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Results: 1 to 20 of 235

1.

Gateways to the FANTOM5 promoter level mammalian expression atlas.

Lizio M, Harshbarger J, Shimoji H, Severin J, Kasukawa T, Sahin S, Abugessaisa I, Fukuda S, Hori F, Ishikawa-Kato S, Mungall CJ, Arner E, Baillie JK, Bertin N, Bono H, de Hoon M, Diehl AD, Dimont E, Freeman TC, Fujieda K, Hide W, Kaliyaperumal R, Katayama T, Lassmann T, Meehan TF, Nishikata K, Ono H, Rehli M, Sandelin A, Schultes EA, 't Hoen PA, Tatum Z, Thompson M, Toyoda T, Wright DW, Daub CO, Itoh M, Carninci P, Hayashizaki Y, Forrest AR, Kawaji H; the FANTOM consortium.

Genome Biol. 2015 Jan 5;16(1):22.

PMID:
25723102
[PubMed - as supplied by publisher]
Free PMC Article
2.

Transcription factor, promoter, and enhancer utilization in human myeloid cells.

Joshi A, Pooley C, Freeman TC, Lennartsson A, Babina M, Schmidl C, Geijtenbeek T; the FANTOM Consortium, Michoel T, Severin J, Itoh M, Lassmann T, Kawaji H, Hayashizaki Y, Carninci P, Forrest AR, Rehli M, Hume DA.

J Leukoc Biol. 2015 Feb 25. pii: jlb.6TA1014-477RR. [Epub ahead of print]

PMID:
25717144
[PubMed - as supplied by publisher]
3.

Gene regulation. Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.

Arner E, Daub CO, Vitting-Seerup K, Andersson R, Lilje B, Drabløs F, Lennartsson A, Rönnerblad M, Hrydziuszko O, Vitezic M, Freeman TC, Alhendi AM, Arner P, Axton R, Baillie JK, Beckhouse A, Bodega B, Briggs J, Brombacher F, Davis M, Detmar M, Ehrlund A, Endoh M, Eslami A, Fagiolini M, Fairbairn L, Faulkner GJ, Ferrai C, Fisher ME, Forrester L, Goldowitz D, Guler R, Ha T, Hara M, Herlyn M, Ikawa T, Kai C, Kawamoto H, Khachigian LM, Klinken SP, Kojima S, Koseki H, Klein S, Mejhert N, Miyaguchi K, Mizuno Y, Morimoto M, Morris KJ, Mummery C, Nakachi Y, Ogishima S, Okada-Hatakeyama M, Okazaki Y, Orlando V, Ovchinnikov D, Passier R, Patrikakis M, Pombo A, Qin XY, Roy S, Sato H, Savvi S, Saxena A, Schwegmann A, Sugiyama D, Swoboda R, Tanaka H, Tomoiu A, Winteringham LN, Wolvetang E, Yanagi-Mizuochi C, Yoneda M, Zabierowski S, Zhang P, Abugessaisa I, Bertin N, Diehl AD, Fukuda S, Furuno M, Harshbarger J, Hasegawa A, Hori F, Ishikawa-Kato S, Ishizu Y, Itoh M, Kawashima T, Kojima M, Kondo N, Lizio M, Meehan TF, Mungall CJ, Murata M, Nishiyori-Sueki H, Sahin S, Nagao-Sato S, Severin J, de Hoon MJ, Kawai J, Kasukawa T, Lassmann T, Suzuki H, Kawaji H, Summers KM, Wells C; FANTOM Consortium, Hume DA, Forrest AR, Sandelin A, Carninci P, Hayashizaki Y.

Science. 2015 Feb 27;347(6225):1010-4. doi: 10.1126/science.1259418. Epub 2015 Feb 12.

PMID:
25678556
[PubMed - in process]
4.

Nuclear transcriptome profiling of induced pluripotent stem cells and embryonic stem cells identify non-coding loci resistant to reprogramming.

Fort A, Yamada D, Hashimoto K, Koseki H, Carninci P.

Cell Cycle. 2015 Feb 9:0. [Epub ahead of print]

PMID:
25664506
[PubMed - as supplied by publisher]
5.

CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses.

Haberle V, Forrest AR, Hayashizaki Y, Carninci P, Lenhard B.

Nucleic Acids Res. 2015 Feb 4. pii: gkv054. [Epub ahead of print]

PMID:
25653163
[PubMed - as supplied by publisher]
Free Article
6.

Telomerase reverse transcriptase regulates microRNAs.

Lassmann T, Maida Y, Tomaru Y, Yasukawa M, Ando Y, Kojima M, Kasim V, Simon C, Daub CO, Carninci P, Hayashizaki Y, Masutomi K.

Int J Mol Sci. 2015 Jan 6;16(1):1192-208. doi: 10.3390/ijms16011192.

PMID:
25569094
[PubMed - in process]
Free PMC Article
7.

Biased allelic expression in human primary fibroblast single cells.

Borel C, Ferreira PG, Santoni F, Delaneau O, Fort A, Popadin KY, Garieri M, Falconnet E, Ribaux P, Guipponi M, Padioleau I, Carninci P, Dermitzakis ET, Antonarakis SE.

Am J Hum Genet. 2015 Jan 8;96(1):70-80. doi: 10.1016/j.ajhg.2014.12.001. Epub 2014 Dec 31.

PMID:
25557783
[PubMed - in process]
8.

CAGE-defined promoter regions of the genes implicated in Rett Syndrome.

Vitezic M, Bertin N, Andersson R, Lipovich L, Kawaji H, Lassmann T, Sandelin A, Heutink P, Goldowitz D, Ha T, Zhang P, Patrizi A, Fagiolini M, Forrest AR, Carninci P, Saxena A.

BMC Genomics. 2014 Dec 24;15(1):1177. [Epub ahead of print]

PMID:
25539566
[PubMed - as supplied by publisher]
Free Article
9.

Characterization of novel transcripts of human papillomavirus type 16 using cap analysis gene expression technology.

Taguchi A, Nagasaka K, Kawana K, Hashimoto K, Kusumoto-Matsuo R, Plessy C, Thomas M, Nakamura H, Bonetti A, Oda K, Kukimoto I, Carninci P, Banks L, Osuga Y, Fujii T.

J Virol. 2015 Feb 15;89(4):2448-52. doi: 10.1128/JVI.03433-14. Epub 2014 Dec 10.

PMID:
25505068
[PubMed - in process]
10.

Genomics: mice in the ENCODE spotlight.

Carninci P.

Nature. 2014 Nov 20;515(7527):346-7. doi: 10.1038/515346a. No abstract available.

PMID:
25409821
[PubMed - indexed for MEDLINE]
11.

The devil in the details of RNA-seq.

Kratz A, Carninci P.

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

PMID:
25203036
[PubMed - in process]
12.

Widespread genome transcription: new possibilities for RNA therapies.

Takahashi H, Carninci P.

Biochem Biophys Res Commun. 2014 Sep 19;452(2):294-301. doi: 10.1016/j.bbrc.2014.08.139. Epub 2014 Sep 1. Review.

PMID:
25193698
[PubMed - indexed for MEDLINE]
Free Article
13.

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 PMC Article
14.

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
15.

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; Fantom Consortium, Beltrami CA, Schneider C.

Stem Cells. 2014 Nov;32(11):2998-3011. doi: 10.1002/stem.1791.

PMID:
25069783
[PubMed - in process]
16.

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 - indexed for MEDLINE]
Free PMC Article
17.

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 - indexed for MEDLINE]
Free PMC Article
18.

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 - indexed for MEDLINE]
19.

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
20.

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
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