Mikita Suyama - Publications

Affiliations: 
Center for Genomic Medicine University of Kyoto, Kyōto-shi, Kyōto-fu, Japan 
Website:
http://www.med.kyoto-u.ac.jp/E/grad_school/introduction/1524/

50 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2017 Yoshihara M, Sato T, Saito D, Ohara O, Kuramoto T, Suyama M. A deletion in the intergenic region upstream of Ednrb causes head spot in the rat strain KFRS4/Kyo. Bmc Genetics. 18: 29. PMID 28356074 DOI: 10.1186/s12863-017-0497-3  0.48
2016 Yoshihara M, Sato T, Saito D, Ohara O, Kuramoto T, Suyama M. Application of target capture sequencing of exons and conserved non-coding sequences to 20 inbred rat strains. Genomics Data. 10: 155-157. PMID 27882299 DOI: 10.1016/j.gdata.2016.11.010  0.48
2016 Yoshihara M, Saito D, Sato T, Ohara O, Kuramoto T, Suyama M. Design and application of a target capture sequencing of exons and conserved non-coding sequences for the rat. Bmc Genomics. 17: 593. PMID 27506932 DOI: 10.1186/s12864-016-2975-9  0.48
2015 Sato T, Suyama M. ChromContact: A web tool for analyzing spatial contact of chromosomes from Hi-C data. Bmc Genomics. 16: 1060. PMID 26666652 DOI: 10.1186/s12864-015-2282-x  1
2015 Yanagihara T, Sanematsu F, Sato T, Uruno T, Duan X, Tomino T, Harada Y, Watanabe M, Wang Y, Tanaka Y, Nakanishi Y, Suyama M, Yoshinori F. Intronic regulation of Aire expression by Jmjd6 for self-tolerance induction in the thymus. Nature Communications. 6: 8820. PMID 26531897 DOI: 10.1038/ncomms9820  1
2015 Shimaji K, Konishi T, Tanaka S, Yoshida H, Kato Y, Ohkawa Y, Sato T, Suyama M, Kimura H, Yamaguchi M. Genomewide identification of target genes of histone methyltransferase dG9a during Drosophila embryogenesis. Genes to Cells : Devoted to Molecular & Cellular Mechanisms. PMID 26334932 DOI: 10.1111/gtc.12281  1
2015 Nishimura T, Sato T, Yamamoto Y, Watakabe I, Ohkawa Y, Suyama M, Kobayashi S, Tanaka M. Sex determination. foxl3 is a germ cell-intrinsic factor involved in sperm-egg fate decision in medaka. Science (New York, N.Y.). 349: 328-31. PMID 26067255 DOI: 10.1126/science.aaa2657  1
2015 Sato T, Suyama M. GenomeCons: a web server for manipulating multiple genome sequence alignments and their consensus sequences. Bioinformatics (Oxford, England). 31: 1293-5. PMID 25480378 DOI: 10.1093/bioinformatics/btu803  1
2014 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. Genome-wide analysis of histone modifications in human endometrial stromal cells. Molecular Endocrinology (Baltimore, Md.). 28: 1656-69. PMID 25073104 DOI: 10.1210/me.2014-1117  1
2014 Yoshihara M, Jiang L, Akatsuka S, Suyama M, Toyokuni S. Genome-wide profiling of 8-oxoguanine reveals its association with spatial positioning in nucleus. Dna Research : An International Journal For Rapid Publication of Reports On Genes and Genomes. 21: 603-12. PMID 25008760 DOI: 10.1093/dnares/dsu023  1
2014 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, ... ... Suyama M, et al. Glycolytic genes are targets of the nuclear receptor Ad4BP/SF-1. Nature Communications. 5: 3634. PMID 24727981 DOI: 10.1038/ncomms4634  1
2014 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, et al. Characterization of common marmoset dysgerminoma-like tumor induced by the lentiviral expression of reprogramming factors. Cancer Science. 105: 402-8. PMID 24521492 DOI: 10.1111/cas.12367  1
2013 Suyama M. Mechanistic insights into mutually exclusive splicing in dynamin 1. Bioinformatics (Oxford, England). 29: 2084-7. PMID 23793749 DOI: 10.1093/bioinformatics/btt368  1
2013 Miyake Y, Toyonaga K, Mori D, Kakuta S, Hoshino Y, Oyamada A, Yamada H, Ono K, Suyama M, Iwakura Y, Yoshikai Y, Yamasaki S. C-type lectin MCL is an FcRγ-coupled receptor that mediates the adjuvanticity of mycobacterial cord factor. Immunity. 38: 1050-62. PMID 23602766 DOI: 10.1016/j.immuni.2013.03.010  1
2013 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. β-Catenin signaling regulates Foxa2 expression during endometrial hyperplasia formation. Oncogene. 32: 3477-82. PMID 22945641 DOI: 10.1038/onc.2012.376  1
2011 Ratanajaraya C, Nishiyama H, Takahashi M, Kawaguchi T, Saito R, Mikami Y, Suyama M, Lathrop M, Yamada R, Ogawa O, Matsuda F. A polymorphism of the POLG2 gene is genetically associated with the invasiveness of urinary bladder cancer in Japanese males. Journal of Human Genetics. 56: 572-6. PMID 21734712 DOI: 10.1038/jhg.2011.60  1
2010 Suyama M, Harrington ED, Vinokourova S, von Knebel Doeberitz M, Ohara O, Bork P. A network of conserved co-occurring motifs for the regulation of alternative splicing. Nucleic Acids Research. 38: 7916-26. PMID 20702423 DOI: 10.1093/nar/gkq705  1
2009 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, et al. Transcriptome complexity in a genome-reduced bacterium. Science (New York, N.Y.). 326: 1268-71. PMID 19965477 DOI: 10.1126/science.1176951  1
2009 Itou J, Suyama M, Imamura Y, Deguchi T, Fujimori K, Yuba S, Kawarabayasi Y, Kawasaki T. Functional and comparative genomics analyses of pmp22 in medaka fish. Bmc Neuroscience. 10: 60. PMID 19534778 DOI: 10.1186/1471-2202-10-60  1
2008 Quijano C, Tomancak P, Lopez-Marti J, Suyama M, Bork P, Milan M, Torrents D, Manzanares M. Selective maintenance of Drosophila tandemly arranged duplicated genes during evolution. Genome Biology. 9: R176. PMID 19087263 DOI: 10.1186/gb-2008-9-12-r176  1
2008 Soldà G, Suyama M, Pelucchi P, Boi S, Guffanti A, Rizzi E, Bork P, Tenchini ML, Ciccarelli FD. Non-random retention of protein-coding overlapping genes in Metazoa. Bmc Genomics. 9: 174. PMID 18416813 DOI: 10.1186/1471-2164-9-174  1
2006 Suyama M, Harrington E, Bork P, Torrents D. Identification and analysis of genes and pseudogenes within duplicated regions in the human and mouse genomes. Plos Computational Biology. 2: e76. PMID 16846249 DOI: 10.1371/journal.pcbi.0020076  1
2006 Suyama M, Torrents D, Bork P. PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Research. 34: W609-12. PMID 16845082 DOI: 10.1093/nar/gkl315  1
2006 Kobayashi A, Tonozuka T, Sato K, Suyama M, Sasaki J, Nyamdawaa B, Sakaguchi M, Sakano Y. Molecular cloning and characterization of an enzyme hydrolyzing p-nitrophenyl alpha-D-glucoside from Bacillus stearothermophilus SA0301. Bioscience, Biotechnology, and Biochemistry. 70: 495-9. PMID 16495668 DOI: 10.1271/bbb.70.495  1
2005 Suyama M, Lathe WC, Bork P. Palindromic repetitive DNA elements with coding potential in Methanocaldococcus jannaschii. Febs Letters. 579: 5281-6. PMID 16182294 DOI: 10.1016/j.febslet.2005.08.051  1
2005 Hillier LW, Graves TA, Fulton RS, Fulton LA, Pepin KH, Minx P, Wagner-McPherson C, Layman D, Wylie K, Sekhon M, Becker MC, Fewell GA, Delehaunty KD, Miner TL, Nash WE, ... ... Suyama M, et al. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. Nature. 434: 724-31. PMID 15815621 DOI: 10.1038/nature03466  0.68
2005 Ciccarelli FD, von Mering C, Suyama M, Harrington ED, Izaurralde E, Bork P. Complex genomic rearrangements lead to novel primate gene function. Genome Research. 15: 343-51. PMID 15710750 DOI: 10.1101/gr.3266405  1
2004 Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, ... ... Suyama M, et al. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 428: 493-521. PMID 15057822 DOI: 10.1038/nature02426  1
2004 Suyama M, Torrents D, Bork P. BLAST2GENE: a comprehensive conversion of BLAST output into independent genes and gene fragments. Bioinformatics (Oxford, England). 20: 1968-70. PMID 15037510 DOI: 10.1093/bioinformatics/bth225  1
2003 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. The human genome: genes, pseudogenes, and variation on chromosome 7. Cold Spring Harbor Symposia On Quantitative Biology. 68: 13-22. PMID 15338598  1
2003 Torrents D, Suyama M, Zdobnov E, Bork P. A genome-wide survey of human pseudogenes. Genome Research. 13: 2559-67. PMID 14656963 DOI: 10.1101/gr.1455503  1
2003 Hillier LW, Fulton RS, Fulton LA, Graves TA, Pepin KH, Wagner-McPherson C, Layman D, Maas J, Jaeger S, Walker R, Wylie K, Sekhon M, Becker MC, O'Laughlin MD, Schaller ME, ... ... Suyama M, et al. The DNA sequence of human chromosome 7. Nature. 424: 157-64. PMID 12853948 DOI: 10.1038/nature01782  0.32
2003 Suyama M, Ohara O. DomCut: prediction of inter-domain linker regions in amino acid sequences. Bioinformatics (Oxford, England). 19: 673-4. PMID 12651735 DOI: 10.1093/bioinformatics/btg031  1
2002 Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, ... ... Suyama M, et al. Initial sequencing and comparative analysis of the mouse genome. Nature. 420: 520-62. PMID 12466850 DOI: 10.1038/nature01262  1
2002 Zdobnov EM, von Mering C, Letunic I, Torrents D, Suyama M, Copley RR, Christophides GK, Thomasova D, Holt RA, Subramanian GM, Mueller HM, Dimopoulos G, Law JH, Wells MA, Birney E, et al. Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science (New York, N.Y.). 298: 149-59. PMID 12364792 DOI: 10.1126/science.1077061  1
2001 Yamamoto-Katayama S, Sato A, Ariyoshi M, Suyama M, Ishihara K, Hirano T, Nakamura H, Morikawa K, Jingami H. Site-directed removal of N-glycosylation sites in BST-1/CD157: effects on molecular and functional heterogeneity. The Biochemical Journal. 357: 385-92. PMID 11439087 DOI: 10.1042/0264-6021:3570385  1
2001 Suyama M, Bork P. Evolution of prokaryotic gene order: genome rearrangements in closely related species. Trends in Genetics : Tig. 17: 10-3. PMID 11163906 DOI: 10.1016/S0168-9525(00)02159-4  1
2000 Suyama M, Doerks T, Braun IC, Sattler M, Izaurralde E, Bork P. Prediction of structural domains of TAP reveals details of its interaction with p15 and nucleoporins. Embo Reports. 1: 53-8. PMID 11256625 DOI: 10.1038/sj.embor.embor627  1
2000 Herold A, Suyama M, Rodrigues JP, Braun IC, Kutay U, Carmo-Fonseca M, Bork P, Izaurralde E. TAP (NXF1) belongs to a multigene family of putative RNA export factors with a conserved modular architecture. Molecular and Cellular Biology. 20: 8996-9008. PMID 11073998 DOI: 10.1128/MCB.20.23.8996-9008.2000  1
2000 Dandekar T, Huynen M, Regula JT, Ueberle B, Zimmermann CU, Andrade MA, Doerks T, Sánchez-Pulido L, Snel B, Suyama M, Yuan YP, Herrmann R, Bork P. Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames. Nucleic Acids Research. 28: 3278-88. PMID 10954595  1
2000 Kikuno R, Nagase T, Suyama M, Waki M, Hirosawa M, Ohara O. HUGE: a database for human large proteins identified in the Kazusa cDNA sequencing project. Nucleic Acids Research. 28: 331-2. PMID 10592264  1
1999 Nagase T, Ishikawa K, Suyama M, Kikuno R, Hirosawa M, Miyajima N, Tanaka A, Kotani H, Nomura N, Ohara O. 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. Dna Research : An International Journal For Rapid Publication of Reports On Genes and Genomes. 6: 63-70. PMID 10231032  1
1999 Suyama M, Nagase T, Ohara O. HUGE: a database for human large proteins identified by Kazusa cDNA sequencing project. Nucleic Acids Research. 27: 338-9. PMID 9847221 DOI: 10.1093/nar/27.1.338  1
1998 Nagase T, Ishikawa K, Suyama M, Kikuno R, Hirosawa M, Miyajima N, Tanaka A, Kotani H, Nomura N, Ohara O. 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. Dna Research : An International Journal For Rapid Publication of Reports On Genes and Genomes. 5: 355-64. PMID 10048485  1
1998 Horimoto K, Suyama M, Toh H, Mori K, Otsuka J. A method for comparing circular genomes from gene locations: application to mitochondrial genomes. Bioinformatics (Oxford, England). 14: 789-802. PMID 9918949  1
1998 Nagase T, Ishikawa K, Suyama M, Kikuno R, Miyajima N, Tanaka A, Kotani H, Nomura N, Ohara O. 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. Dna Research : An International Journal For Rapid Publication of Reports On Genes and Genomes. 5: 277-86. PMID 9872452  1
1998 Ishikawa K, Nagase T, Suyama M, Miyajima N, Tanaka A, Kotani H, Nomura N, Ohara O. Prediction of the coding sequences of unidentified human genes. X. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro. Dna Research : An International Journal For Rapid Publication of Reports On Genes and Genomes. 5: 169-76. PMID 9734811  1
1997 Suyama M, Matsuo Y, Nishikawa K. Comparison of protein structures using 3D profile alignment. Journal of Molecular Evolution. 44: S163-73. PMID 9071025 DOI: 10.1007/PL00000065  1
1995 Suyama M, Nishioka T, Oda J. Searching for common sequence patterns among distantly related proteins. Protein Engineering. 8: 1075-80. PMID 8819973  1
1993 Suyama M, Ogiwara A, Nishioka T, Oda J. Searching for amino acid sequence motifs among enzymes: The Enzyme-Reaction Database Computer Applications in the Biosciences. 9: 9-15. PMID 8435774  1
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