Publications

Original Articles

1. Kodai Yamaura, Naomichi Takemata, Masashi Kariya, Ayami Osaka, Sonoko Ishino, Masataka Yamauchi, Tomonori Tamura, Itaru Hamachi, Shoji Takada, Yoshizumi Ishino, Haruyuki Atomi
   Chromosomal domain formation by archaeal SMC, a roadblock protein, and DNA structure
   Nature Communications 16, 1312 (2025)
   doi: 10.1038/s41467-025-56197-y
2. Hayato Hirai, Naomichi Takemata, Miki Tamura, Kunihiro Ohta
   Facultative heterochromatin formation in rDNA is essential for cell survival during nutritional starvation
   Nucleic Acids Research 50(7), 3727-3744 (2022)
   doi: 10.1093/nar/gkac175
3. Naomichi Takemata, Stephen D. Bell
   High-resolution analysis of chromosome conformation in hyperthermophilic archaea
   STAR Protocols 2(2), 100562-100562 (2021)
   doi: 10.1016/j.xpro.2021.100562
4. Naomichi Takemata, Stephen D. Bell
   Chromosome conformation capture assay combined with biotin enrichment for hyperthermophilic archaea
   STAR Protocols 2(2), 100576-100576 (2021)
   doi: 10.1016/j.xpro.2021.100576
5. Naomichi Takemata, Stephen D. Bell
   Multi-scale architecture of archaeal chromosomes
   Molecular Cell 81 (3), 473-487 (2021)
   doi: 10.1016/j.molcel.2020.12.001
6. Naomichi Takemata, Rachel Y. Samson, Stephen D. Bell
   Physical and Functional Compartmentalization of Archaeal Chromosomes
   Cell 179(1), 165-179 (2019)
   doi: 10.1016/j.cell.2019.08.036
7. Naomichi Takemata, Arisa Oda, Takatomi Yamada, Josephine Galipon, Tomoichiro Miyoshi, Yutaka Suzuki, Sumio Sugano, Charles S. Hoffman, Kouji Hirota, Kunihiro Ohta
   Local potentiation of stress-responsive genes by upstream noncoding transcription
   Nucleic Acids Research 44(11), 5174-89 (2016)
   doi: 10.1093/nar/gkw142
8. Arisa Oda, Naomichi Takemata, Yoshito Hirata, Tomoichiro Miyoshi, Yutaka Suzuki, Sumio Sugano, Kunihiro Ohta
   Dynamic transition of transcription and chromatin landscape during fission yeast adaptation to glucose starvation
   Genes to Cells 20(5), 392-407 (2015)
   doi: 10.1111/gtc.12229
9. Ryuta Asada, Naomichi Takemata, Charles S. Hoffman, Kunihiro Ohta, Kouji Hirota
   Antagonistic controls of chromatin and mRNA start site selection by Tup family corepressors and the CCAAT-binding factor
   Molecular and Cellular Biology 35(5), 847-55 (2015)
   doi: 10.1128/MCB.00924-14

Review Articles

1. Elyza Pilatowski-Herzing, Rachel Y. Samson, Naomichi Takemata, Catherine Badel, Peter B. Bohall, Stephen D. Bell
   Capturing chromosome conformation in Crenarchaea
   Molecular Microbiology 123 (2), 101-108 (2025)
2. Naomichi Takemata
   How Do Thermophiles Organize Their Genomes?
   Microbes and Environments 39 (5), ME23087 (2024)
3. Naomichi Takemata, Stephen D. Bell
   Emerging views of genome organization in Archaea
   Journal of Cell Science 133 (10), jcs243782 (2020)
4. Naomichi Takemata, Kunihiro Ohta
   Role of non-coding RNA transcription around gene regulatory elements in transcription factor recruitment
   RNA biology 14(1), 1-5 (2017)   

Books

1. SMC Proteins
   山浦 昂大、竹俣 直道（担当:分担執筆）　2025年10月（ISBN: 9781071650042）
2. 大規模データで困ったときに、まず図を描くことからはじめる生命科学データ解析 : 解析のゴールドスタンダードを学び、生成AIとの対話でPython・Rを使いこなす
   竹俣 直道（担当:分担執筆）　羊土社　 2025年7月（ISBN: 9784758122825）
3. Computational Methods for 3D Genome Analysis 
   竹俣 直道（担当:分担執筆）　2024年9月（ISBN: 9781071641354）