論文リスト

2015年
Genomewide identification of target genes of histone methyltransferase dG9a during Drosophila embryogenesis.
Shimaji K, Konishi T, Tanaka S, Yoshida H, Kato Y, Ohkawa Y, Sato T, Suyama M, Kimura H, Yamaguchi M.
Genes Cells , (in press)
DNA methylation and gene expression dynamics during spermatogonial stem cell differentiation in the early postnatal mouse testis.
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.
BMC Genomics 16, 624,2015.
Mutations in CDCA7 and HELLS cause immunodeficiency-centromeric instability-facial anomalies syndrome.
Thijssen PE, Ito Y, Grillo G, Wang J, Velasco G, Nitta H, Unoki M, Yoshihara M, Suyama M, Sun Y, Lemmers RJ, de Greef JC, Gennery A, Picco P, Kloeckener-Gruissem B, Güngör T, Reisli I, Picard C, Kebaili K, Roquelaure B, Iwai T, Kondo I, Kubota T, van Ostaijen-Ten Dam MM, van Tol MJ, Weemaes C, Francastel C, van der Maarel SM, Sasaki H.
Nat Commun. 6, 7870, 2015.
Sex determination. foxl3 is a germ cell-intrinsic factor involved in sperm-egg fate decision in medaka.
Nishimura T, Sato T, Yamamoto Y, Watakabe I, Ohkawa Y, Suyama M, Kobayashi S, Tanaka M.
Science 349, 328-331, 2015.
GenomeCons: a web server for manipulating multiple genome sequence alignments and their consensus sequences.
Sato T, Suyama M.
Bioinformatics 31, 1293-1295, 2015.
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2014年
Genome-wide analysis of DNA methylation dynamics during early human development.
Okae H, Chiba H, Hiura H, Hamada H, Sato A, Utsunomiya T, Kikuchi H, Yoshida H, Tanaka A, Suyama M, Arima T.
PLoS Genet. 10, e1004868, 2014.
Genome-wide analysis of histone modifications in human endometrial stromal cells.
Tamura I, Ohkawa Y, Sato T, Suyama M, Jozaki K, Okada M, Lee L, Maekawa R, Asada H, Sato S, Yamagata Y, Tamura H, Sugino N.
Mol Endocrinol. 28, 1656-1669, 2014.
Genome-wide profiling of 8-oxoguanine reveals its association with spatial positioning in nucleus.
Yoshihara M, Jiang L, Akatsuka S, Suyama M, Toyokuni S.
DNA Res. 21, 603-612, 2014.
Glycolytic genes are targets of the nuclear receptor Ad4BP/SF-1.
Baba T, Otake H, Sato T, Miyabayashi K, Shishido Y, Wang CY, Shima Y, Kimura H, Yagi M, Ishihara Y, Hino S, Ogawa H, Nakao M, Yamazaki T, Kang D, Ohkawa Y, Suyama M, Chung BC, Morohashi K.
Nat Commun. 5, 3634, 2014.
Characterization of common marmoset dysgerminoma like tumor induced by the lentiviral expression of reprogramming factors.
Yamaguchi S, Marumoto T, Nii T, Kawano H, Liao J, Nagai Y, Okada M, Takahashi A, Inoue H, Sasaki E, Fujii H, Okano S, Ebise H, Sato T, Suyama M, Okano H, Miura Y, Tani K.
Cancer Sci. 105, 402-408, 2014.
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2013年
The rs6983267 SNP Is Associated with MYC Transcription Efficiency, Which Promotes Progression and Worsens Prognosis of Colorectal Cancer.
Takatsuno Y, Mimori K, Yamamoto K, Sato T, Niida A, Inoue H, Imoto S, Kawano S, Yamaguchi R, Toh H, Iinuma H, Ishimaru S, Ishii H, Suzuki S, Tokudome S, Watanabe M, Tanaka JI, Kudo SE, Mochizuki H, Kusunoki M, Yamada K, Shimada Y, Moriya Y, Miyano S, Sugihara K, Mori M.
Ann. Surg. Oncol. 20, 1395-1402, 2013.
Microarray analysis reveals that high mobility group A1 is involved in colorectal cancer metastasis.
Takahashi Y, Sawada G, Sato T, Kurashige J, Mima K, Matsumura T, Uchi R, Ueo H, Ishibashi M, Takano Y, Akiyoshi S, Eguchi H, Sudo T, Sugimachi K, Tanaka J, Kudo SE, Doki Y, Mori M, Mimori K.
Oncol. Rep. 30, 1488-1496, 2013.
β-Catenin signaling regulates Foxa2 expression during endometrial hyperplasia formation.
Villacorte M, Suzuki K, Hirasawa A, Ohkawa Y, Suyama M, Maruyama T, Aoki D, Ogino Y, Miyagawa S, Terabayashi T, Tomooka Y, Nakagata N, Yamada G.
Oncogene. 32, 3477-3482, 2013.
C-type lectin MCL is an FcRγ-coupled receptor that mediates the adjuvanticity of mycobacterial cord factor.
Miyake Y, Toyonaga K, Mori D, Kakuta S, Hoshino Y, Oyamada A, Yamada H, Ono K, Suyama M, Iwakura Y, Yoshikai Y, Yamasaki S.
Immunity. 38, 1050-1062, 2013.
Mechanistic insights into mutually exclusive splicing in dynamin 1.
Suyama M.
Bioinformatics. 29, 2084-2087, 2013.
Plastin3 is a novel marker for circulating tumor cells undergoing the epithelial-mesenchymal transition and is associated with colorectal cancer prognosis.
Yokobori T, Iinuma H, Shimamura T, Imoto S, Sugimachi K, Ishii H, Iwatsuki M, Ota D, Ohkuma M, Iwaya T, Nishida N, Kogo R, Sudo T, Tanaka F, Shibata K, Toh H, Sato T, Barnard GF, T. Fukagawa T, Yamamoto S, Nakanishi H, Sasaki S, Miyano S, Watanabe T, Kuwano H, Mimori K, Pantel K, Mori M.
Cancer Res. 73, 2059-2069, 2013.
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2012年
Copy number loss of FBXW7 is related to gene expression and poor prognosis in esophageal squamous cell carcinoma.
Yokobori T, Mimori K, Iwatsuki M, Ishii H, Tanaka F, Sato T, Toh H, Sudo T, Iwaya T, Tanaka Y, Onoyama I, Kuwano H, Nakayama KI, Mori M.
Int. J. Onco. 41, 253-259, 2012.
Increased risk for CRC in diabetic patients with the nonrisk allele of SNPs at 8q24.
Ishimaru S, Mimori K, Yamamoto K, Inoue H, Imoto S, Kawano S, Yamaguchi R, Sato T, Toh H, Iinuma H, Maeda T, Ishii H, Suzuki S,Tokudome S, Watanabe M, Tanaka J, Kudo SE, Sugihara K, Hase K, Mochizuki H, Kusunoki M, Yamada K, Shimada Y, Moriya Y, Barnard GF, Miyano S, Mori M.
Ann. Surg. Oncol. 19, 2853-2858, 2012.
2011年
A polymorphism of the POLG2 gene is genetically associated with the invasiveness of urinary bladder cancer in Japanese males.
Ratanajaraya C, Nishiyama H, Takahashi M, Kawaguchi T, Saito R, Mikami Y, Suyama M, Lathrop M, Yamada R, Ogawa O, Matsuda F.
J. Hum. Genet. 56, 572-576, 2011.
2010年
A network of conserved co-occurring motifs for the regulation of alternative splicing.
Suyama M, Harrington ED, Vinokourova S, von Knebel Doeberitz M, Ohara O, Bork P.
Nucleic Acids Res. 38, 7916-7926, 2010.
この論文は、Nucleic Acid Researchのエディターによりトップ5%の論文に選ばれ、紹介記事付きで掲載されました。
2009年
Transcriptome complexity in a genome-reduced bacterium.
Güell M, van Noort V, Yus E, Chen WH, Leigh-Bell J, Michalodimitrakis K, Yamada T, Arumugam M, Doerks T, Kühner S, Rode M, Suyama M, Schmidt S, Gavin AC, Bork P, Serrano L.
Science 326, 1268-1271, 2009.
Functional and comparative genomics analyses of pmp22 in medaka fish.
Itou J, Suyama M, Imamura Y, Deguchi T, Fujimori K, Yuba S, Kawarabayasi Y, Kawasaki T.
BMC Neurosci. 10, 60, 2009.
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2008年
Selective maintenance of Drosophila tandemly arranged arranged duplicated genes during evolution.
Quijano C, Tomancak P, Lopez-Marti J, Suyama M, Bork P, Milan M, Torrents D, Manzanares M.
Genome Biol. 9, R176, 2008.
Non-random retention of protein-coding overlapping genes in Metazoa.
Soldà G, Suyama M, Pelucchi P, Boi S, Guffanti A, Rizzi E, Bork P, Tenchini ML, Ciccarelli FD.
BMC Genomics 9, 174, 2008.
2006年
Identification and analysis of genes and pseudogenes within duplicated regions in the human and mouse Genomes.
Suyama M, Harrington E, Bork P, Torrents D.
PLoS Comput. Biol. 2, e76, 2006.
PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments.
Suyama M, Torrents D, Bork P.
Nucleic Acids Res. 34, W609-W612, 2006.
この論文は、同義置換、非同義置換率を計るのに必要とされるコドンアライメントを作成するためのプログラム開発についてのものです。このプログラムにより、置換率を容易に計算することが可能となり、多くのユーザーに使用されています。被引用回数はすでに300回を超えています。
Molecular cloning and characterization of an enzyme hydrolyzing p-nitrophenyl α-D-glucoside from Bacillus stearothermophilus SA0301.
Kobayashi A, Tonozuka T, Sato K, Suyama M, Sasaki J, Nyamdawaa B, Sakaguchi M, Sakano Y.
Biosci. Biotechnol. Biochem. 70, 495-499, 2006.
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2005年
Palindromic repetitive DNA elements with coding potential in Methanocaldococcus jannaschii.
Suyama M, Lathe WC, Bork P.
FEBS Lett. 579, 5281-5286, 2005.
Initial sequence of the chimpanzee genome and comparison with the human genome.
Mikkelsen TS et al.
Nature 437, 69-87, 2005.
Generation and annotation of the DNA sequences of human chromosomes 2 and 4.
Hillier LW et al.
Nature 434, 724-731, 2005
Complex genomic rearrangements lead to novel primate gene function.
Ciccarelli F, von Mering C, Suyama M, Harrington E, Izaurralde E, Bork P.
Genome Res. 15, 343-351, 2005.
2004年
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.
Hillier LW et al.
Nature 432, 695-716, 2004.
Genome sequence of the Brown Norway rat yields insights into mammalian evolution.
Gibbs RA et al.
Nature 428, 493-521, 2004.
BLAST2GENE: a comprehensive conversion of BLAST output into independent genes and gene Fragments.
Suyama M, Torrents D, Bork P.
Bioinformatics 20, 1968-1970, 2004.
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2003年
The human genome: genes, pseudogenes, and variation on chromosome 7.
Waterston RH, Hillier LW, Fulton LA, Fulton RS, Graves TA, Pepin KH, Bork P, Suyama M, Torrents D, Chinwalla AT, Mardis ER, McPherson JD, Wilson RK.
Cold Spring Harb. Symp. Quant. Biol. 68, 13-22, 2003.
A genome-wide survey of human pseudogenes.
Torrents D, Suyama M, Zdobnov E, Bork P.
Genome Res. 13, 2559-2567, 2003.
The DNA sequence of human chromosome 7.
Hillier LW et al.
Nature 424, 157-164, 2003.
DomCut: prediction of inter-domain linker regions in amino acid sequences.
Suyama M, Ohara O.
Bioinformatics 19, 673-674, 2003.
2002年
Initial sequencing and comparative analysis of the mouse genome.
Waterston RH et al.
Nature 420, 520-562, 2002.
Comparative genome and proteome analysis of anopheles gambiae and Drosophila melanogaster.
Zdobnov EM, von Mering C, Letunic I, Torrents D, Suyama M et al.
Science 298, 149-159, 2002.
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2001年
Site-directed removal of N-glycosylation sites in BST-1/CD157: effects on molecular and functional Heterogeneity.
Yamamoto-Katayama S, Sato A, Ariyoshi M, Suyama M, Ishihara K, Hirano T, Nakamura H, Morikawa K, Jingami H.
Biochem. J. 357, 385-392, 2001.
Evolution of prokaryotic gene order: genome rearrangements in closely related species.
Suyama M, Bork P.
Trends Genet. 17, 10-13, 2001.
2000年
TAP (NXF1) belongs to a multigene family of putative RNA export factors with a conserved molular architecture.
Herold A, Suyama M, Rodrigues JP, Braun IC, Kutay U, Carmo-Fonseca M, Bork P, Izaurralde E.
Mol. Cell. Biol. 20, 8996-9008, 2000.
この論文は、Elisa Izaurraldeのグループとの共同研究で、RNAの核外輸送に関与するタンパク質について、そのアイソフォーム毎の局在化を調べたものです。モデル生物ごとにそれぞれのアイソフォームの構造を比較ゲノム解析で明らかにしました。当時はヒトゲノム配列決定が完了しておらず、断片的なコンティグ情報を手作業で繋ぎ合わせて遺伝子構造を決めました。それらの構造の模式図と局在化の顕微鏡写真を合成したイメージが表紙に採用されました。
Prediction of structural domains of TAP reveals details of its interaction with p15 and nucleoporins.
Suyama M, Doerks T, Braun IC, Sattler M, Izaurralde E, Bork P.
EMBO Rep. 1, 53-58, 2000.
Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames.
Dandekar T, Huynen M, Regula JT, Ueberle B, Zimmermann CU, Andrade MA, Doerks T, Sanchez-Pulido L, Snel B, Suyama M, Yuan YP, Herrmann R, Bork P.
Nucleic Acids Res. 28, 3278-3288, 2000.
HUGE: a database for human large proteins identified in the Kazusa cDNA sequencing project.
Kikuno R, Nagase T, Suyama M, Waki M, Hirosama M, Ohara O.
Nucleic Acids Res. 28, 331-332, 2000.
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1999年
Prediction of the coding sequences of unidentified human genes. XIII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro.
Nagase T, Ishikawa K, Suyama M, Kikuno R, Hirosawa M, Miyajima N, Tanaka A, Kotani H, Nomura N, Ohara O.
DNA Res. 6, 63-70, 1999.
HUGE: a database for human large proteins identified by Kazusa cDNA sequencing project.
Suyama M, Nagase T, Ohara O.
Nucleic Acids Res. 27, 338-339, 1999.
1998年
Prediction of the coding sequences of unidentified human genes. XII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro.
Nagase T, Ishikawa K, Suyama M, Kikuno R, Hirosama M, Miyajima N, Tanaka A, Kotani H, Nomura N, Ohara O.
DNA Res. 5, 355-364, 1998.
A method for comparing circular genomes from gene locations: application to mitochondrial genomes.
Horimoto K, Suyama M, Toh H, Mori K, Otsuka J.
Bioinformatics 14, 789-802, 1998.
Prediction of the coding sequences of unidentified human genes. XI. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro.
Nagase T, Ishikawa K, Suyama M, Kikuno R, Miyajima N, Tanaka A, Kotani H, Nomura N, Ohara O.
DNA Res. 5, 277-286, 1998.
Prediction of the coding sequences of unidentified human genes. X. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro.
Ishikawa K, Nagase T, Suyama M, Miyajima N, Tanaka A, Kotani H, Nomura N, Ohara O.
DNA Res. 5, 169-176, 1998.
Purification and some properties of an extracellular oligo-1,6-glucosidase from Bacillus stearothermophilus SA0301.
Tonozuka T, Sato K, Sakaguchi M, Suyama M, Sekine K, Sakano Y.
J. Appl. Glycosci. 45, 397-400, 1998.
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1997年
Comparison of protein structures using 3D profile alignment.
Suyama M, Matsuo Y, Nishikawa K.
J. Mol. Evol. 44 (suppl. 1), S163-S173, 1997.
1995年
Searching for common sequence patterns among distantly related proteins.
Suyama M, Nishioka T, Oda J.
Protein Eng. 8, 1075-1080, 1995.
1993年
Searching for amino acid sequence motifs among enzymes: the Enzyme-Reaction Database.
Suyama M, Ogiwara A, Nishioka T, Oda J.
Comput. Appl. Biosci. 9, 9-15, 1993.
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