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Page 1
The Human Cell Atlas: Technical approaches and challenges.
Hon CC, Shin JW, Carninci P, Stubbington MJT. Hon CC, et al. Among authors: shin jw. Brief Funct Genomics. 2018 Jul 1;17(4):283-294. doi: 10.1093/bfgp/elx029. Brief Funct Genomics. 2018. PMID: 29092000 Free PMC article. Review.
C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution.
Kouno T, Moody J, Kwon AT, Shibayama Y, Kato S, Huang Y, Böttcher M, Motakis E, Mendez M, Severin J, Luginbühl J, Abugessaisa I, Hasegawa A, Takizawa S, Arakawa T, Furuno M, Ramalingam N, West J, Suzuki H, Kasukawa T, Lassmann T, Hon CC, Arner E, Carninci P, Plessy C, Shin JW. Kouno T, et al. Among authors: shin jw. Nat Commun. 2019 Jan 21;10(1):360. doi: 10.1038/s41467-018-08126-5. Nat Commun. 2019. PMID: 30664627 Free PMC article.
Single-cell transcriptomics reveals expansion of cytotoxic CD4 T cells in supercentenarians.
Hashimoto K, Kouno T, Ikawa T, Hayatsu N, Miyajima Y, Yabukami H, Terooatea T, Sasaki T, Suzuki T, Valentine M, Pascarella G, Okazaki Y, Suzuki H, Shin JW, Minoda A, Taniuchi I, Okano H, Arai Y, Hirose N, Carninci P. Hashimoto K, et al. Among authors: shin jw. Proc Natl Acad Sci U S A. 2019 Nov 26;116(48):24242-24251. doi: 10.1073/pnas.1907883116. Epub 2019 Nov 12. Proc Natl Acad Sci U S A. 2019. PMID: 31719197 Free PMC article.
The choice of negative control antisense oligonucleotides dramatically impacts downstream analysis depending on the cellular background.
Ducoli L, Agrawal S, Hon CC, Ramilowski JA, Sibler E, Tagami M, Itoh M, Kondo N, Abugessaisa I, Hasegawa A, Kasukawa T, Suzuki H, Carninci P, Shin JW, de Hoon MJL, Detmar M. Ducoli L, et al. Among authors: shin jw. BMC Genom Data. 2021 Sep 14;22(1):33. doi: 10.1186/s12863-021-00992-1. BMC Genom Data. 2021. PMID: 34521352 Free PMC article.
Deep sequencing of short capped RNAs reveals novel families of noncoding RNAs.
de Hoon M, Bonetti A, Plessy C, Ando Y, Hon CC, Ishizu Y, Itoh M, Kato S, Lin D, Maekawa S, Murata M, Nishiyori H, Shin JW, Stolte J, Suzuki AM, Tagami M, Takahashi H, Thongjuea S, Forrest ARR, Hayashizaki Y, Kere J, Carninci P. de Hoon M, et al. Among authors: shin jw. Genome Res. 2022 Aug 12;32(9):1727-35. doi: 10.1101/gr.276647.122. Online ahead of print. Genome Res. 2022. PMID: 35961773 Free PMC article.
Antisense-oligonucleotide-mediated perturbation of long non-coding RNA reveals functional features in stem cells and across cell types.
Yip CW, Hon CC, Yasuzawa K, Sivaraman DM, Ramilowski JA, Shibayama Y, Agrawal S, Prabhu AV, Parr C, Severin J, Lan YJ, Dostie J, Petri A, Nishiyori-Sueki H, Tagami M, Itoh M, López-Redondo F, Kouno T, Chang JC, Luginbühl J, Kato M, Murata M, Yip WH, Shu X, Abugessaisa I, Hasegawa A, Suzuki H, Kauppinen S, Yagi K, Okazaki Y, Kasukawa T, de Hoon M, Carninci P, Shin JW. Yip CW, et al. Among authors: shin jw. Cell Rep. 2022 Dec 27;41(13):111893. doi: 10.1016/j.celrep.2022.111893. Cell Rep. 2022. PMID: 36577377 Free article.
Single-nucleotide variant calling in single-cell sequencing data with Monopogen.
Dou J, Tan Y, Kock KH, Wang J, Cheng X, Tan LM, Han KY, Hon CC, Park WY, Shin JW, Jin H, Wang Y, Chen H, Ding L, Prabhakar S, Navin N, Chen R, Chen K. Dou J, et al. Among authors: shin jw. Nat Biotechnol. 2024 May;42(5):803-812. doi: 10.1038/s41587-023-01873-x. Epub 2023 Aug 17. Nat Biotechnol. 2024. PMID: 37592035 Free PMC article.
1,141 results