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Items: 1 to 20 of 102

1.

spongeScan: A web for detecting microRNA binding elements in lncRNA sequences.

Furió-Tarí P, Tarazona S, Gabaldón T, Enright AJ, Conesa A.

Nucleic Acids Res. 2016 May 19. pii: gkw443. [Epub ahead of print]

2.

Liquid chromatography coupled to tandem and high resolution mass spectrometry for the characterisation of ofloxacin transformation products after titanium dioxide photocatalysis.

Jimenez-Villarin J, Serra-Clusellas A, Martínez C, Conesa A, Garcia-Montaño J, Moyano E.

J Chromatogr A. 2016 Apr 22;1443:201-10. doi: 10.1016/j.chroma.2016.03.063. Epub 2016 Mar 23.

PMID:
27025791
3.

A survey of best practices for RNA-seq data analysis.

Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A, Szcześniak MW, Gaffney DJ, Elo LL, Zhang X, Mortazavi A.

Genome Biol. 2016 Jan 26;17:13. doi: 10.1186/s13059-016-0881-8.

4.

Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data.

Okonechnikov K, Conesa A, García-Alcalde F.

Bioinformatics. 2016 Jan 15;32(2):292-4. doi: 10.1093/bioinformatics/btv566. Epub 2015 Oct 1.

5.

Methylome profiling reveals functions and genes which are differentially methylated in serrated compared to conventional colorectal carcinoma.

Conesa-Zamora P, García-Solano J, Turpin Mdel C, Sebastián-León P, Torres-Moreno D, Estrada E, Tuomisto A, Wilce J, Mäkinen MJ, Pérez-Guillermo M, Conesa A.

Clin Epigenetics. 2015 Sep 17;7(1):101. doi: 10.1186/s13148-015-0128-7. eCollection 2015.

6.

Comparative RNA-seq analysis of the Tritrichomonas foetus PIG30/1 isolate from pigs reveals close association with Tritrichomonas foetus BP-4 isolate 'bovine genotype'.

Morin-Adeline V, Mueller K, Conesa A, Šlapeta J.

Vet Parasitol. 2015 Sep 15;212(3-4):111-7. doi: 10.1016/j.vetpar.2015.08.012. Epub 2015 Aug 14.

PMID:
26315127
7.

RNAseq analysis of Aspergillus fumigatus in blood reveals a just wait and see resting stage behavior.

Irmer H, Tarazona S, Sasse C, Olbermann P, Loeffler J, Krappmann S, Conesa A, Braus GH.

BMC Genomics. 2015 Aug 27;16:640. doi: 10.1186/s12864-015-1853-1.

8.

Cognitive Impairment After Sleep Deprivation Rescued by Transcranial Magnetic Stimulation Application in Octodon degus.

Estrada C, López D, Conesa A, Fernández-Gómez FJ, Gonzalez-Cuello A, Toledo F, Tunez I, Blin O, Bordet R, Richardson JC, Fernandez-Villalba E, Herrero MT.

Neurotox Res. 2015 Nov;28(4):361-71. doi: 10.1007/s12640-015-9544-x. Epub 2015 Jul 21.

PMID:
26194615
9.

Data quality aware analysis of differential expression in RNA-seq with NOISeq R/Bioc package.

Tarazona S, Furió-Tarí P, Turrà D, Pietro AD, Nueda MJ, Ferrer A, Conesa A.

Nucleic Acids Res. 2015 Dec 2;43(21):e140. doi: 10.1093/nar/gkv711. Epub 2015 Jul 16.

10.

Two independent epigenetic biomarkers predict survival in neuroblastoma.

Yáñez Y, Grau E, Rodríguez-Cortez VC, Hervás D, Vidal E, Noguera R, Hernández M, Segura V, Cañete A, Conesa A, Font de Mora J, Castel V.

Clin Epigenetics. 2015 Feb 27;7(1):16. doi: 10.1186/s13148-015-0054-8. eCollection 2015.

11.

[Ileocolic fistulas after radiotherapy for endometrial carcinoma].

Alcaide N, Velayos B, Redondo GG, Rosa EB, Conesa AM, Salazar LF, Jiménez I, González JM.

Gastroenterol Hepatol. 2016 Jan;39(1):23-4. doi: 10.1016/j.gastrohep.2014.12.009. Epub 2015 Feb 18. Spanish. No abstract available.

PMID:
25700805
12.

Comparative transcriptomics reveals striking similarities between the bovine and feline isolates of Tritrichomonas foetus: consequences for in silico drug-target identification.

Morin-Adeline V, Lomas R, O'Meally D, Stack C, Conesa A, Šlapeta J.

BMC Genomics. 2014 Nov 5;15:955. doi: 10.1186/1471-2164-15-955.

13.

Understanding disease mechanisms with models of signaling pathway activities.

Sebastian-Leon P, Vidal E, Minguez P, Conesa A, Tarazona S, Amadoz A, Armero C, Salavert F, Vidal-Puig A, Montaner D, Dopazo J.

BMC Syst Biol. 2014 Oct 25;8:121. doi: 10.1186/s12918-014-0121-3.

14.

Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures.

Munro SA, Lund SP, Pine PS, Binder H, Clevert DA, Conesa A, Dopazo J, Fasold M, Hochreiter S, Hong H, Jafari N, Kreil DP, Łabaj PP, Li S, Liao Y, Lin SM, Meehan J, Mason CE, Santoyo-Lopez J, Setterquist RA, Shi L, Shi W, Smyth GK, Stralis-Pavese N, Su Z, Tong W, Wang C, Wang J, Xu J, Ye Z, Yang Y, Yu Y, Salit M.

Nat Commun. 2014 Sep 25;5:5125. doi: 10.1038/ncomms6125.

PMID:
25254650
15.

STATegra EMS: an Experiment Management System for complex next-generation omics experiments.

Hernández-de-Diego R, Boix-Chova N, Gómez-Cabrero D, Tegner J, Abugessaisa I, Conesa A.

BMC Syst Biol. 2014;8 Suppl 2:S9. doi: 10.1186/1752-0509-8-S2-S9. Epub 2014 Mar 13.

16.

The common ground of genomics and systems biology.

Conesa A, Mortazavi A.

BMC Syst Biol. 2014;8 Suppl 2:S1. doi: 10.1186/1752-0509-8-S2-S1. Epub 2014 Mar 13. Review.

17.

Data integration in the era of omics: current and future challenges.

Gomez-Cabrero D, Abugessaisa I, Maier D, Teschendorff A, Merkenschlager M, Gisel A, Ballestar E, Bongcam-Rudloff E, Conesa A, Tegnér J.

BMC Syst Biol. 2014;8 Suppl 2:I1. doi: 10.1186/1752-0509-8-S2-I1. Epub 2014 Mar 13. Review.

18.

Pathway network inference from gene expression data.

Ponzoni I, Nueda M, Tarazona S, Götz S, Montaner D, Dussaut J, Dopazo J, Conesa A.

BMC Syst Biol. 2014;8 Suppl 2:S7. doi: 10.1186/1752-0509-8-S2-S7. Epub 2014 Mar 13.

19.

Relationship between genome and epigenome--challenges and requirements for future research.

Almouzni G, Altucci L, Amati B, Ashley N, Baulcombe D, Beaujean N, Bock C, Bongcam-Rudloff E, Bousquet J, Braun S, Bressac-de Paillerets B, Bussemakers M, Clarke L, Conesa A, Estivill X, Fazeli A, Grgurević N, Gut I, Heijmans BT, Hermouet S, Houwing-Duistermaat J, Iacobucci I, Ilaš J, Kandimalla R, Krauss-Etschmann S, Lasko P, Lehmann S, Lindroth A, Majdič G, Marcotte E, Martinelli G, Martinet N, Meyer E, Miceli C, Mills K, Moreno-Villanueva M, Morvan G, Nickel D, Niesler B, Nowacki M, Nowak J, Ossowski S, Pelizzola M, Pochet R, Potočnik U, Radwanska M, Raes J, Rattray M, Robinson MD, Roelen B, Sauer S, Schinzer D, Slagboom E, Spector T, Stunnenberg HG, Tiligada E, Torres-Padilla ME, Tsonaka R, Van Soom A, Vidaković M, Widschwendter M.

BMC Genomics. 2014 Jun 18;15:487. doi: 10.1186/1471-2164-15-487.

20.

Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series.

Nueda MJ, Tarazona S, Conesa A.

Bioinformatics. 2014 Sep 15;30(18):2598-602. doi: 10.1093/bioinformatics/btu333. Epub 2014 Jun 3.

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