Nikaido Itoshi 二階堂愛

… Alternative Names

NIKAIDO Itoshi 二階堂愛

二階堂愛ニカイドウイトシ

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Researcher Number	00383290
Other IDs
Affiliation (Current)	2025: 東京科学大学, 総合研究院, 教授 2025: 国立研究開発法人理化学研究所, 最先端研究プラットフォーム連携(TRIP)事業本部, チームディレクター
Affiliation (based on the past Project Information) *help	2019 – 2024: 国立研究開発法人理化学研究所, 生命機能科学研究センター, チームリーダー 2017 – 2018: 国立研究開発法人理化学研究所, 生命機能科学研究センター, ユニットリーダー 2016: 独立行政法人理化学研究所, 情報基盤センター, ユニットリーダー 2015: 国立研究開発法人理化学研究所, 情報基盤センター, ユニットリーダー 2013 – 2014: 独立行政法人理化学研究所, 情報基盤センター, ユニットリーダー 2004: 埼玉医科大学, 医学部, 研究員
Review Section/Research Field	Principal Investigator System genome science Except Principal Investigator Medium-sized Section 45:Biology at organismal to population levels and anthropology, and related fields / Transformative Research Areas, Section (III) / Biomedical engineering/Biomaterial science and engineering / Medium-sized Section 53:Organ-based internal medicine and related fields / Genome biology / Biological Sciences
Keywords	Principal Investigator バイオインフォマティクス Except Principal Investigator オミックス解析 / ゲノム / 細胞性粘菌 / アメーボゾア / 細胞極性 / 細胞間接着 / 形態形成 / 神経細胞 / 遺伝子発現 … More / オミックス / 神経回路 / 細胞型 / バイオインフォマティクス / オミクス解析 / シングルセル / hiPSダブルノックイン / β細胞 / single cell / hiPS / single cell analysis / beta cell / がんゲノム / 多層オミックス / ゲノム解析 / プロテオーム / ＲＮＡ / 免疫 / 腫瘍免疫 / 分子標的治療 / 分子分類 / 肝胆膵がん / ヒストン修飾 / セントロメア / 次世代シーケンサー / CYP19 / プロモーター / 転写 / SEVENS法 / ヌクレオソーム / クロマチン / マイクロアレイ / 遺伝子 / 遺伝学 / 脂質 Less

Exploring evolution of multicellularity and ancient molecular mechanisms underlying morphogenetic movement in amoebozoa
- Principal Investigator
  
  澤井哲
- Project Period (FY)
  2023 – 2026
- Research Category
  
  Grant-in-Aid for Scientific Research (A)
- Review Section
  
  Medium-sized Section 45:Biology at organismal to population levels and anthropology, and related fields
- Research Institution
  The University of Tokyo
Development of comprehensive cell type census technology for adaptive neuronal circuits
- Principal Investigator
  
  郷康広
- Project Period (FY)
  2021 – 2025
- Research Category
  
  Grant-in-Aid for Transformative Research Areas (A)
- Review Section
  
  Transformative Research Areas, Section (III)
- Research Institution
  University of Hyogo
  Center for Novel Science Initatives, National Institutes of Natural Sciences
Multi-omics analysis for hepato-biliary-pancreatic cancers
- Principal Investigator
  
  Nakagawa Hidewaki
- Project Period (FY)
  2018 – 2020
- Research Category
  
  Grant-in-Aid for Scientific Research (A)
- Review Section
  
  Medium-sized Section 53:Organ-based internal medicine and related fields
- Research Institution
  Institute of Physical and Chemical Research
Development and finding the mechanism of pancreatic beta cell differentiation from hiPS cells through Single cell analysis
- Principal Investigator
  
  Sugahara Izumi
- Project Period (FY)
  2015 – 2017
- Research Category
  
  Grant-in-Aid for Young Scientists (B)
- Research Field
  
  Biomedical engineering/Biomaterial science and engineering
- Research Institution
  National Center for Global Health and Medicine
  Saitama Medical University
Chromatin structure as a determinant of transcriptional activity
- Principal Investigator
  
  Ishihara Satoru
- Project Period (FY)
  2014 – 2016
- Research Category
  
  Grant-in-Aid for Scientific Research (C)
- Research Field
  
  Genome biology
- Research Institution
  Fujita Health University
Model of mRNA transcription and transcriptional factor bindingPrincipal Investigator
- Principal Investigator
  
  NIKAIDO Itoshi
- Project Period (FY)
  2013 – 2015
- Research Category
  
  Grant-in-Aid for Young Scientists (B)
- Research Field
  
  System genome science
- Research Institution
  Institute of Physical and Chemical Research
遺伝学とトランスクリプトームの統合による高脂血症の遺伝子ネットワークの解明
- Principal Investigator
  
  Okazaki Yasushi
- Project Period (FY)
  2004
- Research Category
  
  Grant-in-Aid for Scientific Research on Priority Areas
- Review Section
  
  Biological Sciences
- Research Institution
  Saitama Medical University

All 2024 2023 2022 2021 2016 2014 2013 2004 Other

All Journal Article Presentation Book

[Book] 新世代フローサイトメトリー活用スタンダード2021
- Author(s)
  芳村美佳，林哲太郎，二階堂愛（分担執筆），清田純、山本拓也（共同編集）
- Total Pages
  320
- Publisher
  羊土社
- ISBN
  9784758122542
- Data Source
  KAKENHI-PLANNED-21H05245
[Book] 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&DRY2014
- Author(s)
  二階堂愛
- Total Pages
  404
- Publisher
  羊土社
- Data Source
  KAKENHI-PROJECT-25830148
[Book] 次世代シーケンサーのその先に -シーケンス技術の現在と未来を考える- 細胞工学2013
- Author(s)
  二階堂愛
- Total Pages
  2
- Publisher
  学研メディカル秀潤社
- Data Source
  KAKENHI-PROJECT-25830148
[Book] NGSによる転写制御ネットワークのモデリング. 実験医学2013
- Author(s)
  二階堂愛
- Total Pages
  4
- Publisher
  羊土社
- Data Source
  KAKENHI-PROJECT-25830148
[Journal Article] Transcriptomic Signatures of WNT-Driven Pathways and Granulosa Cell-Oocyte Interactions during Primordial Follicle Activation.2024
- Author(s)
  Hinako M. Takase, Tappei Mishina, Tetsutaro Hayashi, Mika Yoshimura, Mariko Kuse, Itoshi Nikaido, Tomoya S. Kitajima.
- Journal Title
  
  bioRxiv
  
  Volume: -
- DOI
  10.1101/2024.02.08.579446
- Open Access
- Data Source
  KAKENHI-PROJECT-22KJ3149, KAKENHI-PLANNED-21H05245
[Journal Article] Sctensor detects many-to-many cell-cell interactions from single cell RNA-sequencing data2023
- Author(s)
  Tsuyuzaki Koki、Ishii Manabu、Nikaido Itoshi
- Journal Title
  
  BMC Bioinformatics
  
  Volume: 24 Issue: 1 Pages: 420-420
- DOI
  10.1186/s12859-023-05490-y
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-23K11312, KAKENHI-PLANNED-21H05245
[Journal Article] Single-cell transcriptomics uncovers EGFR signaling-mediated gastric progenitor cell differentiation in stomach homeostasis2023
- Author(s)
  Takada Hitomi、Sasagawa Yohei、Yoshimura Mika、Tanaka Kaori、Iwayama Yoshimi、Hayashi Tetsutaro、Isomura-Matoba Ayako、Nikaido Itoshi、Kurisaki Akira
- Journal Title
  
  Nature Communications
  
  Volume: 14 Issue: 1 Pages: 3750-3750
- DOI
  10.1038/s41467-023-39113-0
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PLANNED-21H05245
[Journal Article] Distinctiveness and continuity in transcriptome and connectivity in the anterior-posterior axis of the paraventricular nucleus of the thalamus2023
- Author(s)
  Shima Yasuyuki、Skibbe Henrik、Sasagawa Yohei、Fujimori Noriko、Iwayama Yoshimi、Isomura-Matoba Ayako、Yano Minoru、Ichikawa Takumi、Nikaido Itoshi、Hattori Nobutaka、Kato Tadafumi
- Journal Title
  
  Cell Reports
  
  Volume: 42 Issue: 10 Pages: 113309-113309
- DOI
  10.1016/j.celrep.2023.113309
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PLANNED-21H05245
[Journal Article] nnTensor: An R package for non-negative matrix/tensordecomposition2023
- Author(s)
  Tsuyuzaki Koki、Nikaido Itoshi
- Journal Title
  
  Journal of Open Source Software
  
  Volume: 8 Issue: 84 Pages: 5015-5015
- DOI
  10.21105/joss.05015
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-23K11312, KAKENHI-PLANNED-21H05245
[Journal Article] Maternal epigenetic factors in embryonic and postnatal development2023
- Author(s)
  Nishimura Hiromi、Ikawa Yayoi、Kajikawa Eriko、Shimizu‐Mizuno Natsumi、Hiver Sylvain、Tabata‐Okamoto Namine、Mori Masashi、Kitajima Tomoya、Hayashi Tetsutaro、Yoshimura Mika、Umeda Mana、Nikaido Itoshi、Kurokawa Mineo、Watanabe Toshio、Hamada Hiroshi
- Journal Title
  
  Genes to Cells
  
  Volume: 28 Issue: 6 Pages: 422-432
- DOI
  10.1111/gtc.13024
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PLANNED-21H05245, KAKENHI-PROJECT-21H02407, KAKENHI-PLANNED-18H05549, KAKENHI-PLANNED-23H04948
[Journal Article] Author Correction: Single-cell transcriptomics uncovers EGFR signaling-mediated gastric progenitor cell differentiation in stomach homeostasis2023
- Author(s)
  Takada Hitomi、Sasagawa Yohei、Yoshimura Mika、Tanaka Kaori、Iwayama Yoshimi、Hayashi Tetsutaro、Isomura-Matoba Ayako、Nikaido Itoshi、Kurisaki Akira
- Journal Title
  
  Nature Communications
  
  Volume: 14 Issue: 1 Pages: 6540-6540
- DOI
  10.1038/s41467-023-41823-4
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PLANNED-21H05245
[Journal Article] A centrifugation-based method for high-throughput biomaterial separation using magnetic microbeads2023
- Author(s)
  Sugishita Hiroki、Hojo Kazunori、Hayashi Tetsutaro、Nikaido Itoshi、Gotoh Yukiko
- Journal Title
  
  bioRxiv
  
  Volume: -
- DOI
  10.1101/2023.04.26.538353
- Open Access
- Data Source
  KAKENHI-PROJECT-22K15118, KAKENHI-PLANNED-21H05245
[Journal Article] WormTensor: a clustering method for time-series whole-brain activity data from C. elegans2023
- Author(s)
  Tsuyuzaki, K., Yamamoto, K., Toyoshima, Y., Sato, H., Kanamori, M., Teramoto, T., Ishihara, T., Iino, Y., and Nikaido, I.
- Journal Title
  
  BMC Bioinformatics
  
  Volume: 24 Issue: 1 Pages: 254-254
- DOI
  10.1186/s12859-023-05230-2
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-23K18149, KAKENHI-PROJECT-21K15182, KAKENHI-PROJECT-23K05958, KAKENHI-PROJECT-23K11312, KAKENHI-PROJECT-20K21805, KAKENHI-PUBLICLY-22H04838, KAKENHI-PLANNED-21H05245
[Journal Article] WUSCHEL-RELATED HOMEOBOX 13 suppresses de novo shoot regeneration via cell fate control of pluripotent callus2023
- Author(s)
  Ogura Nao、Sasagawa Yohei、Ito Tasuku、Tameshige Toshiaki、Kawai Satomi、Sano Masaki、Doll Yuki、Iwase Akira、Kawamura Ayako、Suzuki Takamasa、Nikaido Itoshi、Sugimoto Keiko、Ikeuchi Momoko
- Journal Title
  
  Science Advances
  
  Volume: 9 Issue: 27
- DOI
  10.1126/sciadv.adg6983
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-23KJ1579, KAKENHI-PROJECT-22K05586, KAKENHI-PUBLICLY-22H04713, KAKENHI-PLANNED-20H05911, KAKENHI-PLANNED-21H05245
[Journal Article] Best practices for reporting throughput in biomedical research2022
- Author(s)
  Herbig Maik、Isozaki Akihiro、Di Carlo Dino、Guck Jochen、Nitta Nao、Damoiseaux Robert、Kamikawaji Shogo、Suyama Eigo、Shintaku Hirofumi、Wu Angela Ruohao、Nikaido Itoshi、Goda Keisuke
- Journal Title
  
  Nature Methods
  
  Volume: 19 Issue: 6 Pages: 633-634
- DOI
  10.1038/s41592-022-01483-6
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-21H05245, KAKENHI-PROJECT-19H05633, KAKENHI-PROJECT-20H00317
[Journal Article] A common pathologic mechanism across cellular origins underlies systemic immune dysregulation in an idiopathic autism mouse model.2022
- Author(s)
  Lin C-W, Septyaningtrias DE, Chao H-W, Konda M, Atarashi K, Takeshita K, Tamada K, Nomura J, Sassagawa Y, Tanaka K, Nikaido I, Honda K, McHugh TL, Takumi T
- Journal Title
  
  Mol Psychiatr
  
  Volume: in press Issue: 8 Pages: 3343-3354
- DOI
  10.1038/s41380-022-01566-y
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16H06316, KAKENHI-PUBLICLY-21H00202, KAKENHI-PROJECT-21H04813, KAKENHI-PROJECT-21K19351, KAKENHI-PROJECT-21K07820, KAKENHI-PLANNED-21H05245, KAKENHI-PROJECT-19K16529
[Journal Article] Enhanced transcriptional heterogeneity mediated by NF-κB super-enhancers2022
- Author(s)
  Wibisana Johannes N.、Inaba Takehiko、Shinohara Hisaaki、Yumoto Noriko、Hayashi Tetsutaro、Umeda Mana、Ebisawa Masashi、Nikaido Itoshi、Sako Yasushi、Okada Mariko
- Journal Title
  
  PLOS Genetics
  
  Volume: 18 Issue: 6 Pages: 1010235-1010235
- DOI
  10.1371/journal.pgen.1010235
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-21H05245, KAKENHI-PROJECT-19H05647, KAKENHI-ORGANIZER-17H06299
[Journal Article] Improved MeSH analysis software tools for farm animals2021
- Author(s)
  Amorim Sabrina T.、Tsuyuzaki Koki、Nikaido Itoshi、Morota Gota
- Journal Title
  
  Animal Genetics
  
  Volume: 53 Issue: 1 Pages: 171-172
- DOI
  10.1111/age.13159
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-21H05245, KAKENHI-PROJECT-19K20406
[Journal Article] Context-dependent wiring of Sox2 regulatory networks for self-renewal of embryonic and trophoblast stem cells2013
- Author(s)
  Adachi K, Nikaido I, Ohta H, Ohtsuka S, Ura H, Kadota M, Wakayama T, Ueda HR, Niwa H.
- Journal Title
  
  Molecular Cell
  
  Volume: 52 Issue: 3 Pages: 380-392
- DOI
  10.1016/j.molcel.2013.09.002
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-12J09944, KAKENHI-PLANNED-21116005, KAKENHI-PLANNED-23115006, KAKENHI-PROJECT-23248048, KAKENHI-PROJECT-25830148
[Journal Article] EICO (Expression-based Imprint Candidate Organizer) : finding disease-related imprinted genes2004
- Author(s)
  Nikaido I.
- Journal Title
  
  Nucleic Acids Research 32
  
  Pages: 548-551
- Data Source
  KAKENHI-PROJECT-16012256
[Presentation] 大規模生成AIとゲノム科学による創薬を目指して2024
- Author(s)
  二階堂愛
- Organizer
  日本薬学会第144年会
- Invited
- Data Source
  KAKENHI-PLANNED-21H05245
[Presentation] 基盤モデルに向けたオミクス計測の未来2023
- Author(s)
  二階堂愛
- Organizer
  AIロボット駆動科学シンポジウム2023
- Invited
- Data Source
  KAKENHI-PLANNED-21H05245
[Presentation] 規模トランスクリプトームとAI創薬2023
- Author(s)
  二階堂愛
- Organizer
  第66回日本腎臓学会学術総会
- Invited
- Data Source
  KAKENHI-PLANNED-21H05245
[Presentation] バイオインフォマティクスとゲノム科学で挑む生命の理解2023
- Author(s)
  二階堂愛
- Organizer
  理化学研究所生命機能科学研究センター発生・再生科学集中レクチャープログラム
- Invited
- Data Source
  KAKENHI-PLANNED-21H05245
[Presentation] データ科学とシングルセルゲノム科学で加速する再生医療研究2022
- Author(s)
  二階堂愛
- Organizer
  第21回日本再生医療学会総会
- Invited
- Data Source
  KAKENHI-PLANNED-21H05245
[Presentation] 健康のためにデータ科学でヒトのすべての細胞を調べ尽くす2022
- Author(s)
  二階堂愛
- Organizer
  東京医科歯科大学難治疾患研究所市民公開講座 -最先端生命科学講座シリーズ第30回-
- Invited
- Data Source
  KAKENHI-PLANNED-21H05245
[Presentation] ゲノムレジリエンス破綻の理解と未来予測2021
- Author(s)
  二階堂愛
- Organizer
  バイオDXの最前線-JST戦略的創造研究推進事業CREST-「データ駆動・AI駆動を中心としたデジタルトランスフォーメーションによる生命科学研究の革新［バイオDX]」キックオフシンポジウム
- Data Source
  KAKENHI-PLANNED-21H05245
[Presentation] 疾患機序に迫る 1細胞トランスクリプトーム技術2021
- Author(s)
  二階堂愛
- Organizer
  第3回 Seeing What's Next〈次世代の可視化技術勉強会〉
- Invited
- Data Source
  KAKENHI-PLANNED-21H05245
[Presentation] 生命科学研究を加速するためのAIを計測と計算の融合から考える2016
- Author(s)
  二階堂愛
- Organizer
  第2回理研・産総研共同シンポジウム
- Place of Presentation
  産業技術研究所 (茨城県・つくば市)
- Year and Date
  2016-02-02
- Invited
- Data Source
  KAKENHI-PROJECT-25830148
[Presentation] BioDevOpsによる再現性のあるDNAシーケンス解析環境の構築2016
- Author(s)
  二階堂愛
- Organizer
  NPO並列生物情報処理イニシアティブシンポジウム
- Place of Presentation
  東京工業大学 (東京都)
- Year and Date
  2016-03-11
- Invited
- Data Source
  KAKENHI-PROJECT-25830148
[Presentation] Estimation of transcriptional activity from ChIP-Seq and transcriptome
- Author(s)
  Itoshi Nikaido
- Organizer
  Computational Science in Epigenetics
- Place of Presentation
  Kobe, Hyogo, Japan
- Year and Date
  2015-02-13 – 2015-02-14
- Invited
- Data Source
  KAKENHI-PROJECT-25830148

1. Okazaki Yasushi (80280733)

# of Collaborated Projects: 2 results

# of Collaborated Products: 0 results
2. Ishihara Satoru (00300723)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
3. SASAGAWA YOHEI (10404344)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
4. Nakagawa Hidewaki (50361621)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
5. Sugahara Izumi (10633000)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
6. Matsumoto Masahito (90321819)

# of Collaborated Projects: 1 results

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7. Nakachi Yutaka (10522097)

# of Collaborated Projects: 1 results

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8. Watanabe Ami (40611421)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
9. 坊農秀雅 (20364789)

# of Collaborated Projects: 1 results

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10. 八木研 (60323482)

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11. 石原直恵 (50571791)

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12. 原田信広 (00189705)

# of Collaborated Projects: 1 results

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13. 井元清哉 (10345027)

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14. 山上裕機 (20191190)

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15. 相方浩 (30403512)

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16. 中村透 (70645796)

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17. 郷康広 (50377123)

# of Collaborated Projects: 1 results

# of Collaborated Products: 2 results
18. 澤井哲 (20500367)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
19. 鈴木誉保 (40442975)

# of Collaborated Projects: 1 results

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20. 露崎弘毅

# of Collaborated Projects: 0 results

# of Collaborated Products: 2 results
21. 内匠透

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# of Collaborated Products: 1 results
22. 椙下紘貴

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# of Collaborated Products: 1 results
23. 飯野雄一

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results

Nikaido Itoshi 二階堂 愛

NIKAIDO Itoshi 二階堂 愛

二階堂 愛 ニカイドウ イトシ

Research Projects

Research Products

Co-Researchers

Exploring evolution of multicellularity and ancient molecular mechanisms underlying morphogenetic movement in amoebozoa

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Development of comprehensive cell type census technology for adaptive neuronal circuits

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Multi-omics analysis for hepato-biliary-pancreatic cancers

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Development and finding the mechanism of pancreatic beta cell differentiation from hiPS cells through Single cell analysis

Principal Investigator

Project Period (FY)

Research Category

Research Field

Research Institution

Chromatin structure as a determinant of transcriptional activity

Principal Investigator

Project Period (FY)

Research Category

Research Field

Research Institution

Model of mRNA transcription and transcriptional factor bindingPrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Research Field

Research Institution

遺伝学とトランスクリプトームの統合による高脂血症の遺伝子ネットワークの解明

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

[Book] 新世代フローサイトメトリー活用スタンダード2021

Author(s)

Total Pages

Publisher

ISBN

Data Source

[Book] 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&DRY2014

Author(s)

Total Pages

Publisher

Data Source

[Book] 次世代シーケンサーのその先に -シーケンス技術の現在と未来を考える- 細胞工学2013

Author(s)

Total Pages

Publisher

Data Source

[Book] NGSによる転写制御ネットワークのモデリング. 実験医学2013

Author(s)

Total Pages

Publisher

Data Source

[Journal Article] Transcriptomic Signatures of WNT-Driven Pathways and Granulosa Cell-Oocyte Interactions during Primordial Follicle Activation.2024

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Sctensor detects many-to-many cell-cell interactions from single cell RNA-sequencing data2023

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Single-cell transcriptomics uncovers EGFR signaling-mediated gastric progenitor cell differentiation in stomach homeostasis2023

Nikaido Itoshi 二階堂愛

NIKAIDO Itoshi 二階堂愛

二階堂愛ニカイドウイトシ