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Items: 1 to 50 of 56

1.

ECCB 2018: The 17th European Conference on Computational Biology.

ECCB 2018 Steering Committee, Hatzigeorgiou AG, Bagos P, Benos PV, Nikolaou C, Moreau Y, Kavakiotis I.

Bioinformatics. 2018 Sep 1;34(17):i595-i598. doi: 10.1093/bioinformatics/bty740. No abstract available.

PMID:
30423102
2.

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.

3.

Identifying Pri-miRNA Transcription Start Sites.

Georgakilas G, Perdikopanis N, Hatzigeorgiou AG.

Methods Mol Biol. 2018;1823:11-31. doi: 10.1007/978-1-4939-8624-8_2.

PMID:
29959670
4.

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.

5.

Defective synaptic connectivity and axonal neuropathology in a human iPSC-based model of familial Parkinson's disease.

Kouroupi G, Taoufik E, Vlachos IS, Tsioras K, Antoniou N, Papastefanaki F, Chroni-Tzartou D, Wrasidlo W, Bohl D, Stellas D, Politis PK, Vekrellis K, Papadimitriou D, Stefanis L, Bregestovski P, Hatzigeorgiou AG, Masliah E, Matsas R.

Proc Natl Acad Sci U S A. 2017 May 2;114(18):E3679-E3688. doi: 10.1073/pnas.1617259114. Epub 2017 Apr 17.

6.

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.

7.

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.

8.

Functional Analysis of miRNAs Using the DIANA Tools Online Suite.

Vlachos IS, Hatzigeorgiou AG.

Methods Mol Biol. 2017;1517:25-50.

PMID:
27924472
9.

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.

10.

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.

11.

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
12.

A Positive Regulatory Loop between a Wnt-Regulated Non-coding RNA and ASCL2 Controls Intestinal Stem Cell Fate.

Giakountis A, Moulos P, Zarkou V, Oikonomou C, Harokopos V, Hatzigeorgiou AG, Reczko M, Hatzis P.

Cell Rep. 2016 Jun 21;15(12):2588-96. doi: 10.1016/j.celrep.2016.05.038. Epub 2016 Jun 9.

13.

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.

14.

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
15.

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.

16.

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.

17.

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.

18.

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
19.

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.

20.

Integrated analysis of microRNA and mRNA expression and association with HIF binding reveals the complexity of microRNA expression regulation under hypoxia.

Camps C, Saini HK, Mole DR, Choudhry H, Reczko M, Guerra-Assunção JA, Tian YM, Buffa FM, Harris AL, Hatzigeorgiou AG, Enright AJ, Ragoussis J.

Mol Cancer. 2014 Feb 11;13:28. doi: 10.1186/1476-4598-13-28.

21.

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.

22.

Online resources for miRNA analysis.

Vlachos IS, Hatzigeorgiou AG.

Clin Biochem. 2013 Jul;46(10-11):879-900. doi: 10.1016/j.clinbiochem.2013.03.006. Epub 2013 Mar 18. Review.

PMID:
23518312
23.

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.

24.

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.

25.

Use of mutagenesis, genetic mapping and next generation transcriptomics to investigate insecticide resistance mechanisms.

Kalajdzic P, Oehler S, Reczko M, Pavlidi N, Vontas J, Hatzigeorgiou AG, Savakis C.

PLoS One. 2012;7(6):e40296. doi: 10.1371/journal.pone.0040296. Epub 2012 Jun 29.

26.

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.

27.

Identification of microRNA-221/222 and microRNA-323-3p association with rheumatoid arthritis via predictions using the human tumour necrosis factor transgenic mouse model.

Pandis I, Ospelt C, Karagianni N, Denis MC, Reczko M, Camps C, Hatzigeorgiou AG, Ragoussis J, Gay S, Kollias G.

Ann Rheum Dis. 2012 Oct;71(10):1716-23. doi: 10.1136/annrheumdis-2011-200803. Epub 2012 May 5.

28.

Accurate microRNA Target Prediction Using Detailed Binding Site Accessibility and Machine Learning on Proteomics Data.

Reczko M, Maragkakis M, Alexiou P, Papadopoulos GL, Hatzigeorgiou AG.

Front Genet. 2012 Jan 18;2:103. doi: 10.3389/fgene.2011.00103. eCollection 2011.

29.

Functional microRNA targets in protein coding sequences.

Reczko M, Maragkakis M, Alexiou P, Grosse I, Hatzigeorgiou AG.

Bioinformatics. 2012 Mar 15;28(6):771-6. doi: 10.1093/bioinformatics/bts043. Epub 2012 Jan 27.

PMID:
22285563
30.

TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support.

Vergoulis T, Vlachos IS, Alexiou P, Georgakilas G, Maragkakis M, Reczko M, Gerangelos S, Koziris N, Dalamagas T, Hatzigeorgiou AG.

Nucleic Acids Res. 2012 Jan;40(Database issue):D222-9. doi: 10.1093/nar/gkr1161. Epub 2011 Dec 1.

31.

DIANA-microT Web server upgrade supports Fly and Worm miRNA target prediction and bibliographic miRNA to disease association.

Maragkakis M, Vergoulis T, Alexiou P, Reczko M, Plomaritou K, Gousis M, Kourtis K, Koziris N, Dalamagas T, Hatzigeorgiou AG.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W145-8. doi: 10.1093/nar/gkr294. Epub 2011 May 6.

32.

The DIANA-mirExTra web server: from gene expression data to microRNA function.

Alexiou P, Maragkakis M, Papadopoulos GL, Simmosis VA, Zhang L, Hatzigeorgiou AG.

PLoS One. 2010 Feb 11;5(2):e9171. doi: 10.1371/journal.pone.0009171.

33.

miRGen 2.0: a database of microRNA genomic information and regulation.

Alexiou P, Vergoulis T, Gleditzsch M, Prekas G, Dalamagas T, Megraw M, Grosse I, Sellis T, Hatzigeorgiou AG.

Nucleic Acids Res. 2010 Jan;38(Database issue):D137-41. doi: 10.1093/nar/gkp888. Epub 2009 Oct 22.

34.

MicroRNA promoter analysis.

Megraw M, Hatzigeorgiou AG.

Methods Mol Biol. 2010;592:149-61. doi: 10.1007/978-1-60327-005-2_11.

PMID:
19802595
35.

Lost in translation: an assessment and perspective for computational microRNA target identification.

Alexiou P, Maragkakis M, Papadopoulos GL, Reczko M, Hatzigeorgiou AG.

Bioinformatics. 2009 Dec 1;25(23):3049-55. doi: 10.1093/bioinformatics/btp565. Epub 2009 Sep 29. Review.

PMID:
19789267
36.

Accurate microRNA target prediction correlates with protein repression levels.

Maragkakis M, Alexiou P, Papadopoulos GL, Reczko M, Dalamagas T, Giannopoulos G, Goumas G, Koukis E, Kourtis K, Simossis VA, Sethupathy P, Vergoulis T, Koziris N, Sellis T, Tsanakas P, Hatzigeorgiou AG.

BMC Bioinformatics. 2009 Sep 18;10:295. doi: 10.1186/1471-2105-10-295.

37.

DIANA-mirPath: Integrating human and mouse microRNAs in pathways.

Papadopoulos GL, Alexiou P, Maragkakis M, Reczko M, Hatzigeorgiou AG.

Bioinformatics. 2009 Aug 1;25(15):1991-3. doi: 10.1093/bioinformatics/btp299. Epub 2009 May 12.

PMID:
19435746
38.

DIANA-microT web server: elucidating microRNA functions through target prediction.

Maragkakis M, Reczko M, Simossis VA, Alexiou P, Papadopoulos GL, Dalamagas T, Giannopoulos G, Goumas G, Koukis E, Kourtis K, Vergoulis T, Koziris N, Sellis T, Tsanakas P, Hatzigeorgiou AG.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W273-6. doi: 10.1093/nar/gkp292. Epub 2009 Apr 30.

39.

A transcription factor affinity-based code for mammalian transcription initiation.

Megraw M, Pereira F, Jensen ST, Ohler U, Hatzigeorgiou AG.

Genome Res. 2009 Apr;19(4):644-56. doi: 10.1101/gr.085449.108. Epub 2009 Jan 13.

40.

The database of experimentally supported targets: a functional update of TarBase.

Papadopoulos GL, Reczko M, Simossis VA, Sethupathy P, Hatzigeorgiou AG.

Nucleic Acids Res. 2009 Jan;37(Database issue):D155-8. doi: 10.1093/nar/gkn809. Epub 2008 Oct 27.

41.

Frequency and fate of microRNA editing in human brain.

Kawahara Y, Megraw M, Kreider E, Iizasa H, Valente L, Hatzigeorgiou AG, Nishikura K.

Nucleic Acids Res. 2008 Sep;36(16):5270-80. doi: 10.1093/nar/gkn479. Epub 2008 Aug 6.

42.

Genomic and epigenetic alterations deregulate microRNA expression in human epithelial ovarian cancer.

Zhang L, Volinia S, Bonome T, Calin GA, Greshock J, Yang N, Liu CG, Giannakakis A, Alexiou P, Hasegawa K, Johnstone CN, Megraw MS, Adams S, Lassus H, Huang J, Kaur S, Liang S, Sethupathy P, Leminen A, Simossis VA, Sandaltzopoulos R, Naomoto Y, Katsaros D, Gimotty PA, DeMichele A, Huang Q, Bützow R, Rustgi AK, Weber BL, Birrer MJ, Hatzigeorgiou AG, Croce CM, Coukos G.

Proc Natl Acad Sci U S A. 2008 May 13;105(19):7004-9. doi: 10.1073/pnas.0801615105. Epub 2008 May 5.

43.

Anti-apoptotic function of a microRNA encoded by the HSV-1 latency-associated transcript.

Gartner JJ, Sethupathy P, Hatzigeorgiou AG, Fraser NW.

Nature. 2008 Jan 31;451(7178):600. doi: 10.1038/nature06621. No abstract available.

PMID:
18235505
44.

Human microRNA-155 on chromosome 21 differentially interacts with its polymorphic target in the AGTR1 3' untranslated region: a mechanism for functional single-nucleotide polymorphisms related to phenotypes.

Sethupathy P, Borel C, Gagnebin M, Grant GR, Deutsch S, Elton TS, Hatzigeorgiou AG, Antonarakis SE.

Am J Hum Genet. 2007 Aug;81(2):405-13. Epub 2007 Jul 12.

45.

Redirection of silencing targets by adenosine-to-inosine editing of miRNAs.

Kawahara Y, Zinshteyn B, Sethupathy P, Iizasa H, Hatzigeorgiou AG, Nishikura K.

Science. 2007 Feb 23;315(5815):1137-40.

46.

miRGen: a database for the study of animal microRNA genomic organization and function.

Megraw M, Sethupathy P, Corda B, Hatzigeorgiou AG.

Nucleic Acids Res. 2007 Jan;35(Database issue):D149-55. Epub 2006 Nov 15.

47.

A guide through present computational approaches for the identification of mammalian microRNA targets.

Sethupathy P, Megraw M, Hatzigeorgiou AG.

Nat Methods. 2006 Nov;3(11):881-6.

PMID:
17060911
48.

Characterization of a spliced exon product of herpes simplex type-1 latency-associated transcript in productively infected cells.

Kang W, Mukerjee R, Gartner JJ, Hatzigeorgiou AG, Sandri-Goldin RM, Fraser NW.

Virology. 2006 Dec 5-20;356(1-2):106-14. Epub 2006 Aug 30.

49.

MicroRNA promoter element discovery in Arabidopsis.

Megraw M, Baev V, Rusinov V, Jensen ST, Kalantidis K, Hatzigeorgiou AG.

RNA. 2006 Sep;12(9):1612-9. Epub 2006 Aug 3.

50.

Anti-apoptotic function of a microRNA encoded by the HSV-1 latency-associated transcript.

Gupta A, Gartner JJ, Sethupathy P, Hatzigeorgiou AG, Fraser NW.

Nature. 2006 Jul 6;442(7098):82-5. Epub 2006 May 31. Retraction in: Gartner JJ, Sethupathy P, Hatzigeorgiou AG, Fraser NW. Nature. 2008 Jan 31;451(7178):600.

PMID:
16738545

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