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Results: 1 to 20 of 225

1.

The devil in the details of RNA-seq.

Kratz A, Carninci P.

Nat Biotechnol. 2014 Sep 9;32(9):882-4. doi: 10.1038/nbt.3015. No abstract available.

PMID:
25203036
[PubMed - in process]
2.

Widespread genome transcription: New possibilities for RNA therapies.

Takahashi H, Carninci P.

Biochem Biophys Res Commun. 2014 Sep 1. pii: S0006-291X(14)01572-1. doi: 10.1016/j.bbrc.2014.08.139. [Epub ahead of print] Review.

PMID:
25193698
[PubMed - as supplied by publisher]
3.

Mesencephalic dopaminergic neurons express a repertoire of olfactory receptors and respond to odorant-like molecules.

Grison A, Zucchelli S, Urzì A, Zamparo I, Lazarevic D, Pascarella G, Roncaglia P, Giorgetti A, Garcia-Esparcia P, Vlachouli C, Simone R, Persichetti F, Forrest AR, Hayashizaki Y, Carloni P, Ferrer I, Lodovichi C, Plessy C; FANTOM Consortium, Carninci P, Gustincich S.

BMC Genomics. 2014 Aug 27;15:729. doi: 10.1186/1471-2164-15-729.

PMID:
25164183
[PubMed - in process]
Free Article
4.

Multiplicity of 5' Cap Structures Present on Short RNAs.

Abdelhamid RF, Plessy C, Yamauchi Y, Taoka M, de Hoon M, Gingeras TR, Isobe T, Carninci P.

PLoS One. 2014 Jul 31;9(7):e102895. doi: 10.1371/journal.pone.0102895. eCollection 2014.

PMID:
25079783
[PubMed - in process]
Free PMC Article
5.

Specific mesothelial signature marks the heterogeneity of mesenchymal stem cells from high-grade serous ovarian cancer.

Verardo R, Piazza S, Klaric E, Ciani Y, Bussadori G, Marzinotto S, Mariuzzi L, Cesselli D, Beltrami AP, Mano M, Itoh M, Kawaji H, Lassmann T, Carninci P, Hayashizaki Y, Forrest AR; the FANTOM consortium, Beltrami CA, Schneider C.

Stem Cells. 2014 Jul 28. doi: 10.1002/stem.1791. [Epub ahead of print]

PMID:
25069783
[PubMed - as supplied by publisher]
6.

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 K, 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 Aug 5;111(31):11467-72. doi: 10.1073/pnas.1317751111. Epub 2014 Jul 21.

PMID:
25049417
[PubMed - in process]
7.

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
8.

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]
9.

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 Aug;24(8):1396-410. doi: 10.1101/gr.164095.113. Epub 2014 Jun 5.

PMID:
24904046
[PubMed - in process]
Free PMC Article
10.

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 - indexed for MEDLINE]
Free PMC Article
11.

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
12.

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 - indexed for MEDLINE]
13.

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 - indexed for MEDLINE]
14.

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]
15.

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
16.

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]
17.

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
18.

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]
19.

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]
20.

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]

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