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Items: 28

1.

CellFishing.jl: an ultrafast and scalable cell search method for single-cell RNA sequencing.

Sato K, Tsuyuzaki K, Shimizu K, Nikaido I.

Genome Biol. 2019 Feb 11;20(1):31. doi: 10.1186/s13059-019-1639-x.

2.

Polysaccharide hydrolase of the hadal zone amphipods Hirondellea gigas.

Kobayashi H, Nagahama T, Arai W, Sasagawa Y, Umeda M, Hayashi T, Nikaido I, Watanabe H, Oguri K, Kitazato H, Fujioka K, Kido Y, Takami H.

Biosci Biotechnol Biochem. 2018 Jul;82(7):1123-1133. doi: 10.1080/09168451.2018.1459178. Epub 2018 Apr 6.

PMID:
29623763
3.

Quartz-Seq2: a high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads.

Sasagawa Y, Danno H, Takada H, Ebisawa M, Tanaka K, Hayashi T, Kurisaki A, Nikaido I.

Genome Biol. 2018 Mar 9;19(1):29. doi: 10.1186/s13059-018-1407-3.

4.

Chromatin remodeler CHD7 regulates the stem cell identity of human neural progenitors.

Chai M, Sanosaka T, Okuno H, Zhou Z, Koya I, Banno S, Andoh-Noda T, Tabata Y, Shimamura R, Hayashi T, Ebisawa M, Sasagawa Y, Nikaido I, Okano H, Kohyama J.

Genes Dev. 2018 Jan 15;32(2):165-180. doi: 10.1101/gad.301887.117. Epub 2018 Feb 9.

5.

Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs.

Hayashi T, Ozaki H, Sasagawa Y, Umeda M, Danno H, Nikaido I.

Nat Commun. 2018 Feb 12;9(1):619. doi: 10.1038/s41467-018-02866-0.

6.

SCODE: an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation.

Matsumoto H, Kiryu H, Furusawa C, Ko MSH, Ko SBH, Gouda N, Hayashi T, Nikaido I.

Bioinformatics. 2017 Aug 1;33(15):2314-2321. doi: 10.1093/bioinformatics/btx194.

7.

Erratum to: Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity.

Sasagawa Y, Nikaido I, Hayashi T, Danno H, Uno KD, Imai T, Ueda HR.

Genome Biol. 2017 Jan 18;18(1):9. doi: 10.1186/s13059-017-1154-x. No abstract available.

8.

An application of MeSH enrichment analysis in livestock.

Morota G, Peñagaricano F, Petersen JL, Ciobanu DC, Tsuyuzaki K, Nikaido I.

Anim Genet. 2015 Aug;46(4):381-7. doi: 10.1111/age.12307. Epub 2015 Jun 2.

9.

A novel single - cell RNA sequencing method for safety and effective cell transplantation.

Nikaido I.

Nihon Rinsho. 2015 Jun;73 Suppl 5:365-8. Japanese. No abstract available.

PMID:
30458080
10.

MeSH ORA framework: R/Bioconductor packages to support MeSH over-representation analysis.

Tsuyuzaki K, Morota G, Ishii M, Nakazato T, Miyazaki S, Nikaido I.

BMC Bioinformatics. 2015 Feb 15;16:45. doi: 10.1186/s12859-015-0453-z.

11.

Context-dependent wiring of Sox2 regulatory networks for self-renewal of embryonic and trophoblast stem cells.

Adachi K, Nikaido I, Ohta H, Ohtsuka S, Ura H, Kadota M, Wakayama T, Ueda HR, Niwa H.

Mol Cell. 2013 Nov 7;52(3):380-92. doi: 10.1016/j.molcel.2013.09.002. Epub 2013 Oct 10.

12.

Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity.

Sasagawa Y, Nikaido I, Hayashi T, Danno H, Uno KD, Imai T, Ueda HR.

Genome Biol. 2013 Apr 17;14(4):R31. doi: 10.1186/gb-2013-14-4-r31. Erratum in: Genome Biol. 2017 Jan 18;18(1):9.

13.

An automated system for high-throughput single cell-based breeding.

Yoshimoto N, Kida A, Jie X, Kurokawa M, Iijima M, Niimi T, Maturana AD, Nikaido I, Ueda HR, Tatematsu K, Tanizawa K, Kondo A, Fujii I, Kuroda S.

Sci Rep. 2013;3:1191. doi: 10.1038/srep01191. Epub 2013 Feb 1.

14.

Transcriptome tomography for brain analysis in the web-accessible anatomical space.

Okamura-Oho Y, Shimokawa K, Takemoto S, Hirakiyama A, Nakamura S, Tsujimura Y, Nishimura M, Kasukawa T, Masumoto KH, Nikaido I, Shigeyoshi Y, Ueda HR, Song G, Gee J, Himeno R, Yokota H.

PLoS One. 2012;7(9):e45373. doi: 10.1371/journal.pone.0045373. Epub 2012 Sep 19.

15.

Quantitative expression profile of distinct functional regions in the adult mouse brain.

Kasukawa T, Masumoto KH, Nikaido I, Nagano M, Uno KD, Tsujino K, Hanashima C, Shigeyoshi Y, Ueda HR.

PLoS One. 2011;6(8):e23228. doi: 10.1371/journal.pone.0023228. Epub 2011 Aug 12.

16.

Id4, a new candidate gene for senile osteoporosis, acts as a molecular switch promoting osteoblast differentiation.

Tokuzawa Y, Yagi K, Yamashita Y, Nakachi Y, Nikaido I, Bono H, Ninomiya Y, Kanesaki-Yatsuka Y, Akita M, Motegi H, Wakana S, Noda T, Sablitzky F, Arai S, Kurokawa R, Fukuda T, Katagiri T, Schönbach C, Suda T, Mizuno Y, Okazaki Y.

PLoS Genet. 2010 Jul 8;6(7):e1001019. doi: 10.1371/journal.pgen.1001019.

17.

Integration of exogenous DNA into mouse embryonic stem cell chromosomes shows preference into genes and frequent modification at junctions.

Suzuki K, Ohbayashi F, Nikaido I, Okuda A, Takaki H, Okazaki Y, Mitani K.

Chromosome Res. 2010 Feb;18(2):191-201. doi: 10.1007/s10577-010-9111-5. Epub 2010 Feb 23.

PMID:
20177773
18.

Identification of novel PPARgamma target genes by integrated analysis of ChIP-on-chip and microarray expression data during adipocyte differentiation.

Nakachi Y, Yagi K, Nikaido I, Bono H, Tonouchi M, Schönbach C, Okazaki Y.

Biochem Biophys Res Commun. 2008 Jul 25;372(2):362-6. doi: 10.1016/j.bbrc.2008.05.037. Epub 2008 May 19.

PMID:
18489901
19.

[Analysis of gene networks during adipogenesis and osteoblastgenesis focusing on the crosstalk and redundant pathways].

Bono H, Yagi K, Nakachi Y, Nikaido I, Okazaki Y.

Tanpakushitsu Kakusan Koso. 2004 Dec;49(17 Suppl):2965-9. Review. Japanese. No abstract available.

PMID:
15669285
20.

EICO (Expression-based Imprint Candidate Organizer): finding disease-related imprinted genes.

Nikaido I, Saito C, Wakamoto A, Tomaru Y, Arakawa T, Hayashizaki Y, Okazaki Y.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D548-51.

21.

Development and evaluation of an automated annotation pipeline and cDNA annotation system.

Kasukawa T, Furuno M, Nikaido I, Bono H, Hume DA, Bult C, Hill DP, Baldarelli R, Gough J, Kanapin A, Matsuda H, Schriml LM, Hayashizaki Y, Okazaki Y, Quackenbush J.

Genome Res. 2003 Jun;13(6B):1542-51.

22.

Discovery of imprinted transcripts in the mouse transcriptome using large-scale expression profiling.

Nikaido I, Saito C, Mizuno Y, Meguro M, Bono H, Kadomura M, Kono T, Morris GA, Lyons PA, Oshimura M, Hayashizaki Y, Okazaki Y; RIKEN GER Group; GSL Members.

Genome Res. 2003 Jun;13(6B):1402-9.

23.

Comprehensive analysis of the mouse metabolome based on the transcriptome.

Bono H, Nikaido I, Kasukawa T, Hayashizaki Y, Okazaki Y; RIKEN GER Group; GSL Members.

Genome Res. 2003 Jun;13(6B):1345-9.

24.

Systematic expression profiling of the mouse transcriptome using RIKEN cDNA microarrays.

Bono H, Yagi K, Kasukawa T, Nikaido I, Tominaga N, Miki R, Mizuno Y, Tomaru Y, Goto H, Nitanda H, Shimizu D, Makino H, Morita T, Fujiyama J, Sakai T, Shimoji T, Hume DA, Hayashizaki Y, Okazaki Y; RIKEN GER Group; GSL Members.

Genome Res. 2003 Jun;13(6B):1318-23.

25.

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs.

Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, Nikaido I, Osato N, Saito R, Suzuki H, Yamanaka I, Kiyosawa H, Yagi K, Tomaru Y, Hasegawa Y, Nogami A, Schönbach C, Gojobori T, Baldarelli R, Hill DP, Bult C, Hume DA, Quackenbush J, Schriml LM, Kanapin A, Matsuda H, Batalov S, Beisel KW, Blake JA, Bradt D, Brusic V, Chothia C, Corbani LE, Cousins S, Dalla E, Dragani TA, Fletcher CF, Forrest A, Frazer KS, Gaasterland T, Gariboldi M, Gissi C, Godzik A, Gough J, Grimmond S, Gustincich S, Hirokawa N, Jackson IJ, Jarvis ED, Kanai A, Kawaji H, Kawasawa Y, Kedzierski RM, King BL, Konagaya A, Kurochkin IV, Lee Y, Lenhard B, Lyons PA, Maglott DR, Maltais L, Marchionni L, McKenzie L, Miki H, Nagashima T, Numata K, Okido T, Pavan WJ, Pertea G, Pesole G, Petrovsky N, Pillai R, Pontius JU, Qi D, Ramachandran S, Ravasi T, Reed JC, Reed DJ, Reid J, Ring BZ, Ringwald M, Sandelin A, Schneider C, Semple CA, Setou M, Shimada K, Sultana R, Takenaka Y, Taylor MS, Teasdale RD, Tomita M, Verardo R, Wagner L, Wahlestedt C, Wang Y, Watanabe Y, Wells C, Wilming LG, Wynshaw-Boris A, Yanagisawa M, Yang I, Yang L, Yuan Z, Zavolan M, Zhu Y, Zimmer A, Carninci P, Hayatsu N, Hirozane-Kishikawa T, Konno H, Nakamura M, Sakazume N, Sato K, Shiraki T, Waki K, Kawai J, Aizawa K, Arakawa T, Fukuda S, Hara A, Hashizume W, Imotani K, Ishii Y, Itoh M, Kagawa I, Miyazaki A, Sakai K, Sasaki D, Shibata K, Shinagawa A, Yasunishi A, Yoshino M, Waterston R, Lander ES, Rogers J, Birney E, Hayashizaki Y; FANTOM Consortium; RIKEN Genome Exploration Research Group Phase I & II Team.

Nature. 2002 Dec 5;420(6915):563-73.

PMID:
12466851
26.

Asb4, Ata3, and Dcn are novel imprinted genes identified by high-throughput screening using RIKEN cDNA microarray.

Mizuno Y, Sotomaru Y, Katsuzawa Y, Kono T, Meguro M, Oshimura M, Kawai J, Tomaru Y, Kiyosawa H, Nikaido I, Amanuma H, Hayashizaki Y, Okazaki Y.

Biochem Biophys Res Commun. 2002 Feb 8;290(5):1499-505.

PMID:
11820791
27.

Functional annotation of a full-length mouse cDNA collection.

Kawai J, Shinagawa A, Shibata K, Yoshino M, Itoh M, Ishii Y, Arakawa T, Hara A, Fukunishi Y, Konno H, Adachi J, Fukuda S, Aizawa K, Izawa M, Nishi K, Kiyosawa H, Kondo S, Yamanaka I, Saito T, Okazaki Y, Gojobori T, Bono H, Kasukawa T, Saito R, Kadota K, Matsuda H, Ashburner M, Batalov S, Casavant T, Fleischmann W, Gaasterland T, Gissi C, King B, Kochiwa H, Kuehl P, Lewis S, Matsuo Y, Nikaido I, Pesole G, Quackenbush J, Schriml LM, Staubli F, Suzuki R, Tomita M, Wagner L, Washio T, Sakai K, Okido T, Furuno M, Aono H, Baldarelli R, Barsh G, Blake J, Boffelli D, Bojunga N, Carninci P, de Bonaldo MF, Brownstein MJ, Bult C, Fletcher C, Fujita M, Gariboldi M, Gustincich S, Hill D, Hofmann M, Hume DA, Kamiya M, Lee NH, Lyons P, Marchionni L, Mashima J, Mazzarelli J, Mombaerts P, Nordone P, Ring B, Ringwald M, Rodriguez I, Sakamoto N, Sasaki H, Sato K, Schönbach C, Seya T, Shibata Y, Storch KF, Suzuki H, Toyo-oka K, Wang KH, Weitz C, Whittaker C, Wilming L, Wynshaw-Boris A, Yoshida K, Hasegawa Y, Kawaji H, Kohtsuki S, Hayashizaki Y; RIKEN Genome Exploration Research Group Phase II Team and the FANTOM Consortium.

Nature. 2001 Feb 8;409(6821):685-90.

PMID:
11217851
28.

Generation of 10,154 expressed sequence tags from a leafy gametophyte of a marine red alga, Porphyra yezoensis.

Nikaido I, Asamizu E, Nakajima M, Nakamura Y, Saga N, Tabata S.

DNA Res. 2000 Jun 30;7(3):223-7.

PMID:
10907854

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