Publications

Scientific papers

Preprint/submitted:

  1. Hinako M. Takase, Tappei Mishina, Tetsutaro Hayashi, Mika Yoshimura, Mariko Kuse, Itoshi Nikaido, Tomoya S. Kitajima. Transcriptomic Signatures of WNT-Driven Pathways and Granulosa Cell-Oocyte Interactions during Primordial Follicle Activation.
  2. Hiroki Sugishita, Kazunori Hojo, Tetsutaro Hayashi, Itoshi Nikaido, Yukiko Gotoh. A centrifugation-based method for high-throughput biomaterial separation using magnetic microbeads, Apr 26, 2023
  3. Ikkyu K, Nikaido I. MTL4MHC2: MHC class II binding prediction using multi-task learning from small training data

Published/in press:

2023

  1. Koki Tsuyuzaki*, Manabu Ishii, Itoshi Nikaido*. ScTensor detects many-to-many cell-cell interactions from single cell RNA-sequencing data. BMC bioinformatics, 24, (1), Nov 7, 2023, 420-420
  2. Yasuyuki Shima, Henrik Skibbe, Yohei Sasagawa, Noriko Fujimori, Yoshimi Iwayama, Ayako Isomura-Matoba, Minoru Yano, Takumi Ichikawa, Itoshi Nikaido, Nobutaka Hattori, Tadafumi Kato. Distinctiveness and continuity in transcriptome and connectivity in the anterior-posterior axis of the paraventricular nucleus of the thalamus. Cell reports, 42, (10), Oct 18, 2023, 113309-113309
  3. Nao Ogura, Yohei Sasagawa, Tasuku Ito, Toshiaki Tameshige, Satomi Kawai, Masaki Sano, Yuki Doll, Akira Iwase, Ayako Kawamura, Takamasa Suzuki, Itoshi Nikaido, Keiko Sugimoto, Momoko Ikeuchi. WUSCHEL-RELATED HOMEOBOX 13 suppresses de novo shoot regeneration via cell fate control of pluripotent callus. Science Advances, 9, (27), Jul 7, 2023
  4. Hitomi Takada*, Yohei Sasagawa*, Mika Yoshimura, Kaori Tanaka, Yoshimi Iwayama, Tetsutaro Hayashi, Ayako Isomura-Matoba, Itoshi Nikaido†, Akira Kurisaki†. Single-cell transcriptomics uncovers EGFR signaling-mediated gastric progenitor cell differentiation in stomach homeostasis. Nature communications, 14, (1), Jun 29, 2023, 3750-3750
  5. Koki Tsuyuzaki*, Kentaro Yamamoto, Yu Toyoshima, Hirofumi Sato, Manami Kanamori, Takayuki Teramoto, Takeshi Ishihara, Yuichi Iino, Itoshi Nikaido*. WormTensor: a clustering method for time-series whole-brain activity data from C. elegans. BMC bioinformatics, 24, (1), Jun 16, 2023, 254-254
  6. Koki Tsuyuzaki, Itoshi Nikaido. nnTensor: An R package for non-negative matrix/tensor decomposition. Journal of Open Source Software. Apr 23, 2023

2022

  1. Johannes N Wibisana, Takehiko Inaba, Hisaaki Shinohara, Noriko Yumoto, Tetsutaro Hayashi, Mana Umeda, Masashi Ebisawa, Itoshi Nikaido, Yasushi Sako, Mariko Okada. Enhanced transcriptional heterogeneity mediated by NF-κB super-enhancers. PLoS genetics 18(6) e1010235 2022/06/01
  2. Maik Herbig, Akihiro Isozaki, Dino Di Carlo, Jochen Guck, Nao Nitta, Robert Damoiseaux, Shogo Kamikawaji, Eigo Suyama, Hirofumi Shintaku, Angela Ruohao Wu, Itoshi Nikaido, Keisuke Goda. Best practices for reporting throughput in biomedical research. Nature methods 2022/05/04
  3. Chia-Wen Lin, Dian E. Septyaningtrias, Hsu-Wen Chao, Mikiko Konda, Koji Atarashi, Kozue Takeshita, Kota Tamada, Jun Nomura, Yohei Sasagawa, Kaori Tanaka, Itoshi Nikaido, Kenya Honda, Thomas J. McHugh, Toru Takumi. A common epigenetic mechanism across different cellular origins underlies systemic immune dysregulation in an idiopathic autism mouse model. Molecular Psychiatry. 02 May 2022.

2021

  1. Sabrina T. Amorim, Koki Tsuyuzaki, Itoshi Nikaido, and Gota Morota. Improved MeSH analysis software tools for farm animals. Animal Genetics. 2021.
  2. Tappei Mishina, Namine Tabata, Tetsutaro Hayashi, Mika Yoshimura, Mana Umeda, Masashi Mori, Yayoi Ikawa, Hiroshi Hamada, Itoshi Nikaido, Tomoya S. Kitajima. Single-oocyte transcriptome analysis reveals aging-associated effects influenced by life stage and calorie restriction. Aging Cell. 10 July 2021.
  3. Satoru Ishihara*, Yohei Sasagawa, Takeru Kameda, Mana Umeda, Hayato Yamashita, Naoe Kotomura, Masayuki Abe, Yohei Shimono, Itoshi Nikaido*. The local state of chromatin compaction at transcription start sites controls transcription levels. Nucleic Acid Research. gkab587. 07 July 2021. (*co-corresponding author)
  4. Ayumi Yamada, Takae Hirasawa, Kayako Nishimura, Chikako Shimura, Naomi Kogo, Kei Fukuda, Madoka Kato, Masaki Yokomori, Tetsutaro Hayashi, Mana Umeda, Mika Yoshimura, Yoichiro Iwakura, Itoshi Nikaido, Shigeyoshi Itohara, Yoichi Shinkai. Derepression of inflammation-related genes link to microglia activation and neural maturation defect in a mouse model of Kleefstra Syndrome. iScience. June 16, 2021
  5. Ritsuko Morita, Noriko Sanzen, Hiroko Sasaki, Tetsutaro Hayashi, Mana Umeda, Mika Yoshimura, Takaki Yamamoto, Tatsuo Shibata, Takaya Abe, Hiroshi Kiyonari, Yasuhide Furuta, Itoshi Nikaido, Hironobu Fujiwara. Tracing the origin of hair follicle stem cells. Nature. 09 June 2021

2020

  1. Tomoyo Sawada, Thomas E. Chater*, Yohei Sasagawa*, Mika Yoshimura, Noriko Fujimori-Tonou, Kaori Tanaka, Kynon J. M. Benjamin, Apuã C. M. Paquola, Jennifer A. Erwin, Yukiko Goda, Itoshi Nikaido, Tadafumi Kato. Developmental Excitation-Inhibition Imbalance Underlying Psychoses Revealed by Single-Cell Analyses of Discordant Twins-Derived Cerebral Organoids. Molecular Psychiatry. 25, 2695–2711. 07 August 2020 (*These authors contributed equally)
  2. Hiroshi Ochiai, Tetsutaro Hayashi, Mana Umeda, Mika Yoshimura, Akihito Harada, Yukiko Shimizu, Kenta Nakano, Noriko Saitoh, Hiroshi Kimura, Zhe Liu, Takashi Yamamoto, Tadashi Okamura, Yasuyuki Ohkawa, Itoshi Nikaido. Genome-wide analysis of transcriptional bursting-induced noise in mammalian cells. Science Advances 17 Jun 2020: Vol. 6, no. 25, eaaz6699.
  3. Hiroki Michida, Hiroaki Imoto, Hisaaki Shinohara, Noriko Yumoto, Masahide Seki, Mana Umeda, Tetsutaro Hayashi, Itoshi Nikaido, Kasukawa Takeya, Yutaka Suzuki, Mariko Okada-Hatakeyama. The number of transcription factors at an enhancer determine switch-like gene expression. Cell Reports. VOLUME 31, ISSUE 9, 107724, JUNE 02, 2020.
  4. Elisabetta Mereu, Atefeh Lafzi, Catia Moutinho, Christoph Ziegenhain, Davis J. McCarthy, Adrian Alvarez, Eduard Batlle, Sagar, Dominic Grün, Julia K. Lau, Stéphane C. Boutet, Chad Sanada, Aik Ooi, Robert C. Jones, Kelly Kaihara, Chris Brampton, Yasha Talaga, Yohei Sasagawa, Kaori Tanaka, Tetsutaro Hayashi, Caroline Braeuning, Cornelius Fischer, Sascha Sauer, Timo Trefzer, Christian Conrad, Xian Adiconis, Lan T. Nguyen, Aviv Regev, Joshua Z. Levin, Swati Parekh, Aleksandar Janjic, Lucas E. Wange, Johannes W. Bagnoli, Wolfgang Enard, Marta Gut, Rickard Sandberg, Itoshi Nikaido, Ivo Gut, Oliver Stegle, Holger Heyn. Benchmarking Single-Cell RNA Sequencing Protocols for Cell Atlas Projects. Nature Biotechnology.
  5. Seiji Shiozawa, Mayutaka Nakajima, Junko Okahara, Yoko Kuortaki, Fumihiko Kisa, Sho Yoshimatsu, Mari Nakamura, Ikuko Koya, Mika Yoshimura, Yohei Sasagawa, Itoshi Nikaido, Erika Sasaki, and Hideyuki Okano. Primed to naïve-like conversion of the common marmoset embryonic stem cells. Stem Cells and Development. 18 Mar 2020.
  6. Haruka Ozaki, Tetsutaro Hayashi, Umeda Mana, Itoshi Nikaido. Millefy: visualizing cell-to-cell heterogeneity in read coverage of single-cell RNA sequencing datasets. BMC Genomics volume 21, Article number: 177, 2020.
  7. Hirotaka Matsumoto, Tetsutaro Hayashi, Haruka Ozaki, Koki Tsuyuzaki, Mana Umeda, Tsuyoshi Iida, Masaya Nakamura, Hideyuki Okano, Itoshi Nikaido. A NMF-based approach to discover overlooked differentially expressed gene regions from single-cell RNA-seq data. NAR Genomics and Bioinformatics, Volume 2, Issue 1, March 2020.
  8. Koki Tsuyuzaki, Hiroyuki Sato, Kenta Sato, Itoshi Nikaido. Benchmarking principal component analysis for large-scale single-cell RNA-sequencing. Genome Biology. 21, Article number: 9, 2020.

2019

  1. Akinori Okumura, Tetsutaro Hayashi, Masashi Ebisawa, Mika Yoshimura, Yohei Sasagawa, Itoshi Nikaido, Yoshihiko Umesono, Makoto Mochii. Cell type-specific transcriptome analysis unveils secreted signaling molecule genes expressed in apical epithelial cap during appendage regeneration. Development Growth and Differentiation. 11 November 2019
  2. Yohei Sasagawa, Tetsutaro Hayashi and Itoshi Nikaido. Strategies for converting RNA to amplifiable cDNA for single-cell RNA sequencing methods. Single Molecular and Single Cell Sequencing. Advances in Experimental Medicine and Biology. Springer (Invited review). Apr 10 2019.
  3. Kenta Sato, Koki Tsuyuzaki, Kentaro Shimizu, Itoshi Nikaido. CellFishing.jl: an ultrafast and scalable cell search method for single-cell RNA-sequencing. Genome Biology. 20, Article number: 31, 2019

2018

  1. Hideki Kobayashi, Takahiko Nagahama, Wataru Arai, Yohei Sasagawa, Mana Umeda, Tetsutaro Hayashi, Itoshi Nikaido, Hiromi Watanabe, Kazumasa Oguri, Hiroshi Kitazawa, Kantaro Fujioka, Yukari Kido, Hideto Takami. Polysaccharide hydrolase of the hadal zone amphipods Hirondellea gigas. Bioscience, Biotechnology, and Biochemistry. 1123-1133, 06 Apr. 2018.
  2. Yohei Sasagawa*, Hiroki Danno*, Hitomi Takada*, Masashi Ebisawa, Tetsutaro Hayashi, Akira Kurisaki†, Itoshi Nikaido†. Quartz-Seq2: a high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads. Genome Biology. 19, Article number: 29. 2018.
  3. Tetsutaro Hayashi*, Haruka Ozaki*, Yohei Sasagawa, Mana Umeda, Hiroki Danno, Itoshi Nikaido. Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs. Nature Communications. 9, Article number: 619, 2018.
  4. MuhChyi Chai, Tsukasa Sanosaka, Hironobu Okuno, Zhi Zhou, Ikuko Koya, Satoe Banno, Tomoko Andoh-Noda, Yoshikuni Tabata, Rieko Shimamura, Tetsutaro Hayashi, Masashi Ebisawa, Yohei Sasagawa, Itoshi Nikaido, Hideyuki Okano, and Jun Kohyama. The chromatin remodeler CHD7 regulates stem cell identity of human neural progenitors. Genes and Development. February 9, 2018, doi: 10.1101/gad.301887.117.
  5. Koki Tsuyuzak and Itoshi Nikaido. Biological Systems as Heterogeneous Information Networks: A Mini-review and Perspectives. HeteroNAM’18. WSDM2018. 2018.

-2017

  1. Matsumoto H, Kiryu H, Furusawa C, Ko MSH, Ko SBH, Gouda N, Hayashi T, Nikaido I. SCODE: An efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation. Bioinformatics, Volume 33, Issue 15, 1 August 2017, Pages 2314–2321.
  2. Haiyang Hu, Masahiro Uesaka, Song Guo, Kotaro Shimai, Tsai-Ming Lu, Fang Li, Satoko Fujimoto, Masato Ishikawa, Shiping Liu, Yohei Sasagawa, Guojie Zhang, Shigeru Kuratani, Jr-Kai Yu, Takehiro G. Kusakabe, Philipp Khaitovich, Naoki Irie; the EXPANDE Consortium. Constrained vertebrate evolution by pleiotropic genes. Nature Ecology & Evolution,1, 1722–1730 2017.
  3. G. Morota, F. Peñagaricano, J. L. Petersen, D. C. Ciobanu, K. Tsuyuzaki and I.
    Nikaido. An application of MeSH enrichment analysis in livestock. Animal Genetics. 2015.
  4. Koki Tsuyuzaki, Gota Morota, Takeru Nakazato, Satoru Miyazaki and Itoshi Nikaido. MeSH ORA framework: R/Bioconductor packages to support MeSH over-representation analysis. BMC Bioinformatics. 2015, 16:45.
  5. Kenjiro Adachi*, Itoshi Nikaido*, Hiroshi Ohta, Satoshi Ohtsuka, Hiroki Ura, Teruhiko Wakayama, Hiroki R. Ueda & Hitoshi Niwa. Context-Dependent Wiring of Sox2 Regulatory Networks for Self-Renewal of Embryonic and Trophoblast Stem Cells. Molecular Cell. 2013. (*Equally contributions)
  6. Sasagawa Y*, Nikaido I*, Hayashi T, Danno H, Uno KD, Imai T and Ueda HR. Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity. Genome Biology. 14. 2013 (*Equally contributions)
  7. Yoshimoto N, Kida A, Xu J, Kurokawa M, Iijima M, Niimi T, Maturana AD, Nikaido I, Ueda HR, Tatematsu K, Tanizawa K, Kondo A, Fujii I & Kuroda S. An automated system for high-throughput single cell-based breeding. Scientific Reports 3, Article number: 1191. 2013.
  8. Okamura-Oho Y, Shimokawa K, Takemoto S, Hirakiyama A, Nakamura S, Tsujimura Y, Nishimura M, Kasukawa T, Masumoto K, Nikaido I, Shigeyoshi Y, Ueda HR, Song G, Gee J, Himeno R, Yokota H. Transcriptome Tomography for Brain Analysis in the Web-Accessible Anatomical Space. PLoS ONE 7(9): e45373. 2012
  9. Kasukawa T*, Masumoto KH*, Nikaido I*, Nagano M, Uno KD, Tsujino K, Hanashima C, Shigeyoshi Y, Ueda HR. Quantitative expression profile of distinct functional regions in the adult mouse brain. PLoS One. 2011;6(8):e23228. Epub 2011 Aug 12. (*Equally contributions)
  10. 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. Id4, a new candidate gene for senile osteoporosis, acts as a molecular switch promoting osteoblast differentiation. PLoS Genet. 2010 Jul 8;6(7):e1001019.
  11. Suzuki K, Ohbayashi F, Nikaido I, Okuda A, Takaki H, Okazaki Y, Mitani K. Integration of exogenous DNA into mouse embryonic stem cell chromosomes shows preference into genes and frequent modification at junctions. Chromosome Res. 2010 Feb;18(2):191-201. Epub 2010 Feb 23.
  12. Nakachi Y, Yagi K, Nikaido I, Bono H, Tonouchi M, Schönbach C, Okazaki Y. Identification of novel PPARgamma target genes by integrated analysis of ChIP-on-chip and microarray expression data during adipocyte differentiation. Biochem Biophys Res Commun. 2008 Jul 25;372(2):362-6. Epub 2008 May 19.
  13. Nikaido I, Saito C, Wakamoto A, Tomaru Y, Arakawa T, Hayashizaki Y, Okazaki Y. EICO (Expression-based Imprint Candidate Organizer): finding disease-related imprinted genes. Nucleic Acids Res. 2004 Jan 1;32:D548-51.
  14. 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. Discovery of imprinted transcripts in the mouse transcriptome using large-scale expression profiling. Genome Res. 2003 Jun;13(6B):1402-9.
  15. 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. Development and evaluation of an automated annotation pipeline and cDNA annotation system. Genome Res. 2003 Jun;13(6B):1542-51.
  16. Bono H, Nikaido I, Kasukawa T, Hayashizaki Y, Okazaki Y; RIKEN GER Group; GSL Members. Comprehensive analysis of the mouse metabolome based on the transcriptome. Genome Res. 2003 Jun;13(6B):1345-9.
  17. 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. Systematic expression profiling of the mouse transcriptome using RIKEN cDNA microarrays. Genome Res. 2003 Jun;13(6B):1318-23.
  18. 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. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature. 2002 Dec 5;420(6915):563-73.
  19. 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. Asb4, Ata3, and Dcn are novel imprinted genes identified by high-throughput screening using RIKEN cDNA microarray. Biochem Biophys Res Commun. 2002 Feb 8;290(5):1499-505.
  20. 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. Functional annotation of a full-length mouse cDNA collection. Nature. 2001 Feb 8;409(6821):685-90.
  21. Nikaido I, Asamizu E, Nakajima M, Nakamura Y, Saga N, Tabata S. Generation of 10,154 expressed sequence tags from a leafy gametophyte of a marine red alga, Porphyra yezoensis. DNA Res. 2000 Jun 30;7(3):223-7.

日本語総説・書籍 (Scientific Review & Books in Japanese)

  • 2019
    • 笹川 洋平, 二階堂 愛 バイオイノベーションに向けて～バイオテクノロジーの新技術からの新しい視点～ 第1章　分子バーコードの視点から 1細胞RNAシーケンス法を支えるバーコード配列技術とcDNA分子変換技術. シーエムシー出版   2019年3月   抜き刷りを以下からリクエストできます。
      https://forms.gle/Rzi4NZiznB763VXx6
  •  2018
    • 二階堂愛. 1細胞トランスクリプトーム技術の最先端. Medical Science Digest. Vol.44, No.1, 2018.
  • 2017
    • 二階堂愛. 1細胞オミックス計測技術. リキッドバイオプシー. シーエムシー出版. 159-164. 2017年8月31日.
      團野宏樹, 二階堂愛. 1細胞トランスクリプトーム解析の高出力化と自動化. 生体の科学. 68(2) 178-184. 2017.
  • 2016
  • 2015
    • 二階堂愛, 1細胞からのlncRNAの網羅的計測. 実験医学増刊. ノンコーディングRNAテキストブック. 2015年10月. 羊土社.
    • 露崎弘毅, 二階堂愛. 1細胞RNA-Seqのヒートマップによる可視化と相互情報量による発現分布差解析 (R+biomaRt+reshap2+ggplot2+entory). 次世代シークエンサーDRY解析教本. 2015年10月. 秀潤社.
    • 二階堂愛, iPS・分化細胞集団の不均質性を1細胞・全遺伝子解像度で高速計測する技術の開発. 再生医療 ー新たな医療を求めてー. 2015(刊行予定). 日本臨牀社
    • 二階堂愛, 笹川洋平. 網羅的な1細胞遺伝子発現計測とデータ解析手法の現状と将来. 2015年1月. 実験医学. 羊土社.
  • 2014
    • 二階堂愛 (編). 次世代シークエンス解析スタンダード〜NGSのポテンシャルを活かしきるWET&DRY. 羊土社. 2014
      • 二階堂愛. RとBioconductorでChIP-seqデータを解析する.
      • 笹川洋平. 二階堂愛. 1細胞から遺伝子発言を網羅的にみる
      • 團野宏樹. 笹川洋平. 二階堂愛. メチル化結合タンパク質でDNAメチル化を定量する.
    • 荒引健, 石田基広, 高橋康介, 林真広, 二階堂愛. R言語上級ハンドブック. シーアンドアール研究所
  • 2013
  • -2011
    • 二階堂愛: オープンソースで学ぶバイオインフォマティクス (1, 2, 4章, 付録A, B). Open Bio Japan編, 東京電機大学出版局. 2008.
    • 二階堂愛: 医学・生物学研究のための検索エンジン活用. バイオデータベースとウェブツールの手とり足とり活用法, 改訂第2版. 羊土社. 2007.
    • 二階堂愛. 知識ベースを利用した分子間相互作用 – IPAの利用法. 分子間相互作用解析ハンドブック. 羊土社. 2007.Itoshi Nikaido: 第4章 2色蛍光スポット型アレイの前処理 (Chapter 4: Preprocessing Two-Color Spotted Arrays), RとBioconductorを用いたバイオインフォマティクス (Bioinformatics and Computational Biology Solutions Using R and Bioconductor), pp. 55-79, Springer Japan, 2007.
    • 二階堂愛. 第5章 セルベースアッセイ (Chapter 5: Cell-Based Assays), RとBioconductorを用いたバイオインフォマティクス (Bioinformatics and Computational Biology Solutions Using R and Bioconductor), pp. 81-105, Springer Japan, 2007.
    • 二階堂愛. 統計解析環境Rのゲノム解析向けライブラリ集 Bioconductor. 人工知能学会誌. vol.22 no.1 (2007年1月)
    • 二階堂愛. バイオインフォマティクスの扉を開き、裾野を広げるKNOB. 特集:バイオインフォマティクスの親潮流, 日本バイオインフォマティクス学会ニュースレター 第12号. Feb. 2006.
    • 二階堂愛. 遺伝学とマイクロアレイの統合による疾患遺伝子の発見. ゲノム情報はこう活かせ！比較ゲノム学を遺伝子・タンパク質の機能解析や疾患遺伝子探索に活用する. 岡崎康司、坊農秀雅 編集 羊土社 ISBN 4-89706-485-6. 2005
    • 二階堂愛. 第2章. 配列の収集と蓄積. バイオインフォマティクス ゲノム配列から機能解析へ 第2版. 岡崎康司、坊農秀雅 監訳 メディカルサイエンスインターナショナル. ISBN4-89592-426-2. (原著 “Bioinformatics: Sequence and Genome Analysis 2nd edition” by David W. Mount Cold Spring Harbor Laboratory Press) 2005.
    • 二階堂愛. ゲノムネットワーク時代を生き抜くためのシグナルパスウェイと遺伝子ネットワークの知識ベース.  2005. テクノトレンド. Bioテクノロジージャーナル. 1-2月号.  羊土社.
    • 二階堂愛. ゲノム医学研究のためのインターネットリソース. ゲノムと疾患. 村松正實 監修 南山堂 ISBN 4-52513-051-2. 2004
    • 坊農秀雅、八木研、仲地豊、二階堂愛、岡崎康司 脂肪・骨芽細胞分化ネットワークのクロストークと冗長性の解明. 2004
    • 二階堂愛. 配列の取扱い.  EMBOSSを用いた配列解析への手引き. JAMBO JAMBO (Japan EMBOSS Users Group). (原著 The Administrator’s Guide by David Martin, Peter Rice, Alan Bleasby)
    • 二階堂愛. EMBOSSを用いた配列解析への手引き. JAMBO JAMBO (Japan EMBOSS Users Group). (原著 The Administrator’s Guide by David Martin, Peter Rice, Alan Bleasby)
    • 二階堂愛. EMBOSSのインストール. EMBOSS管理者の手引き. JAMBO (Japan EMBOSS Users Group). (原著 The Administrator’s Guide by David Martin, Peter Rice, Alan Bleasby)
    • 二階堂愛. 第2章. 配列の収集と蓄積. バイオインフォマティクス ゲノム配列から機能解析へ. 岡崎康司、坊農秀雅 監訳 メディカルサイエンスインターナショナル ISBN4-89592-307-X. (原著 “Bioinformatics: Sequence and Genome Analysis” by David W. Mount Cold Spring Harbor Laboratory Press)