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Ryo Nakaki · SciRah

Researcher profile · Semantic Scholar

Ryo Nakaki

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Ryo Nakaki — researcher profile on SciRah

h-index: 19
Works: 41
Citations: 1,830

Most-cited papers

ChIP‐Atlas: a data‐mining suite powered by full integration of public ChIP‐seq data
Shinya Oki, T. Ohta, Go Shioi, H. Hatanaka +6 more
2018EMBO Reports679 citations Open access
Semantic Scholar
H3K4/H3K9me3 Bivalent Chromatin Domains Targeted by Lineage-Specific DNA Methylation Pauses Adipocyte Differentiation.
Yoshihiro Matsumura, Ryo Nakaki, T. Inagaki, Ayano Yoshida +11 more
2015Molecules and Cells196 citations Open access
Semantic Scholar
Extracellular Acidic pH Activates the Sterol Regulatory Element-Binding Protein 2 to Promote Tumor Progression.
Ayano Kondo, S. Yamamoto, Ryo Nakaki, T. Shimamura +6 more
2017Cell Reports177 citations Open access
Semantic Scholar
NFIA co-localizes with PPARγ and transcriptionally controls the brown fat gene program
Yuta Hiraike, H. Waki, Jingjun Yu, Masahiro Nakamura +22 more
2017Nature Cell Biology91 citations Open access
Semantic Scholar
Histone demethylase JMJD1A coordinates acute and chronic adaptation to cold stress via thermogenic phospho-switch
Yohei Abe, Yosuke Fujiwara, Hiroki Takahashi, Yoshihiro Matsumura +13 more
2018Nature Communications84 citations Open access
Semantic Scholar
Downregulation of ERG and FLI1 expression in endothelial cells triggers endothelial-to-mesenchymal transition
Nao Nagai, H. Ohguchi, Ryo Nakaki, Yoshihiro Matsumura +4 more
2018PLoS Genetics68 citations Open access
Semantic Scholar
Diminished nuclear RNA decay upon Salmonella infection upregulates antibacterial noncoding RNAs
Katsutoshi Imamura, A. Takaya, Y. Ishida, Yayoi Fukuoka +16 more
2018EMBO Journal61 citations Open access
Semantic Scholar
Coordinated demethylation of H3K9 and H3K27 is required for rapid inflammatory responses of endothelial cells
Yoshiki Higashijima, Yusuke Matsui, T. Shimamura, Ryo Nakaki +21 more
2018bioRxiv52 citations Open access
Semantic Scholar
Dynamically and epigenetically coordinated GATA/ETS/SOX transcription factor expression is indispensable for endothelial cell differentiation
Yasuharu Kanki, Ryo Nakaki, T. Shimamura, Taichi Matsunaga +9 more
2017Nucleic Acids Research49 citations Open access
Semantic Scholar
The FBXL10/KDM2B Scaffolding Protein Associates with Novel Polycomb Repressive Complex-1 to Regulate Adipogenesis*
T. Inagaki, S. Iwasaki, Yoshihiro Matsumura, T. Kawamura +14 more
2014Journal of Biological Chemistry43 citations Open access
Semantic Scholar
JMJD1A is a signal-sensing scaffold that regulates acute chromatin dynamics via SWI/SNF association for thermogenesis
Yohei Abe, R. Rozqie, Yoshihiro Matsumura, T. Kawamura +16 more
2015Nature Communications41 citations Open access
Semantic Scholar
Comprehensive epigenome characterization reveals diverse transcriptional regulation across human vascular endothelial cells
Ryuichiro Nakato, Y. Wada, Ryo Nakaki, G. Nagae +32 more
2019Epigenetics & Chromatin36 citations Open access
Semantic Scholar
Novel lnc RNA regulated by HIF‐1 inhibits apoptotic cell death in the renal tubular epithelial cells under hypoxia
I. Mimura, Y. Hirakawa, Yasuharu Kanki, N. Kushida +5 more
2017Physiological Reports36 citations Open access
Semantic Scholar
Type I Interferon Delivery by iPSC-Derived Myeloid Cells Elicits Antitumor Immunity via XCR1+ Dendritic Cells.
N. Tsuchiya, Rong Zhang, T. Iwama, Norihiro Ueda +21 more
2019Cell Reports32 citations Open access
Semantic Scholar
Dynamics of chromatin accessibility during TGF-β-induced EMT of Ras-transformed mammary gland epithelial cells
Mayu Arase, Yusuke Tamura, Natsumi Kawasaki, Kazunobu Isogaya +6 more
2017Scientific Reports28 citations Open access
Semantic Scholar
Increased PDGFRB and NF-κB signaling caused by highly prevalent somatic mutations in intracranial aneurysms
Yasuyuki Shima, Shota Sasagawa, N. Ota, R. Oyama +36 more
2023Science Translational Medicine25 citations
Semantic Scholar
Genome-wide analysis revealed that DZNep reduces tubulointerstitial fibrosis via down-regulation of pro-fibrotic genes
I. Mimura, Y. Hirakawa, Yasuharu Kanki, Ryo Nakaki +4 more
2018Scientific Reports23 citations Open access
Semantic Scholar
TET1 upregulation drives cancer cell growth through aberrant enhancer hydroxymethylation of HMGA2 in hepatocellular carcinoma
K. Shirai, G. Nagae, M. Seki, Yotaro Kudo +14 more
2021Cancer Science22 citations Open access
Semantic Scholar
PERK inhibition attenuates vascular remodeling in pulmonary arterial hypertension caused by BMPR2 mutation
Takashi Shimizu, Yoshiki Higashijima, Yasuharu Kanki, Ryo Nakaki +3 more
2021Science Signaling19 citations
Semantic Scholar
Bivalent-histone-marked immediate-early gene regulation is vital for VEGF-responsive angiogenesis.
Yasuharu Kanki, M. Muramatsu, Yuri Miyamura, Kenta Kikuchi +12 more
2022Cell Reports17 citations Open access
Semantic Scholar
Spatiotemporal dynamics of SETD5-containing NCoR–HDAC3 complex determines enhancer activation for adipogenesis
Yoshihiro Matsumura, R. Ito, Ayumu Yajima, Rei Yamaguchi +26 more
2021Nature Communications15 citations Open access
Semantic Scholar
Integrative analysis of transcription factor occupancy at enhancers and disease risk loci in noncoding genomic regions
Shinya Oki, T. Ohta, Go Shioi, H. Hatanaka +6 more
2017bioRxiv15 citations Open access
Semantic Scholar
Inhibition of cardiac PERK signaling promotes peripartum cardiac dysfunction
Takashi Shimizu, Akashi Taguchi, Yoshiki Higashijima, Yasuharu Kanki +3 more
2021Scientific Reports9 citations Open access
Semantic Scholar
A novel ab initio identification system of transcriptional regulation motifs in genome DNA sequences based on direct comparison scheme of signal/noise distributions
Ryo Nakaki, Jiyoung Kang, M. Tateno
2012Nucleic Acids Research7 citations Open access
Semantic Scholar
Low-dose radiation induces unstable gene expression in developing human iPSC-derived retinal ganglion organoids
Mari Katsura, Y. Urade, Hiroko Nansai, Mika Kobayashi +11 more
2023Scientific Reports6 citations Open access
Semantic Scholar
Low-Dose Radiation Disrupts the Transcription Cascade of PAX6
Mari Katsura, Y. Urade, Hiroko Nansai, Mika Kobayashi +11 more
20213 citations Open access
Semantic Scholar
MicroRNA-320a/b is a Therapeutic Target and Biomarker for Peripartum Cardiomyopathy
Takashi Shimizu, Akashi Taguchi, Yoshihiro Higashijima, Yasuharu Kanki +3 more
20210 citations Open access
Semantic Scholar
Regulatory networks defining human corneal limbal epithelial cells identity through epigenomes.
Suguru Nakagawa, Ryo Nakaki, S. Yamagami, T. Usui +1 more
20180 citations
Semantic Scholar
RyuGoo-Saba: a CWL-based execution engine utilizing cloud resources for big data analysis in life science
Hirotaka Suetake, Ryo Nakaki
20180 citations Open access
Semantic Scholar
Investigation of sprouting angiogenesis using single cell transcriptome analysis
Y. Uchijima, H. Tozawa, Kazuo Tonami, Y. Kurihara +11 more
20170 citations
Semantic Scholar
Comprehensive and integrative analyses with a novel ChIP-seq and DNase-seq database
Shinya Oki, T. Ohta, Go Shioi, H. Hatanaka +6 more
20160 citations
Semantic Scholar
Co-localization of NFIA and PPARγ controls the brown fat gene program
H. Waki, Yuta Hiraike, Yu Jing, Masahiro Nakamura +16 more
20160 citations
Semantic Scholar
Epigenetic Thermoregulatory Mechanism Regulated by JMJD1A-containing Protein Complex
T. Inagaki, Yohei Abe, R. Rozqie, Yoshihiro Matsumura +6 more
20160 citations
Semantic Scholar
The integration of dynamic epigenetic data in vascular endothelial cells
Yasuharu Kanki, Jun‐ichi Suehiro, Ryo Nakaki, T. Osawa +4 more
20150 citations
Semantic Scholar
Correlation between loss of active histone marks and induction of DNA methylation during Epstein-Barr virus infection
Sayaka Funata, K. Matsusaka, R. Yamanaka, Ryo Nakaki +3 more
20150 citations
Semantic Scholar
Genome-wide chromatin interactome analysis by NGS
A. Okabe, S. Tsutsumi, Ryo Nakaki, H. Aburatani
20150 citations
Semantic Scholar
1I1448 MODIC : a novel ab inito identification system of transcription factor binding motifs in genome DNA sequences(Bioinformatics & Bioengineering,Oral Presentation,The 50th Annual Meeting of the Biophysical Society of Japan)
M. Tateno, Ryo Nakaki, Jiyoung Kang
20120 citations Open access
Semantic Scholar
1E1336 Improvement of a parameter-tuning-free identification system of transcriptional factor binding sites in genome DNA sequences(Genome biology, Bioinformatics,The 49th Annual Meeting of the Biophysical Society of Japan)
Ryo Nakaki, M. Tateno
20110 citations Open access
Semantic Scholar
Development of a Novel Algorithm for Identifying Transcription Factor Binding Motifs in the Genome DNA Sequences
Ryo Nakaki, M. Tateno
20110 citations Open access
Semantic Scholar
2SD-05 Theoretical and computational quantum structural biology for understanding functional mechanisms of biological macromolecular systems(2SD Sail on, Quantum Structural Biology,The 49th Annual Meeting of the Biophysical Society of Japan)
M. Tateno, Jiyoung Kang, Ryo Nakaki
20110 citations Open access
Semantic Scholar
3P291 Development of an "ab initio" identification system of transcriptional factor binding motifs in genome DNA sequences(Genome biology: Genome analysis,The 48th Annual Meeting of the Biophysical Society of Japan)
Ryo Nakaki, M. Tateno
20100 citations Open access
Semantic Scholar

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H. Aburatani×23
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Yasuharu Kanki×12
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Yoshihiro Matsumura×6

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H. Kimura — researcher profile on SciRah

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S. Yamamoto — researcher profile on SciRah

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Yohei Abe — researcher profile on SciRah

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