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Transcriptome analysis of recurrently deregulated genes across multiple cancers identifies new pan-cancer biomarkers.

Kaczkowski B, Tanaka Y, Kawaji H, Sandelin A, Andersson R, Itoh M, Lassmann T; FANTOM5 consortium, Hayashizaki Y, Carninci P, Forrest AR.

Cancer Res. 2015 Nov 9. pii: canres.0484.2015. [Epub ahead of print]


DeepCAGE Transcriptomics Reveal an Important Role of the Transcription Factor MAFB in the Lymphatic Endothelium.

Dieterich LC, Klein S, Mathelier A, Sliwa-Primorac A, Ma Q, Hong YK, Shin JW, Hamada M, Lizio M, Itoh M, Kawaji H, Lassmann T, Daub CO, Arner E, Carninci P, Hayashizaki Y, Forrest AR, Wasserman WW, Detmar M.

Cell Rep. 2015 Nov 17;13(7):1493-504. doi: 10.1016/j.celrep.2015.10.002. Epub 2015 Nov 5.


Deficiency of multidrug resistance 2 contributes to cell transformation through oxidative stress.

Tebbi A, Levillayer F, Jouvion G, Fiette L, Soubigou G, Varet H, Boudjadja N, Cairo S, Hashimoto K, Suzuki AM, Carninci P, Carissimo A, di Bernardo D, Wei Y.

Carcinogenesis. 2015 Nov 5. pii: bgv156. [Epub ahead of print]


CAGE profiling of ncRNAs in hepatocellular carcinoma reveals widespread activation of retroviral LTR promoters in virus-induced tumors.

Hashimoto K, Suzuki AM, Dos Santos A, Desterke C, Collino A, Ghisletti S, Braun E, Bonetti A, Fort A, Qin XY, Radaelli E, Kaczkowski B, Forrest AR, Kojima S, Samuel D, Natoli G, Buendia MA, Faivre J, Carninci P.

Genome Res. 2015 Oct 28. [Epub ahead of print]


Discovery and functional analysis of lncRNAs: Methodologies to investigate an uncharacterized transcriptome.

Kashi K, Henderson L, Bonetti A, Carninci P.

Biochim Biophys Acta. 2015 Oct 23. pii: S1874-9399(15)00216-3. doi: 10.1016/j.bbagrm.2015.10.010. [Epub ahead of print]


STAP cells are derived from ES cells.

Konno D, Kasukawa T, Hashimoto K, Itoh T, Suetsugu T, Miura I, Wakana S, Carninci P, Matsuzaki F.

Nature. 2015 Sep 24;525(7570):E4-5. doi: 10.1038/nature15366. No abstract available.


Expression Specificity of Disease-Associated lncRNAs: Toward Personalized Medicine.

Nguyen Q, Carninci P.

Curr Top Microbiol Immunol. 2015 Aug 30. [Epub ahead of print]


SINEUPs: A new class of natural and synthetic antisense long non-coding RNAs that activate translation.

Zucchelli S, Cotella D, Takahashi H, Carrieri C, Cimatti L, Fasolo F, Jones MH, Sblattero D, Sanges R, Santoro C, Persichetti F, Carninci P, Gustincich S.

RNA Biol. 2015;12(8):771-9. doi: 10.1080/15476286.2015.1060395.


Paradigm shifts in genomics through the FANTOM projects.

de Hoon M, Shin JW, Carninci P.

Mamm Genome. 2015 Oct;26(9-10):391-402. doi: 10.1007/s00335-015-9593-8. Epub 2015 Aug 8.


The frequent evolutionary birth and death of functional promoters in mouse and human.

Young RS, Hayashizaki Y, Andersson R, Sandelin A, Kawaji H, Itoh M, Lassmann T, Carninci P; FANTOM Consortium, Bickmore WA, Forrest AR, Taylor MS.

Genome Res. 2015 Oct;25(10):1546-57. doi: 10.1101/gr.190546.115. Epub 2015 Jul 30.


Krimper Enforces an Antisense Bias on piRNA Pools by Binding AGO3 in the Drosophila Germline.

Sato K, Iwasaki YW, Shibuya A, Carninci P, Tsuchizawa Y, Ishizu H, Siomi MC, Siomi H.

Mol Cell. 2015 Aug 20;59(4):553-63. doi: 10.1016/j.molcel.2015.06.024. Epub 2015 Jul 23.


A draft network of ligand-receptor-mediated multicellular signalling in human.

Ramilowski JA, Goldberg T, Harshbarger J, Kloppman E, Lizio M, Satagopam VP, Itoh M, Kawaji H, Carninci P, Rost B, Forrest AR.

Nat Commun. 2015 Jul 22;6:7866. doi: 10.1038/ncomms8866.


Promoter-level expression clustering identifies time development of transcriptional regulatory cascades initiated by ErbB receptors in breast cancer cells.

Mina M, Magi S, Jurman G, Itoh M, Kawaji H, Lassmann T, Arner E, Forrest AR, Carninci P, Hayashizaki Y, Daub CO; FANTOM Consortium, Okada-Hatakeyama M, Furlanello C.

Sci Rep. 2015 Jul 16;5:11999. doi: 10.1038/srep11999.


Redefining the transcriptional regulatory dynamics of classically and alternatively activated macrophages by deepCAGE transcriptomics.

Roy S, Schmeier S, Arner E, Alam T, Parihar SP, Ozturk M, Tamgue O, Kawaji H, de Hoon MJ, Itoh M, Lassmann T, Carninci P, Hayashizaki Y, Forrest AR, Bajic VB, Guler R; Fantom Consortium, Brombacher F, Suzuki H.

Nucleic Acids Res. 2015 Aug 18;43(14):6969-82. doi: 10.1093/nar/gkv646. Epub 2015 Jun 27.


Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium.

Yu NY, Hallström BM, Fagerberg L, Ponten F, Kawaji H, Carninci P, Forrest AR; Fantom Consortium, Hayashizaki Y, Uhlén M, Daub CO.

Nucleic Acids Res. 2015 Aug 18;43(14):6787-98. doi: 10.1093/nar/gkv608. Epub 2015 Jun 27.


Engineering mammalian cell factories with SINEUP noncoding RNAs to improve translation of secreted proteins.

Patrucco L, Chiesa A, Soluri MF, Fasolo F, Takahashi H, Carninci P, Zucchelli S, Santoro C, Gustincich S, Sblattero D, Cotella D.

Gene. 2015 Sep 15;569(2):287-93. doi: 10.1016/j.gene.2015.05.070. Epub 2015 Jun 2.


SINEUPs are modular antisense long non-coding RNAs that increase synthesis of target proteins in cells.

Zucchelli S, Fasolo F, Russo R, Cimatti L, Patrucco L, Takahashi H, Jones MH, Santoro C, Sblattero D, Cotella D, Persichetti F, Carninci P, Gustincich S.

Front Cell Neurosci. 2015 May 13;9:174. doi: 10.3389/fncel.2015.00174. eCollection 2015.


HSA21 Single-Minded 2 (Sim2) Binding Sites Co-Localize with Super-Enhancers and Pioneer Transcription Factors in Pluripotent Mouse ES Cells.

Letourneau A, Cobellis G, Fort A, Santoni F, Garieri M, Falconnet E, Ribaux P, Vannier A, Guipponi M, Carninci P, Borel C, Antonarakis SE.

PLoS One. 2015 May 8;10(5):e0126475. doi: 10.1371/journal.pone.0126475. eCollection 2015.


Transcriptional dynamics reveal critical roles for non-coding RNAs in the immediate-early response.

Aitken S, Magi S, Alhendi AM, Itoh M, Kawaji H, Lassmann T, Daub CO, Arner E, Carninci P, Forrest AR, Hayashizaki Y; FANTOM Consortium, Khachigian LM, Okada-Hatakeyama M, Semple CA.

PLoS Comput Biol. 2015 Apr 17;11(4):e1004217. doi: 10.1371/journal.pcbi.1004217. eCollection 2015 Apr.


Expression analysis of the long non-coding RNA antisense to Uchl1 (AS Uchl1) during dopaminergic cells' differentiation in vitro and in neurochemical models of Parkinson's disease.

Carrieri C, Forrest AR, Santoro C, Persichetti F, Carninci P, Zucchelli S, Gustincich S.

Front Cell Neurosci. 2015 Apr 1;9:114. doi: 10.3389/fncel.2015.00114. eCollection 2015.

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