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Items: 1 to 20 of 201

1.

ggsashimi: Sashimi plot revised for browser- and annotation-independent splicing visualization.

Garrido-Martín D, Palumbo E, Guigó R, Breschi A.

PLoS Comput Biol. 2018 Aug 17;14(8):e1006360. doi: 10.1371/journal.pcbi.1006360. [Epub ahead of print]

PMID:
30118475
2.

Towards a complete map of the human long non-coding RNA transcriptome.

Uszczynska-Ratajczak B, Lagarde J, Frankish A, Guigó R, Johnson R.

Nat Rev Genet. 2018 Sep;19(9):535-548. doi: 10.1038/s41576-018-0017-y. Review.

PMID:
29795125
3.

The reference epigenome and regulatory chromatin landscape of chronic lymphocytic leukemia.

Beekman R, Chapaprieta V, Russiñol N, Vilarrasa-Blasi R, Verdaguer-Dot N, Martens JHA, Duran-Ferrer M, Kulis M, Serra F, Javierre BM, Wingett SW, Clot G, Queirós AC, Castellano G, Blanc J, Gut M, Merkel A, Heath S, Vlasova A, Ullrich S, Palumbo E, Enjuanes A, Martín-García D, Beà S, Pinyol M, Aymerich M, Royo R, Puiggros M, Torrents D, Datta A, Lowy E, Kostadima M, Roller M, Clarke L, Flicek P, Agirre X, Prosper F, Baumann T, Delgado J, López-Guillermo A, Fraser P, Yaspo ML, Guigó R, Siebert R, Martí-Renom MA, Puente XS, López-Otín C, Gut I, Stunnenberg HG, Campo E, Martin-Subero JI.

Nat Med. 2018 Jun;24(6):868-880. doi: 10.1038/s41591-018-0028-4. Epub 2018 May 21.

PMID:
29785028
4.

Expression of the transcribed ultraconserved region 70 and the related long non-coding RNA AC092652.2-202 has prognostic value in Chronic Lymphocytic Leukaemia.

Bomben R, Roisman A, D'Agaro T, Castellano G, Baumann T, Delgado J, López-Guillermo A, Zucchetto A, Dal-Bo M, Bravin V, Slavutsky I, Vlasova A, Guigó R, Martin-Subero JI, Chapaprieta V, Beekman R, Martin-García D, Beà S, Salaverria I, Aymerich M, Campo E, Gattei V, Hernández L.

Br J Haematol. 2018 Apr 24. doi: 10.1111/bjh.15237. [Epub ahead of print] No abstract available.

PMID:
29687884
5.

Comparative transcriptomics across 14 Drosophila species reveals signatures of longevity.

Ma S, Avanesov AS, Porter E, Lee BC, Mariotti M, Zemskaya N, Guigo R, Moskalev AA, Gladyshev VN.

Aging Cell. 2018 Apr 19:e12740. doi: 10.1111/acel.12740. [Epub ahead of print]

6.

The effects of death and post-mortem cold ischemia on human tissue transcriptomes.

Ferreira PG, Muñoz-Aguirre M, Reverter F, Sá Godinho CP, Sousa A, Amadoz A, Sodaei R, Hidalgo MR, Pervouchine D, Carbonell-Caballero J, Nurtdinov R, Breschi A, Amador R, Oliveira P, Çubuk C, Curado J, Aguet F, Oliveira C, Dopazo J, Sammeth M, Ardlie KG, Guigó R.

Nat Commun. 2018 Feb 13;9(1):490. doi: 10.1038/s41467-017-02772-x.

7.

The discovery potential of RNA processing profiles.

Pagès A, Dotu I, Pallarès-Albanell J, Martí E, Guigó R, Eyras E.

Nucleic Acids Res. 2018 Feb 16;46(3):e15. doi: 10.1093/nar/gkx1115.

8.

High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing.

Lagarde J, Uszczynska-Ratajczak B, Carbonell S, Pérez-Lluch S, Abad A, Davis C, Gingeras TR, Frankish A, Harrow J, Guigo R, Johnson R.

Nat Genet. 2017 Dec;49(12):1731-1740. doi: 10.1038/ng.3988. Epub 2017 Nov 6.

9.

Data Resources for Human Functional Genomics.

Ardlie KG, Guigó R.

Curr Opin Syst Biol. 2017 Feb;1:75-79. doi: 10.1016/j.coisb.2016.12.019. Epub 2017 Feb 22. No abstract available.

10.

Selenoprofiles: A Computational Pipeline for Annotation of Selenoproteins.

Santesmasses D, Mariotti M, Guigó R.

Methods Mol Biol. 2018;1661:17-28. doi: 10.1007/978-1-4939-7258-6_2.

PMID:
28917034
11.

Comparative transcriptomics in human and mouse.

Breschi A, Gingeras TR, Guigó R.

Nat Rev Genet. 2017 Jul;18(7):425-440. doi: 10.1038/nrg.2017.19. Epub 2017 May 8. Review.

PMID:
28479595
12.

LncATLAS database for subcellular localization of long noncoding RNAs.

Mas-Ponte D, Carlevaro-Fita J, Palumbo E, Hermoso Pulido T, Guigo R, Johnson R.

RNA. 2017 Jul;23(7):1080-1087. doi: 10.1261/rna.060814.117. Epub 2017 Apr 6.

13.

Brain Transcriptome Sequencing of a Natural Model of Alzheimer's Disease.

Altimiras F, Uszczynska-Ratajczak B, Camara F, Vlasova A, Palumbo E, Newhouse S, Deacon RM, Farias LA, Hurley MJ, Loyola DE, Vásquez RA, Dobson R, Guigó R, Cogram P.

Front Aging Neurosci. 2017 Mar 20;9:64. doi: 10.3389/fnagi.2017.00064. eCollection 2017. No abstract available.

14.

Genomic history of the origin and domestication of common bean unveils its closest sister species.

Rendón-Anaya M, Montero-Vargas JM, Saburido-Álvarez S, Vlasova A, Capella-Gutierrez S, Ordaz-Ortiz JJ, Aguilar OM, Vianello-Brondani RP, Santalla M, Delaye L, Gabaldón T, Gepts P, Winkler R, Guigó R, Delgado-Salinas A, Herrera-Estrella A.

Genome Biol. 2017 Mar 29;18(1):60. doi: 10.1186/s13059-017-1190-6.

15.

Scalable Design of Paired CRISPR Guide RNAs for Genomic Deletion.

Pulido-Quetglas C, Aparicio-Prat E, Arnan C, Polidori T, Hermoso T, Palumbo E, Ponomarenko J, Guigo R, Johnson R.

PLoS Comput Biol. 2017 Mar 2;13(3):e1005341. doi: 10.1371/journal.pcbi.1005341. eCollection 2017 Mar.

16.

Computational identification of the selenocysteine tRNA (tRNASec) in genomes.

Santesmasses D, Mariotti M, Guigó R.

PLoS Comput Biol. 2017 Feb 13;13(2):e1005383. doi: 10.1371/journal.pcbi.1005383. eCollection 2017 Feb.

17.

Ten Simple Rules on How to Organize a Scientific Retreat.

Ponomarenko J, Garrido R, Guigó R.

PLoS Comput Biol. 2017 Feb 2;13(2):e1005344. doi: 10.1371/journal.pcbi.1005344. eCollection 2017 Feb. No abstract available.

18.

Discovery of Cancer Driver Long Noncoding RNAs across 1112 Tumour Genomes: New Candidates and Distinguishing Features.

Lanzós A, Carlevaro-Fita J, Mularoni L, Reverter F, Palumbo E, Guigó R, Johnson R.

Sci Rep. 2017 Jan 27;7:41544. doi: 10.1038/srep41544.

19.

ChimPipe: accurate detection of fusion genes and transcription-induced chimeras from RNA-seq data.

Rodríguez-Martín B, Palumbo E, Marco-Sola S, Griebel T, Ribeca P, Alonso G, Rastrojo A, Aguado B, Guigó R, Djebali S.

BMC Genomics. 2017 Jan 3;18(1):7. doi: 10.1186/s12864-016-3404-9.

20.

Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx.

Abascal F, Corvelo A, Cruz F, Villanueva-Cañas JL, Vlasova A, Marcet-Houben M, Martínez-Cruz B, Cheng JY, Prieto P, Quesada V, Quilez J, Li G, García F, Rubio-Camarillo M, Frias L, Ribeca P, Capella-Gutiérrez S, Rodríguez JM, Câmara F, Lowy E, Cozzuto L, Erb I, Tress ML, Rodriguez-Ales JL, Ruiz-Orera J, Reverter F, Casas-Marce M, Soriano L, Arango JR, Derdak S, Galán B, Blanc J, Gut M, Lorente-Galdos B, Andrés-Nieto M, López-Otín C, Valencia A, Gut I, García JL, Guigó R, Murphy WJ, Ruiz-Herrera A, Marques-Bonet T, Roma G, Notredame C, Mailund T, Albà MM, Gabaldón T, Alioto T, Godoy JA.

Genome Biol. 2016 Dec 14;17(1):251.

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