar/gkx396.
25.Franke V, Ganesh S, Karlic R, Malik R, Pasulka J, Horvat F, Kuzman M, Fulka H, Cernohorska M, Urbanova J, Svobodova E, Ma J,
 Suzuki Y, Aoki F, Schultz RM, Vlahovicek K, Svoboda P.
 Long terminal repeats power evolution of genes and gene expression programs in mammalian oocytes and zygotes.
 Genome Res. 2017 Aug;27(8):1384-1394. doi: 10.1101/gr.216150.116. Epub 2017 May 18.
26.Takahashi Y, Sugimachi K, Yamamoto K, Niida A, Shimamura T, Sato T, Watanabe M, Tanaka J, Kudo S, Sugihara K, Hase K,
 Kusunoki M, Yamada K, Shimada Y, Moriya Y, Suzuki Y, Miyano S, Mori M, Mimori K.
 Japanese genome-wide association study identifies a significant colorectal cancer susceptibility locus at chromosome 10p14.
 Cancer Sci. 2017 Sep 4. doi: 10.1111/cas.13391. [Epub ahead of print]
27.Imai K, Tarumoto N, Misawa K, Runtuwene LR, Sakai J, Hayashida K, Eshita Y, Maeda R, Tuda J, Murakami T, Maesaki S, Suzuki Y,
 Yamagishi J, Maeda T.
 A novel diagnostic method for malaria using loop-mediated isothermal amplification (LAMP) and MinION? nanopore sequencer.
 BMC Infect Dis. 2017 Sep 13;17(1):621. doi: 10.1186/s12879-017-2718-9.
28.Yamazaki T, Ichihara K, Suzuki R, Oshima K, Miyamura S, Kuwano K, Toyoda A, Suzuki Y, Sugano S, Hattori M, Kawano S.
 Genomic structure and evolution of the mating type locus in the green seaweed Ulva partita.
 Sci Rep. 2017 Sep 15;7(1):11679. doi: 10.1038/s41598-017-11677-0.
29.Zhang H, Kiuchi T, Wang L, Kawamoto M, Suzuki Y, Sugano S, Banno Y, Katsuma S, Shimada T.
 Bm-muted, orthologous to mouse muted and encoding a subunit of the BLOC-1 complex, is responsible for the otm translucent
 mutation of the silkworm Bombyx mori.
 Gene. 2017 Sep 20;629:92-100. doi: 10.1016/j.gene.2017.07.071. Epub 2017 Jul 30.
30.Asahi H, Inoue SI, Niikura M, Kunigo K, Suzuki Y, Kobayashi F, Sendo F.
 Profiling molecular factors associated with pyknosis and developmental arrest induced by an opioid receptor antagonist and
 dihydroartemisinin in Plasmodium falciparum.
 PLoS One. 2017 Sep 21;12(9):e0184874. doi: 10.1371/journal.pone.0184874. eCollection 2017.
31.Takayama KI, Suzuki T, Fujimura T, Yamada Y, Takahashi S, Homma Y, Suzuki Y, Inoue S.
 Dysregulation of spliceosome gene expression in advanced prostate cancer by RNA-binding protein PSF.
 Proc Natl Acad Sci U S A. 2017 Sep 26;114(39):10461-10466. doi: 10.1073/pnas.1706076114. Epub 2017 Sep 11.
32.Yamamoto Y, Gotoh S, Korogi Y, Seki M, Konishi S, Ikeo S, Sone N, Nagasaki T, Matsumoto H, Muro S, Ito I, Hirai T, Kohno T,
 Suzuki Y, Mishima M.
 Long-term expansion of alveolar stem cells derived from human iPS cells in organoids.
 Nat Methods. 2017 Oct 2. doi: 10.1038/nmeth.4448. [Epub ahead of print]
33.Shinozaki E, Yoshino T, Yamazaki K, Muro K, Yamaguchi K, Nishina T, Yuki S, Shitara K, Bando H, Mimaki S, Nakai C, Matsushima K,
 Suzuki Y, Akagi K, Yamanaka T, Nomura S, Fujii S, Esumi H, Sugiyama M, Nishida N, Mizokami M, Koh Y, Abe Y, Ohtsu A,
 Tsuchihara K.
 Clinical significance of BRAF non-V600E mutations on the therapeutic effects of anti-EGFR monoclonal antibody treatment in patients
 with pretreated metastatic colorectal cancer: the Biomarker Research for anti-EGFR monoclonal Antibodies by Comprehensive Cancer
 genomics (BREAC) study.
 Br J Cancer. 2017 Oct 3. doi: 10.1038/bjc.2017.308. [Epub ahead of print]
34.Bowman JL, Kohchi T, Yamato KT, Jenkins J, Shu S, Ishizaki K, Yamaoka S, Nishihama R, Nakamura Y, Berger F, Adam C, Aki SS,
 Althoff F, Araki T, Arteaga-Vazquez MA, Balasubrmanian S, Barry K, Bauer D, Boehm CR, Briginshaw L, Caballero-Perez J, Catarino B,
 Chen F, Chiyoda S, Chovatia M, Davies KM, Delmans M, Demura T, Dierschke T, Dolan L, Dorantes-Acosta AE, Eklund DM, Florent SN,
 Flores-Sandoval E, Fujiyama A, Fukuzawa H, Galik B, Grimanelli D, Grimwood J, Grossniklaus U, Hamada T, Haseloff J,
 Hetherington AJ, Higo A, Hirakawa Y, Hundley HN, Ikeda Y, Inoue K, Inoue SI, Ishida S, Jia Q, Kakita M, Kanazawa T, Kawai Y,
 Kawashima T, Kennedy M, Kinose K, Kinoshita T, Kohara Y, Koide E, Komatsu K, Kopischke S, Kubo M, Kyozuka J, Lagercrantz U,
 Lin SS, Lindquist E, Lipzen AM, Lu CW, De Luna E, Martienssen RA, Minamino N, Mizutani M, Mizutani M, Mochizuki N, Monte I,
 Mosher R, Nagasaki H, Nakagami H, Naramoto S, Nishitani K, Ohtani M, Okamoto T, Okumura M, Phillips J, Pollak B, Reinders A,
 Rovekamp M, Sano R, Sawa S, Schmid MW, Shirakawa M, Solano R, Spunde A, Suetsugu N, Sugano S, Sugiyama A, Sun R, Suzuki Y,
 Takenaka M, Takezawa D, Tomogane H, Tsuzuki M, Ueda T, Umeda M, Ward JM, Watanabe Y, Yazaki K, Yokoyama R, Yoshitake Y,
 Yotsui I, Zachgo S, Schmutz J.
 Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome.
 Cell. 2017 Oct 5;171(2):287-304.e15. doi: 10.1016/j.cell.2017.09.030.
35.Nojiri T, Arai M, Suzuki Y, Kumazoe M, Tokudome T, Miura K, Hino J, Hosoda H, Miyazato M,
 Okumura M, Kawaoka S, Kangawa K.  Transcriptome analysis reveals a role for the endothelial ANP-GC-A signaling in interfering
 with pre-metastatic niche formation by solid cancers.
 Oncotarget. 2017 May 25;8(39):65534-65547. doi: 10.18632/oncotarget.18032. eCollection 2017 Sep 12
36.Rosikiewicz W, Suzuki Y, Makalowska I.
 OverGeneDB: a database of 5' end protein coding overlapping genes in human and mouse genomes.
 Nucleic Acids Res. 2018 Jan 4;46(D1):D186-D193. doi: 10.1093/nar/gkx948.
37.Hashimoto S, Tabuchi Y, Yurino H, Hirohashi Y, Deshimaru S, Asano T, Mariya T, Oshima K, Takamura Y, Ukita Y, Ametani A,
 Kondo N, Monma N, Takeda T, Misu S, Okayama T, Ikeo K, Saito T, Kaneko S, Suzuki Y, Hattori M, Matsushima K, Torigoe T.
 Comprehensive single-cell transcriptome analysis reveals heterogeneity in endometrioid adenocarcinoma tissues.
 Sci Rep. 2017 Oct 27;7(1):14225. doi: 10.1038/s41598-017-14676-3.
38.Suzuki A, Suzuki M, Mizushima-Sugano J, Frith MC, Makalowski W, Kohno T, Sugano S, Tsuchihara K, Suzuki Y.
 Sequencing and phasing cancer mutations in lung cancers using a long-read portable sequencer.
 DNA Res. 2017 Dec 1;24(6):585-596. doi: 10.1093/dnares/dsx027.
39.Suzuki A, Kawano S, Mitsuyama T, Suyama M, Kanai Y, Shirahige K, Sasaki H, Tokunaga K, Tsuchihara K, Sugano S,
 Nakai K, Suzuki Y.  DBTSS/DBKERO for integrated analysis of transcriptional regulation.
 Nucleic Acids Res. 2018 Jan 4;46(D1):D229-D238. doi: 10.1093/nar/gkx1001.
40.Cui X, Mino T, Yoshinaga M, Nakatsuka Y, Hia F, Yamasoba D, Tsujimura T, Tomonaga K, Suzuki Y,
 Uehata T, Takeuchi O.
 Regnase-1 and Roquin Nonredundantly Regulate Th1 Differentiation Causing Cardiac Inflammation and Fibrosis.
 J Immunol. 2017 Dec 15;199(12):4066-4077. doi: 10.4049/jimmunol.1701211. Epub 2017 Nov 10.
41.Ushijima T, Hanada K, Gotoh E, Yamori W, Kodama Y, Tanaka H, Kusano M, Fukushima A, Tokizawa M, Yamamoto YY,
 Tada Y, Suzuki Y, Matsushita T.
 Light Controls Protein Localization through Phytochrome-Mediated Alternative Promoter Selection.
 Cell. 2017 Nov 30;171(6):1316-1325.e12. doi: 10.1016/j.cell.2017.10.018. Epub 2017 Nov 9.
42.Umeda K, Tanaka S, Ihara F, Yamagishi J, Suzuki Y, Nishikawa Y.
 Transcriptional profiling of Toll-like receptor 2-deficient primary murine brain cells
 during Toxoplasma gondii infection.
 PLoS One. 2017 Nov 14;12(11):e0187703. doi: 10.1371/journal.pone.0187703. eCollection 2017.
43.Sekimoto N, Suzuki Y, Sugano S.
 Decreased KPNB1 Expression is Induced by PLK1 Inhibition and Leads to Apoptosis in Lung Adenocarcinoma.
 J Cancer. 2017 Nov 6;8(19):4125-4140. doi: 10.7150/jca.21802. eCollection 2017.
44.Arishima T, Sasaki S, Isobe T, Ikebata Y, Shimbara S, Ikeda S, Kawashima K, Suzuki Y, Watanabe M,
 Sugano S, Mizoshita K, Sugimoto Y.
 Maternal variant in the upstream of FOXP3 gene on the X chromosome is associated with recurrent infertility
 in Japanese Black cattle.
 BMC Genet. 2017 Dec 6;18(1):103. doi: 10.1186/s12863-017-0573-8.
45.Kudoh T, Takahashi M, Osabe T, Toyoda A, Hirakawa H, Suzuki Y, Ohmido N, Onodera Y.
 Molecular insights into the non-recombining nature of the spinach male-determining region.
 Mol Genet Genomics. 2018 Apr;293(2):557-568. doi: 10.1007/s00438-017-1405-2. Epub 2017 Dec 8.
46.Yamada T, Imamachi N, Onoguchi-Mizutani R, Imamura K, Suzuki Y, Akimitsu N.
 5'-Bromouridine IP Chase (BRIC)-Seq to Determine RNA Half-Lives.
 Methods Mol Biol. 2018;1720:1-13. doi: 10.1007/978-1-4939-7540-2_1.
47.Wong MKS, Tsukada T, Ogawa N, Pipil S, Ozaki H, Suzuki Y, Iwasaki W, Takei Y.
 A sodium binding system alleviates acute salt stress during seawater acclimation in eels.
 Zoological Lett. 2017 Dec 12;3:22. doi: 10.1186/s40851-017-0081-8. eCollection 2017.
48.Sakai E, Nakayama M, Oshima H, Kouyama Y, Niida A, Fujii S, Ochiai A, Nakayama KI, Mimori K,
 Suzuki Y, Hong CP, Ock CY, Kim SJ, Oshima M.
 Combined Mutation of Apc, Kras, and Tgfbr2 Effectively Drives Metastasis of Intestinal Cancer.
 Cancer Res. 2018 Mar 1;78(5):1334-1346. doi: 10.1158/0008-5472.CAN-17-3303. Epub 2017 Dec 27.
49.Wojtkowska M, Buczek D, Suzuki Y, Shabardina V, Makałowski W, Kmita H.
 The emerging picture of the mitochondrial protein import complexes of Amoebozoa supergroup.
 BMC Genomics. 2017 Dec 29;18(1):997. doi: 10.1186/s12864-017-4383-1.
50.Firouzi S, Farmanbar A, Nakai K, Iwanaga M, Uchimaru K, Utsunomiya A, Suzuki Y, Watanabe T.
 Clonality of HTLV-1-infected T cells as a risk indicator for development and progression of adult T-cell leukemia.
 Blood Adv. 2017 Jun 27;1(15):1195-1205. doi: 10.1182/bloodadvances.2017005900. eCollection 2017 Jun 27.

2016

英文論文
1.Wong MK, Pipil S, Ozaki H, Suzuki Y, Iwasaki W, Takei Y.
 Flexible selection of diversified Na(+)/K(+)-ATPase α-subunit isoforms for osmoregulation in teleosts.
 Zoological Lett. 2016 Aug 3;2:15. doi: 10.1186/s40851-016-0050-7. eCollection 2016.
2.Yasuma K, Yasunaga J, Takemoto K, Sugata K, Mitobe Y, Takenouchi N, Nakagawa M, Suzuki Y, Matsuoka M.
 HTLV-1 bZIP Factor Impairs Anti-viral Immunity by Inducing Co-inhibitory Molecule, T Cell Immunoglobulin and ITIM Domain (TIGIT).
 PLoS Pathog. 2016 Jan 6;12(1):e1005372. doi: 10.1371/journal.ppat.1005372. eCollection 2016 Jan.
3.Higashi K, Tobe T, Kanai A, Uyar E, Ishikawa S, Suzuki Y, Ogasawara N, Kurokawa K, Oshima T.
 H-NS Facilitates Sequence Diversification of Horizontally Transferred DNAs during Their Integration in Host Chromosomes.
 PLoS Genet. 2016 Jan 20;12(1):e1005796. doi: 10.1371/journal.pgen.1005796. eCollection 2016 Jan.
4.Jinda W, Poungvarin N, Taylor TD, Suzuki Y, Thongnoppakhun W, Limwongse C, Lertrit P, Suriyaphol P, Atchaneeyasakul LO.
 A novel start codon mutation of the MERTK gene in a patient with retinitis pigmentosa.
 Molecular Vision2016; 22:342-351 Received 28 January 2016 | Accepted 19 April 2016 | Published 21 April 2016.
5.Tanabe H, Seki M, Itoh M, Deepak A, Lal P, Horiuchi T, Suzuki Y, Kawakami K.
 Fluorescence-Activated Cell Sorting and Gene Expression Profiling of GFP-Positive Cells from Transgenic Zebrafish Lines.
 Methods Mol Biol. 2016;1451:93-106. doi: 10.1007/978-1-4939-3771-4_7.
6.Yamamoto R, Abe K, Suzuki Y, Suzuki MG, Aoki F.
 Characterization of gene expression in mouse embryos at the 1-cell stage.
 J Reprod Dev. 2016;62(1):87-92. doi: 10.1262/jrd.2015-131. Epub 2015 Nov 22.
7.Yokomori R, Shimai K, Nishitsuji K, Suzuki Y, Kusakabe T, Nakai K.
 Genome-wide identification and characterization of transcription start sites and promoters in the tunicate Ciona intestinalis.
 Genome Res. 2016; 26: 140-150
8.Uchi R, Takahashi Y, Niida A, Shimamura T, Hirata H, Sugimachi K, Sawada G, Iwaya T, Kurashige J, Shinden Y, Iguchi T, Eguchi H,
 Chiba K, Shiraishi Y, Nagae G, Yoshida K, Nagata Y, Haeno H, Yamamoto H, Ishii H, Doki Y, Iinuma H, Sasaki S, Nagayama S,
 Yamada K, Yachida S, Kato M, Shibata T, Oki E, Saeki H, Shirabe K, Oda Y, Maehara Y, Komune S, Mori M, Suzuki Y, Yamamoto K,
 Aburatani H, Ogawa S, Miyano S, Mimori K.
 Integrated Multiregional Analysis Proposing a New Model of Colorectal Cancer Evolution.
 PLoS Genet. 2016 Feb 18;12(2):e1005778. doi: 10.1371/journal.pgen.1005778. eCollection 2016.
9.Tan E, Kinoshita S, Suzuki Y, Ineno T, Tamaki K, Kera A, Muto K, Yada T, Kitamura S, Asakawa S, Watabe S.
 Different gene expression profiles between normal and thermally selected strains of rainbow trout, Oncorhynchus mykiss, as revealed
 by comprehensive transcriptome analysis.
 Gene. 2016 Feb 1;576(2 Pt 1):637-43. doi: 10.1016/j.gene.2015.10.028. Epub 2015 Oct 22.
10.Buczek D, Wojtkowska M, Suzuki Y, Sonobe S, Nishigami Y, Antoniewicz M, Kmita H, Maka?owski W.
 Protein import complexes in the mitochondrial outer membrane of Amoebozoa representatives.
 BMC Genomics. 2016 Feb 6;17:99. doi: 10.1186/s12864-016-2402-2.
11.Sasamoto Y, Hayashi R, Park SJ, Saito-Adachi M, Suzuki Y, Kawasaki S, Quantock A, Nakai K, Tsujikawa M, Nishida K.
 PAX6 Isoforms, along with Reprogramming Factors, Differentially Regulate the Induction of Cornea-specific Genes.
 Scientific Reports 6, Article number: 20807 (2016 Feb 22) doi:10.1038/srep20807
12.Takei S, Togo-Ohno M, Suzuki Y, Kuroyanagi H.
 Evolutionarily conserved autoregulation of alternative pre-mRNA splicing by ribosomal protein L10a.
 Nucleic Acids Res. 2016 Mar 9. pii: gkw152. [Epub ahead of print]
13.Huang F, Dang Z, Suzuki Y, Horiuchi T, Yagi K, Kouguchi H, Irie T, Kim K, Oku Y.
 Analysis on Gene Expression Profile in Oncospheres and Early Stage Metacestodes from Echinococcus multilocularis.
 PLOS, Published: April 19, 2016. http://dx.doi.org/10.1371/journal.pntd.0004634
14.Oshima M, Hasegawa N, Mochizuki-Kashio M, Muto T, Miyagi S, Koide S, Yabata S, Wendt GR, Saraya A, Wang C, Shimoda K,
 Suzuki Y, Iwama A.
 Ezh2 regulates the Lin28/let-7 pathway to restrict activation of fetal gene signature in adult hematopoietic stem cells.
 Exp Hematol. 2016 Apr;44(4):282-96.e3. doi: 10.1016/j.exphem.2015.12.009. Epub 2016 Jan 7.
15.Sawada G, Niida A, Uchi R, Hirata H, Shimamura T, Suzuki Y, Shiraishi Y, Chiba K, Imoto S, Takahashi Y, Iwaya T, Sudo T,
 Hayashi T, Takai H, Kawasaki Y, Matsukawa T, Eguchi H, Sugimachi K, Tanaka F, Suzuki H, Yamamoto K, Ishii H, Shimizu M,
 Yamazaki H, Yamazaki M, Tachimori Y, Kajiyama Y, Natsugoe S, Fujita H, Mafune K, Tanaka Y, Kelsell DP, Scott CA, Tsuji S, Yachida S,
 Shibata T, Sugano S, Doki Y, Akiyama T, Aburatani H, Ogawa S, Miyano S, Mori M, Mimori K.
 Genomic Landscape of Esophageal Squamous Cell Carcinoma in a Japanese Population.
 Gastroenterology. 2016 May;150(5):1171-82. doi: 10.1053/j.gastro.2016.01.035. Epub 2016 Feb 10.
16.Suzuki S, Kato H, Suzuki Y, Chikashige Y, Hiraoka Y, Kimura H, Nagao K, Obuse C, Takahata S, Murakami Y.
 Histone H3K36 trimethylation is essential for multiple silencing mechanisms in fission yeast.
 Nucleic Acids Res. 2016 May 19;44(9):4147-62. doi: 10.1093/nar/gkw008. Epub 2016 Jan 20.
17.Takemata N, Oda A, Yamada T, Galipon J, Miyoshi T, Suzuki Y, Sugano S, Hoffman CS, Hirota K, Ohta K.
 Local potentiation of stress-responsive genes by upstream noncoding transcription.
 Nucleic Acids Res. 2016 Jun 20;44(11):5174-89. doi: 10.1093/nar/gkw142. Epub 2016 Mar 3.
18.Hohmann AF, Martin LJ, Minder JL, Roe JS, Shi J, Steurer S, Bader G, McConnell D, Pearson M, Gerstberger T, Gottschamel T,
 Thompson D, Suzuki Y, Koegl M, Vakoc CR.
 Sensitivity and engineered resistance of myeloid leukemia cells to BRD9 inhibition.
 Nat Chem Biol. 2016 Jul 4. doi: 10.1038/nchembio.2115. [Epub ahead of print]
19.Ueno K, Iwagawa T, Kuribayashi H, Baba Y, Nakauchi H, Murakami A, Nagasaki M, Suzuki Y, Watanabe S.
 Transition of differential histone H3 methylation in photoreceptors and other retinal cells during retinal differentiation.
 Sci Rep. 2016 Jul 5;6:29264. doi: 10.1038/srep29264.
20.Maruzuru Y, Koyanagi N, Takemura N, Uematsu S, Matsubara D, Suzuki Y, Arii J, Kato A, Kawaguchi Y.
 p53 Is a Host Cell Regulator during Herpes Simplex Encephalitis.
 J Virol. 2016 Jul 11;90(15):6738-45. doi: 10.1128/JVI.00846-16. Print 2016 Aug 1.
21.Imae K, Saito Y, Kizaki H, Ryuno H, Mao H, Miyashita A, Suzuki Y, Sekimizu K, Kaito C.
 Novel nucleoside diphosphatase contributes to Staphylococcus aureus virulence.
 J Biol Chem. 2016 Jul 15. pii: jbc.M116.721845. [Epub ahead of print]
22.Koso H, Tsuhako A, Lai CY, Baba Y, Otsu M, Ueno K, Nagasaki M, Suzuki Y, Watanabe S.
 Conditional rod photoreceptor ablation reveals Sall1 as a microglial marker and regulator of microglial morphology in the retina.
 Glia. 2016 Jul 26. doi: 10.1002/glia.23038. [Epub ahead of print]
23.Uno A, Nakamura R, Tsukahara T, Qu W, Sugano S, Suzuki Y, Morishita S, Takeda H.
 Comparative Analysis of Genome and Epigenome in Closely Related Medaka Species Identifies Conserved Sequence Preferences for
 DNA Hypomethylated Domains.
 Zoolog Sci. 2016 Aug;33(4):358-65. doi: 10.2108/zs160030.
24.Mimaki S, Totsuka Y, Suzuki Y, Nakai C, Goto M, Kojima M, Arakawa H, Takemura S, Tanaka S, Marubashi S, Kinoshita M,
 Matsuda T, Shibata T, Nakagama H, Ochiai A, Kubo S, Nakamori S, Esumi H, Tsuchihara K.
 Hypermutation and unique mutational signatures of occupational cholangiocarcinoma in printing workers exposed to haloalkanes.
 Carcinogenesis. 2016 Aug;37(8):817-26. doi: 10.1093/carcin/bgw066. Epub 2016 Jun 7.
25.Fukumura K, Wakabayashi S, Kataoka N, Sakamoto H, Suzuki Y, Nakai K, Mayeda A, Inoue K.
 The Exon Junction Complex Controls the Efficient and Faithful Splicing of a Subset of Transcripts Involved in Mitotic Cell-Cycle
 Progression.
 Int J Mol Sci. 2016 Aug 2;17(8). pii: E1153. doi: 10.3390/ijms17081153.
26.Koide S, Oshima M, Takubo K, Yamazaki S, Nitta E, Saraya A, Aoyama K, Kato Y, Miyagi S, Nakajima-Takagi Y, Chiba T, Matsui H,
 Arai F, Suzuki Y, Kimura H, Nakauchi H, Suda T, Shinkai Y, Iwama A.
 Setdb1 maintains hematopoietic stem and progenitor cells by restricting the ectopic activation of nonhematopoietic genes.
 Blood. 2016 Aug 4;128(5):638-49. doi: 10.1182/blood-2016-01-694810. Epub 2016 Jun 14.
27.Sasaki S, Hasegawa K, Higashi T, Suzuki Y, Sugano S, Yasuda Y, Sugimoto Y.
 A missense mutation in solute carrier family 12, member 1 (SLC12A1) causes hydrallantois in Japanese Black cattle.
 BMC Genomics. 2016 Sep 9;17(1):724. doi: 10.1186/s12864-016-3035-1.
28.Ueda M, Iguchi T, Masuda T, Nakahara Y, Hirata H, Uchi R, Niida A, Momose K, Sakimura S, Chiba K, Eguchi H, Ito S, Sugimachi K,
  Yamasaki M, Suzuki Y, Miyano S, Doki Y, Mori M, Mimori K.
 Somatic mutations in plasma cell-free DNA are diagnostic markers for esophageal squamous cell carcinoma recurrence.
 Oncotarget. 2016 Sep 20;7(38):62280-62291. doi: 10.18632/oncotarget.11409.
29.Hashimoto T, Horikawa DD, Saito Y, Kuwahara H, Kozuka-Hata H, Shin-I T, Minakuchi Y, Ohishi K, Motoyama A, Aizu T, Enomoto A,
  Kondo K, Tanaka S, Hara Y, Koshikawa S, Sagara H, Miura T, Yokobori S, Miyagawa K, Suzuki Y, Kubo T, Oyama M, Kohara Y,
 Fujiyama A, Arakawa K, Katayama T, Toyoda A, Kunieda T.
 Extremotolerant tardigrade genome and improved radiotolerance of human cultured cells by tardigrade-unique protein.
 Nat Commun. 2016 Sep 20;7:12808. doi: 10.1038/ncomms12808.
30.Session AM, Uno Y, Kwon T, Chapman JA, Toyoda A, Takahashi S, Fukui A, Hikosaka A, Suzuki A, Kondo M, van Heeringen SJ,
  Quigley I, Heinz S, Ogino H, Ochi H, Hellsten U, Lyons JB, Simakov O, Putnam N, Stites J, Kuroki Y, Tanaka T, Michiue T, Watanabe M,
  Bogdanovic O, Lister R, Georgiou G, Paranjpe SS, van Kruijsbergen I, Shu S, Carlson J, Kinoshita T, Ohta Y, Mawaribuchi S, Jenkins J,
  Grimwood J, Schmutz J, Mitros T, Mozaffari SV, Suzuki Y, Haramoto Y, Yamamoto TS, Takagi C, Heald R, Miller K, Haudenschild C,
  Kitzman J, Nakayama T, Izutsu Y, Robert J, Fortriede J, Burns K, Lotay V, Karimi K, Yasuoka Y, Dichmann DS, Flajnik MF, Houston DW,
  Shendure J, DuPasquier L, Vize PD, Zorn AM, Ito M, Marcotte EM, Wallingford JB, Ito Y, Asashima M, Ueno N, Matsuda Y, Veenstra GJ,
  Fujiyama A, Harland RM, Taira M, Rokhsar DS.
 Genome evolution in the allotetraploid frog Xenopus laevis.
 Nature. 2016 Oct 20;538(7625):336-343. doi: 10.1038/nature19840.
31.Koso H, Tsuhako A, Lai CY, Baba Y, Otsu M, Ueno K, Nagasaki M, Suzuki Y, Watanabe S.
 Conditional rod photoreceptor ablation reveals Sall1 as a microglial marker and regulator of microglial morphology in the retina.
 Glia. 2016 Nov;64(11):2005-24. doi: 10.1002/glia.23038. Epub 2016 Jul 26.
32.Hoshino A, Jayakumar V, Nitasaka E, Toyoda A, Noguchi H, Itoh T, Shin-I T, Minakuchi Y, Koda Y, Nagano AJ, Yasugi M, Honjo MN,
  Kudoh H, Seki M, Kamiya A, Shiraki T, Carninci P, Asamizu E, Nishide H, Tanaka S, Park KI, Morita Y, Yokoyama K, Uchiyama I,
  Tanaka Y, Tabata S, Shinozaki K, Hayashizaki Y, Kohara Y, Suzuki Y, Sugano S, Fujiyama A, Iida S, Sakakibara Y.
 Genome sequence and analysis of the Japanese morning glory Ipomoea nil.
 Nat Commun. 2016 Nov 8;7:13295. doi: 10.1038/ncomms13295.
33.Maruyama K, Kawasaki T, Hamaguchi M, Hashimoto M, Furu M, Ito H, Fujii T, Takemura N, Karuppuchamy T, Kondo T, Kawasaki T,
  Fukasaka M, Misawa T, Saitoh T, Suzuki Y, Martino MM, Kumagai Y, Akira S.
 Bone-protective Functions of Netrin 1 Protein.
 J Biol Chem. 2016 Nov 11;291(46):23854-23868. Epub 2016 Sep 28.
34.Sano T, Kawata K, Ohno S, Yugi K, Kakuda H, Kubota H, Uda S, Fujii M, Kunida K, Hoshino D, Hatano A, Ito Y, Sato M, Suzuki Y,
  Kuroda S.
 Selective control of up-regulated and down-regulated genes by temporal patterns and doses of insulin.
 Sci Signal. 2016 Nov 22;9(455):ra112.
35.Kumagai Y, Vandenbon A, Teraguchi S, Akira S, Suzuki Y.
 Genome-wide map of RNA degradation kinetics patterns in dendritic cells after LPS stimulation facilitates identification of primary
  sequence and secondary structure motifs in mRNAs.
 BMC Genomics. 2016 Dec 22;17(Suppl 13):1032. doi: 10.1186/s12864-016-3325-7.
36.Shoji K, Suzuki Y, Sugano S, Shimada T, Katsuma S.
 Artificial "ping-pong" cascade of PIWI-interacting RNA in silkworm cells.
 RNA. 2017 Jan;23(1):86-97. Epub 2016 Oct 24.

2015

英文論文
1. Tani H, Imamachi N, Mizutani R, Imamura K, Kwon Y, Miyazaki S, Maekawa S, Suzuki Y, Akimitsu N.  
 Genome-Wide Analysis of Long Noncoding RNA Turnover.
 Methods Mol Biol. 2015;1262:305-20. doi: 10.1007/978-1-4939-2253-6_19.
2. Nishimura M, Tanaka S, Ihara F, Muroi Y, Yamagishi J, Furuoka H, Suzuki Y, Nishikawa Y.
  Transcriptome and Histopathological Changes in Mouse Brain Infected with Neospora caninum.
 SCIENTIFIC REPORTS SREP-14-08991.3d 2015 Jan 21.
3. Yamaguchi K, Komura M, Yamaguchi R, Imoto S, Shimizu E, Kasuya S, Shibuya T, Hatakeyama S, Takahashi N, Ikenoue T, Hata K,
 Tsurita G, Shinozaki M, Suzuki Y, Sugano S, Miyano S, Furukawa Y.
 Detection of APC mosaicism by next-generation sequencing in an FAP patient.
 Journal of Human Genetics. 2015 Feb 26. doi: 10.1038/jhg.2015.14.
4. Maekawa S, Imamachi N, Irie T, Tani H, Matsumoto K, Mizutani R, Imamura K, Kakeda M, Yada T, Sugano S, Suzuki Y,
 Akimitsu N.
 Analysis of RNA decay factor mediated RNA stability contributions on RNA abundance.
 BMC Genomics. 16, 154, 2015.
5. Lertwattanasakul N, Kosaka T, Hosoyama A, Suzuki Y, Rodrussamee N, Matsutani M, Murata M, Fujimoto N, Suprayogi,
 Tsuchikane K, Limtong S, Fujita N, Yamada M.
 Genetic basis of the highly efficient yeast Kluyveromyces marxianus: complete genome sequence and transcriptome analyses.
 Biotechnology for Biofuels. 8:47 DOI 10.1186/s13068-015-0227-x, 2015
6. Suzuki A, Matsushima K, Makinoshima H, Sugano S, Kohno T, Tsuchihara K, Suzuki Y.
 Single-cell analysis of lung adenocarcinoma cell lines reveals diverse expression patterns of individual cells invoked by a molecular
 target drug treatment.
 Genome Biology 2015 April 3, 16 :66
7. Kobayashi N, Suzuki Y, Schoenfeld LW, Muller CA, Nieduszynski C, Wolfe KH, Tanaka TU.
 Discovery of an unconventional centromere in budding yeast redefines evolution of point centromeres.
 Current Biology. 2015 Aug 3;25(15):2026-33. doi: 10.1016/j.cub.2015.06.023. Epub 2015 Jul 9.
8. Mino T, Murakawa Y, Fukao A, Vandenbon A, Wessels H, Ori D, Uehata T, Tartey S, Akira S, Suzuki Y,Vinuesa C, Ohler U,
 Standley D, Markus La M, Fujiwara T, Takeuchi O.
 Regnase-1 and Roquin Regulate a Common Element in Inflammatory mRNAs by Spatiotemporally Distinct Mechanisms.
 Cell2015 May 21;161(5):1058-73. doi: 10.1016/j.cell.2015.04.029.
9. Shigemizu D, Aiba T, Nakagawa H, Ozaki K, Miya F, Satake W, Toda T, Miyamoto Y, Fujimoto A, Suzuki Y, Kubo M, Tsunoda T,
 Shimizu W, Tanaka T.
 Exome analyses of long QT syndrome reveal candidate pathogenic mutations in calmodulin-interacting genes.
 PLoS One. Jul 1;10(7):e0130329. doi: 10.1371/journal.pone.0130329. eCollection 2015.
10. Handa Y, Nishide H, Takeda N, Suzuki Y, Kawaguchi M, Saito K.
 RNA-seq Transcriptional Profiling of an Arbuscular Mycorrhiza Provides Insights into Regulated and Coordinated Gene Expression in
 Lotus japonicus and Rhizophagus irregularis.
 Plant and Cell Physiology 2015; doi: 10.1093/pcp/pcv071
11. Sutani T, Sakata T, Nakato R, Masuda K, Ishibashi M, Yamashita D, Suzuki Y, Hirano T, Bando M, Shirahige K.
 Condensin targets and reduces unwound DNA structure associated with transcription in mitotic chromosome condensation.
 Nature communications. 2015 Jul 23;6:7815. doi: 10.1038/ncomms8815.
12. Mwangi S, Attardo G, Suzuki Y, Aksoy S,Christoffels A.
 TSS seq based core promoter architecture in blood feeding Glossina morsitans morsitans vector of Trypanosomiasis.
 BMC Genomics. 2015 Sept 22, 16:722 doi:10.1186/s12864-015-1921-6
13. Kubota S, Iwasaki T, Hanada K, Nagano A, Fujiyama A, Toyoda A, Sugano S, Suzuki Y, Hikosaka K, Ito M, Morinaga S.
 A Genome Scan for Genes Underlying Microgeographic-Scale Local Adaptation in a Wild Arabidopsis Species.
 PLOS Genetics. DOI: 10.1371/journal.pgen.1005361. 14 July 2015.
14. Fukui T, Kawamoto M, Shoji K, Kiuchi T, Sugano S, Shimada T, Suzuki Y, Katsuma S.
 The Endosymbiotic Bacterium Wolbachia Selectively Kills Male Hosts by Targeting the Masculinizing Gene.
 PLOS Pathogens. 2015 Jul 14;11(7):e1005048. doi: 10.1371/journal.ppat.1005048. eCollection 2015.
15. Bahnassawy L, Perumal TM, Gonzalez-Cano L, Hillje AL, Taher L Makalowski W, Suzuki Y, Fuellen G, Sol AD, Schwamborn JC.
 TRIM32 modulates pluripotency entry and exit by directly regulating Oct4 stability.
 Scientific Reports. 2015 Aug 26;5:13456. doi: 10.1038/srep13456.
16. Hirano M, Satake W, Ihara K, Tsuge I, Kondo S, Saida K, Betsui H, Okubo K, Sakamoto H, Ueno S, Ikuno Y, Ishihara R, Iwahashi H,
 Ohishi M, Mano T, Yamashita T, Suzuki Y, Nakamura Y, Kusunoki S, Toda T.
 The first nationwide survey and genetic analyses of Bardet-Biedl syndrome.
 PLOS One. 2015 Sep 1;10(9):e0136317. doi: 10.1371/journal.pone.0136317. eCollection 2015.
17. Kubo N, Toh H, Shirane K, Shirakawa T, Kobayashi H, Sato T, Sone H, Sato Y, Tomizawa S, Tsurusaki Y, Shibata H, Saitsu H,
 Suzuki Y, Matsumoto N, Suyama M, Kono T, Ohbo K, Sasaki H.
 DNA Methylation and Gene Expression Dynamics during Spermatogonial Stem Cell Differentiation in the Early Postnatal Mouse Testis.
 BMC Genomics. 2015 Aug 20;16(1):624. doi: 10.1186/s12864-015-1833-5.
18. Mizutani R, Imamachi N, Suzuki Y, Yoshida H, Tochigi N, Oonishi T, Suzuki Y, Akimitsu N.
 Oncofetal protein IGF2BP3 facilitates the activity of proto-oncogene protein EIF4E through the destabilization of EIF4E-BP2 mRNA.
 Oncogene. 2015 Nov 2. doi: 10.1038/onc.2015.410.

2014

英文論文
1. Yasuoka Y, Suzuki Y, Takahashi S, Someya H, Sudou N, Haramoto Y, Cho KW, Asashima M, Sugano S, Taira M.
 Occupancy of tissue-specific cis-regulatory modules by Otx2 and TLE/Groucho for embryonic head specification.
 Nat Commun. 2014 Jul 9;5:4322. doi: 10.1038/ncomms5322.
2. Yamagishi J, Natori A, Tolba ME, Mongan AE, Sugimoto C, Katayama T, Kawashima S, Makalowski W, Maeda R, Eshita Y, Tuda J,
 Suzuki Y.
 Interactive Transcriptome Analysis of Malaria Patients and Infecting Plasmodium falciparum.
 Genome Res. 2014 Sep;24(9):1433-44. doi: 10.1101/gr.158980.113. Epub 2014 Aug 4.
3. Kiuchi T, Koga H, Kawamoto M, Shoji K, Sakai H, Arai Y, Ishihara G, Kawaoka S, Sugano S, Shimada T, Suzuki Y, Suzuki MG,
 Katsuma S.
 A single female-specific piRNA is the primary determiner of sex in the silkworm.
 Nature. 2014 May 29;509(7502):633-6. doi: 10.1038/nature13315. Epub 2014 May 14.
4. International Glossina Genome Initiative. 
  Genome sequence of the tsetse fly (Glossina morsitans): vector of African trypanosomiasis.
 Science. 2014 Apr 25;344(6182):380-6. doi: 10.1126/science.1249656.
5. Ariizumi T, Kishimoto S, Kakami R, Maoka T, Hirakawa H, Suzuki Y, Ozeki Y, Shirasawa K, Bernillon S, Okabe Y, Moing A, Asamizu E,
 Rothan C, Ohmiya A, Ezura H. Corresponding Author: Tohru Ariizumi Handling Editor: Kazuki Saito.
 Identification of the Carotenoid Modifying Gene PALE YELLOW PETAL 1 as an Essential Factor in Xanthophyll Esterification and Yellow
 Flower Pigmentation in Tomato (Solanum lycopersicum).
 Plant J. 2014 Aug;79(3):453-65. doi: 10.1111/tpj.12570. Epub 2014 Jul 2.
6. Runtuwene LR, Konishi E, Yamanaka A, Makino Y, Suzuki Y, Takasaki T, Kurane I, Kobayashi T, Eshita Y.
 Dengue transmission model by means of viremic adult immuno-competent mouse.
 Parasites & Vectors 2014, 7:143
7. Seki M, Masaki H, Arauchi T, Nakauchi H, Sugano S, Suzuki Y.
 A comparison of the rest complex binding patterns in embryonic stem cells and epiblast stem cells.
 PLoS One. 2014 Apr 21;9(4):e95374. doi: 10.1371/journal.pone.0095374. eCollection 2014.
8. Negishi M, Wongpalee SP, Sarkar S, Park J, Lee KY, Shibata Y, Reon BJ, Abounader R, Suzuki Y, Sugano S, Dutta A.
 A New lncRNA, APTR, Associates with and Represses the CDKN1A/p21 Promoter by Recruiting Polycomb Proteins.
 PLoS One. 2014 Apr 18;9(4):e95216. doi: 10.1371/journal.pone.0095216. eCollection 2014.
9. Kanda S, Tanigawa S, Ohmori T, Taguchi A, Kudo K, Suzuki Y, Sato Y, Hino S, Sander M, Perantoni AO, Sugano S, Nakao M,
 Nishinakamura R.
 Sall1 Maintains Nephron Progenitors and Nascent Nephrons by Acting as Both an Activator and a Repressor.
 J Am Soc Nephrol. 2014 Apr 17.
10. Furuta Y, Namba-Fukuyo H, Shibata TF, Nishiyama T, Shigenobu S, Suzuki Y, Sugano S, Hasebe M, Kobayashi I.
 Methylome diversification through changes in DNA methyltransferase sequence specificity.
 PLoS Genet. 2014 Apr 10;10(4):e1004272. doi: 10.1371/journal.pgen.1004272. eCollection 2014 Apr.
11. Yoshitane H, Ozaki H, Terajima H, Du NH, Suzuki Y, Fujimori T, Kosaka N, Shimba S, Sugano S, Takagi T, Iwasaki W, Fukada Y.
 CLOCK-controlled polyphonic regulation of circadian rhythms through canonical and noncanonical E-boxes.
 Mol Cell Biol. 2014 May;34(10):1776-87. doi: 10.1128/MCB.01465-13. Epub 2014 Mar 3.
12. Firouzi S, Lopez Y, Suzuki Y, Nakai K, Sugano S, Yamochi T, Watanabe T.
 Development and validation of a new high-throughput method to investigate the clonality of HTLV-1-infected cells based on provirus
 integration sites.
 Genome Medicine. 2014 June
13. Imamura K, Imamachi N, Akizuki G, Kumakura M, Kawaguchi A, Nagata K,Kato A, Kawaguchi Y, Sato H, Yoneda M, Kai C,
 Yada T, Suzuki Y, Yamada T, Ozawa T, Kaneki K, Inoue T, Kobayashi M, Kodama T, Wada Y, Sekimizu K, Akimitsu N.
 Long Noncoding RNA NEAT1-Dependent SFPQ Relocation from Promoter Region to Paraspeckle Mediates IL8 Expression upon Immune
 Stimuli.
 Mol Cell. 2014 Feb 6;53(3):393-406. doi: 10.1016/j.molcel.2014.01.009.
14. Matsumoto K, Suzuki A, Wakaguri H, Sugano S, Suzuki Y.
 Construction of mate pair full-length cDNAs libraries and characterization of transcriptional start sites and termination sites.
 Nucleic Acids Res. 2014 Dec 1;42(16):e125. doi: 10.1093/nar/gku600. Epub 2014 Jul 17.
15. SEQC/MAQC-III Consortium.
  A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control
 Consortium.
 Nat Biotech, pp903 ? 914. Sept, 2014. doi:10.1038/nbt.2957
16. Igarashi H, Suzuki Y, Kwee IL, Nakada T.
 Water influx into cerebrospinal fluid is significantly reduced in senile plaque bearing transgenic mice, supporting beta-amyloid
 clearance hypothesis of Alzheimer's disease.
 Neurol Res. 2014 Dec;36(12):1094-8. doi: 10.1179/1743132814Y.0000000434. Epub 2014 Aug 1.
17. Shoji K, Hara K, Kawamoto M, Kiuchi T, Kawaoka S, Sugano S, Shimada T, Suzuki Y, Katsuma S.
 Silkworm HP1a transcriptionally enhances highly expressed euchromatic genes via association with their transcription start sites.
 Nucleic Acids Res. 2015 Feb 1;42(18):11462-71. doi: 10.1093/nar/gku862. Epub 2014 Sep 18.
18. Kuroyanagi H, Takei S, Suzuki Y.
 Comprehensive analysis of mutually exclusive alternative splicing in C. elegans.
 Worm. 2014 Mar 31;3:e28459. doi: 10.4161/worm.28459. eCollection 2014.
19. Yamagishi J, Wakaguri H, Yokoyama N, Yamashita R, Suzuki Y, Xuan X, Igarashi I.
 The Babesia bovis gene and promoter model: an update from full-length EST analysis.
 BMC Genomics. 2014 Aug 13;15:678. doi: 10.1186/1471-2164-15-678.
20. Zhang H, Kudoh J, Shimizu A, Tan E, Suzuki Y, Saito K, Hirose Y, Watabe S, Asakawa S, Kinoshita S, Okano H.
 Dramatic improvement in genome assembly achieved using doubled-haploid genomes.
 Scientific Reports 2014 Oct 27
21. Suzuki A, Wakaguri H, Yamashita R, Kawano S, Tsuchihara K, Sugano S, Suzuki Y, Nakai K.
 DBTSS as an integrative platform for transcriptome, epigenome and genome sequence variation data.
 Nucleic Acids Research 2014; doi: 10.1093/nar/gku1080
22. Shoji K, Hara K, Kawamoto M, Kiuchi T, Kawaoka S, Sugano S, Shimada T, Suzuki Y, Katsuma S.
 Silkworm HP1a transcriptionally enhances highly expressed euchromatic genes via association with their transcription start sites.
 Nucleic Acids Res. 2015;42(18):11462-71. doi: 10.1093/nar/gku862. Epub 2014 Sep 18.
23. Suzuki A, Makinoshima H, Wakaguri H, Esumi H, Sugano S, Kohno T, Tsuchihara K, Suzuki Y.
 Aberrant transcriptional regulations in cancers: genome, transcriptome and epigenome analysis of lung adenocarcinoma cell lines.
 Nucleic Acids Res. 2014 Nov 6. pii: gku885.
24. Vandenbon A, Teraguchi S, Takeuchi O, Suzuki Y, Standley D.
 Dynamics of enhancers in myeloid antigen presenting cells upon LPS stimulation.
 BMC Genomics 2014, 15(Suppl 10):S4 doi:10.1186/1471-2164-15-S10-S4
25. Maekawa S, Suzuki A, Sugano S, Suzuki Y.
 RNA sequencing: from sample preparation to analysis.
 Methods Mol. Biol. 2014. 1164, 51?65.

2013

英文論文
1. Kuroyanagi H, Watanabe Y, Suzuki Y and Hagiwara M.
 Position-dependent and neuron-specific splicing regulation by the CELF family RNA-binding protein UNC-75 in Caenorhabditis elegans.  NAR. 41(7), 4015-25, 2013
2. Hashimoto S1, Ogoshi K, Sasaki A, Abe J, Qu W, Nakatani Y, Ahsan B, Oshima K, Shand FH, Ametani A, Suzuki Y, Kaneko S, Wada T,
 Hattori M, Sugano S, Morishita S, Matsushima K.
 Coordinated changes in DNA methylation in antigen-specific memory CD4 T cells. Journal of Immunology. 190(8),4076-91
 J Immunol. 2013 Apr 15;190(8):4076-91. doi: 10.4049/jimmunol.1202267. Epub 2013 Mar 18.
3. Suzuki A, Mimaki S, Yamane Y, Kawase A, Matsushima K, Suzuki M, Goto K, Sugano S, Esumi H, Suzuki Y, Tsuchihara K.
 Identification and Characterization of Cancer Mutations in Japanese Lung Adenocarcinoma without Sequencing of Normal Tissue
 Counterparts.
 PLoS One. 8(9),e73484, 2013
4. Kanematsu S, Tanimoto K, Suzuki Y, Sugano S.
 Screening for possible miRNA-mRNA associations in a colon cancer cell line.
 Gene. S0378-1119(13)01021-4, 2013
5. 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. Malt1-induced cleavage of regnase-1 in CD4(+) helper T cells regulates immune
 activation.
 Cell. 153(5):1036-49. 2013.
6. Sato Y, Yoshizato T, Shiraishi Y, Maekawa S, Okuno Y, Kamura T, Shimamura T, Sato-Otsubo A, Nagae G, Suzuki H, Nagata Y,
 Yoshida K, Kon A, Suzuki Y, Chiba K, Tanaka H, Niida A, Fujimoto A, Tsunoda T, Morikawa T, Maeda D, Kume H, Sugano S,
 Fukayama M, Aburatani H, Sanada M, Miyano S, Homma Y, Ogawa S.
 Integrated molecular analysis of clear-cell renal cell carcinoma.
 Nat Genet. 45:860-867, 2013.
7. Imamachi N, Tani H, Mizutani R, Imamura K,Irie T, Suzuki Y, Akimitsu N.
 BRIC-seq: a genome-wide approach for determining RNA stability in mammalian cells.
 Methods. 2014 May 1;67(1):55-63. doi: 10.1016/j.ymeth.2013.07.014. Epub 2013 Jul 17.
8. Hata K, Takashima R, Amano K, Ono K, Nakanishi M, Yoshida M, Wakabayashi M, Matsuda A, Maeda Y, Suzuki Y, Sugano S,
 Whitson RH, Nishimura R, Yoneda T.
 Arid5b facilitates chondrogenesis by recruiting the histone demethylase Phf2 to Sox9-regulated genes.
 Nat Commun. 2013;4:2850. doi: 10.1038/ncomms3850.
9. Muto T, Sashida G, Oshima M, Wendt GR, Mochizuki-Kashio M, Nagata Y, Sanada M, Miyagi S, Saraya A, Kamio A, Nagae G,
 Nakaseko C, Yokote K, Shimoda K, Koseki H, Suzuki Y, Sugano S, Aburatani H, Ogawa S, Iwama A.
 Concurrent loss of Ezh2 and Tet2 cooperates in the pathogenesis of myelodysplastic disorders.
 J Exp Med. 2013 Nov 18;210(12):2627-39. doi: 10.1084/jem.20131144. Epub 2013 Nov 11.
10. Nishikawa H, Iga M, Yamaguchi J, Saito K, Kataoka H, Suzuki Y, Sugano S, Fujiwara H.
 Molecular basis of wing coloration in a Batesian mimic butterfly, Papilio polytes.
 Sci Rep. 2013 Nov 11;3:3184. doi: 10.1038/srep03184.
11. Tolba ME, Kobayashi S, Imada M, Suzuki Y, Sugano S.
 Giardia lamblia transcriptome analysis using TSS-Seq and RNA-Seq.
 PLoS One. 2013 Oct 7;8(10):e76184. doi: 10.1371/journal.pone.0076184. eCollection 2013.
12.Watanabe T, Oyama T, Asada M, Harada D, Ito Y, Inagawa M, Suzuki Y, Sugano S, Katsube K, Karsenty G, Komori T, Kitagawa M,
 Asahara H.
 MAML1 enhances the transcriptional activity of Runx2 and plays a role in bone development.
 PLoS Genet. 9(1):e1003132. 2013.
13. Nikaido M, Noguchi H, Nishihara H, Toyoda A, Suzuki Y, Kajitani R, Suzuki H, Okuno M, Aibara M, Ngatunga BP, Mzighani SI,
 Kalombo HW, Masengi KW, Tuda J, Nogami S, Maeda R, Iwata M, Abe Y, Fujimura K, Okabe M, Amano T, Maeno A, Shiroishi T, Itoh T,
 Sugano S, Kohara Y, Fujiyama A, Okada N.
 Coelacanth genomes reveal signatures for evolutionary transition from water to land.
 Genome Res. 23:1740-1748, 2013.
14. Hosokawa H, Tanaka T, Suzuki Y, Iwamura C, Ohkubo S, Endoh K, Kato M, Endo Y, Onodera A, Tumes DJ, Kanai A, Sugano S,
 Nakayama T.
 Functionally distinct Gata3/Chd4 complexes coordinately establish T helper 2 (Th2) cell identity.
 Proc Natl Acad Sci U S A. 110(12):4691-6. 2013.
15. Tumes DJ, Onodera A, Suzuki A, Shinoda K, Endo Y, Iwamura C, Hosokawa H, Koseki H, Tokoyoda K, Suzuki Y, Motohashi S,
 Nakayama T.
 The polycomb protein Ezh2 regulates differentiation and plasticity of CD4(+) T helper type 1 and type 2 cells.
 Immunity. 39(5):819-32. 2013.

2012

英文論文
1. Kawaoka S, Mitsutake H, Kiuchi T, Kobayashi M, Yoshikawa M, Suzuki Y, Sugano S, Shimada T, Kobayashi J, Tomari Y, Katsuma S.
 A role for transcription from a piRNA cluster in de novo piRNA production.
 RNA. 18:265-273, 2012
2. Tani H, Mizutani R, Salam KA, Tano K, Ijiri K, Wakamatsu A, Isogai T, Suzuki Y, Akimitsu N.
 Genome-wide determination of RNA stability reveals hundreds of short-lived non-coding transcripts in mammals.
 Genome Res. 2012 Feb 27 [Epub ahead of print].
3. Amiruddin N, Lee XW, Blake DP, Suzuki Y, Tay YL, Lim LS, Tomley FM, Watanabe J, Sugimoto C, Wan KL.
 Characterisation of full-length cDNA sequences provides insights into the Eimeria tenella transcriptome.
 BMC Genomics. 2012 Jan 13;13(1):21
4. Kobayashi H, Sakurai T, Imai M, Takahashi N, Fukuda A, Yayoi O, Sato S, Nakabayashi K, Hata K, Sotomaru Y, Suzuki Y, Kono T.
 Contribution of intragenic DNA methylation in mouse gametic DNA methylomes to establish oocyte-specific heritable marks.
 PLoS Genet. 2012 Jan;8(1):e1002440.
5. Yamashita R, Sugano S, Suzuki Y, Nakai K.
 DBTSS: DataBase of Transcriptional Start Sites progress report in 2012.
 Nucleic Acids Res. 40: D150-D154, 2012.
6. Tani H, Imamachi N, Salam KA, Mizutani R, Ijiri K, Irie T, Yada T, Suzuki Y, Akimitsu N.
 Identification of hundreds of novel UPF1 target transcripts by direct determination of whole transcriptome stability.
 RNA Biol. 2012 Nov;9(11):1370-9. doi: 10.4161/rna.22360. Epub 2012 Oct 12.
7. Mizutani R, Wakamatsu A, Tanaka N, Yoshida H, Tochigi N, Suzuki Y, Oonishi T, Tani H, Tano K, Ijiri K, Isogai T, Akimitsu N.
 Identification and characterization of novel genotoxic stress-inducible nuclear long noncoding RNAs in mammalian cells.
 PLoS One. 2012;7(4):e34949. doi: 10.1371/journal.pone.0034949. Epub 2012 Apr 19.
8. Qu W, Hashimoto S, Shimada A, Nakatani Y, Ichikawa K, Saito TL, Ogoshi K, Matsushima K, Suzuki Y, Sugano S, Takeda H,
 Morishita S.
 Genome-wide genetic variations are highly correlated with proximal DNA methylation patterns.
 Genome Res. 22:1419-1425, 2012.
9. Kawaoka S, Hara K, Shoji K, Kobayashi M, Shimada T, Sugano S, Tomari Y, Suzuki Y, Katsuma S.
 The comprehensive epigenome map of piRNA clusters.
 Nucleic Acids Res. 2013 Feb 1;41(3):1581-90. doi: 10.1093/nar/gks1275. 2012.
10. Deardorff MA, Bando M, Nakato R, Watrin E, Itoh T, Minamino M, Saitoh K, Komata M, Katou Y, Clark D, Cole KE, De Baere E,
 Decroos C, Di Donato N, Ernst S, Francey LJ, Gyftodimou Y, Hirashima K, Hullings M, Ishikawa Y, Jaulin C, Kaur M, Kiyono T,
 Lombardi PM, Magnaghi-Jaulin L, Mortier GR, Nozaki N, Petersen MB, Seimiya H, Siu VM, Suzuki Y, Takagaki K, Wilde JJ, Willems PJ,
 Prigent C, Gillessen-Kaesbach G, Christianson DW, Kaiser FJ, Jackson LG, Hirota T, Krantz ID, Shirahige K.
 HDAC8 mutations in Cornelia de Lange syndrome affect the cohesin acetylation cycle.
 Nature. 489(7415):313-7. 2012.

招待講演
1. Yutaka Suzuki “Integrative Transcriptome Analysis” FIRST symposium, March, 2012, Osaka, Japan.

2011

英文論文
1. Van Heeringen SJ, Akhtar W, Jacobi UG, Akkers RC, Suzuki Y, Veenstra GJ.
 Nucleotide composition-linked divergence of vertebrate core promoter architecture.
 Genome Res. 21: 410-421, 2011.
2. Yang X, Xu S; HUGO Pan-Asian SNP Consortium; Indian Genome Variation Consortium.
 Identification of close relatives in the HUGO Pan-Asian SNP database.
 PLoS One. 2011;6(12):e29502.
3. Renfree MB, Papenfuss AT, Deakin JE, Lindsay J, Heider T, Belov K, Rens W, Waters PD, Pharo EA, Shaw G, Wong ES, Lefevre CM,
 Nicholas KR, Kuroki Y, Wakefield MJ, Zenger KR, Wang C, Ferguson-Smith M, Nicholas FW, Hickford D, Yu H, Short KR, Siddle HV,
 Frankenberg SR, Chew KY, Menzies BR, Stringer JM, Suzuki S, Hore TA, Delbridge ML, Patel H, Mohammadi A, Schneider NY, Hu Y,
 O'Hara W, Al Nadaf S, Wu C, Feng ZP, Cocks BG, Wang J, Flicek P, Searle SM, Fairley S, Beal K, Herrero J, Carone DM, Suzuki Y,
 Sugano S, Toyoda A, Sakaki Y, Kondo S, Nishida Y, Tatsumoto S, Mandiou I, Hsu A, McColl KA, Lansdell B, Weinstock G, Kuczek E,
 McGrath A, Wilson P, Men A, Hazar-Rethinam M, Hall A, Davis J, Wood D, Williams S, Sundaravadanam Y, Muzny DM, Jhangiani SN,
 Lewis LR, Morgan MB, Okwuonu GO, Ruiz SJ, Santibanez J, Nazareth L, Cree A, Fowler G, Kovar CL, Dinh HH, Joshi V, Jing C, Lara F,
 Thornton R, Chen L, Deng J, Liu Y, Shen JY, Song XZ, Edson J, Troon C, Thomas D, Stephens A, Yapa L, Levchenko T, Gibbs RA,
 Cooper DW, Speed TP, Fujiyama A, M Graves JA, O'Neill RJ, Pask AJ, Forrest SM, Worley KC.
 Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and
 development.
 Genome Biol. 2011 Dec 21;12(12):414. [Epub ahead of print]
4. Okamura K, Yamashita R, Takimoto N, Nishitsuji K, Suzuki Y, Kusakabe TG, Nakai K.
 Profiling ascidian promoters as the primordial type of vertebrate promoter.
 BMC Genomics. 2011 Nov 30;12 Suppl 3:S7.
5. Yada T, Yoshida K, Morita M, Taniguchi T, Irie T, Suzuki Y.
 Linear regression models predicting strength of transcriptional activity of promoters.
 Genome Inform. 25: 53-60, 2011.
6. Yamagishi J, Watanabe J, Goo YK, Masatani T, Suzuki Y, Xuan X.
 Characterization of Toxoplasma gondii 5' UTR with Encyclopedic TSS Information.
 J Parasitol. 2011 Oct 1 [Epub ahead of print].
7. Avasthi TS, Devi SH, Taylor TD, Kumar N, Baddam R, Kondo S, Suzuki Y, Lamouliatte H, Megraud F, Ahmed N.
 Genomes of two chronological isolates (Helicobacter pylori 2017 and 2018) of the West African Helicobacter pylori strain 908 obtained
 from a single patient.
 J Bacteriol. 193: 3385-3386, 2011.
8. Renfree MB, Papenfuss AT, Deakin JE, Lindsay J, Heider T, Belov K, Rens W, Waters PD, Pharo EA, Shaw G, Wong ES, Lefevre CM,
 Nicholas KR, Kuroki Y, Wakefield MJ, Zenger KR, Wang C, Ferguson-Smith M, Nicholas FW, Hickford D, Yu H, Short KR, Siddle HV,
 Frankenberg SR, Chew KY, Menzies BR, Stringer JM, Suzuki S, Hore TA, Delbridge ML, Mohammadi A, Schneider NY, Hu Y, O'Hara W,
 Al Nadaf S, Wu C, Feng ZP, Cocks BG, Wang J, Flicek P, Searle SM, Fairley S, Beal K, Herrero J, Carone DM, Suzuki Y, Sugano S,
 Toyoda A, Sakaki Y, Kondo S, Nishida Y, Tatsumoto S, Mandiou I, Hsu A, McColl KA, Lansdell B, Weinstock G, Kuczek E, McGrath A,
 Wilson P, Men A, Hazar-Rethinam M, Hall A, Davis J, Wood D, Williams S, Sundaravadanam Y, Muzny DM, Jhangiani SN, Lewis LR,
 Morgan MB, Okwuonu GO, Ruiz SJ, Santibanez J, Nazareth L, Cree A, Fowler G, Kovar CL, Dinh HH, Joshi V, Jing C, Lara F,
 Thornton R, Chen L, Deng J, Liu Y, Shen JY, Song XZ, Edson J, Troon C, Thomas D, Stephens A, Yapa L, Levchenko T, Gibbs RA,
 Cooper DW, Speed TP, Fujiyama A, M Graves JA, O'Neill RJ, Pask AJ, Forrest SM, Worley KC.
 Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and
 development.
 Genome Biol. 2011 Aug 29;12(8):R81. [Epub ahead of print]
9. Yoshida K, Sanada M, Shiraishi Y, Nowak D, Nagata Y, Yamamoto R, Sato Y, Sato-Otsubo A, Kon A, Nagasaki M, Chalkidis G,
 Suzuki Y, Shiosaka M, Kawahata R, Yamaguchi T, Otsu M, Obara N, Sakata-Yanagimoto M, Ishiyama K, Mori H, Nolte F,
 Hofmann WK, Miyawaki S, Sugano S, Haferlach C, Koeffler HP, Shih LY, Haferlach T, Chiba S, Nakauchi H, Miyano S, Ogawa S.
 Frequent pathway mutations of splicing machinery in myelodysplasia.
 Nature. 478:64-69, 2011.
10. Kanai A, Suzuki K, Tanimoto K, Mizushima-Sugano J, Suzuki Y, Sugano S.
 Characterization of STAT6 Target Genes in Human B Cells and Lung Epithelial Cells.
 DNA Res. 2011 Aug 9. [Epub ahead of print]
11. Kawaoka S, Arai Y, Kadota K, Suzuki Y, Hara K, Sugano S, Shimizu K, Tomari Y, Shimada T, Katsuma S.
 Zygotic amplification of secondary piRNAs during silkworm embryogenesis.
 RNA. 2011 Jul;17(7):1401-7. Epub 2011 May 31.
12. Horiuchi S, Onodera A, Hosokawa H, Watanabe Y, Tanaka T, Sugano S, Suzuki Y, Nakayama T.
 Genome-wide analysis reveals unique regulation of transcription of Th2-specific genes by GATA3.
 J Immunol. 2011 Jun 1;186(11):6378-89. Epub 2011 May 2.
13. Irie T, Park SJ, Yamashita R, Seki M, Yada T, Sugano S, Nakai K, Suzuki Y.
 Predicting promoter activities of primary human DNA sequences.
 Nucleic Acids Res. 2011 Jun 1;39(11):e75. Epub 2011 Apr 12.
14. Kim RN, Kim DW, Choi SH, Chae SH, Nam SH, Kim DW, Kim A, Kang A, Park KH, Lee YS, Hirai M, Suzuki Y, Sugano S,
 Hashimoto K, Kim DS, Park HS.
 Major chimpanzee-specific structural changes in sperm development-associated genes.
 Funct Integr Genomics. 2011 Apr 12. [Epub ahead of print]
15. Hatin WI, Nur-Shafawati AR, Zahri MK, Xu S, Jin L, Tan SG, Rizman-Idid M, Zilfalil BA; HUGO Pan-Asian SNP Consortium.
 Population genetic structure of peninsular Malaysia Malay sub-ethnic groups.
 PLoS One. 2011 Apr 5;6(4):e18312.
16. Takeuchi Y, Fujino Y, Fukushima K, Watanabe M, Nakagawa T, Ohno K, Sasaki N, Yamagishi J, Wakaguri H, Sugano S, Kawano S,
 Fujisaki K, Sugimoto C, Watanabe J, Suzuki Y, Kimata I, Xuan X.
 Construction and analysis of full-length cDNA library of Cryptosporidium parvum.
 Parasitol Int. 2011 Mar 21. [Epub ahead of print]
17. Yamashita R, Sathira NP, Kanai A,Tanimoto K, Arauchi T, Tanaka Y, Hashimoto SI, Sugano S, Nakai K, Suzuki Y.
 Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis.
 Genome Res. 21:775-789 2011.
18. Irie T, Park SJ, Yamashita R, Seki M, Yada T, Sugano S, Nakai K, Suzuki Y.
 Predicting promoter activities of primary human DNA sequences.
 Nucleic Acids Res. 2011 Jun 1;39(11):e75. 2011.
19. Tuda J, Mongan AE, Tolba ME, Imada M, Yamagishi J, Xuan X, Wakaguri H, Sugano S, Sugimoto C, Suzuki Y.
 Full-parasites: database of full-length cDNAs of apicomplexa parasites, 2010 update.
 Nucleic Acids Res. 39: D625-D631,2011.
20. Tani H, Mizutani R, Salam KA, Tano K, Ijiri K, Wakamatsu A, Isogai T, Suzuki Y, Akimitsu N.
 Genome-wide determination of RNA stability reveals hundreds of short-lived non-coding transcripts in mammals.
 Genome Res. 22(5):947-56. 2012.

和文総説
1. 鈴木穣、次世代シークエンスデータの解析の実際~エキソーム、ChIP-Seq、RNA-Seqを中心にして、 実験医学増刊号使えるデータベース・ウェブツール、351-356(2011)。
2. 鈴木穣、トランスクリプトーム解析、細胞工学30, 817-822 (2011)。

招待講演
1. Yutaka Suzuki “Transcriptome Analysis of Apicomplexa Parasites” Symposium of Parasite Genomics, February, 2011, Sapporo, Japan.
2. Yutaka Suzuki “Transcriptome Analysis” Poznan Summer School of Bioinformatics, July, 2011, Poznan, Poland.

2010

英文論文
1. Tuda J, Mongan AE, Tolba ME, Imada M, Yamagishi J, Xuan X, Wakaguri H, Sugano S, Sugimoto C, Suzuki Y.
 Full-parasites: database of full-length cDNAs of apicomplexa parasites, 2010 update.
 Nucleic Acids Res. 39: D625-D631,2011. 2010 Nov 4. [Epub ahead of print]
2. Sathirapongsasuti JF, Sathira N, Suzuki Y, Huttenhower C, Sugano S.
 Ultraconserved cDNA segments in the human transcriptome exhibit resistance to folding and implicate function in translation and
 alternative splicing.
 Nucleic Acids Res. 39: 1967-1979,2011. 2010 Nov 9. [Epub ahead of print]
3. Onodera A, Yamashita M, Endo Y, Kuwahara M, Tofukuji S, Hosokawa H, Kanai A, Suzuki Y, Nakayama T.
 STAT6-mediated displacement of polycomb by trithorax complex establishes long-term maintenance of GATA3 expression in T helper
 type 2 cells.
 J Exp Med. 2010 Oct 25;207(11):2493-506. Epub 2010 Oct 18.
4. Tanimoto K, Tsuchihara K, Kanai A, Arauchi T, Esumi H, Suzuki Y, Sugano S.
 Genome-wide identification and annotation of HIF-1α binding sites in two cell lines using massively parallel sequencing.
 Hugo J. 4:35-48, 2010.
5. Hatanaka F, Matsubara C, Myung J, Yoritaka T, Kamimura N, Tsutsumi S, Kanai A, Suzuki Y, Sassone-Corsi P, Aburatani H,
 Sugano S, Takumi T.
 Genome-wide profiling of the core clock protein BMAL1 targets reveals strict relationship with metabolism.
 Mol Cell Biol. 30:5636-5648, 2010. 2010 Oct 11. [Epub ahead of print]
6. Terashima M, Ishimura A, Yoshida M, Suzuki Y, Sugano S, Suzuki T.
 The tumor suppressor Rb and its related Rbl2 genes are regulated by Utx histone demethylase.
 Biochem Biophys Res Commun.399:238-244, 2010. Epub 2010 Jul 30.
7. Mangone M, Manoharan AP, Thierry-Mieg D, Thierry-Mieg J, Han T, Mackowiak S, Mis E, Zegar C, Gutwein MR, Khivansara V, Attie O,
 Chen K, Salehi-Ashtiani K, Vidal M, Harkins TT, Bouffard P, Suzuki Y, Sugano S, Kohara Y, Rajewsky N, Piano F, Gunsalus KC, Kim JK.
 The Landscape of C. elegans 3'UTRs.
 Science. 329:432-435, 2010.
8. Yamagishi J, Wakaguri H, Ueno A, Goo YK, Tolba M, Igarashi M, Nishikawa Y, Sugimoto C, Sugano S, Suzuki Y, Watanabe J,
 Xuan X.
 High-Resolution Characterization of Toxoplasma gondii Transcriptome with a Massive Parallel Sequencing Method.
 DNA Res. 17:233-243, 2010.
9. Kuroshu RM, Watanabe J, Sugano S, Morishita S, Suzuki Y, Kasahara M.
 Cost-effective sequencing of full-length cDNA clones powered by a de novo-reference hybrid assembly.
 PLoS One. 5:e10517 2010.
10. Sathira N, Yamashita R, Tanimoto K,Kanai A, Arauchi T, Kanematsu S, Nakai K, Suzuki Y, Sugano S.
 Characterization of Transcription Start Sites of Putative Non-coding RNAs by Multifaceted Use of Massively Paralleled Sequencer.
 DNA Res. 17:169-182, 2010.
11. Suzuki S, Tanaka T, Poyurovsky MV, Nagano H, Mayama T, Ohkubo S, Lokshin M, Hosokawa H, Nakayama T, Suzuki Y, Sugano S,
 Sato E, Nagao T, Yokote K, Tatsuno I, Prives C.
 Phosphate-activated glutaminase (GLS2), a p53-inducible regulator of glutamine metabolism and reactive oxygen species.
 Proc Natl Acad Sci U S A. 107:7461-7466, 2010.
12. Hodo Y, Hashimoto SI, Honda M, Yamashita T, Suzuki Y, Sugano S, Kaneko S, Matsushima K.
 Comprehensive gene expression analysis of 5'-end of mRNA identified novel intronic transcripts associated with hepatocellular
 carcinoma.
 Genomics. 95:217-223, 2010.
13. Takeda J, Suzuki Y, Sakate R, Sato Y, Gojobori T, Imanishi T, Sugano S.
 H-DBAS: human-transcriptome database for alternative splicing: update 2010.
 Nucleic Acids Res. 38:D86-90, 2010.
14. Yamashita R, Wakaguri H, Sugano S, Suzuki Y, Nakai K.
 DBTSS provides a tissue specific dynamic view of Transcription Start Sites.
 Nucleic Acids Res. 38:D98-104 2010.

和文総説
1. 鈴木穣、菅野純夫 完全長cDNAライブラリーの作成、新遺伝子工学ハンドブック 42-49 (2010)

招待講演
1. Yutaka Suzuki “Transcriptome Analysis” Poznan Summer School of Bioinformatics, August, 2010, Poznan, Poland.
2. Yutaka Suzuki ”Human Transcriptome Analysis using Illumina GA”, Illumina Users’ Meeting, April, 2010, Phuket, Thailand.

2009

英文論文
1. HUGO Pan-Asian SNP Consortium, Abdulla MA, Ahmed I, Assawamakin A, Bhak J, Brahmachari SK, Calacal GC, Chaurasia A,
 Chen CH, Chen J, Chen YT, Chu J, Cutiongco-de la Paz EM, De Ungria MC, Delfin FC, Edo J, Fuchareon S, Ghang H, Gojobori T, Han J,
 Ho SF, Hoh BP, Huang W, Inoko H, Jha P, Jinam TA, Jin L, Jung J, Kangwanpong D, Kampuansai J, Kennedy GC, Khurana P, Kim HL,
 Kim K, Kim S, Kim WY, Kimm K, Kimura R, Koike T, Kulawonganunchai S, Kumar V, Lai PS, Lee JY, Lee S, Liu ET, Majumder PP,
 Mandapati KK, Marzuki S, Mitchell W, Mukerji M, Naritomi K, Ngamphiw C, Niikawa N, Nishida N, Oh B, Oh S, Ohashi J, Oka A, Ong R,
 Padilla CD, Palittapongarnpim P, Perdigon HB, Phipps ME, Png E, Sakaki Y, Salvador JM, Sandraling Y, Scaria V, Seielstad M, Sidek MR,
 Sinha A, Srikummool M, Sudoyo H, Sugano S, Suryadi H, Suzuki Y, Tabbada KA, Tan A, Tokunaga K, Tongsima S, Villamor LP,
 Wang E, Wang Y, Wang H, Wu JY, Xiao H, Xu S, Yang JO, Shugart YY, Yoo HS, Yuan W, Zhao G, Zilfalil BA; Indian Genome Variation
 Consortium.
 Mapping human genetic diversity in Asia.
 Science. 326:1541-1545, 2009.
2. Osada N, Hirata M, Tanuma R, Suzuki Y, Sugano S, Terao K, Kusuda J, Kameoka Y, Hashimoto K, Takahashi I.
 Collection of Macaca fascicularis cDNAs derived from bone marrow, kidney, liver, pancreas, spleen, and thymus.
 BMC Res Notes. 2009 Sep 29;2(1):199. [Epub ahead of print]
3. Kimura K, Suzuki Y, Sugano S, Koike A.
 Computation of Rank and Select Functions on Hierarchical Binary String and Its Application to Genome Mapping Problems for
 Short-Read DNA Sequences.
 J Comput Biol. 2009 Sep 22. [Epub ahead of print]
4. Ishimura A, Terashima M, Kimura H, Akagi K, Suzuki Y, Sugano S, Suzuki T.
 Jmjd2c histone demethylase enhances the expression of Mdm2 oncogene.
 Biochem Biophys Res Commun. 389:366-371, 2009.
5. Wakaguri H, Suzuki Y, Sasaki M, Sugano S, Watanabe J.
 Inconsistencies of genome annotations in apicomplexan parasites revealed by 5'-end-one-pass and full-length sequences of
 oligo-capped cDNAs.
 BMC Genomics. 2009 Jul 15;10(1): 312.
6. Kawaoka S, Hayashi N, Suzuki Y, Abe H, Sugano S, Tomari Y, Shimada T, Katsuma S.
 The Bombyx ovary-derived cell line endogenously expresses PIWI/PIWI-interacting RNA complexes.
 RNA 15: 1258-1264, 2009.
7. Tsuchihara K, Suzuki Y, Wakaguri H, Irie T, Tanimoto K, Hashimoto SI, Matsushima K, Mizushima-Sugano J, Yamashita R,
 Nakai K, Bentley D, Esumi H, Sugano S.
 Massive transcriptional start site analysis of human genes in hypoxia cells.
 Nucleic Acids Res. 37: 2249-2263, 2009. 2009 Feb 22. [Epub ahead of print]
8. Hashimoto S, Qu W, Ahsan B, Ogoshi K, Sasaki A, Nakatani Y, Lee Y, Ogawa M, Ametani A, Suzuki Y, Sugano S, Lee CC, Nutter RC,
 Morishita S, Matsushima K.
 High-resolution analysis of the 5'-end transcriptome using a next generation DNA sequencer.
 PLoS ONE. 2009;4(1):e4108. Epub 2009 Jan 1.
9. Sasaki S, Mello CC, Shimada A, Nakatani Y, Hashimoto SI, Ogawa M, Matsushima K, Gu SG, Kasahara M, Ahsan B, Sasaki A, Saito T,
 Suzuki Y, Sugano S, Kohara Y, Takeda H, Fire A, Morishita S.
 Chromatin-Associated Periodicity in Genetic Variation Downstream of Transcriptional Start Sites.
 Science. 32:401-404, 2009.

和文総説
1. 鈴木穣、土原一哉, 次世代高速シークエンサーによるRNA解析, 蛋白質核酸酵54, 1256-1263 (2009)。

2008

英文論文
1. International Silkworm Genome Consortium.
 The genome of a lepidopteran model insect, the silkworm Bombyx mori.
 Insect Biochem Mol Biol. 38:1036-1045, 2008.
2. Lee YS, Choi SL, Kim TH, Lee JA, Kim HK, Kim H, Jang DJ, Lee JJ, Lee S, Sin GS, Kim CB, Suzuki Y, Sugano S, Kubo T, Moroz LL,
 Kandel ER, Bhak J, Kaang BK.
 Transcriptome analysis and identification of regulators for long-term plasticity in Aplysia kurodai.
 Proc Natl Acad Sci U S A. 105:18602-18607, 2008
3. Wakaguri H, Suzuki Y, Katayama T, Kawashima S, Kibukawa E, Hiranuka K, Sasaki M, Sugano S, Watanabe J.
 Full-Malaria/Parasites and Full-Arthropods: databases of full-length cDNAs of parasites and arthropods, update 2009.
 Nucleic Acids Res. 37:D520-D525, 2009 Nov 4. 2008[Epub ahead of print]
4. Takeda J, Suzuki Y, Sakate R, Sato Y, Seki M, Irie T, Takeuchi N, Ueda T, Nakao M, Sugano S, Gojobori T, Imanishi T.
 Low conservation and species-specific evolution of alternative splicing in humans and mice: comparative genomics analysis using
 well-annotated full-length cDNAs.
 Nucleic Acids Res. 36: 6386-6395, 2008.
5. Yoshikawa F, Sato Y, Tohyama K, Akagi T, Hashikawa T, Nagakura-Takagi Y, Sekine Y, Morita N, Baba H, Suzuki Y, Sugano S,
 Sato A, Furuichi T.
 Opalin, a transmembrane sialylglycoprotein located in the CNS myelin paranodal loop membrane.
 J Biol Chem. 283:20830-20840, 2008 May 19. [Epub ahead of print]
6. Yamashita R, Suzuki Y, Takeuchi N, Wakaguri H, Ueda T, Sugano S, Nakai K.
 Comprehensive detection of human terminal oligo-pyrimidine (TOP) genes and analysis of their characteristics.
 Nucleic Acids Res. 36: 3707-3715, 2008.
7. Nakao N, Ono H, Yamamura T, Anraku T, Takagi T, Higashi K, Yasuo S, Katou Y, Kageyama S, Uno Y, Kasukawa T, Iigo M, Sharp PJ,
 Iwasawa A, Suzuki Y, Sugano S, Niimi T, Mizutani M, Namikawa T, Ebihara S, Ueda HR, Yoshimura T.
 Thyrotrophin in the pars tuberalis triggers photoperiodic response.
 Nature. 452:317-322, 2008.
8. Davuluri RV, Suzuki Y, Sugano S, Plass C, Huang TH.
 The functional consequences of alternative promoter use in mammalian genomes.
 Trends Genet. 24:167-177, 2008.
9. Osada N, Hashimoto K, Kameoka Y, Hirata M, Tanuma R, Uno Y, Inoue I, Hida M, Suzuki Y, Sugano S, Terao K, Kusuda J,
 Takahashi I.
 Large-scale analysis of Macaca fascicularis transcripts and inference of genetic divergence between M. fascicularis and M. mulatta.
 BMC Genomics. 2008 Feb 24;9:90.
10. Uno Y, Suzuki Y, Wakaguri H, Sakamoto Y, Sano H, Osada N, Hashimoto K, Sugano S, Inoue I.
 Expressed sequence tags from cynomolgus monkey (Macaca fascicularis) liver: A systematic identification of drug-metabolizing
 enzymes.
 FEBS Lett. 582:351-358, 2008.
11. 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.
 The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts.
 Nucleic Acids Res. 36: D793-D799, 2008.
12. Rensing SA, Lang D, Zimmer AD, Terry A, Salamov A, Shapiro H, Nishiyama T, Perroud PF, Lindquist EA, Kamisugi Y, Tanahashi T,
 Sakakibara K, Fujita T, Oishi K, Shin-I T, Kuroki Y, Toyoda A, Suzuki Y, Hashimoto S, Yamaguchi K, Sugano S, Kohara Y, Fujiyama A,
 Anterola A, Aoki S, Ashton N, Barbazuk WB, Barker E, Bennetzen JL, Blankenship R, Cho SH, Dutcher SK, Estelle M, Fawcett JA,
 Gundlach H, Hanada K, Heyl A, Hicks KA, Hughes J, Lohr M, Mayer K, Melkozernov A, Murata T, Nelson DR, Pils B, Prigge M, Reiss B,
 Renner T, Rombauts S, Rushton PJ, Sanderfoot A, Schween G, Shiu SH, Stueber K, Theodoulou FL, Tu H, Van de Peer Y, Verrier PJ,
 Waters E, Wood A, Yang L, Cove D, Cuming AC, Hasebe M, Lucas S, Mishler BD, Reski R, Grigoriev IV, Quatrano RS, Boore JL.
 The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants.
 Science. 319: 64-69, 2008.
13. Wakaguri H, Yamashita R, Suzuki Y, Sugano S, Nakai K.
 DBTSS: database of transcription start sites, progress report 2008.
 Nucleic Acids Res. 36: D97-D100, 2008

2007

英文論文
1. Okabe T, Ohmori Y, Tanigami A, Hishigaki H, Suzuki Y, Sugano S, Kawaguchi A, Nakaya H, Wakitani S. Detection of gene expression
 in synovium of patients with osteoarthritis using a random sequencing method.
 Acta Orthop. 78: 687-692, 2007.
2. Yamamoto YY, Ichida H, Abe T, Suzuki Y, Sugano S, Obokata J. Differentiation of core promoter architecture between plants and
 mammals revealed by LDSS analysis.
 Nucleic Acids Res. 35: 6219-6226, 2007.
3. Muramatsu S, Wakabayashi M, Ohno T, Amano K, Ooishi R, Sugahara T, Shiojiri S, Tashiro K,Suzuki Y, Nishimura R, Kuhara S,  
 Sugano S, Yoneda T, Matsuda A. Functional gene screening system identified TRPV4 as a regulator of chondrogenic differentiation.
 J Biol Chem. 282: 32158-32167, 2007.
4. Tsuritani K, Irie T, Yamashita R, Sakakibara Y, Wakaguri H, Kanai A, Mizushima-Sugano J, Sugano S, Nakai K, Suzuki Y.
 Distinct class of putative "non-conserved" promoters in humans: Comparative studies of alternative promoters of human and mouse
 genes.
 Genome Res. 17: 1005-1014, 2007.
5. Sakakibara Y, Irie T, Suzuki Y, Yamashita R, Wakaguri H, Kanai A, Chiba J, Takagi T, Mizushima-Sugano J, Hashimoto SI,  
 Nakai K, Sugano S.
 Intrinsic Promoter Activities of Primary DNA Sequences in the Human Genome.
 DNA Res. 14: 71-77, 2007.
6. Watanabe J, Wakaguri H, Sasaki M, Suzuki Y, Sugano S.
 Comparasite: a database for comparative study of transcriptomes of parasites defined by full-length cDNAs.
 Nucleic Acids Res.35: D431-438, 2007. Epub 2006 Dec 6.
7. Takeda J, Suzuki Y, Nakao M, Kuroda T, Sugano S, Gojobori T, Imanishi T.
 H-DBAS: alternative splicing database of completely sequenced and manually annotated full-length cDNAs based on H-Invitational.
 Nucleic Acids Res. 35: D104-D109, 2007. Epub 2006 Nov 27.
8. Oyama M, Kozuka-Hata H, Suzuki Y, Semba K, Yamamoto T, Sugano S.
 Diversity of translation start sites may define increased complexity of the human short ORFeome.
 Mol Cell Proteomics. 2007 Feb 21; [Epub ahead of print]
9. Funaguma S, Hashimoto S, Suzuki Y, Omuro N, Sugano S, Mita K, Katsuma S, Shimada T.
 SAGE analysis of early oogenesis in the silkworm, Bombyx mori.
 Insect Biochem Mol Biol.37:147-154, 2007. Epub 2006 Nov 15.

2006

英文論文
1. Cheong J, Yamada Y, Yamashita R, Irie T, Kanai A, Wakaguri H, Nakai K, Ito T, Saito I, Sugano S, Suzuki Y.
 Diverse DNA methylation statuses at alternative promoters of human genes in various tissues.
 DNA Res. 2006;13:155-167. Epub 2006 Oct 26.
2. Takeda J, Suzuki Y, Nakao M, Barrero RA, Koyanagi KO, Jin L, Motono C, Hata H, Isogai T, Nagai K, Otsuki T, Kuryshev V,
 Shionyu M, Yura K, Go M, Thierry-Mieg J, Thierry-Mieg D, Wiemann S, Nomura N, Sugano S, Gojobori T, Imanishi T.
 Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely
 sequenced and manually annotated full-length cDNAs.
 Nucleic Acids Res. 2006;34:3917-3928. Epub 2006 Aug 12.
3. Khan A, Bohme U, Kelly KA, Adlem E, Brooks K, Simmonds M, Mungall K, Quail MA, Arrowsmith C, Chillingworth T, Churcher C,
 Harris D, Collins M, Fosker N, Fraser A, Hance Z, Jagels K, Moule S, Murphy L, O'Neil S, Rajandream MA, Saunders D, Seeger K,
 Whitehead S, Mayr T, Xuan X, Watanabe J, Suzuki Y, Wakaguri H, Sugano S, Sugimoto C, Paulsen I, Mackey AJ, Roos DS, Hall N,
 Berriman M, Barrell B, Sibley LD, Ajioka JW.
 Common inheritance of chromosome Ia associated with clonal expansion of Toxoplasma gondii.
 Genome Res. 2006 16:1119-1125. Epub 2006 Aug 10.
4. Suzuki Y, Sugano S.
 Transcriptome analyses of human genes and applications for proteome analyses.
 Curr Protein Pept Sci. 7:147-163, 2006.
5. Tsai CC, Huang KW, Chen HF, Zhan BW, Lai YH, Lee FH, Lin CY, Ho YC, Chao YW, Su YC, Jane SW, Chen YC, Hsu CI, Li PH, Hsu HC,
 Suzuki Y, Sugano S, Lin JY.
 Gene expression analysis of human hepatocellular carcinoma by using full-length cDNA library.
 J Biomed Sci. 2006 13:241-249.
6. Yamashita R, Suzuki Y, Wakaguri H, Tsuritani K, Nakai K, Sugano S.
 DBTSS: DataBase of Human Transcription Start Sites, progress report 2006.
 Nucleic Acids Res.2006 34:D86-89.
7. Kimura K, Wakamatsu A, Suzuki Y, Ota T, Nishikawa T, Yamashita R, Yamamoto J, Sekine M, Tsuritani K, Wakaguri H, Ishii S,
 Sugiyama T, Saito K, Isono Y, Irie R, Kushida N, Yoneyama T, Otsuka R, Kanda K, Yokoi T, Kondo H, Wagatsuma M, Murakawa K,
 Ishida S, Ishibashi T, Takahashi-Fujii A, Tanase T, Nagai K, Kikuchi H, Nakai K, Isogai T, Sugano S.
 Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human
 genes.
 Genome Res. 2006 16:55-65. Epub 2005 Dec 12.

2005

英文論文
1. Tahira T, Baba S, Higasa K, Kukita Y, Suzuki Y, Sugano S, Hayashi K.
 dbQSNP: A database of SNPs in human promoter regions with allele frequency information determined by single-strand conformation
 polymorphism-based methods.
 Hum Mutat. 26:69-77, 2005
2. Osada N, Hirata M, Tanuma R, Kusuda J, Hida M, Suzuki Y, Sugano S, Gojobori T, Shen CK, Wu CI, Hashimoto K.
 Substitution Rate and Structural Divergence of 5'UTR Evolution: Comparative Analysis Between Human and Cynomolgus Monkey
 cDNAs.
 Mol Biol Evol. 22: 1976-1982,2005. 2005 Jun 8; [Epub ahead of print]
3. Yamashita R, Suzuki Y, Sugano S, Nakai K. Genome-wide analysis reveals strong correlation between CpG islands with nearby
 transcription start sites of genes and their tissue specificity.
 Gene. 350:129-136, 2005.
4. Otsuki T, Ota T, Nishikawa T, Hayashi K, Suzuki Y, Yamamoto J, Wakamatsu A, Hayashi H, Matsuzaki O, Muramatsu S, Tsuchiya Y,
 Harada T, Suzuki Y, Sugano S, Matsuda A, Nishida E.
 Centaurin-alpha 1 is a PI3K dependent activator of ERK1/2 map kinases.
 J Biol Chem. 2005 Nov 14; [Epub ahead of print]

和文総説
1. 鈴木穣、山下理宇、菅野純夫、中井謙太, DBTSS転写開始点データベース, 実験医学増刊号データベース手とり足とり活用法, 65-71 (2005)

2004

英文論文
1. Gerhard DS, Wagner L, Feingold EA, Shenmen CM, Grouse LH, Schuler G, Klein SL, Old S, Rasooly R, Good P, Guyer M, Peck AM,
 Derge JG, Lipman D, Collins FS, Jang W, Sherry S, Feolo M, Misquitta L, Lee E, Rotmistrovsky K, Greenhut SF, Schaefer CF, Buetow K,
 Bonner TI, Haussler D, Kent J, Kiekhaus M, Furey T, Brent M, Prange C, Schreiber K, Shapiro N, Bhat NK, Hopkins RF, Hsie F, Driscoll T,
 Soares MB, Casavant TL, Scheetz TE, Brown-stein MJ, Usdin TB, Toshiyuki S, Carninci P, Piao Y, Dudekula DB, Ko MS, Kawakami K,
 Suzuki Y, Sugano S, Gruber CE, Smith MR, Simmons B, Moore T, Waterman R, Johnson SL, Ruan Y, Wei CL, Mathavan S,
 Gunaratne PH, Wu J, Garcia AM, Hulyk SW, Fuh E, Yuan Y, Sneed A, Kowis C, Hodgson A, Muzny DM, McPherson J, Gibbs RA, Fahey J,
 Helton E, Ketteman M, Madan A, Rodrigues S, Sanchez A, Whiting M, Madari A, Young AC, Wetherby KD, Granite SJ, Kwong PN,
 Brinkley CP, Pearson RL, Bouffard GG, Blakesly RW, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM,
 Butterfield YS, Griffith M, Griffith OL, Krzywinski MI, Liao N, Morrin R, Palmquist D, Petrescu AS, Skalska U, Smailus DE, Stott JM,
 Schnerch A, Schein JE, Jones SJ, Holt RA, Baross A, Marra MA, Clifton S, Makowski KA, Bosak S, Malek J; MGC Project Team.
 The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).
 Genome Res. 14:2121-2127,2004.
2. Suzuki Y, Yamashita R, Shirota M, Sakakibara Y, Chiba J, Mizushima-Sugano J, Kel AE, Arakawa T, Carninci P, Kawai J,
 Hayashizaki Y, Takagi T, Nakai K, Sugano S.
 Large-scale collection and characterization of promoters of human and mouse genes.
 In Silico Biol. 4(3):0036 [Epub ahead of print] 2004
3. Bajic VB, Tan SL, Suzuki Y, Sugano S.
 Promoter prediction analysis on the whole human genome.
 Nat Biotechnol. 22: 1467-1473, 2004
4. Suzuki Y, Yamashita R, Shirota M, Sakakibara Y, Chiba J, Mizushima-Sugano J, Nakai K, Sugano S.
 Sequence comparison of human and mouse genes reveals a homologous block structure in the promoter regions.
 Genome Res. 14:1711-1718, 2004.
5. Niida A, Hiroko T, Kasai M, Furukawa Y, Nakamura Y, Suzuki Y, Sugano S, Akiyama T.
 DKK1, a negative regulator of Wnt signaling, is a target of the beta-catenin/TCF pathway.
 Oncogene. 23:8520-8526, 2004.
6. Oyama M, Itagaki C, Hata H, Suzuki Y, Izumi T, Natsume T, Isobe T, Sugano S.
 Analysis of small human proteins reveals the translation of upstream open reading frames of mRNAs.
 Genome Res. 10B: 2048-2052, 2004.
7. Yamada S, Ohira M, Horie H, Ando K, Takayasu H, Suzuki Y, Sugano S, Hirata T, Goto T, Matsunaga T, Hiyama E, Hayashi Y,
 Ando H, Suita S, Kaneko M, Sasaki F, Hashizume K, Ohnuma N, Nakagawara A.
 Expression profiling and differential screening between hepatoblastomas and the corresponding normal livers: identification of high
 expression of the PLK1 oncogene as a poor-prognostic indicator of hepatoblastomas.
 Oncogene. 2004 23:5901-5911.
8. Huang DY, Kuo YY, Lai JS, Suzuki Y, Sugano S, Chang ZF.
 GATA-1 and NF-Y cooperate to mediate erythroid-specific transcription of Gfi-1B gene.
 Nucleic Acids Res. 2004 32:3935-3946.
9. Hashimoto SI, Suzuki Y, Kasai Y, Morohoshi K, Yamada T, Sese J, Morishita S, Sugano S, Matsushima K.
 5'-end SAGE for the analysis of transcriptional start sites.
 Nat Biotechnol. 22: 1146-1149, 2004 Epub Aug 8
10. Yu L, Frith MC, Suzuki Y, Peterfreund RA, Gearan T, Sugano S, Schwarzschild MA, Weng Z, Fink JS, Chen JF.
 Characterization of genomic organization of the adenosine A2A receptor gene by molecular and bioinformatics analyses.
 Brain Res. 1000:156-173, 2004.
11. Imanishi T, Itoh T, Suzuki Y, O'Donovan C, Fukuchi S, Koyanagi KO, Barrero RA, Tamura T, Yamaguchi-Kabata Y, Tanino M, Yura K,
 Miyazaki S, Ikeo K, Homma K, Kasprzyk A, Nishikawa T, Hirakawa M, Thierry-Mieg J, Thierry-Mieg D, Ashurst J, Jia L, Nakao M,
 Thomas MA, Mulder N, Karavidopoulou Y, Jin L, Kim S, Yasuda T, Lenhard B, Eveno E, Suzuki Y, Yamasaki C, Takeda JI, Gough C,
 Hilton P, Fujii Y, Sakai H, Tanaka S, Amid C, Bellgard M, Bonaldo Md M, Bono H, Bromberg SK, Brookes AJ, Bruford E, Carninci P,
 Chelala C, Couillault C, Souza SJ, Debily MA, Devignes MD, Dubchak I, Endo T, Estreicher A, Eyras E, Fukami-Kobayashi K,
 R Gopinath G, Graudens E, Hahn Y, Han M, Han ZG, Hanada K, Hanaoka H, Harada E, Hashimoto K, Hinz U, Hirai M, Hishiki T,
 Hopkinson I, Imbeaud S, Inoko H, Kanapin A, Kaneko Y, Kasukawa T, Kelso J, Kersey P, Kikuno R, Kimura K, Korn B, Kuryshev V,
 Makalowska I, Makino T, Mano S, Mariage-Samson R, Mashima J, Matsuda H, Mewes HW, Minoshima S, Nagai K, Nagasaki H,
 Nagata N, Nigam R, Ogasawara O, Ohara O, Ohtsubo M, Okada N, Okido T, Oota S, Ota M, Ota T, Otsuki T, Piatier-Tonneau D,
 Poustka A, Ren SX, Saitou N, Sakai K, Sakamoto S, Sakate R, Schupp I, Servant F, Sherry S, Shiba R, Shimizu N, Shimoyama M,
 Simpson AJ, Soares B, Steward C, Suwa M, Suzuki M, Takahashi A, Tamiya G, Tanaka H, Taylor T, Terwilliger JD, Unneberg P,
 Veeramachaneni V, Watanabe S, Wilming L, Yasuda N, Yoo HS, Stodolsky M, Makalowski W, Go M, Nakai K, Takagi T, Kanehisa M,
 Sakaki Y, Quackenbush J, Okazaki Y, Hayashizaki Y, Hide W, Chakraborty R, Nishikawa K, Sugawara H, Tateno Y, Chen Z, Oishi M,
 Tonellato P, Apweiler R, Okubo K, Wagner L, Wiemann S, Strausberg RL, Isogai T, Auffray C, Nomura N, Gojobori T, Sugano S.
 Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones.
 PLoS Biol. 2004 Apr 20 [Epub ahead of print]
12. Matsuzaki M, Misumi O, Shin-I T, Maruyama S, Takahara M, Miyagishima SY, Mori T, Nishida K, Yagisawa F, Nishida K, Yoshida Y,
 Nishimura Y, Nakao S, Kobayashi T, Momoyama Y, Higashiyama T, Minoda A, Sano M, Nomoto H, Oishi K, Hayashi H, Ohta F,
 Nishizaka S, Haga S, Miura S, Morishita T, Kabeya Y, Terasawa K, Suzuki Y, Ishii Y, Asakawa S, Takano H, Ohta N, Kuroiwa H,
 Tanaka K, Shimizu N, Sugano S, Sato N, Nozaki H, Ogasawara N, Kohara Y, Kuroiwa T.
 Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D.
 Nature. 428: 653-657, 2004.
13. Ota T, Suzuki Y, Nishikawa T, Otsuki T, Sugiyama T, Irie R, Wakamatsu A, Hayashi K, Sato H, Nagai K, Kimura K, Makita H,
 Sekine M, Obayashi M, Nishi T, Shibahara T, Tanaka T, Ishii S, Yamamoto J, Saito K, Kawai Y, Isono Y, Nakamura Y, Nagahari K,
 Murakami K, Yasuda T, Iwayanagi T, Wagatsuma M, Shiratori A, Sudo H, Hosoiri T, Kaku Y, Kodaira H, Kondo H, Sugawara M,
 Takahashi M, Kanda K, Yokoi T, Furuya T, Kikkawa E, Omura Y, Abe K, Kamihara K, Katsuta N, Sato K, Tanikawa M, Yamazaki M,
 Ninomiya K, Ishibashi T, Yamashita H, Murakawa K, Fujimori K, Tanai H, Kimata M, Watanabe M, Hiraoka S, Chiba Y, Ishida S, Ono Y,
 Takiguchi S, Watanabe S, Yosida M, Hotuta T, Kusano J, Kanehori K, Takahashi-Fujii A, Hara H, Tanase TO, Nomura Y, Togiya S,
 Komai F, Hara R, Takeuchi K, Arita M, Imose N, Musashino K, Yuuki H, Oshima A, Sasaki N, Aotsuka S, Yoshikawa Y, Matsunawa H,
 Ichihara T, Shiohata N, Sano S, Moriya S, Momiyama H, Satoh N, Takami S, Terashima Y, Suzuki O, Nakagawa S, Senoh A,
 Mizoguchi H, Goto Y, Shimizu F, Wakebe H, Hishigaki H, Watanabe T, Sugiyama A, Takemoto M, Kawakami B, Yamazaki M,
 Watanabe K, Kumagai A, Itakura S, Fukuzumi Y, Fujimori Y, Komiyama M, Tashiro H, Tanigami A, Fujiwara T, Ono T, Yamada K, Fujii Y,
 Ozaki K, Hirao M, Ohmori Y, Kawabata A, Hikiji T, Kobatake N, Inagaki H, Ikema Y, Okamoto S, Okitani R, Kawakami T, Noguchi S,
 Itoh T, Shigeta K, Senba T, Matsumura K, Nakajima Y, Mizuno T, Morinaga M, Sasaki M, Togashi T, Oyama M, Hata H, Watanabe M,
 Komatsu T, Mizushima-Sugano J, Satoh T, Shirai Y, Takahashi Y, Nakagawa K, Okumura K, Nagase T, Nomura N, Kikuchi H, Masuho Y,
 Yamashita R, Nakai K, Yada T, Nakamura Y, Ohara O, Isogai T, Sugano S.
 Complete sequencing and characterization of 21,243 full-length human cDNAs.
 Nat Genet. 36:40-45, 2004.
14. Watanabe J., Sasaki M., Suzuki Y. and Sugano S.
 Full-malaria 2004: an enlarged database for comparative studies of full-length cDNAs of malaria parasites, Plasmodium species.
 Nucleic Acids Res. 32: D334-338, 2004.
15. Suzuki Y., Yamashita R., Sugano S. and Nakai K.
 DBTSS, DataBase of Transcriptional Start Sites: progress report 2004.
 Nucleic Acids Res. 32: D78-81, 2004.

2003

英文論文
1. Yamashita R, Suzuki Y, Nakai K, Sugano S.
 Small open reading frames in 5' untranslated regions of mRnas.
 C R Biol. 326:987-991, 2003.
2. Clark M. S., Edwards Y. J., Peterson D, Clifton S. W., Thompson A. J., Sasaki M., Suzuki Y., Kikuchi K., Watabe S., Kawakami K.,
  Sugano S., Elgar G., Johnson S. L.
 Fugu ESTs: new resources for transcription analysis and genome annotation.
 Genome Res 13: 2747-2753, 2003.
3. Ohira M, Morohashi A, Inuzuka H, Shishikura T, Kawamoto T, Kageyama H, Nakamura Y, Isogai E, Takayasu H, Sakiyama S,
 Suzuki Y, Sugano S, Goto T, Sato S, Nakagawara A
 Expression profiling and characterization of 4200 genes cloned from primary neuroblastomas: identification of 305 genes differentially
 expressed between favorable and unfavorable subsets.
 Oncogene. 22:5525-5536. 2003
4. Tsai CC, Chung YD, Lee HJ, Chang WH, Suzuki Y, Sugano S, Lin JY.
 Large-scale sequencing analysis of the full-length cDNA library of human hepatocellular carcinoma.
 J Biomed Sci 10: 636-643. 2003.
5. Ohira M, Morohashi A, Nakamura Y, Isogai E, Furuya K, Hamano S, Machida T, Aoyama M, Fukumura M, Miyazaki K, Suzuki Y,
 Sugano S, Hirato J, Nakagawara A.
 Neuroblastoma oligo-capping cDNA project: toward the understanding of the genesis and biology of neuroblastoma.
 Cancer Lett. 197: 63-8, 2003.
6. 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, 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, Kawai J, Carninci P,
 Adachi J, Aizawa K, Arakawa T, Fukuda S, Hara A, Hashidume 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;
 Rice Full-Length cDNA Consortium; National Institute of Agrobiological Sciences Rice Full-Length cDNA Project Team;
 Foundation of Advancement of International Science Genome Sequencing & Analysis Group; RIKEN. Collection, mapping, and
 annotation of over 28,000 cDNA clones from japonica rice.
 Science. 301: 376-379, 2003.
7. Shibui-Nihei A, Ohmori Y, Yoshida K, Imai J, Oosuga I, Iidaka M, Suzuki Y, Mizushima-Sugano J, Yoshitomo-Nakagawa K, Sugano S.
 The 5' terminal oligopyrimidine tract of human elongation factor 1A-1 gene functions as a transcriptional initiator and produces a
 variable number of Us at the transcriptional level. Gene. 311: 137-45, 2003.
8. Matsuda A, Suzuki Y, Honda G, Muramatsu S, Matsuzaki O, Nagano Y, Doi T, Shimotohno K, Harada T, Nishida E, Hayashi H,
 Sugano S.
 Large-scale identification and characterization of human genes that activate NF-kappaB and MAPK signaling pathways.
 Oncogene. 22: 3307-3318, 2003.
9. Suzuki Y, Sugano S.
 Construction of a full-length enriched and a 5'-end enriched cDNA library using the oligo-capping method.
 Methods Mol Biol. 221: 73-91, 2003.
10. Xie GX, Han X, Ito E, Yanagisawa Y, Maruyama K, Sugano S, Suzuki Y, Wang Y, Gabriel A, Stevens SK, Mitchell J, Sharma M,
 Palmer PP.
 Gene structure, dual-promoters and mRNA alternative splicing of the human and mouse regulator of G protein signaling GAIP/RGS19.
 J Mol Biol. 325: 721-732, 2003.

2002

英文論文
1. Komatsu T, Suzuki Y, Imai J, Sugano S, Hida M, Tanigami A, Muroi S, Yamada Y, Hanaoka K.
 Molecular cloning, mRNA expression and chromosomal localization of mouse angiotensin-converting enzyme-related carboxypeptidase
  (mACE2).
 DNA Seq. 13:217-220. 2002.
2. Shiroki K, Ohsawa C, Sugi N, Wakiyama M, Miura K, Watanabe M, Suzuki Y, Sugano S.
 Internal ribosome entry site-mediated translation of Smad5 in vivo: requirement for a nuclear event.
 Nucleic Acids Res 30: 2851-2861. . 2002
3. Takamatsu K, Maekawa K, Togashi T, Choi DK, Suzuki Y, Taylor TD, Toyoda A, Sugano S, Fujiyama A, Hattori M, Sakaki Y,
 Takeda T.
 Identification of two novel primate-specific genes in DSCR.
 DNA Res. 9: 89-97. 2002
4. Ueda R. H, Chen W, Adachi A, Wakamatsu H, Hayashi S, Takasugi T, Nagano M, Nakahama K, Suzuki Y, Sugano S, Iino M,
  Shigeyoshi Y, Hashimoto S.
 A Transcription Factor Response Element for Gene Expression During Circadian Night.
 Nature 418: 534-539, 2002.
5. Suzuki Y, Yamashita R, Nakai K, Sugano S.
 DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs.
 Nucleic Acids Res. 30: 328-331, 2002.
6. Osada N, Hida M, Kusuda J, Tanuma R, Hirata M, Hirai M, Terao K, Suzuki Y, Sugano S, Hashimoto K.
 Prediction of unidentified human genes on the basis of sequence similarity to novel cDNAs from cynomolgus monkey brain.
 Genome Biol. 3: RESEARCH0006, 2002.
7. Nishikawa T, Ota T, Kawai Y, Ishii S, Saito K, Yamamoto J, Wakamatsu A, Ozawa M, Suzuki Y, Sugano S, Isogai T.
 Database and analysis system for cDNA clones obtained from full-length enriched cDNA libraries.
 In Silico Biol. 2: 5-18, 2002.
8. Omori Y, Imai J, Suzuki Y, Watanabe S, Tanigami A, Sugano S.
 OASIS is a transcriptional activator of CREB/ATF family with a transmembrane domain.
 Biochem Biophys Res Commun. 293: 470-477, 2002.
9. Sugiyama T, Ishii S, Yamamoto J, Irie R, Saito K, Otuki T, Wakamatsu A, Suzuki Y, Hio Y, Ota T, Nishikawa T, Sugano S, Masuho Y,
 Isogai T.
 cDNA macroarray analysis of gene expression in synoviocytes stimulated with TNFalpha.
 FEBS Lett. 517: 121-128, 2002.
10. Shiroki K, Ohsawa C, Sugi N, Wakiyama M, Miura K, Watanabe M, Suzuki Y, Sugano S.
 Internal ribosome entry site-mediated translation of Smad5 in vivo: requirement for a nuclear event.
 Nucleic Acids Res. 30: 2851-2861 2002.
11. Watanabe J, Sasaki M, Suzuki Y, Sugano S.
 Analysis of transcriptomes of human malaria parasite Plasmodium falciparum using full-length enriched library: identification of novel
  genes and diverse transcription start sites of messenger RNAs.
 Gene. 2002 291: 105-113, 2002.

2001

英文論文
1. Nishikawa T, Ota T, Kawai Y, Ishii S, Saito K, Yamamoto JI, Wakamatsu A, Ozawa M, Suzuki Y, Sugano S, Isocal T.
 Comparison of sequences of cDNA clones obtained from oligo-capping cDNA libraries with those from unigene.
 DNA Res. 8: 255-262, 2001.
2. Hida, M., Suzuki, Y., Sugano, S.
 Full-length cDNA libraries: Reagents for functional studies of the nervous system.
 In Method in genomic neuroscience. Edited by Chen, H. R. and Moldin, S. O. (CRC press FL). Pp207-227, 2001.
3. Osada N, Hida M, Kususda J, Tanuma R, Iseki K, Hirata M, Suto Y, Hirai M, Terao K, Suzuki Y, Sugano S, Hashimoto K.
 Assignment of 118 novel cDNAs of cynomolgus monkey brain to human chromosomes.
 Gene. 275: 31-37, 2001.
4. Nishimoto M, Fukushima A, Miyagi S, Suzuki Y, Sugano S, Matsuda Y, Hori Ta, Muramatsu M, Okuda A.
 Structural analyses of the utf1 gene encoding a transcriptional coactivator expressed in pluripotent embryonic stem cells.
 Biochem Biophys Res Commun.285: 945-953, 2001.
5. Suzuki Y, Sugano S.
 Construction of full-length-enriched cDNA libraries. The oligo-capping method.
 Methods Mol Biol. 175: 143-153, 2001.
6. Suzuki Y, Taira H, Tsunoda T, Mizushima-Sugano J, Sese J, Hata H, Ota T, Isogai T, Tanaka T, Morishita S, Okubo K, Sakaki Y,
  Nakamura Y, Suyama A, Sugano S.
 Diverse transcriptional initiation revealed by fine, large-scale mapping of mRNA start sites.
 EMBO Rep. 2: 388-393, 2001.
7. Suzuki Y, Tsunoda T, Sese J, Taira H, Mizushima-Sugano J, Hata H, Ota T, Isogai T, Tanaka T, Nakamura Y, Suyama A, Sakaki Y,
  Morishita S, Okubo K, Sugano S.
 Identification and characterization of the potential promoter regions of 1031 kinds of human genes.
 Genome Res. 11: 677-684, 2001.
8. Omori Y, Imai J, Watanabe M, Komatsu T, Suzuki Y, Kataoka K, Watanabe S, Tanigami A, Sugano S.
 CREB-H: a novel mammalian transcription factor belonging to the CREB/ATF family and functioning via the box-B element with a
  liver-specific expression.
 Nucleic Acids Res. 29: 2154-2162, 2001.
9. Choi DK, Suzuki Y, Yoshimura S, Togashi T, Hida M, Taylor TD, Wang Y, Sugano S, Hattori M, Sakaki Y.
 Molecular cloning and characterization of a gene expressed in mouse developing tongue, mDscr5 gene, a homolog of human DSCR5
  (Down syndrome Critical Region gene 5).
 Mamm Genome. 12: 347-351, 2001.
10. Shibui, A., Ohmori, Y., Suzuki, Y., Sasaki, M., Nogami, S., Sugano, S., Watanabe, J.
 Effect of DNA vaccine in murine malaria using a full-length cDNA library.
 Res. Commun. Mol. Path. And Pharmacology.109: 147-157, 2001.
11. Yudate, H. T., Suwa, M., Irie, R., Matsui, H., Nishikawa, T., Nakamura, Y., Yamaguchi, D., Peng, Z. Z., Yamamoto, T., Nagai, K.,
  Hayashi, K., Otsuki, T., Sugiyama, T., Ota, T., Suzuki, Y., Sugano, S., Isogai, T., Masuho, Y.
 HUNT: launch of a full-length cDNA database from the helix research institute.
 Nucl. Acid Res. 29: 185-188, 2001.

2000

英文論文
1. Takasaki J., Kamohara M., Matsumoto M., Saito T., Sugimoto T., Ohishi T., Ishii H., Ota T., Nishikawa T., Kawai Y., Masuho Y.,
 Isogai T., Suzuki Y., Sugano S., Furuichi K.
 Related the molecular characterization and tissue distribution of the human cysteinyl leukotriene CysLT(2) receptor.
 Biochem Biophys Res Commun. 274: 316-322, 2000.
2. Campbell H. D., Kamei M., Claudianos C., Woollatt E., Sutherland G. R., Suzuki Y., Hida M., Sugano S., Young I. G.
 Human and mouse homologues of the drosophila melanogaster tweety (tty) gene: A novel gene family encoding predicted
 transmembrane proteins.
 Genomics. 68: 89-92, 2000.
3. Davuluri R. V., Suzuki Y., Sugano S., Zhang M. Q.
 CART classification of human 5' UTR sequences.
 Genome Res. 10: 1807-1816, 2000.
4. Ohira M., Shishikura T., Kawamoto T., Inuzuka H., Morohashi A., Takayasu H., Kageyama H., Takada N., Takahashi M., Sakiyama S.,
 Suzuki Y., Sugano S., Kuma H., Nozawa I., Nakagawara A.
 Hunting the subset-specific genes of neuroblastoma: Expression profiling and differential screening of the full-length-enriched
 oligo-capping cDNA libraries.
 Med Pediatr Oncol. 35: 547-549, 2000.
5. Kawamoto T., Shishikura T., Ohira M., Takayasu H., Morohashi A., Takada N., Takahashi M., Suzuki Y., Sugano S., Hori T.,
  Nakagawara A.
 Association between favorable neuroblastoma and high expression of the novel metalloproteinase gene, nbla3145/XCE, cloned by
 differential screening of the full-length-enriched oligo-capping neuroblastoma cDNA libraries.
 Med Pediatr Oncol. 35: 628-631, 2000.
6. Osada, N., Kusuda, J., Suzuki, Y., Sugano, S., Hashimoto, K.
 Sequnce analysis, gene expression, and chromosomal assignment of mouse Borg4 gene and its human orthologue.
 J. Hum. Genet. 45: 374-377, 2000
7. Suzuki, Y., Ishihara, D., Sasaki, M., Nakagawa, H., Hata, H., Tsunoda, T., Watanabe, M., Komatsu, T., Ota, T., Isogai, T.,
  Suyama, A., Sugano, S.
 Statistical analysis of 5' untranslated region of human mRNA using "Oligo-capping" cDNA libraries.
 Genomis 64: 286-297, 2000.

1999

英文論文
1. Xie, G. X., Ito, E., Maruyama, K., Suzuki, Y., Sugano, S., Sharma, M., Pietruck, C., Palmer, P. P.
 The promoter region of human prepro-nociceptin gene and its regulation by cyclic AMP and steroid hormones.
 Gene 238: 427-436, 1999
2. Kim, M., Tezuka, T., Suzuki, Y., Sugano, S., Hirai, M., Yamamoto, T.
 Molecular cloning and characterization of a novel Cbl-family gene, cbl-c.
 Gene 139: 145-154, 1999.
3. Seki, N., Hattori, A., Hayashi, A., Kozuma, S., Sasaki, M., Suzuki, Y., Sugano, S., Muramatsu, M., Saito, T.
 Cloning and expression profile of mouse and human genes, Rnf11/RNF11, a novel RING-H2 finger protein.
 Biochem. Biophy. Acta 1489: 421-427, 1999
4. Seki, N., Hayashi, A., Hattori, A., Kozuma, S., Sasaki, M., Suzuki, Y., Sugano, S., Muramatsu, M., Saito, T.
 cDNA cloning, tissue expression, and chromosomal assigment of a mouse gene, encoding a 127 kDa UV-damaged DNA binding protein  which is defective in XPE cells.
 DNA Res. 6: 319-322, 1999
5. Shibui, A., Tsunoda, T., Seki, N., Suzuki Y., Sugano, S., Sugane, K.
 Cloning, expression analysis and chromosomal localization of a novel butyrophilin like receptor.
 J. Hum. Genet. 44: 249-252, 1999
6. Shibui, A., Tsunoda, T., Seki, N., Suzuki Y., Sugane, K., Sugano, S.
 Isolation and chromosomal mapping of human homolog of intestinal Na+/PO4 cotransporter.
 J. Hum. Genet. 44: 190-192, 1999
7. Ito, E., Yanagisawa, Y., Iwahashi, Y., Suzuki, Y., Nagasaki, H., Akiyama, Y., Sugano, S., Yuasa, Y., Maruyama, K.
 A core promoter and a frequent single-nucleotide polymorphism of the mismatch repair gene hMLH1.
 Biochem. Biophys. Res. Comm.256: 488-494, 1999.
8. Ito, E., Iwahashi, Y., Yanagisawa, Y., Suzuki, Y., Sugano, S., Yuasa, Y., Maruyama, K.
 Two short sequences have positive effects on the human p27 kip1 gene transcription,
 Gene 228: 93-100, 1999.
9. Seki, N., Hattori, A., Sugano, S., Suzuki, Y., Nakagawara, A., Muramatsu, M., Hori, T., Saito, T.
 A novel human gene whose product shares significant homology with the bovine brain-specific protein p25 on chromosome 5p15.3.
 J. Hum. Genet. 44: 121-122, 1999.

1998

英文論文
1. Seki N, Hattori A, Sugano S, Suzuki Y, Nakagawara A, Ohhira M, Muramatsu M, Hori T, Saito T.
 Isolation, tissue expression, and chromosomal assignment of a novel human gene which encodes a protein with RING finger motif.
 J Hum Genet. 1998;43(4):272-4.
2. Seki N, Muramatsu M, Sugano S, Suzuki Y, Nakagawara A, Ohhira M, Hayashi A, Hori T, Saito T.
 Cloning, expression analysis, and chromosomal localization of HIP1R, an isolog of huntingtin interacting protein (HIP1).
 J Hum Genet. 1998;43(4):268-71.
3. Seki N, Sugano S, Suzuki Y, Nakagawara A, Ohira M, Muramatsu M, Saito T, Hori T. I
 solation, tissue expression, and chromosomal assignment of human RGS5, a novel G-protein signaling regulator gene.
 J Hum Genet. 1998;43(3):202-5.

1997

英文論文
1. Suzuki Y, Yoshitomo-Nakagawa K, Maruyama K, Suyama A, Sugano S.
 Construction and characterization of a full length-enriched and a 5'-end-enriched cDNA library.
 Gene. 1997 Oct 24;200(1-2):149-56.

1996

英文論文
1. Yu YS, Suzuki Y, Yoshitomo K, Muramatsu M, Yamaguchi N, Sugano S.
 The promoter structure of TGF-beta type II receptor revealed by "oligo-capping" method and deletion analysis.
 Biochem Biophys Res Commun.1996 Aug 5;225(1):302-6.