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A field guide to cultivating computational biology.
Way GP, Greene CS, Carninci P, Carvalho BS, de Hoon M, Finley SD, Gosline SJC, Lȇ Cao KA, Lee JSH, Marchionni L, Robine N, Sindi SS, Theis FJ, Yang JYH, Carpenter AE, Fertig EJ. Way GP, et al. Among authors: de hoon m. PLoS Biol. 2021 Oct 7;19(10):e3001419. doi: 10.1371/journal.pbio.3001419. eCollection 2021 Oct. PLoS Biol. 2021. PMID: 34618807 Free PMC article.
FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions.
Severin J, Waterhouse AM, Kawaji H, Lassmann T, van Nimwegen E, Balwierz PJ, de Hoon MJ, Hume DA, Carninci P, Hayashizaki Y, Suzuki H, Daub CO, Forrest AR. Severin J, et al. Among authors: de hoon mj. Genome Biol. 2009;10(4):R39. doi: 10.1186/gb-2009-10-4-r39. Epub 2009 Apr 19. Genome Biol. 2009. PMID: 19374773 Free PMC article.
Redefinition of the human mast cell transcriptome by deep-CAGE sequencing.
Motakis E, Guhl S, Ishizu Y, Itoh M, Kawaji H, de Hoon M, Lassmann T, Carninci P, Hayashizaki Y, Zuberbier T, Forrest AR, Babina M; FANTOM consortium. Motakis E, et al. Among authors: de hoon m. Blood. 2014 Apr 24;123(17):e58-67. doi: 10.1182/blood-2013-02-483792. Epub 2014 Mar 26. Blood. 2014. PMID: 24671954 Free PMC article.
Paradigm shifts in genomics through the FANTOM projects.
de Hoon M, Shin JW, Carninci P. de Hoon M, et al. Mamm Genome. 2015 Oct;26(9-10):391-402. doi: 10.1007/s00335-015-9593-8. Epub 2015 Aug 8. Mamm Genome. 2015. PMID: 26253466 Free PMC article.
Recounting the FANTOM CAGE-Associated Transcriptome.
Imada EL, Sanchez DF, Collado-Torres L, Wilks C, Matam T, Dinalankara W, Stupnikov A, Lobo-Pereira F, Yip CW, Yasuzawa K, Kondo N, Itoh M, Suzuki H, Kasukawa T, Hon CC, de Hoon MJL, Shin JW, Carninci P, Jaffe AE, Leek JT, Favorov A, Franco GR, Langmead B, Marchionni L. Imada EL, et al. Among authors: de hoon mjl. Genome Res. 2020 Jul;30(7):1073-1081. doi: 10.1101/gr.254656.119. Epub 2020 Feb 20. Genome Res. 2020. PMID: 32079618 Free PMC article.
Comparative transcriptomics of primary cells in vertebrates.
Alam T, Agrawal S, Severin J, Young RS, Andersson R, Arner E, Hasegawa A, Lizio M, Ramilowski JA, Abugessaisa I, Ishizu Y, Noma S, Tarui H, Taylor MS, Lassmann T, Itoh M, Kasukawa T, Kawaji H, Marchionni L, Sheng G, R R Forrest A, Khachigian LM, Hayashizaki Y, Carninci P, de Hoon MJL. Alam T, et al. Among authors: de hoon mjl. Genome Res. 2020 Jul;30(7):951-961. doi: 10.1101/gr.255679.119. Epub 2020 Jul 27. Genome Res. 2020. PMID: 32718981 Free PMC article.
79 results