論文リスト

The impact of selective HDAC inhibitors on the transcriptome of early mouse embryos

Shao R, Suzuki T, Suyama M & Tsukada Y

BMC Genomics, 2024

Exome-wide benchmark of difficult-to-sequence regions using short-read next-generation DNA sequencing

Hijikata A, Suyama M, Kikugawa S, Matoba R, Naruto T, Enomoto Y, Kurosawa K, Harada N, Yanagi K, Kaname T, Miyako K, Takazawa M, Sasai H, Hosokawa J, Itoga S, Yamaguchi T, Kosho T, Matsubara K, Kuroki Y, Fukami M, Adachi K, Nanba E, Tsuchida N, Uchiyama Y, Matsumoto N, Nishimura N, Ohara O

Nucleic Acids Research, 2023

主導機関であるかずさDNA研からのプレスリリースはこちらです

MUC1-C IS A COMMON DRIVER OF ACQUIRED OSIMERTINIB RESISTANCE IN NON-SMALL CELL LUNG CANCER

Haratake N, Ozawa H, Morimoto Y, Yamashita N, Daimon T, Bhattacharya A, Wang K, Nakashoji A, Isozaki H, Shimokawa M, Kikutake C, Suyama M, Hashinokuchi A, Takada K, Takenaka T, Yoshizumi T, Mitsudomi T, Aaron N Hata, Kufe D

Journal of Thoracic Oncology, 2023

Pan-cancer analysis of whole-genome doubling and its association with patient prognosis

Kikutake C, Suyama M

BMC cancer, 2023

Possible involvement of silent mutations in cancer pathogenesis and evolution

Kikutake C, Suyama M

Scientific Reports, 2023

Increased neutrophils in inflammatory bowel disease accelerate the accumulation of amyloid plaques in the mouse model of Alzheimer’s disease

Kaneko R, Matsui A, Watanabe M, Harada Y, Kanamori M, Awata N, Kawazoe M, Takao T, Kobayashi Y, Kikutake C, Suyama M, Saito T, Takaomi C Saido, Ito M

Inflammation and Regeneration, 2023

Prostaglandin E2 receptor Ptger4b regulates female-specific peptidergic neurons and female sexual receptivity in medaka

Fleming T, Kikuchi Y, Nakajo M, Tachizawa M, Inazumi T, Tsuchiya S, Sugimoto Y, Saito D, Suyama M, Ohkawa Y, Baba T, Morohashi KI, Okubo K

Commun Biol.,2022

Tmsb10 triggers fetal Leydig differentiation by suppressing the RAS/ERK pathway

Inoue M, Baba T, Takahashi F, Terao M, Yanai S, Shima Y, Saito D, Sugihara K, Miura T, Takada S, Suyama M, Ohkawa Y, Morohashi KI

Commun Biol.,2022

Genome-wide identification of copy neutral loss of heterozygosity reveals its possible association with spatial positioning of chromosomes

Kim H, Suyama M

Hum. Mol. Genet.,2022

Genome-wide identification of exon extension/shrinkage events induced by splice-site-creating mutations

Qu Z, Sakaguchi N, Kikutake C, Suyama M

RNA Biol.,2022

Drosophila transcription factor NF-Y suppresses transcription of the lipase 4 gene, a key gene for lipid storage

Yoshioka Y, Anzai K, Kowada R, Hiratsuka K, Hirayabu T, Yasuda M, Ohkawa Y, Sato T, Suyama M, Yoshida H, Yamaguchi M.

Exp. Cell Res.,2022

In Vitro Generation of Brain Regulatory T Cells by Co-culturing With Astrocytes

Yamamoto S, Matsui A, Ohyagi M, Kikutake C, Harada Y, Iizuka-Koga M, Suyama M, Yoshimura A, Ito M.

Frontiers Immunol.,2022

Identification of a drug-response gene in multiple myeloma through longitudinal single-cell transcriptome sequencing

Masuda T, Haji S, Nakashima Y, Tsuda M, Kimura D, Takamatsu A, Iwahashi N, Umakoshi H, Shiratsuchi M, Kikutake C, Suyama M, Ohkawa Y, Ogawa Y.

Iscience,2022

Pan-cancer analysis of mutations in open chromatin regions and their possible association with cancer pathogenesis

Kikutake C, Suyama M.

Cancer Medicine,2022

Mapping of promoter usage QTL using RNA-seq data reveals their contributions to complex traits

Kubota N, Suyama M.

PLoS Comput Biol.,2022

Pervasive occurrence of splice-site-creating mutations and their possible involvement in genetic disorders

Sakaguchi N, Suyama M.

npj Genomic Medicine,2022

Kastor and Polluks polypeptides encoded by a single gene locus cooperatively regulate VDAC and spermatogenesis

Mise S, Matsumoto A, Shimada K, Hosaka T, Takahashi M, Ichihara K, Shimizu H, Shiraishi C, Saito D, Suyama M, Yasuda T, Ide T, Izumi Y, Bamba T, Kimura-Someya T, Shirouzu M, Miyata H, Ikawa M, Nakayama KI.

Nat Commun.,2022

The microRNA cluster C19MC confers differentiation potential into trophoblast lineages upon human pluripotent stem cells

Kobayashi N, Okae H, Hiura H, Kubota N, Kobayashi EH, Shibata S, Oike A, Hori T, Kikutake C, Hamada H, Kaji H, Suyama M, Bortolin-Cavaillé ML, Cavaillé J, Arima T.

Nat Commun.,2022

Sex differences in metabolic pathways are regulated by Pfkfb3 and Pdk4 expression in rodent muscle

Christianto A, Baba T, Takahashi F, Inui K, Inoue M, Suyama M, Ono Y, Ohkawa Y, Morohashi KI.

Commun Biol.,2021

A ubiquitin-like protein encoded by the “noncoding” RNA TINCR promotes keratinocyte proliferation and wound healing

Nita A, Matsumoto A, Tang R, Shiraishi C, Ichihara K, Saito D, Suyama M, Yasuda T, Tsuji G, Furue M, Katayama B, Ozawa T, Murata T, Dainichi T, Kabashima K, Hatano A, Matsumoto M, Nakayama KI.

PLoS Genet.,2021

Sexual fate of murine external genitalia development: Conserved transcriptional competency for male-biased genes in both sexes

Kajioka D, Suzuki K, Matsushita S, Hino S, Sato T, Takada S, Isono K, Takeo T, Kajimoto M, Nakagata N, Nakao M, Suyama M, DeFalco T, Miyagawa S, Yamada G.

bioRxiv,2021

Functional variants in hematopoietic transcription factor footprints and their roles in the risk of immune system diseases

Kubota N, Suyama M.

bioRxiv,2021

Identification of SLC38A7 as a Prognostic Marker and Potential Therapeutic Target of Lung Squamous Cell Carcinoma

Haratake N, Hu Q, Okamoto T, Jogo T, Toyokawa G, Kinoshita F, Takenaka T, Tagawa T, Iseda N, Itoh S, Yamada Y, Oda Y, Shimokawa M, Kikutake C, Suyama M., Unoki M, Sasaki H, Mori M

Ann Surg.,2021

Pan-cancer analysis of non-coding recurrent mutations and their possible involvement in cancer pathogenesis

Kikutake C,Yoshihara M, Suyama M.

NAR Cancer., 2021

In silico identification of pseudo-exon activation events in personal genome and transcriptome data

Sakaguchi N, Suyama M.

RNA Biol., 2020

Augmented oxidative stress increases 8-oxoguanine preferentially in the transcriptionally active genomic regions.

Akatsuka S, Li GH, Kawaguchi S, Takahashi T, Yoshihara M, Suyama M, Toyokuni S.

Free Radical Research. 2020

Comparative genomic analysis of inbred rat strains reveals the existence of ancestral polymorphisms.

Kim H,Yoshihara M,Suyama M.

Mamm Genome. 2020

An integrated analysis of public genomic data unveils a possible functional mechanism of psoriasis risk via a long-range ERRFI1 enhancer.

Kubota N, Suyama M.

BMC Med. Genomics 13, 8, 2020

A Prediction Model for Detrusor Underactivity Based on Symptoms and Noninvasive Test Parameters in Men with Lower Urinary Tract Symptoms: An Analysis from a Large Group of Patients Undergoing Pressure Flow Studies.

Namitome R, Takei M, Takahashi R, Kikutake C, Yokomizo A, Yamaguchi O, Eto M.

J Urol. 2019

Current progress and issues of cancer genomic medicine in Kyushu University Hospital

Ito M, Kawaji H, Kubo M, Oki E, Iwama E, Maeda T, Ogawa M, Ochiai M, Shikada S, Yamamoto H, Suzuki M, Todaka K, Nakashima N,Yoshihara M,Suyama M, Baba E, Akashi K, Nakanishi Y.

Ann Oncol. 30, Issue Supplement_6, 2019

Metabolically and immunologically beneficial impact of extra virgin olive and flaxseed oils on composition of gut microbiota in mice.

Millman J, Okamoto S, Kimura A, Uema T, Higa M, Yonamine M, Namba T, Ogata E, Yamazaki S, Shimabukuro M, Tsutsui M, Matsushita M, Ikematsu S, Masuzaki H.

Eur J Nutr. 2019

CLEC3A, MMP7, and LCN2 as novel markers for predicting recurrence in resected G1 and G2 pancreatic neuroendocrine tumors.

Miki M, Oono T, Fujimori N, Takaoka T, Kawabe K, Miyasaka Y, Ohtsuka T, Saito D, Nakamura M, Ohkawa Y, Oda Y ,Suyama M, Ito T, Ogawa Y.

Cancer Med. 8, 3748-3760, 2019

Zfp281 Shapes the Transcriptome of Trophoblast Stem Cells and Is Essential for Placental Development.

Ishiuchi T, Ohishi H, Sato T, Kamimura S, Yorino M, Abe S, Suzuki A, Wakayama T, Suyama M, Sasaki H.

Cell Rep. 27, 1742-1754, 2019

Novel components of germline sex determination acting downstream of foxl3 in medaka.

Kikuchi M, Nishimura T, Saito D, Shigenobu S, Takada R, Gutierrez-Triana JA, Cerdán JLM, Takada S, Wittbrodt J, Suyama M, Tanaka M.

Dev Biol. 445, 80-89, 2019

よくわかるバイオインフォマティクス入門

藤博幸・編

須山先生が共著者であるバイオインフォマティクスの入門書です。バイオインフォマティクスの勉強を始めたいけど、何から勉強したらいいのかな、という方は是非読まれてみてはいかがでしょうか？バイオインフォマティクスの幅広い分野が網羅されており、非常に参考になる一冊です。須山先生は第６章「ゲノム解析」の執筆を担当しました。

Pan-cancer analysis of intratumor heterogeneity associated with patient prognosis using multidimensional measures.

Kikutake C, Yoshihara M, Sato T, Saito D, Suyama M.

Oncotarget 9, 37689-37699, 2018

Fetal Leydig cells dedifferentiate and serve as adult Leydig stem cells.

Shima Y, Miyabayashi K, Sato T, Suyama M, Ohkawa Y, Doi M, Okamura H, Suzuki K.

Development 145, 23, 2018

Concomitant Intraductal Papillary Mucinous Neoplasm in Pancreatic Ductal Adenocarcinoma Is an Independent Predictive Factor for the Occurrence of New Cancer in the Remnant Pancreas.

Matsuda R, Miyasaka Y, Ohishi Y, Yamamoto T, Saeki K, Mochidome N, Abe A, Ozono K, Shindo K, Ohtsuka T, Kikutake C, Nakamura M, Oda Y.

Ann Surg. 2018

Mouse polycomb group gene Cbx2 promotes osteoblastic but suppresses adipogenic differentiation in postnatal long bones.

Katoh-Fukui Y, Baba T, Sato T, Otake H, Nagakui-Noguchi Y, Shindo M, Suyama M, Ohkawa Y, Tsumura H, Morohashi KI, Fukami M.

Bone 120, 219-231, 2018

Intratumor heterogeneity of HMCN1 mutant alleles associated with poor prognosis in patients with breast cancer.

Kikutake C, Yoshihara M, Sato T, Saito D, Suyama M.

Oncotarget 9, 33337-33347, 2018

Ad4BP/SF-1 regulates cholesterol synthesis to boost the production of steroids.

Baba T, Otake H, Inoue M, Sato T, Ishihara Y, Moon JY, Tsuchiya M, Miyabayashi K, Ogawa H, Shima Y, Wang L, Sato R, Yamazaki T, Suyama M, Nomura M, Choi MH, Ohkawa Y, Morohashi KI.

Communications Biology 1, 18, 2018.

The Autism-Related Protein CHD8 Cooperates with C/EBPβ to Regulate Adipogenesis.

Kita Y, Katayama Y, Shiraishi T, Oka T, Sato T, Suyama M, Ohkawa Y, Miyata K, Oike Y, Shirane M, Nishiyama M, Nakayama KI.

Cell Rep. 23, 1988-2000, 2018.

Identification of a candidate enhancer for DMRT3 involved in spastic cerebral palsy pathogenesis.

Kubota N, Yokoyama T, Hoshi N, Suyama M.

Biochem Biophys Res Commun. 496, 133-139, 2018.

Derivation of Human Trophoblast Stem Cells.

Okae H, Toh H, Sato T, Hiura H, Takahashi S, Shirane K, Kabayama Y, Suyama M, Sasaki H, Arima T.

Cell Stem Cell 22, 50-63.e6, 2018.

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Identification of Secretory Leukoprotease Inhibitor As an Endogenous Negative Regulator in Allergic Effector Cells.

Matsuba S, Yabe-Wada T, Takeda K, Sato T, Suyama M, Takai T, Kikuchi T, Nukiwa T, Nakamura A.

Frontiers Immunol. 8, 1538, 2017.

DBTSS/DBKERO for integrated analysis of transcriptional regulation.

Suzuki A, Kawano S, Mitsuyama T, Suyama M, Kanai Y, Shirahige K, Sasaki H, Tokunaga K, Tsuchihara K, Sugano S, Nakai K, Suzuki Y.

Nucleic Acids Res. 46, D229-D238, 2017.

Histone methyltransferase G9a is a key regulator of the starvation-induced behaviors in Drosophila melanogaster.

Shimaji K, Tanaka R, Maeda T, Ozaki M, Yoshida H, Ohkawa Y, Sato T, Suyama M, Yamaguchi M.

Sci Rep. 7, 14763, 2017.

Identification of Candidate Genes for Generalized Tonic-Clonic Seizures in Noda Epileptic Rat.

Kuramoto T, Voigt B, Nakanishi S, Kitada K, Nakamura T, Wakamatsu K, Yoshihara M, Suyama M, Uemura R, Tanaka M, Kuwamura M, Shimizu S, Ohno Y, Sasa M, Serikawa T.

Behav Genet. 47, 609-619, 2017.

Control of tissue size and development by a regulatory element in the yorkie 3'UTR.

Umegawachi T, Yoshida H, Koshida H, Yamada M, Ohkawa Y, Sato T, Suyama M, Krause HM, Yamaguchi M.

Am J Cancer Res. 7, 673-687, 2017.

A deletion in the intergenic region upstream of Ednrb causes head spot in the rat strain KFRS4/Kyo.

Yoshihara M, Sato T, Saito D, Ohara O, Kuramoto T, Suyama M.

BMC Genet. 18, 29, 2017.

Role of Ad4-binding protein/steroidogenic factor 1 in regulating NADPH production in adrenocortical Y-1 cells.

Li B, Baba T, Miyabayashi K, Sato T, Shima Y, Ichinose T, Miura D, Ohkawa Y, Suyama M, Morohashi KI.

Endocr J. 64, 315-324, 2017.

Differential lactate and cholesterol synthetic activities in XY and XX Sertoli cells.

Shishido Y, Baba T, Sato T, Shima Y, Miyabayashi K, Inoue M, Akiyama H, Kimura H, Kanai Y, Ishihara Y, Haraguchi S, Miyazaki A, Rozman D, Yamazaki T, Choi MH, Ohkawa Y, Suyama M, Morohashi KI.

Sci Rep. 7, 41912,2017.

Software updates in the Illumina HiSeq platform affect whole-genome bisulfite sequencing.

Toh H, Shirane K, Miura F, Kubo N, Ichiyanagi K, Hayashi K, Saitou M, Suyama M, Ito T, Sasaki H.

BMC Genomics. 18, 31, 2017.

Alterations in fetal Leydig cell gene expression during fetal and adult development.

Miyabayashi K, Shima Y, Inoue M, Sato T, Baba T, Ohkawa Y, Suyama M, Morohashi KI.

Sex Dev. 11, 53-63, 2017.

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Application of target capture sequencing of exons and conserved non-coding sequences to 20 inbred rat strains.

Yoshihara M, Sato T, Saito D, Ohara O, Kuramoto T, Suyama M.

Genom Data. 10, 155-157, 2016.

Allele-Specific Methylome and Transcriptome Analysis Reveals Widespread Imprinting in the Human Placenta.

Hamada H, Okae H, Toh H, Chiba H, Hiura H, Shirane K, Sato T, Suyama M, Yaegashi N, Sasaki H, Arima T.

Am J Hum Genet. 99, 1045-1058, 2016.

CHD8 haploinsufficiency results in autistic-like phenotypes in mice.

Katayama Y, Nishiyama M, Shoji H, Ohkawa Y, Kawamura A, Sato T, Suyama M, Takumi T, Miyakawa T, Nakayama KI.

Nature 537, 675-679, 2016.

Design and application of a target capture sequencing of exons and conserved non-coding sequences for the rat.

Yoshihara M, Saito D, Sato T, Ohara O, Kuramoto T, Suyama M.

BMC Genomics. 17, 593, 2016.

TLR signals posttranscriptionally regulate the cytokine trafficking mediator sortilin.

Yabe-Wada T, Matsuba S, Takeda K, Sato T, Suyama M, Ohkawa Y, Takai T, Shi H, Philpott CC, Nakamura A.

Sci Rep. 6, 26566, 2016.

Isolation and Characterization of Fetal Leydig Progenitor Cells of Male Mice.

Inoue M, Shima Y, Miyabayashi K, Tokunaga K, Sato T, Baba T, Ohkawa Y, Akiyama H, Suyama M, Morohashi K.

Endocrinology. 157, 1222-1233, 2016.

Androgen Regulates Mafb Expression Through its 3'UTR During Mouse Urethral Masculinization.

Matsushita S, Suzuki K, Ogino Y, Hino S, Sato T, Suyama M, Matsumoto T, Omori A, Inoue S, Yamada G.

Endocrinology. 157, 844-857, 2016.

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ChromContact: A web tool for analyzing spatial contact of chromosomes from Hi-C data.

Sato T, Suyama M.

BMC Genomics. 16, 1060, 2015.

Intronic regulation of Aire expression by Jmjd6 for self-tolerance induction in the thymus.

Yanagihara T, Sanematsu F, Sato T, Uruno T, Duan X, Tomino T, Harada Y, Watanabe M, Wang Y, Tanaka Y, Nakanishi Y, Suyama M, Fukui Y.

Nat Commun. 6, 8820, 2015.

Linkage disequilibrium analysis of allelic heterogeneity in DNA methylation.

Saito D, Suyama M.

Epigenetics. 10, 1093-1098, 2015.

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. 20, 902-914, 2015.

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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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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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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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.

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.

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。

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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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.

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1000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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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.

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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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.

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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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.

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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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.

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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Comparison of protein structures using 3D profile alignment.

Suyama M, Matsuo Y, Nishikawa K.

J. Mol. Evol. 44 (suppl. 1), S163-S173, 1997.

Searching for common sequence patterns among distantly related proteins.

Suyama M, Nishioka T, Oda J.

Protein Eng. 8, 1075-1080, 1995.

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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