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Items: 21

1.

microCLIP super learning framework uncovers functional transcriptome-wide miRNA interactions.

Paraskevopoulou MD, Karagkouni D, Vlachos IS, Tastsoglou S, Hatzigeorgiou AG.

Nat Commun. 2018 Sep 6;9(1):3601. doi: 10.1038/s41467-018-06046-y.

2.

DIANA-TarBase v8: a decade-long collection of experimentally supported miRNA-gene interactions.

Karagkouni D, Paraskevopoulou MD, Chatzopoulos S, Vlachos IS, Tastsoglou S, Kanellos I, Papadimitriou D, Kavakiotis I, Maniou S, Skoufos G, Vergoulis T, Dalamagas T, Hatzigeorgiou AG.

Nucleic Acids Res. 2018 Jan 4;46(D1):D239-D245. doi: 10.1093/nar/gkx1141.

3.

BUFET: boosting the unbiased miRNA functional enrichment analysis using bitsets.

Zagganas K, Vergoulis T, Paraskevopoulou MD, Vlachos IS, Skiadopoulos S, Dalamagas T.

BMC Bioinformatics. 2017 Sep 6;18(1):399. doi: 10.1186/s12859-017-1812-8.

4.

A perspective on AKT 25-plus years after its discovery.

Paraskevopoulou MD, Tsichlis PN.

Sci Signal. 2017 Jul 4;10(486). pii: eaan8791. doi: 10.1126/scisignal.aan8791.

PMID:
28676491
5.

Neuronal ELAVL proteins utilize AUF-1 as a co-partner to induce neuron-specific alternative splicing of APP.

Fragkouli A, Koukouraki P, Vlachos IS, Paraskevopoulou MD, Hatzigeorgiou AG, Doxakis E.

Sci Rep. 2017 Mar 14;7:44507. doi: 10.1038/srep44507.

6.

Erratum to: The whole genome sequence of the Mediterranean fruit fly, Ceratitis capitata (Wiedemann), reveals insights into the biology and adaptive evolution of a highly invasive pest species.

Papanicolaou A, Schetelig MF, Arensburger P, Atkinson PW, Benoit JB, Bourtzis K, Castañera P, Cavanaugh JP, Chao H, Childers C, Curril I, Dinh H, Doddapaneni H, Dolan A, Dugan S, Friedrich M, Gasperi G, Geib S, Georgakilas G, Gibbs RA, Giers SD, Gomulski LM, González-Guzmán M, Guillem-Amat A, Han Y, Hatzigeorgiou AG, Hernández-Crespo P, Hughes DS, Jones JW, Karagkouni D, Koskinioti P, Lee SL, Malacrida AR, Manni M, Mathiopoulos K, Meccariello A, Munoz-Torres M, Murali SC, Murphy TD, Muzny DM, Oberhofer G, Ortego F, Paraskevopoulou MD, Poelchau M, Qu J, Reczko M, Robertson HM, Rosendale AJ, Rosselot AE, Saccone G, Salvemini M, Savini G, Schreiner P, Scolari F, Siciliano P, Sim SB, Tsiamis G, Ureña E, S Vlachos I, Werren JH, Wimmer EA, Worley KC, Zacharopoulou A, Richards S, Handler AM.

Genome Biol. 2017 Jan 18;18(1):11. doi: 10.1186/s13059-017-1155-9. No abstract available.

7.

RNAcentral: a comprehensive database of non-coding RNA sequences.

The RNAcentral Consortium, Petrov AI, Kay SJE, Kalvari I, Howe KL, Gray KA, Bruford EA, Kersey PJ, Cochrane G, Finn RD, Bateman A, Kozomara A, Griffiths-Jones S, Frankish A, Zwieb CW, Lau BY, Williams KP, Chan PP, Lowe TM, Cannone JJ, Gutell R, Machnicka MA, Bujnicki JM, Yoshihama M, Kenmochi N, Chai B, Cole JR, Szymanski M, Karlowski WM, Wood V, Huala E, Berardini TZ, Zhao Y, Chen R, Zhu W, Paraskevopoulou MD, Vlachos IS, Hatzigeorgiou AG, Ma L, Zhang Z, Puetz J, Stadler PF, McDonald D, Basu S, Fey P, Engel SR, Cherry JM, Volders PJ, Mestdagh P, Wower J, Clark MB, Quek XC, Dinger ME.

Nucleic Acids Res. 2017 Jan 4;45(D1):D128-D134. doi: 10.1093/nar/gkw1008. Epub 2016 Oct 28.

8.

The whole genome sequence of the Mediterranean fruit fly, Ceratitis capitata (Wiedemann), reveals insights into the biology and adaptive evolution of a highly invasive pest species.

Papanicolaou A, Schetelig MF, Arensburger P, Atkinson PW, Benoit JB, Bourtzis K, Castañera P, Cavanaugh JP, Chao H, Childers C, Curril I, Dinh H, Doddapaneni H, Dolan A, Dugan S, Friedrich M, Gasperi G, Geib S, Georgakilas G, Gibbs RA, Giers SD, Gomulski LM, González-Guzmán M, Guillem-Amat A, Han Y, Hatzigeorgiou AG, Hernández-Crespo P, Hughes DS, Jones JW, Karagkouni D, Koskinioti P, Lee SL, Malacrida AR, Manni M, Mathiopoulos K, Meccariello A, Munoz-Torres M, Murali SC, Murphy TD, Muzny DM, Oberhofer G, Ortego F, Paraskevopoulou MD, Poelchau M, Qu J, Reczko M, Robertson HM, Rosendale AJ, Rosselot AE, Saccone G, Salvemini M, Savini G, Schreiner P, Scolari F, Siciliano P, Sim SB, Tsiamis G, Ureña E, Vlachos IS, Werren JH, Wimmer EA, Worley KC, Zacharopoulou A, Richards S, Handler AM.

Genome Biol. 2016 Sep 22;17(1):192. doi: 10.1186/s13059-016-1049-2. Erratum in: Genome Biol. 2017 Jan 18;18(1):11.

9.

DIANA-TarBase and DIANA Suite Tools: Studying Experimentally Supported microRNA Targets.

Paraskevopoulou MD, Vlachos IS, Hatzigeorgiou AG.

Curr Protoc Bioinformatics. 2016 Sep 7;55:12.14.1-12.14.18. doi: 10.1002/cpbi.12.

PMID:
27603020
10.

DIANA-mirExTra v2.0: Uncovering microRNAs and transcription factors with crucial roles in NGS expression data.

Vlachos IS, Vergoulis T, Paraskevopoulou MD, Lykokanellos F, Georgakilas G, Georgiou P, Chatzopoulos S, Karagkouni D, Christodoulou F, Dalamagas T, Hatzigeorgiou AG.

Nucleic Acids Res. 2016 Jul 8;44(W1):W128-34. doi: 10.1093/nar/gkw455. Epub 2016 May 20.

11.

Analyzing MiRNA-LncRNA Interactions.

Paraskevopoulou MD, Hatzigeorgiou AG.

Methods Mol Biol. 2016;1402:271-286. doi: 10.1007/978-1-4939-3378-5_21.

PMID:
26721498
12.

DIANA-LncBase v2: indexing microRNA targets on non-coding transcripts.

Paraskevopoulou MD, Vlachos IS, Karagkouni D, Georgakilas G, Kanellos I, Vergoulis T, Zagganas K, Tsanakas P, Floros E, Dalamagas T, Hatzigeorgiou AG.

Nucleic Acids Res. 2016 Jan 4;44(D1):D231-8. doi: 10.1093/nar/gkv1270. Epub 2015 Nov 26.

13.

DIANA-miRGen v3.0: accurate characterization of microRNA promoters and their regulators.

Georgakilas G, Vlachos IS, Zagganas K, Vergoulis T, Paraskevopoulou MD, Kanellos I, Tsanakas P, Dellis D, Fevgas A, Dalamagas T, Hatzigeorgiou AG.

Nucleic Acids Res. 2016 Jan 4;44(D1):D190-5. doi: 10.1093/nar/gkv1254. Epub 2015 Nov 19.

14.

DIANA-miRPath v3.0: deciphering microRNA function with experimental support.

Vlachos IS, Zagganas K, Paraskevopoulou MD, Georgakilas G, Karagkouni D, Vergoulis T, Dalamagas T, Hatzigeorgiou AG.

Nucleic Acids Res. 2015 Jul 1;43(W1):W460-6. doi: 10.1093/nar/gkv403. Epub 2015 May 14.

15.

microTSS: accurate microRNA transcription start site identification reveals a significant number of divergent pri-miRNAs.

Georgakilas G, Vlachos IS, Paraskevopoulou MD, Yang P, Zhang Y, Economides AN, Hatzigeorgiou AG.

Nat Commun. 2014 Dec 10;5:5700. doi: 10.1038/ncomms6700.

PMID:
25492647
16.

DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions.

Vlachos IS, Paraskevopoulou MD, Karagkouni D, Georgakilas G, Vergoulis T, Kanellos I, Anastasopoulos IL, Maniou S, Karathanou K, Kalfakakou D, Fevgas A, Dalamagas T, Hatzigeorgiou AG.

Nucleic Acids Res. 2015 Jan;43(Database issue):D153-9. doi: 10.1093/nar/gku1215. Epub 2014 Nov 21.

17.

BiDaS: a web-based Monte Carlo BioData Simulator based on sequence/feature characteristics.

Paraskevopoulou MD, Vlachos IS, Athanasiadis E, Spyrou G.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W582-6. doi: 10.1093/nar/gkt420. Epub 2013 May 28.

18.

DIANA-microT web server v5.0: service integration into miRNA functional analysis workflows.

Paraskevopoulou MD, Georgakilas G, Kostoulas N, Vlachos IS, Vergoulis T, Reczko M, Filippidis C, Dalamagas T, Hatzigeorgiou AG.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W169-73. doi: 10.1093/nar/gkt393. Epub 2013 May 16.

19.

DIANA-LncBase: experimentally verified and computationally predicted microRNA targets on long non-coding RNAs.

Paraskevopoulou MD, Georgakilas G, Kostoulas N, Reczko M, Maragkakis M, Dalamagas TM, Hatzigeorgiou AG.

Nucleic Acids Res. 2013 Jan;41(Database issue):D239-45. doi: 10.1093/nar/gks1246. Epub 2012 Nov 28.

20.

miRNA regulons associated with synaptic function.

Paschou M, Paraskevopoulou MD, Vlachos IS, Koukouraki P, Hatzigeorgiou AG, Doxakis E.

PLoS One. 2012;7(10):e46189. doi: 10.1371/journal.pone.0046189. Epub 2012 Oct 8.

21.

DIANA miRPath v.2.0: investigating the combinatorial effect of microRNAs in pathways.

Vlachos IS, Kostoulas N, Vergoulis T, Georgakilas G, Reczko M, Maragkakis M, Paraskevopoulou MD, Prionidis K, Dalamagas T, Hatzigeorgiou AG.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W498-504. doi: 10.1093/nar/gks494. Epub 2012 May 30.

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