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Results: 1 to 20 of 220

1.

PAPD5-mediated 3' adenylation and subsequent degradation of miR-21 is disrupted in proliferative disease.

Boele J, Persson H, Shin JW, Ishizu Y, Newie IS, Søkilde R, Hawkins SM, Coarfa C, Ikeda K, Takayama KI, Horie-Inoue K, Ando Y, Burroughs AM, Sasaki C, Suzuki C, Sakai M, Aoki S, Ogawa A, Hasegawa A, Lizio M, Kaida K, Teusink B, Carninci P, Suzuki H, Inoue S, Gunaratne PH, Rovira C, Hayashizaki Y, de Hoon MJ.

Proc Natl Acad Sci U S A. 2014 Jul 21. pii: 201317751. [Epub ahead of print]

PMID:
25049417
[PubMed - as supplied by publisher]
2.

Comparative validation of the D. melanogaster modENCODE transcriptome annotation.

Chen ZX, Sturgill D, Qu J, Jiang H, Park S, Boley N, Suzuki AM, Fletcher AR, Plachetzki DC, FitzGerald PC, Artieri CG, Atallah J, Barmina O, Brown JB, Blankenburg KP, Clough E, Dasgupta A, Gubbala S, Han Y, Jayaseelan JC, Kalra D, Kim YA, Kovar CL, Lee SL, Li M, Malley JD, Malone JH, Mathew T, Mattiuzzo NR, Munidasa M, Muzny DM, Ongeri F, Perales L, Przytycka TM, Pu LL, Robinson G, Thornton RL, Saada N, Scherer SE, Smith HE, Vinson C, Warner CB, Worley KC, Wu YQ, Zou X, Cherbas P, Kellis M, Eisen MB, Piano F, Kionte K, Fitch DH, Sternberg PW, Cutter AD, Duff MO, Hoskins RA, Graveley BR, Gibbs RA, Bickel PJ, Kopp A, Carninci P, Celniker SE, Oliver B, Richards S.

Genome Res. 2014 Jul;24(7):1209-23. doi: 10.1101/gr.159384.113.

PMID:
24985915
[PubMed - in process]
Free PMC Article
3.

Detecting Expressed Genes Using CAGE.

Murata M, Nishiyori-Sueki H, Kojima-Ishiyama M, Carninci P, Hayashizaki Y, Itoh M.

Methods Mol Biol. 2014;1164:67-85. doi: 10.1007/978-1-4939-0805-9_7.

PMID:
24927836
[PubMed - in process]
4.

Digital expression profiling of the compartmentalized translatome of Purkinje neurons.

Kratz A, Beguin P, Kaneko M, Chimura T, Suzuki AM, Matsunaga A, Kato S, Bertin N, Lassmann T, Vigot R, Carninci P, Plessy C, Launey T.

Genome Res. 2014 Jun 5. pii: gr.164095.113. [Epub ahead of print]

PMID:
24904046
[PubMed - as supplied by publisher]
Free Article
5.

MOIRAI: a compact workflow system for CAGE analysis.

Hasegawa A, Daub C, Carninci P, Hayashizaki Y, Lassmann T.

BMC Bioinformatics. 2014 May 16;15:144. doi: 10.1186/1471-2105-15-144.

PMID:
24884663
[PubMed - in process]
Free PMC Article
6.

RECLU: a pipeline to discover reproducible transcriptional start sites and their alternative regulation using capped analysis of gene expression (CAGE).

Ohmiya H, Vitezic M, Frith MC, Itoh M, Carninci P, Forrest AR, Hayashizaki Y, Lassmann T; FANTOM Consortium.

BMC Genomics. 2014 Apr 25;15:269. doi: 10.1186/1471-2164-15-269.

PMID:
24779366
[PubMed - in process]
Free PMC Article
7.

Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance.

Fort A, Hashimoto K, Yamada D, Salimullah M, Keya CA, Saxena A, Bonetti A, Voineagu I, Bertin N, Kratz A, Noro Y, Wong CH, de Hoon M, Andersson R, Sandelin A, Suzuki H, Wei CL, Koseki H; FANTOM Consortium, Hasegawa Y, Forrest AR, Carninci P.

Nat Genet. 2014 Jun;46(6):558-66. doi: 10.1038/ng.2965. Epub 2014 Apr 28.

PMID:
24777452
[PubMed - in process]
8.

Systemic identification of estrogen-regulated genes in breast cancer cells through cap analysis of gene expression mapping.

Yamaga R, Ikeda K, Boele J, Horie-Inoue K, Takayama K, Urano T, Kaida K, Carninci P, Kawai J, Hayashizaki Y, Ouchi Y, de Hoon M, Inoue S.

Biochem Biophys Res Commun. 2014 May 9;447(3):531-6. doi: 10.1016/j.bbrc.2014.04.033. Epub 2014 Apr 16.

PMID:
24746470
[PubMed - in process]
9.

Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation.

Morikawa H, Ohkura N, Vandenbon A, Itoh M, Nagao-Sato S, Kawaji H, Lassmann T, Carninci P, Hayashizaki Y, Forrest AR, Standley DM, Date H, Sakaguchi S; FANTOM Consortium.

Proc Natl Acad Sci U S A. 2014 Apr 8;111(14):5289-94. doi: 10.1073/pnas.1312717110. Epub 2014 Mar 27.

PMID:
24706905
[PubMed - indexed for MEDLINE]
10.

Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing.

Kawaji H, Lizio M, Itoh M, Kanamori-Katayama M, Kaiho A, Nishiyori-Sueki H, Shin JW, Kojima-Ishiyama M, Kawano M, Murata M, Ninomiya-Fukuda N, Ishikawa-Kato S, Nagao-Sato S, Noma S, Hayashizaki Y, Forrest AR, Carninci P; FANTOM Consortium.

Genome Res. 2014 Apr;24(4):708-17. doi: 10.1101/gr.156232.113. Epub 2014 Mar 27.

PMID:
24676093
[PubMed - in process]
Free PMC Article
11.

Transcription and enhancer profiling in human monocyte subsets.

Schmidl C, Renner K, Peter K, Eder R, Lassmann T, Balwierz PJ, Itoh M, Nagao-Sato S, Kawaji H, Carninci P, Suzuki H, Hayashizaki Y, Andreesen R, Hume DA, Hoffmann P, Forrest AR, Kreutz MP, Edinger M, Rehli M; FANTOM consortium.

Blood. 2014 Apr 24;123(17):e90-9. doi: 10.1182/blood-2013-02-484188. Epub 2014 Mar 26.

PMID:
24671955
[PubMed - indexed for MEDLINE]
12.

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.

Blood. 2014 Apr 24;123(17):e58-67. doi: 10.1182/blood-2013-02-483792. Epub 2014 Mar 26.

PMID:
24671954
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

The enhancer and promoter landscape of human regulatory and conventional T-cell subpopulations.

Schmidl C, Hansmann L, Lassmann T, Balwierz PJ, Kawaji H, Itoh M, Kawai J, Nagao-Sato S, Suzuki H, Andreesen R, Hayashizaki Y, Forrest AR, Carninci P, Hoffmann P, Edinger M, Rehli M; FANTOM consortium.

Blood. 2014 Apr 24;123(17):e68-78. doi: 10.1182/blood-2013-02-486944. Epub 2014 Mar 26.

PMID:
24671953
[PubMed - indexed for MEDLINE]
14.

Analysis of the DNA methylome and transcriptome in granulopoiesis reveals timed changes and dynamic enhancer methylation.

Rönnerblad M, Andersson R, Olofsson T, Douagi I, Karimi M, Lehmann S, Hoof I, de Hoon M, Itoh M, Nagao-Sato S, Kawaji H, Lassmann T, Carninci P, Hayashizaki Y, Forrest AR, Sandelin A, Ekwall K, Arner E, Lennartsson A; FANTOM consortium.

Blood. 2014 Apr 24;123(17):e79-89. doi: 10.1182/blood-2013-02-482893. Epub 2014 Mar 26.

PMID:
24671952
[PubMed - indexed for MEDLINE]
15.

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, Lassmann T, Itoh M, Summers KM, Suzuki H, Daub CO, Kawai J, Heutink P, Hide W, Freeman TC, Lenhard B, Bajic VB, Taylor MS, Makeev VJ, Sandelin A, Hume DA, Carninci P, Hayashizaki Y.

Nature. 2014 Mar 27;507(7493):462-70. doi: 10.1038/nature13182.

PMID:
24670764
[PubMed - indexed for MEDLINE]
16.

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; FANTOM Consortium, Forrest AR, Carninci P, Rehli M, Sandelin A.

Nature. 2014 Mar 27;507(7493):455-61. doi: 10.1038/nature12787.

PMID:
24670763
[PubMed - indexed for MEDLINE]
17.

Diversity and dynamics of the Drosophila transcriptome.

Brown JB, Boley N, Eisman R, May GE, Stoiber MH, Duff MO, Booth BW, Wen J, Park S, Suzuki AM, Wan KH, Yu C, Zhang D, Carlson JW, Cherbas L, Eads BD, Miller D, Mockaitis K, Roberts J, Davis CA, Frise E, Hammonds AS, Olson S, Shenker S, Sturgill D, Samsonova AA, Weiszmann R, Robinson G, Hernandez J, Andrews J, Bickel PJ, Carninci P, Cherbas P, Gingeras TR, Hoskins RA, Kaufman TC, Lai EC, Oliver B, Perrimon N, Graveley BR, Celniker SE.

Nature. 2014 Mar 16. doi: 10.1038/nature12962. [Epub ahead of print]

PMID:
24670639
[PubMed - as supplied by publisher]
18.

Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines.

Rye M, Sandve GK, Daub CO, Kawaji H, Carninci P, Forrest AR, Drabløs F; FANTOM consortium.

BMC Genomics. 2014 Mar 26;15:120. doi: 10.1186/1471-2164-15-120.

PMID:
24669905
[PubMed - in process]
Free PMC Article
19.

NanoCAGE analysis of the mouse olfactory epithelium identifies the expression of vomeronasal receptors and of proximal LINE elements.

Pascarella G, Lazarevic D, Plessy C, Bertin N, Akalin A, Vlachouli C, Simone R, Faulkner GJ, Zucchelli S, Kawai J, Daub CO, Hayashizaki Y, Lenhard B, Carninci P, Gustincich S.

Front Cell Neurosci. 2014 Feb 18;8:41. doi: 10.3389/fncel.2014.00041. eCollection 2014.

PMID:
24600346
[PubMed]
Free PMC Article
20.

Two independent transcription initiation codes overlap on vertebrate core promoters.

Haberle V, Li N, Hadzhiev Y, Plessy C, Previti C, Nepal C, Gehrig J, Dong X, Akalin A, Suzuki AM, van IJcken WF, Armant O, Ferg M, Strähle U, Carninci P, Müller F, Lenhard B.

Nature. 2014 Mar 20;507(7492):381-5. doi: 10.1038/nature12974. Epub 2014 Feb 16.

PMID:
24531765
[PubMed - indexed for MEDLINE]

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