Author

Naoto Kondo

RIKEN

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Organism:human· 4 Approach:statistical model· 4 Assay:bulk RNA-seq· 3 Research Focus:differential expression· 3 Research Focus:gene regulatory network inference· 3 Assay:CITE-seq· 1 Research Focus:database / resource· 1 Research Focus:fine-mapping· 1

Frequent Co-Authors

Masayoshi ItohiD· 4 shared Kayoko YasuzawaiD· 3 shared Piero CarninciiD· 3 shared Albin SandeliniD· 2 shared Alexander V. FavoroviD· 2 shared Chi Wai YipiD· 2 shared Chikashi C. TeraoiD· 2 shared Chung-Chau HoniD· 2 shared

Activity by Year

2018-2021 · peak 2/yr

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10 top collaborators · 44 mutual co-author links

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4 shared papersGenomics

Masayoshi ItohORCID

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4 papers

Recent·Most cited

Systematic identification of cis-interacting lncRNAs and their targets

Saumya Agrawal, Ivan V. Kulakovskiy, Jessica Severin, Masaru Koido, Tanvir Alam, Imad Abugessaisa, Andrey Buyan, Howard Y. Chang, Josée Dostie, Masayoshi Itoh, Juha Kere, Naoto Kondo, Yunjing Li, Vsevolod J. Makeev, Mickaël Mendez, , Michiel de Hoon

The paper identifies cis-interacting lncRNAs and their targets using RNA-chromatin and Hi-C data across 18 human cell types.

bioRxiv · Jan 13, 2021 · PreprintGenomics

Functional Annotation of Human Long Non-Coding RNAs via Molecular Phenotyping

Jordan A. Ramilowski, Chi Wai Yip, Saumya Agrawal, Jen-Chien Chang, Yari Ciani, Ivan V. Kulakovskiy, Mickaël Mendez, Jasmine Li Ching Ooi, John F. Ouyang, Nick Parkinson, Andreas Petri, Leonie Roos, Jessica Severin, Kayoko Yasuzawa, Imad Abugessaisa, , Chinatsu Yamamoto

The paper functionally annotates human long non-coding RNAs by systematically knocking down 285 lncRNAs and analyzing molecular phenotypes using CAGE sequencing.

Genome Research · Jul 1, 2020Peer-reviewedGenomics

Recounting the FANTOM Cage Associated Transcriptome

Eddie L. Imada, Diego Fernando Sanchez, Leonardo Collado‐Torres, Christopher Wilks, Tejasvi Matam, Wikum Dinalankara, Alexey Stupnikov, Francisco Pereira Lobo, Chi-Wai Yip, Kayoko Yasuzawa, Naoto Kondo, Masayoshi Itoh, Harukazu Suzuki, Takeya Kasukawa, Chung-Chau Hon, , Luigi Marchionni

The paper presents FC-R2, an expanded transcriptome atlas of over 109,000 genes, including lncRNAs, and demonstrates its utility in analyzing gene expression across normal and diseased human samples.

Genome Research · Jul 1, 2020Peer-reviewedGenomics

Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease.

John Kenneth Baillie, Andrew D. Bretherick, Chris Haley, Sara Clohisey, Alan Gray, Lucile P. A. Neyton, Jeffrey C. Barrett, Eli A. Stahl, Albert Tenesa, Robin Andersson, James B. Brown, Geoffrey J. Faulkner, Marina Lizio, Ulf Schaefer, Carsten O. Daub, , David Arthur Hume

The paper identifies shared expression patterns of genetic variants across tissues and cell types, enabling fine mapping of disease-associated variants and revealing key cell types involved in disease pathogenesis.

PLoS Computational Biology · Mar 1, 2018Peer-reviewedGenomics