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Items: 1 to 20 of 305

1.

Conserved temporal ordering of promoter activation implicates common mechanisms governing the immediate early response across cell types and stimuli.

Vacca A, Itoh M, Kawaji H, Arner E, Lassmann T, Daub CO, Carninci P, Forrest ARR, Hayashizaki Y; FANTOM Consortium, Aitken S, Semple CA.

Open Biol. 2018 Aug;8(8). pii: 180011. doi: 10.1098/rsob.180011.

2.

Transcriptional landscape of Mycobacterium tuberculosis infection in macrophages.

Roy S, Schmeier S, Kaczkowski B, Arner E, Alam T, Ozturk M, Tamgue O, Parihar SP, Kawaji H, Itoh M, Lassmann T, Carninci P, Hayashizaki Y, Forrest ARR, Guler R, Bajic VB, Brombacher F, Suzuki H.

Sci Rep. 2018 Apr 30;8(1):6758. doi: 10.1038/s41598-018-24509-6.

3.

Prevention of hepatocellular carcinoma by targeting MYCN-positive liver cancer stem cells with acyclic retinoid.

Qin XY, Suzuki H, Honda M, Okada H, Kaneko S, Inoue I, Ebisui E, Hashimoto K, Carninci P, Kanki K, Tatsukawa H, Ishibashi N, Masaki T, Matsuura T, Kagechika H, Toriguchi K, Hatano E, Shirakami Y, Shiota G, Shimizu M, Moriwaki H, Kojima S.

Proc Natl Acad Sci U S A. 2018 May 8;115(19):4969-4974. doi: 10.1073/pnas.1802279115. Epub 2018 Apr 23.

4.

From "Cellular" RNA to "Smart" RNA: Multiple Roles of RNA in Genome Stability and Beyond.

Michelini F, Jalihal AP, Francia S, Meers C, Neeb ZT, Rossiello F, Gioia U, Aguado J, Jones-Weinert C, Luke B, Biamonti G, Nowacki M, Storici F, Carninci P, Walter NG, d'Adda di Fagagna F.

Chem Rev. 2018 Apr 25;118(8):4365-4403. doi: 10.1021/acs.chemrev.7b00487. Epub 2018 Mar 30.

PMID:
29600857
5.

Target-enrichment sequencing for detailed characterization of small RNAs.

Nguyen Q, Aguado J, Iannelli F, Suzuki AM, Rossiello F, d'Adda di Fagagna F, Carninci P.

Nat Protoc. 2018 Apr;13(4):768-786. doi: 10.1038/nprot.2018.001. Epub 2018 Mar 22.

PMID:
29565901
6.

Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease.

Baillie JK, Bretherick A, Haley CS, Clohisey S, Gray A, Neyton LPA, Barrett J, Stahl EA, Tenesa A, Andersson R, Brown JB, Faulkner GJ, Lizio M, Schaefer U, Daub C, Itoh M, Kondo N, Lassmann T, Kawai J; IIBDGC Consortium, Mole D, Bajic VB, Heutink P, Rehli M, Kawaji H, Sandelin A, Suzuki H, Satsangi J, Wells CA, Hacohen N, Freeman TC, Hayashizaki Y, Carninci P, Forrest ARR, Hume DA.

PLoS Comput Biol. 2018 Mar 1;14(3):e1005934. doi: 10.1371/journal.pcbi.1005934. eCollection 2018 Mar.

7.

Structural determinants of the SINE B2 element embedded in the long non-coding RNA activator of translation AS Uchl1.

Podbevšek P, Fasolo F, Bon C, Cimatti L, Reißer S, Carninci P, Bussi G, Zucchelli S, Plavec J, Gustincich S.

Sci Rep. 2018 Feb 16;8(1):3189. doi: 10.1038/s41598-017-14908-6.

8.

Identification of functional features of synthetic SINEUPs, antisense lncRNAs that specifically enhance protein translation.

Takahashi H, Kozhuharova A, Sharma H, Hirose M, Ohyama T, Fasolo F, Yamazaki T, Cotella D, Santoro C, Zucchelli S, Gustincich S, Carninci P.

PLoS One. 2018 Feb 7;13(2):e0183229. doi: 10.1371/journal.pone.0183229. eCollection 2018.

9.

Correction to: Relatively frequent switching of transcription start sites during cerebellar development.

Zhang P, Dimont E, Ha T, Swanson DJ, Itoh M, Kawaji H, Lassmann T, Daub CO, Arner E; FANTOM Consortium, Carninci P, Hayashizaki Y, Forrest ARR, Hide W, Goldowitz D.

BMC Genomics. 2018 Jan 11;19(1):39. doi: 10.1186/s12864-017-4291-4.

10.

Discovery of Transcription Factors Novel to Mouse Cerebellar Granule Cell Development Through Laser-Capture Microdissection.

Zhang PGY, Yeung J, Gupta I, Ramirez M, Ha T, Swanson DJ, Nagao-Sato S, Itoh M, Kawaji H, Lassmann T, Daub CO, Arner E, de Hoon M; FANTOM consortium, Carninci P, Forrest ARR, Hayashizaki Y, Goldowitz D.

Cerebellum. 2018 Jun;17(3):308-325. doi: 10.1007/s12311-017-0912-3.

PMID:
29307116
11.

The Human Cell Atlas.

Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Göttgens B, Hacohen N, Haniffa M, Hemberg M, Kim S, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundberg E, Lundeberg J, Majumder P, Marioni JC, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe'er D, Phillipakis A, Ponting CP, Quake S, Reik W, Rozenblatt-Rosen O, Sanes J, Satija R, Schumacher TN, Shalek A, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton M, Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt F, Weissman J, Wold B, Xavier R, Yosef N; Human Cell Atlas Meeting Participants.

Elife. 2017 Dec 5;6. pii: e27041. doi: 10.7554/eLife.27041.

12.

Monitoring transcription initiation activities in rat and dog.

Lizio M, Mukarram AK, Ohno M, Watanabe S, Itoh M, Hasegawa A, Lassmann T, Severin J, Harshbarger J, Abugessaisa I, Kasukawa T, Hon CC, Carninci P, Hayashizaki Y, Forrest ARR, Kawaji H.

Sci Data. 2017 Nov 28;4:170173. doi: 10.1038/sdata.2017.173.

13.

The effect of genetic variation on promoter usage and enhancer activity.

Garieri M, Delaneau O, Santoni F, Fish RJ, Mull D, Carninci P, Dermitzakis ET, Antonarakis SE, Fort A.

Nat Commun. 2017 Nov 7;8(1):1358. doi: 10.1038/s41467-017-01467-7.

14.

The Human Cell Atlas: Technical approaches and challenges.

Hon CC, Shin JW, Carninci P, Stubbington MJT.

Brief Funct Genomics. 2018 Jul 1;17(4):283-294. doi: 10.1093/bfgp/elx029.

15.

Transcription start site profiling of 15 anatomical regions of the Macaca mulatta central nervous system.

Francescatto M, Lizio M, Philippens I, Bontrop R, Sakai M, Watanabe S, Itoh M, Hasegawa A, Lassmann T, Severin J, Harshbarger J, Abugessaisa I, Kasukawa T, Carninci P, Hayashizaki Y, Forrest ARR, Kawaji H, Rizzu P, Heutink P.

Sci Data. 2017 Oct 31;4:170163. doi: 10.1038/sdata.2017.163.

16.

SCPortalen: human and mouse single-cell centric database.

Abugessaisa I, Noguchi S, Böttcher M, Hasegawa A, Kouno T, Kato S, Tada Y, Ura H, Abe K, Shin JW, Plessy C, Carninci P, Kasukawa T.

Nucleic Acids Res. 2018 Jan 4;46(D1):D781-D787. doi: 10.1093/nar/gkx949.

17.

Linking FANTOM5 CAGE peaks to annotations with CAGEscan.

Bertin N, Mendez M, Hasegawa A, Lizio M, Abugessaisa I, Severin J, Sakai-Ohno M, Lassmann T, Kasukawa T, Kawaji H, Hayashizaki Y, Forrest ARR, Carninci P, Plessy C.

Sci Data. 2017 Oct 3;4:170147. doi: 10.1038/sdata.2017.147.

18.

Transcriptome Analysis Uncovers a Growth-Promoting Activity of Orosomucoid-1 on Hepatocytes.

Qin XY, Hara M, Arner E, Kawaguchi Y, Inoue I, Tatsukawa H, Furutani Y, Nagatsuma K, Matsuura T, Wei F, Kikuchi J, Sone H, Daub C, Kawaji H, Lassmann T, Itoh M, Suzuki H, Carninci P, Hayashizaki Y; FANTOM consortium, Kokudo N, Forrest ARR, Kojima S.

EBioMedicine. 2017 Oct;24:257-266. doi: 10.1016/j.ebiom.2017.09.008. Epub 2017 Sep 12.

19.

Systematic analysis of transcription start sites in avian development.

Lizio M, Deviatiiarov R, Nagai H, Galan L, Arner E, Itoh M, Lassmann T, Kasukawa T, Hasegawa A, Ros MA, Hayashizaki Y, Carninci P, Forrest ARR, Kawaji H, Gusev O, Sheng G.

PLoS Biol. 2017 Sep 5;15(9):e2002887. doi: 10.1371/journal.pbio.2002887. eCollection 2017 Sep.

20.

The FANTOM5 collection, a data series underpinning mammalian transcriptome atlases in diverse cell types.

Kawaji H, Kasukawa T, Forrest A, Carninci P, Hayashizaki Y.

Sci Data. 2017 Aug 29;4:170113. doi: 10.1038/sdata.2017.113.

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