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Items: 50

1.

Missense Mutations in NKAP Cause a Disorder of Transcriptional Regulation Characterized by Marfanoid Habitus and Cognitive Impairment.

Fiordaliso SK, Iwata-Otsubo A, Ritter AL, Quesnel-Vallières M, Fujiki K, Nishi E, Hancarova M, Miyake N, Morton JEV, Lee S, Hackmann K, Bando M, Masuda K, Nakato R, Arakawa M, Bhoj E, Li D, Hakonarson H, Takeda R, Harr M, Keena B, Zackai EH, Okamoto N, Mizuno S, Ko JM, Valachova A, Prchalova D, Vlckova M, Pippucci T, Seiler C, Choi M, Matsumoto N, Di Donato N, Barash Y, Sedlacek Z, Shirahige K, Izumi K.

Am J Hum Genet. 2019 Sep 30. pii: S0002-9297(19)30348-9. doi: 10.1016/j.ajhg.2019.09.009. [Epub ahead of print]

PMID:
31587868
2.

The novel lncRNA CALIC upregulates AXL to promote colon cancer metastasis.

Kawasaki Y, Miyamoto M, Oda T, Matsumura K, Negishi L, Nakato R, Suda S, Yokota N, Shirahige K, Akiyama T.

EMBO Rep. 2019 Aug;20(8):e47052. doi: 10.15252/embr.201847052. Epub 2019 Jul 29.

PMID:
31353791
3.

Cux2 refines the forelimb field by controlling expression of Raldh2 and Hox genes.

Ueda S, Cordeiro IR, Moriyama Y, Nishimori C, Kai KI, Yu R, Nakato R, Shirahige K, Tanaka M.

Biol Open. 2019 Feb 1;8(2). pii: bio040584. doi: 10.1242/bio.040584.

4.

Colonic endoscopic mucosal resection in patients taking anticoagulants: Is heparin bridging therapy necessary?

Fujita M, Murao T, Osawa M, Hirai S, Fukushima S, Yo S, Nakato R, Ishii M, Matsumoto H, Tamaki T, Sakakibara T, Shiotani A.

J Dig Dis. 2018 May;19(5):288-294. doi: 10.1111/1751-2980.12598. Epub 2018 May 27.

PMID:
29687957
5.

Sensitive and robust assessment of ChIP-seq read distribution using a strand-shift profile.

Nakato R, Shirahige K.

Bioinformatics. 2018 Jul 15;34(14):2356-2363. doi: 10.1093/bioinformatics/bty137.

PMID:
29528371
6.

Combined Loss of JMJD1A and JMJD1B Reveals Critical Roles for H3K9 Demethylation in the Maintenance of Embryonic Stem Cells and Early Embryogenesis.

Kuroki S, Nakai Y, Maeda R, Okashita N, Akiyoshi M, Yamaguchi Y, Kitano S, Miyachi H, Nakato R, Ichiyanagi K, Shirahige K, Kimura H, Shinkai Y, Tachibana M.

Stem Cell Reports. 2018 Apr 10;10(4):1340-1354. doi: 10.1016/j.stemcr.2018.02.002. Epub 2018 Mar 8.

7.

Expectoration of Cryptosporidium Parasites in Sputum of Human Immunodeficiency Virus-Positive and -Negative Adults.

Mor SM, Ascolillo LR, Nakato R, Ndeezi G, Tumwine JK, Okwera A, Sponseller JK, Tzipori S, Griffiths JK.

Am J Trop Med Hyg. 2018 Apr;98(4):1086-1090. doi: 10.4269/ajtmh.17-0741. Epub 2018 Feb 1.

8.

Hypergastrinemia in Long-Term Use of Proton Pump Inhibitors.

Shiotani A, Katsumata R, Gouda K, Fukushima S, Nakato R, Murao T, Ishii M, Fujita M, Matsumoto H, Sakakibara T.

Digestion. 2018;97(2):154-162. doi: 10.1159/000484688. Epub 2018 Jan 8.

PMID:
29310112
9.

The HSF1-PARP13-PARP1 complex facilitates DNA repair and promotes mammary tumorigenesis.

Fujimoto M, Takii R, Takaki E, Katiyar A, Nakato R, Shirahige K, Nakai A.

Nat Commun. 2017 Nov 21;8(1):1638. doi: 10.1038/s41467-017-01807-7.

10.

Statistical Analysis and Quality Assessment of ChIP-seq Data with DROMPA.

Nakato R, Shirahige K.

Methods Mol Biol. 2018;1672:631-643. doi: 10.1007/978-1-4939-7306-4_41.

PMID:
29043652
11.

Differences in the clinical course of 516 Japanese patients with upper gastrointestinal bleeding between weekday and weekend admissions.

Fujita M, Manabe N, Murao T, Osawa M, Hirai S, Fukushima S, Shogen Y, Nakato R, Ishii M, Matsumoto H, Hata J, Shiotani A.

Scand J Gastroenterol. 2017 Dec;52(12):1365-1370. doi: 10.1080/00365521.2017.1377762. Epub 2017 Sep 19.

PMID:
28925290
12.

New ultrasonographic screening method for oropharyngeal dysphagia: tissue Doppler imaging.

Manabe N, Haruma K, Nakato R, Kusunoki H, Kamada T, Hata J.

Am J Physiol Gastrointest Liver Physiol. 2018 Jan 1;314(1):G32-G38. doi: 10.1152/ajpgi.00019.2017. Epub 2017 Sep 1.

13.

MRG15-mediated tethering of PALB2 to unperturbed chromatin protects active genes from genotoxic stress.

Bleuyard JY, Fournier M, Nakato R, Couturier AM, Katou Y, Ralf C, Hester SS, Dominguez D, Rhodes D, Humphrey TC, Shirahige K, Esashi F.

Proc Natl Acad Sci U S A. 2017 Jul 18;114(29):7671-7676. doi: 10.1073/pnas.1620208114. Epub 2017 Jul 3.

14.

Genome-Wide Target Analyses of Otx2 Homeoprotein in Postnatal Cortex.

Sakai A, Nakato R, Ling Y, Hou X, Hara N, Iijima T, Yanagawa Y, Kuwano R, Okuda S, Shirahige K, Sugiyama S.

Front Neurosci. 2017 May 31;11:307. doi: 10.3389/fnins.2017.00307. eCollection 2017.

15.

Two Components of Aversive Memory in Drosophila, Anesthesia-Sensitive and Anesthesia-Resistant Memory, Require Distinct Domains Within the Rgk1 Small GTPase.

Murakami S, Minami-Ohtsubo M, Nakato R, Shirahige K, Tabata T.

J Neurosci. 2017 May 31;37(22):5496-5510. doi: 10.1523/JNEUROSCI.3648-16.2017. Epub 2017 Apr 17.

16.

Decreased cohesin in the brain leads to defective synapse development and anxiety-related behavior.

Fujita Y, Masuda K, Bando M, Nakato R, Katou Y, Tanaka T, Nakayama M, Takao K, Miyakawa T, Tanaka T, Ago Y, Hashimoto H, Shirahige K, Yamashita T.

J Exp Med. 2017 May 1;214(5):1431-1452. doi: 10.1084/jem.20161517. Epub 2017 Apr 13.

17.

Effects of Capsaicin on Older Patients with Oropharyngeal Dysphagia: A Double-Blind, Placebo-Controlled, Crossover Study.

Nakato R, Manabe N, Shimizu S, Hanayama K, Shiotani A, Hata J, Haruma K.

Digestion. 2017;95(3):210-220. doi: 10.1159/000463382. Epub 2017 Mar 21. Erratum in: Digestion. 2017;96(3):184.

PMID:
28319947
18.

Age-Related Differences in Clinical Characteristics and Esophageal Motility in Patients with Dysphagia.

Nakato R, Manabe N, Kamada T, Matsumoto H, Shiotani A, Hata J, Haruma K.

Dysphagia. 2017 Jun;32(3):374-382. doi: 10.1007/s00455-016-9763-1. Epub 2016 Dec 2.

PMID:
27913915
19.

Helicobacter pylori Eradication with Proton Pump Inhibitors or Potassium-Competitive Acid Blockers: The Effect of Clarithromycin Resistance.

Matsumoto H, Shiotani A, Katsumata R, Fujita M, Nakato R, Murao T, Ishii M, Kamada T, Haruma K, Graham DY.

Dig Dis Sci. 2016 Nov;61(11):3215-3220. Epub 2016 Sep 22.

PMID:
27659671
20.

Regulation of Unfolded Protein Response via Protein S-nitrosylation.

Ohkubo Y, Nakato R, Uehara T.

Yakugaku Zasshi. 2016;136(6):801-4. doi: 10.1248/yakushi.15-00292-1. Review. Japanese.

21.

Molecular Detection of H. pylori Using Adherent Gastric Mucous to Biopsy Forceps.

Matsumoto H, Shiotani A, Nishibayashi H, Kamada T, Kimura T, Fujimura Y, Nakato R, Murao T, Fujita M, Haruma K.

Helicobacter. 2016 Dec;21(6):548-553. doi: 10.1111/hel.12310. Epub 2016 Apr 8.

PMID:
27061611
22.

Recent advances in ChIP-seq analysis: from quality management to whole-genome annotation.

Nakato R, Shirahige K.

Brief Bioinform. 2017 Mar 1;18(2):279-290. doi: 10.1093/bib/bbw023. Review.

23.

Regulation of the unfolded protein response via S-nitrosylation of sensors of endoplasmic reticulum stress.

Nakato R, Ohkubo Y, Konishi A, Shibata M, Kaneko Y, Iwawaki T, Nakamura T, Lipton SA, Uehara T.

Sci Rep. 2015 Oct 8;5:14812. doi: 10.1038/srep14812.

24.

Replication-Coupled PCNA Unloading by the Elg1 Complex Occurs Genome-wide and Requires Okazaki Fragment Ligation.

Kubota T, Katou Y, Nakato R, Shirahige K, Donaldson AD.

Cell Rep. 2015 Aug 4;12(5):774-87. doi: 10.1016/j.celrep.2015.06.066. Epub 2015 Jul 23.

25.

Condensin targets and reduces unwound DNA structures associated with transcription in mitotic chromosome condensation.

Sutani T, Sakata T, Nakato R, Masuda K, Ishibashi M, Yamashita D, Suzuki Y, Hirano T, Bando M, Shirahige K.

Nat Commun. 2015 Jul 23;6:7815. doi: 10.1038/ncomms8815.

26.

The Deubiquitinating Enzyme USP7 Regulates Androgen Receptor Activity by Modulating Its Binding to Chromatin.

Chen ST, Okada M, Nakato R, Izumi K, Bando M, Shirahige K.

J Biol Chem. 2015 Aug 28;290(35):21713-23. doi: 10.1074/jbc.M114.628255. Epub 2015 Jul 14.

27.

Assembly of Slx4 signaling complexes behind DNA replication forks.

Balint A, Kim T, Gallo D, Cussiol JR, Bastos de Oliveira FM, Yimit A, Ou J, Nakato R, Gurevich A, Shirahige K, Smolka MB, Zhang Z, Brown GW.

EMBO J. 2015 Aug 13;34(16):2182-97. doi: 10.15252/embj.201591190. Epub 2015 Jun 25.

28.

Esco1 Acetylates Cohesin via a Mechanism Different from That of Esco2.

Minamino M, Ishibashi M, Nakato R, Akiyama K, Tanaka H, Kato Y, Negishi L, Hirota T, Sutani T, Bando M, Shirahige K.

Curr Biol. 2015 Jun 29;25(13):1694-706. doi: 10.1016/j.cub.2015.05.017. Epub 2015 Jun 4.

29.

Germline gain-of-function mutations in AFF4 cause a developmental syndrome functionally linking the super elongation complex and cohesin.

Izumi K, Nakato R, Zhang Z, Edmondson AC, Noon S, Dulik MC, Rajagopalan R, Venditti CP, Gripp K, Samanich J, Zackai EH, Deardorff MA, Clark D, Allen JL, Dorsett D, Misulovin Z, Komata M, Bando M, Kaur M, Katou Y, Shirahige K, Krantz ID.

Nat Genet. 2015 Apr;47(4):338-44. doi: 10.1038/ng.3229. Epub 2015 Mar 2.

30.

The chromosomal association of the Smc5/6 complex depends on cohesion and predicts the level of sister chromatid entanglement.

Jeppsson K, Carlborg KK, Nakato R, Berta DG, Lilienthal I, Kanno T, Lindqvist A, Brink MC, Dantuma NP, Katou Y, Shirahige K, Sjögren C.

PLoS Genet. 2014 Oct 16;10(10):e1004680. doi: 10.1371/journal.pgen.1004680. eCollection 2014 Oct.

31.

ATF1 modulates the heat shock response by regulating the stress-inducible heat shock factor 1 transcription complex.

Takii R, Fujimoto M, Tan K, Takaki E, Hayashida N, Nakato R, Shirahige K, Nakai A.

Mol Cell Biol. 2015 Jan;35(1):11-25. doi: 10.1128/MCB.00754-14. Epub 2014 Oct 13.

32.

Dimeric combinations of MafB, cFos and cJun control the apoptosis-survival balance in limb morphogenesis.

Suda N, Itoh T, Nakato R, Shirakawa D, Bando M, Katou Y, Kataoka K, Shirahige K, Tickle C, Tanaka M.

Development. 2014 Jul;141(14):2885-94. doi: 10.1242/dev.099150.

33.

Chromatin immunoprecipitation protocol for mammalian cells.

Komata M, Katou Y, Tanaka H, Nakato R, Shirahige K, Bando M.

Methods Mol Biol. 2014;1164:33-8. doi: 10.1007/978-1-4939-0805-9_4.

PMID:
24927833
34.

BRCA2 coordinates the activities of cell-cycle kinases to promote genome stability.

Yata K, Bleuyard JY, Nakato R, Ralf C, Katou Y, Schwab RA, Niedzwiedz W, Shirahige K, Esashi F.

Cell Rep. 2014 Jun 12;7(5):1547-1559. doi: 10.1016/j.celrep.2014.04.023. Epub 2014 May 15.

35.

Safety of gastrointestinal endoscopic biopsy in patients taking antithrombotics.

Fujita M, Shiotani A, Murao T, Ishii M, Yamanaka Y, Nakato R, Matsumoto H, Tarumi K, Manabe N, Kamada T, Hata J, Haruma K.

Dig Endosc. 2015 Jan;27(1):25-9. doi: 10.1111/den.12303. Epub 2014 Apr 27.

PMID:
24766557
36.

A cohesin-independent role for NIPBL at promoters provides insights in CdLS.

Zuin J, Franke V, van Ijcken WF, van der Sloot A, Krantz ID, van der Reijden MI, Nakato R, Lenhard B, Wendt KS.

PLoS Genet. 2014 Feb 13;10(2):e1004153. doi: 10.1371/journal.pgen.1004153. eCollection 2014 Feb.

37.

Histone variants enriched in oocytes enhance reprogramming to induced pluripotent stem cells.

Shinagawa T, Takagi T, Tsukamoto D, Tomaru C, Huynh LM, Sivaraman P, Kumarevel T, Inoue K, Nakato R, Katou Y, Sado T, Takahashi S, Ogura A, Shirahige K, Ishii S.

Cell Stem Cell. 2014 Feb 6;14(2):217-27. doi: 10.1016/j.stem.2013.12.015.

38.

Smc5/6-mediated regulation of replication progression contributes to chromosome assembly during mitosis in human cells.

Gallego-Paez LM, Tanaka H, Bando M, Takahashi M, Nozaki N, Nakato R, Shirahige K, Hirota T.

Mol Biol Cell. 2014 Jan;25(2):302-17. doi: 10.1091/mbc.E13-01-0020. Epub 2013 Nov 20.

39.

The dynamics of genome replication using deep sequencing.

Müller CA, Hawkins M, Retkute R, Malla S, Wilson R, Blythe MJ, Nakato R, Komata M, Shirahige K, de Moura AP, Nieduszynski CA.

Nucleic Acids Res. 2014 Jan;42(1):e3. doi: 10.1093/nar/gkt878. Epub 2013 Oct 1.

40.

Recurrent mutations in multiple components of the cohesin complex in myeloid neoplasms.

Kon A, Shih LY, Minamino M, Sanada M, Shiraishi Y, Nagata Y, Yoshida K, Okuno Y, Bando M, Nakato R, Ishikawa S, Sato-Otsubo A, Nagae G, Nishimoto A, Haferlach C, Nowak D, Sato Y, Alpermann T, Nagasaki M, Shimamura T, Tanaka H, Chiba K, Yamamoto R, Yamaguchi T, Otsu M, Obara N, Sakata-Yanagimoto M, Nakamaki T, Ishiyama K, Nolte F, Hofmann WK, Miyawaki S, Chiba S, Mori H, Nakauchi H, Koeffler HP, Aburatani H, Haferlach T, Shirahige K, Miyano S, Ogawa S.

Nat Genet. 2013 Oct;45(10):1232-7. doi: 10.1038/ng.2731. Epub 2013 Aug 18.

PMID:
23955599
41.

DROMPA: easy-to-handle peak calling and visualization software for the computational analysis and validation of ChIP-seq data.

Nakato R, Itoh T, Shirahige K.

Genes Cells. 2013 Jul;18(7):589-601. doi: 10.1111/gtc.12058. Epub 2013 May 15.

42.

Eukaryotic replisome components cooperate to process histones during chromosome replication.

Foltman M, Evrin C, De Piccoli G, Jones RC, Edmondson RD, Katou Y, Nakato R, Shirahige K, Labib K.

Cell Rep. 2013 Mar 28;3(3):892-904. doi: 10.1016/j.celrep.2013.02.028. Epub 2013 Mar 14.

43.

PRDM14 ensures naive pluripotency through dual regulation of signaling and epigenetic pathways in mouse embryonic stem cells.

Yamaji M, Ueda J, Hayashi K, Ohta H, Yabuta Y, Kurimoto K, Nakato R, Yamada Y, Shirahige K, Saitou M.

Cell Stem Cell. 2013 Mar 7;12(3):368-82. doi: 10.1016/j.stem.2012.12.012. Epub 2013 Jan 17.

44.

Telomere-binding protein Taz1 controls global replication timing through its localization near late replication origins in fission yeast.

Tazumi A, Fukuura M, Nakato R, Kishimoto A, Takenaka T, Ogawa S, Song JH, Takahashi TS, Nakagawa T, Shirahige K, Masukata H.

Genes Dev. 2012 Sep 15;26(18):2050-62. doi: 10.1101/gad.194282.112.

45.

HDAC8 mutations in Cornelia de Lange syndrome affect the cohesin acetylation cycle.

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.

Nature. 2012 Sep 13;489(7415):313-7. doi: 10.1038/nature11316.

46.

Replisome stability at defective DNA replication forks is independent of S phase checkpoint kinases.

De Piccoli G, Katou Y, Itoh T, Nakato R, Shirahige K, Labib K.

Mol Cell. 2012 Mar 9;45(5):696-704. doi: 10.1016/j.molcel.2012.01.007. Epub 2012 Feb 9.

47.

The inheritance of histone modifications depends upon the location in the chromosome in Saccharomyces cerevisiae.

Masumoto H, Nakato R, Kanemaki M, Shirahige K, Hachinohe M.

PLoS One. 2011;6(12):e28980. doi: 10.1371/journal.pone.0028980. Epub 2011 Dec 21.

48.

Origin association of Sld3, Sld7, and Cdc45 proteins is a key step for determination of origin-firing timing.

Tanaka S, Nakato R, Katou Y, Shirahige K, Araki H.

Curr Biol. 2011 Dec 20;21(24):2055-63. doi: 10.1016/j.cub.2011.11.038. Epub 2011 Dec 8.

49.

[A case report: small cell carcinoma of the ureter].

Koizumi K, Nakato R, Inoue Y, Yanagisawa Y, Kobayashi M.

Hinyokika Kiyo. 2011 Jan;57(1):21-4. Japanese.

50.

Cgaln: fast and space-efficient whole-genome alignment.

Nakato R, Gotoh O.

BMC Bioinformatics. 2010 Apr 30;11:224. doi: 10.1186/1471-2105-11-224.

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