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Genome-wide analysis of mammalian promoter architecture and evolution.
Nat Genet. 2006 Jun;38(6):626-35. doi: 10.1038/ng1789. Epub 2006 Apr 28.
Nat Genet. 2006.
PMID: 16645617
The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.
FANTOM Consortium; Suzuki H, Forrest AR, van Nimwegen E, Daub CO, Balwierz PJ, Irvine KM, Lassmann T, Ravasi T, Hasegawa Y, de Hoon MJ, Katayama S, Schroder K, Carninci P, Tomaru Y, Kanamori-Katayama M, Kubosaki A, Akalin A, Ando Y, Arner E, Asada M, Asahara H, Bailey T, Bajic VB, Bauer D, Beckhouse AG, Bertin N, Björkegren J, Brombacher F, Bulger E, Chalk AM, Chiba J, Cloonan N, Dawe A, Dostie J, Engström PG, Essack M, Faulkner GJ, Fink JL, Fredman D, Fujimori K, Furuno M, Gojobori T, Gough J, Grimmond SM, Gustafsson M, Hashimoto M, Hashimoto T, Hatakeyama M, Heinzel S, Hide W, Hofmann O, Hörnquist M, Huminiecki L, Ikeo K, Imamoto N, Inoue S, Inoue Y, Ishihara R, Iwayanagi T, Jacobsen A, Kaur M, Kawaji H, Kerr MC, Kimura R, Kimura S, Kimura Y, Kitano H, Koga H, Kojima T, Kondo S, Konno T, Krogh A, Kruger A, Kumar A, Lenhard B, Lennartsson A, Lindow M, Lizio M, Macpherson C, Maeda N, Maher CA, Maqungo M, Mar J, Matigian NA, Matsuda H, Mattick JS, Meier S, Miyamoto S, Miyamoto-Sato E, Nakabayashi K, Nakachi Y, Nakano M, Nygaard S, Okayama T, Okazaki Y, Okuda-Yabukami H, Orlando V, Otomo J, Pachkov M, Petrovsky N, Plessy C, Quackenbush J, Radovanovic A, Rehli M, Saito R, Sandelin A,…
See abstract for full author list ➔
FANTOM Consortium, et al.
Nat Genet. 2009 May;41(5):553-62. doi: 10.1038/ng.375. Epub 2009 Apr 19.
Nat Genet. 2009.
PMID: 19377474
Free PMC article.
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An atlas of active enhancers across human cell types and tissues.
Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T, Ntini E, Arner E, Valen E, Li K, Schwarzfischer L, Glatz D, Raithel J, Lilje B, Rapin N, Bagger FO, Jørgensen M, Andersen PR, Bertin N, Rackham O, Burroughs AM, Baillie JK, Ishizu Y, Shimizu Y, Furuhata E, Maeda S, Negishi Y, Mungall CJ, Meehan TF, Lassmann T, Itoh M, Kawaji H, Kondo N, Kawai J, Lennartsson A, Daub CO, Heutink P, Hume DA, Jensen TH, Suzuki H, Hayashizaki Y, Müller F, Forrest ARR, Carninci P, Rehli M, Sandelin A.
Andersson R, et al.
Nature. 2014 Mar 27;507(7493):455-461. doi: 10.1038/nature12787.
Nature. 2014.
PMID: 24670763
Free PMC article.
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Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs.
Maeda N, Kasukawa T, Oyama R, Gough J, Frith M, Engström PG, Lenhard B, Aturaliya RN, Batalov S, Beisel KW, Bult CJ, Fletcher CF, Forrest AR, Furuno M, Hill D, Itoh M, Kanamori-Katayama M, Katayama S, Katoh M, Kawashima T, Quackenbush J, Ravasi T, Ring BZ, Shibata K, Sugiura K, Takenaka Y, Teasdale RD, Wells CA, Zhu Y, Kai C, Kawai J, Hume DA, Carninci P, Hayashizaki Y.
Maeda N, et al.
PLoS Genet. 2006 Apr;2(4):e62. doi: 10.1371/journal.pgen.0020062.
PLoS Genet. 2006.
PMID: 16683036
Free PMC article.
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Unamplified cap analysis of gene expression on a single-molecule sequencer.
Kanamori-Katayama M, Itoh M, Kawaji H, Lassmann T, Katayama S, Kojima M, Bertin N, Kaiho A, Ninomiya N, Daub CO, Carninci P, Forrest AR, Hayashizaki Y.
Kanamori-Katayama M, et al.
Genome Res. 2011 Jul;21(7):1150-9. doi: 10.1101/gr.115469.110. Epub 2011 May 19.
Genome Res. 2011.
PMID: 21596820
Free PMC article.
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A promoter-level mammalian expression atlas.
FANTOM Consortium and the RIKEN PMI and CLST (DGT); Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M, Itoh M, Andersson R, Mungall CJ, Meehan TF, Schmeier S, Bertin N, Jørgensen M, Dimont E, Arner E, Schmidl C, Schaefer U, Medvedeva YA, Plessy C, Vitezic M, Severin J, Semple C, Ishizu Y, Young RS, Francescatto M, Alam I, Albanese D, Altschuler GM, Arakawa T, Archer JA, Arner P, Babina M, Rennie S, Balwierz PJ, Beckhouse AG, Pradhan-Bhatt S, Blake JA, Blumenthal A, Bodega B, Bonetti A, Briggs J, Brombacher F, Burroughs AM, Califano A, Cannistraci CV, Carbajo D, Chen Y, Chierici M, Ciani Y, Clevers HC, Dalla E, Davis CA, Detmar M, Diehl AD, Dohi T, Drabløs F, Edge AS, Edinger M, Ekwall K, Endoh M, Enomoto H, Fagiolini M, Fairbairn L, Fang H, Farach-Carson MC, Faulkner GJ, Favorov AV, Fisher ME, Frith MC, Fujita R, Fukuda S, Furlanello C, Furino M, Furusawa J, Geijtenbeek TB, Gibson AP, Gingeras T, Goldowitz D, Gough J, Guhl S, Guler R, Gustincich S, Ha TJ, Hamaguchi M, Hara M, Harbers M, Harshbarger J, Hasegawa A, Hasegawa Y, Hashimoto T, Herlyn M, Hitchens KJ, Ho Sui SJ, Hofmann OM, Hoof I, Hori F, Huminiecki L, Iida K, Ikawa T, …
See abstract for full author list ➔
FANTOM Consortium and the RIKEN PMI and CLST (DGT), et al. Among authors: kanamori katayama m.
Nature. 2014 Mar 27;507(7493):462-70. doi: 10.1038/nature13182.
Nature. 2014.
PMID: 24670764
Free PMC article.
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FANTOM5 CAGE profiles of human and mouse samples.
Noguchi S, Arakawa T, Fukuda S, Furuno M, Hasegawa A, Hori F, Ishikawa-Kato S, Kaida K, Kaiho A, Kanamori-Katayama M, Kawashima T, Kojima M, Kubosaki A, Manabe RI, Murata M, Nagao-Sato S, Nakazato K, Ninomiya N, Nishiyori-Sueki H, Noma S, Saijyo E, Saka A, Sakai M, Simon C, Suzuki N, Tagami M, Watanabe S, Yoshida S, Arner P, Axton RA, Babina M, Baillie JK, Barnett TC, Beckhouse AG, Blumenthal A, Bodega B, Bonetti A, Briggs J, Brombacher F, Carlisle AJ, Clevers HC, Davis CA, Detmar M, Dohi T, Edge ASB, Edinger M, Ehrlund A, Ekwall K, Endoh M, Enomoto H, Eslami A, Fagiolini M, Fairbairn L, Farach-Carson MC, Faulkner GJ, Ferrai C, Fisher ME, Forrester LM, Fujita R, Furusawa JI, Geijtenbeek TB, Gingeras T, Goldowitz D, Guhl S, Guler R, Gustincich S, Ha TJ, Hamaguchi M, Hara M, Hasegawa Y, Herlyn M, Heutink P, Hitchens KJ, Hume DA, Ikawa T, Ishizu Y, Kai C, Kawamoto H, Kawamura YI, Kempfle JS, Kenna TJ, Kere J, Khachigian LM, Kitamura T, Klein S, Klinken SP, Knox AJ, Kojima S, Koseki H, Koyasu S, Lee W, Lennartsson A, Mackay-Sim A, Mejhert N, Mizuno Y, Morikawa H, Morimoto M, Moro K, Morris KJ, Motohashi H, Mummery CL, Nakachi Y, Nakahara F, Nakamura T, Nakamura Y, Nozaki T, Ogi…
See abstract for full author list ➔
Noguchi S, et al. Among authors: kanamori katayama m.
Sci Data. 2017 Aug 29;4:170112. doi: 10.1038/sdata.2017.112.
Sci Data. 2017.
PMID: 28850106
Free PMC article.
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The transcriptional landscape of the mammalian genome.
Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, Kodzius R, Shimokawa K, Bajic VB, Brenner SE, Batalov S, Forrest AR, Zavolan M, Davis MJ, Wilming LG, Aidinis V, Allen JE, Ambesi-Impiombato A, Apweiler R, Aturaliya RN, Bailey TL, Bansal M, Baxter L, Beisel KW, Bersano T, Bono H, Chalk AM, Chiu KP, Choudhary V, Christoffels A, Clutterbuck DR, Crowe ML, Dalla E, Dalrymple BP, de Bono B, Della Gatta G, di Bernardo D, Down T, Engstrom P, Fagiolini M, Faulkner G, Fletcher CF, Fukushima T, Furuno M, Futaki S, Gariboldi M, Georgii-Hemming P, Gingeras TR, Gojobori T, Green RE, Gustincich S, Harbers M, Hayashi Y, Hensch TK, Hirokawa N, Hill D, Huminiecki L, Iacono M, Ikeo K, Iwama A, Ishikawa T, Jakt M, Kanapin A, Katoh M, Kawasawa Y, Kelso J, Kitamura H, Kitano H, Kollias G, Krishnan SP, Kruger A, Kummerfeld SK, Kurochkin IV, Lareau LF, Lazarevic D, Lipovich L, Liu J, Liuni S, McWilliam S, Madan Babu M, Madera M, Marchionni L, Matsuda H, Matsuzawa S, Miki H, Mignone F, Miyake S, Morris K, Mottagui-Tabar S, Mulder N, Nakano N, Nakauchi H, Ng P, Nilsson R, Nishiguchi S, Nishikawa S, Nori F, Ohara O, Okazaki Y, Orlando V, Pang KC, Pavan W…
See abstract for full author list ➔
Carninci P, et al.
Science. 2005 Sep 2;309(5740):1559-63. doi: 10.1126/science.1112014.
Science. 2005.
PMID: 16141072
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The combination of gene perturbation assay and ChIP-chip reveals functional direct target genes for IRF8 in THP-1 cells.
Kubosaki A, Lindgren G, Tagami M, Simon C, Tomaru Y, Miura H, Suzuki T, Arner E, Forrest AR, Irvine KM, Schroder K, Hasegawa Y, Kanamori-Katayama M, Rehli M, Hume DA, Kawai J, Suzuki M, Suzuki H, Hayashizaki Y.
Kubosaki A, et al.
Mol Immunol. 2010 Aug;47(14):2295-302. doi: 10.1016/j.molimm.2010.05.289. Epub 2010 Jun 22.
Mol Immunol. 2010.
PMID: 20573402
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Automated workflow for preparation of cDNA for cap analysis of gene expression on a single molecule sequencer.
Itoh M, Kojima M, Nagao-Sato S, Saijo E, Lassmann T, Kanamori-Katayama M, Kaiho A, Lizio M, Kawaji H, Carninci P, Forrest AR, Hayashizaki Y.
Itoh M, et al.
PLoS One. 2012;7(1):e30809. doi: 10.1371/journal.pone.0030809. Epub 2012 Jan 30.
PLoS One. 2012.
PMID: 22303458
Free PMC article.
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