Yamanaka Soichiro

ヤマナカソウイチロウ | Yamanaka Soichiro

Affiliation and department：
Job title：准教授

Research field (3)： Genetics , Developmental biology , Genomics

Research keywords (8)： high throughput sequencer , mouse , RNA-binding protein , transposon , heterochromatin , gonocyte , germ cell , Epigenetics

Research theme for competitive and other funds (13)：

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Papers (20)：

Muhammad Tahir, Shehroz S. Khan, James Davie, Soichiro Yamanaka, Ahmed Ashraf. LOCO-EPI: Leave-one-chromosome-out (LOCO) as a benchmarkingparadigm for deep learning based prediction of enhancer-promoterinteractions. Applied Intelligence. 2025. 55. 71
Muhammad Tahir, Mahboobeh Norouzi, Shehroz S. Khan, James R. Davie, Soichiro Yamanaka, Ahmed Ashraf. Artificial intelligence and deep learning algorithms for epigenetic sequence analysis: A review for epigeneticists and AI experts. Computers in Biology and Medicine. 2024. 183. 109302-109302
Peilin Li, Tatsuya Fujisawa, Haruka Narita, Yuta Uneme, Masahide Seki, Mengwen Hu, Ryohei Narumi, Satoshi H. Namekawa, Shehroz S. Khan, James R. Davie, et al. Priming Epigenetic Landscape at Gene Promoters through Transcriptional Activation in Mammalian Germ Cells. bioRxiv. 2024
Muhammad Tahir, Shehroz Khan, James Davie, Soichiro Yamanaka, Ahmed Ashraf. TransformerChrome: Transformer-based Model for Prediction of Gene Expression from Histone Modifications. The 37th Canadian Conference on Artificial Intelligence. 2024
Yuta Uneme, Ryu Maeda, Gen Nakayama, Haruka Narita, Naoki Takeda, Ryuji Hiramatsu, Hidenori Nishihara, Ryuichiro Nakato, Yoshiakira Kanai, Kimi Araki, et al. Morc1 reestablishes H3K9me3 heterochromatin on piRNA-targeted transposons in gonocytes. Proceedings of the National Academy of Sciences of the United States of America. 2024. 121. 13. e2317095121

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MISC (3)：

山中総一郎. マウス胎仔期の雄性生殖細胞におけるクロマチン構造変換の発見. 生化学. 2021. 93. 9. 152-156
Soichiro Yamanaka, Yusuke Kishi, Haruhiko Siomi. Chapter Eighteen - ATAC-seq method applied to embryonic germ cells and neural stem cells from mouse: Practical tips and modifications. Epigenetics Methods. 2020. 18. 371-386
Epigenetic Modifications Induced by Various Types of Small RNAs. 2015. 34. 9. 862-867

Lectures and oral presentations (3)：

Ectopic expression of genes by polycomb deregulation in mouse gonocytes
(第46回日本分子生物学会年会 2023)
マウスゴノサイトでのポリコーム脱制御による遺伝子の異所的発現
(第三回有性生殖研究会 2023)
Chromatin programming and reprogramming in mouse gonocyte
(CEEHRC (Canadian Epigenetics and Environment Health Research Consortium) and IHEC (International Human Epigenome Consortium) Joint Annual Meeting 2022)

Professional career (1)：

Work history (4)：

2019/04 - 現在 Department of Biological Sciences, Graduate School of Science, The University of Tokyo Associate Professor
2017/06 - 2019/03 Keio University School of Medicine Assistant Professor
2013/03 - 2017/05 Keio University School of Medicine Instructor
2010/09 - 2013/02 National Institutes of Health Visiting fellow

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