Publications


Things I've authored

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Selected

  1. Maragkakis M, et al., DIANA-microT web server: elucidating miRNA functions through target prediction. Nucleic Acids Res. 37, W273–6, (2009). more…
    (500+ citations)

  2. Maragkakis M, et al., Accurate miRNA target prediction correlates with protein repression levels. BMC Bioinformatics 10, 295 (2009). more…
    (340+ citations)

  3. Maragkakis M*, Vergoulis T*, et al., DIANA-microT Web server upgrade supports Fly and Worm miRNA target prediction and bibliographic miRNA to disease association. Nucleic Acids Res. 39, W145–8 (2011). more…
    (100+ citations)

  4. Reczko M*, Maragkakis M*, et al., Functional microRNA targets in protein coding sequences. Bioinformatics 28, 771–776 (2012). more…
    (240+ citations)

  5. Vourekas A*, Zheng K*, Fu Q*, Maragkakis M*, et al., The RNA helicase MOV10L1 binds piRNA precursors to initiate piRNA processing. Genes & Development 29, 617–629 (2015). more…

  6. Maragkakis M*, Alexiou P*, Nakaya T, Mourelatos Z, CLIPSeqTools - A novel bioinformatics CLIP-Seq analysis suite. RNA 22, 1–9 (2016). more…

  7. Vourekas A, ALexiou P, Vrettos N, Maragkakis M, Mourelatos Z, Sequence-dependent but not sequence-specific piRNA adhesion traps mRNAs to the germ plasm. Nature 531, 390–394 (2016). more…
    (Highlighted in: Dev Cell. 37:9-10, 2016)

  8. Ibrahim F*, Maragkakis M*, Alexiou P, Mourelatos Z, Ribothrypsis, a novel process of canonical mRNA decay, mediates ribosome-phased mRNA endonucleolysis. Nat. Struct. Mol. Biol., (2018). more…
    (selected for journal cover and research highlight)

Publications

  1. 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, DIANA-microT web server: elucidating miRNA functions through target prediction. Nucleic Acids Res. 37, W273–6, (2009). more…

  2. Papadopoulos GL, Alexiou P, Maragkakis M, Reczko M, Hatzigeorgiou AG, DIANA-mirPath: Integrating human and mouse miRNAs in pathways. Bioinformatics. 25, 1991–1993 (2009). more…

  3. 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, Accurate miRNA target prediction correlates with protein repression levels. BMC Bioinformatics 10, 295 (2009). more…

  4. Alexiou P, Maragkakis M, Papadopoulos GL, Reczko M, Hatzigeorgiou AG, Lost in translation: an assessment and perspective for computational miRNA target identification. Bioinformatics 25, 3049–3055 (2009). more…

  5. Alexiou P, Maragkakis M, Papadopoulos GL, Simmosis VA, Zhang L, Hatzigeorgiou AG, The DIANA-mirExTra web server: from gene expression data to miRNA function. PLoS One 5, e9171 (2010). more…

  6. Iizasa H, Wulff BE, Alla NR, Maragkakis M, Megraw M, Hatzigeorgiou A, Iwakiri D, Takada K, Wiedmer A, Showe L, Lieberman P, Nishikura K, Editing of Epstein-Barr virus-encoded BART6 miRNAs controls their dicer targeting and consequently affects viral latency. J. Biol Chem. 285, 33358–33370 (2010). more…

  7. Alexiou P, Maragkakis M, Hatzigeorgiou AG, Online resources for miRNA analysis. J. Nucleic Acids Investig. 2, 2–5 (2011). more…

  8. Maragkakis M*, Vergoulis T*, Alexiou P, Reczko M, Plomaritou K, Gousis M, Kourtis K, Koziris N, Dalamagas T, Hatzigeorgiou AG, DIANA-microT Web server upgrade supports Fly and Worm miRNA target prediction and bibliographic miRNA to disease association. Nucleic Acids Res. 39, W145–8 (2011). more…

  9. Reczko M*, Maragkakis M*, Alexiou P, Papadopoulos GL, Hatzigeorgiou AG, Accurate microRNA target prediction using detailed binding site accessibility and machine learning on proteomics data. Front. Genet. 2, 103 (2011). more…

  10. Vergoulis T, Vlachos IS, Alexiou P, Georgakilas G, Maragkakis M, Reczko M, Gerangelos S, Koziris N, Dalamagas T, Hatzigeorgiou AG, TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support. Nucleic Acids Res. 40, D222–9 (2012). more…

  11. Reczko M*, Maragkakis M*, Alexiou P, Grosse I, Hatzigeorgiou AG, Functional microRNA targets in protein coding sequences. Bioinformatics 28, 771–776 (2012). more…

  12. Vlachos IS, Kostoulas N, Vergoulis T, Georgakilas G, Reczko M, Maragkakis M, Paraskevopoulou MD, Prionidis K, Dalamagas T, Hatzigeorgiou AG, DIANA miRPath v. 2.0: investigating the combinatorial effect of microRNAs in pathways. Nucleic Acids Res. 40, W498–504 (2012). more…

  13. Vourekas A, Zheng Q, Alexiou P*, Maragkakis M*, Kirino Y, Gregory BD, Mourelatos Z, Target RNA repertoire of Mili and Miwi reveals piRNA biogenesis and function of Miwi in spermiogenesis. Nat. Struct. Mol. Biol. 19, 773–781 (2012). more…

  14. Paraskevopoulou MD, Georgakilas G, Kostoulas N, Reczko M, Maragkakis M, Dalamagas TM, Hatzigeorgiou AG, DIANA-LncBase: experimentally verified and computationally predicted microRNA targets on long non-coding RNAs. Nucleic Acids Res. 41, D239–45 (2013). more…

  15. Ibrahim F, Maragkakis M*, Alexiou P*, Maronski AM, Dichter AM, Mourelatos Z, Identification of in vivo, conserved, TAF15 RNA binding sites reveals the impact of TAF15 on the neuronal transcriptome. Cell Reports 3, 301–308 (2013). more…

  16. Nakaya T, Alexiou P*, Maragkakis M*, Chang A, Mourelatos Z, FUS regulates genes coding for RNA binding proteins in neurons by binding to their highly conserved introns. RNA 19, 498–509 (2013). more…

  17. Honda S, Kirino Y, Maragkakis M, Alexiou P, Ohtaki A, Murali R, Mourelatos Z, Kirino Y, Mitochondrial protein BmPAPI modulates the length of mature piRNAs. RNA 19, 1405–1418 (2013). more…

  18. Liu X, Zheng Q, Vrettos N, Maragkakis M, Alexiou P, Gregory BD, Mourelatos Z, A MicroRNA precursor surveillance system in quality control of MicroRNA synthesis. Molecular Cell 55, 868–879 (2014). more…

  19. Vourekas A*, Zheng K*, Fu Q*, Maragkakis M*, Alexiou P, Pillai RS, Mourelatos Z, Wang PJ, The RNA helicase MOV10L1 binds piRNA precursors to initiate piRNA processing. Genes & Development 29, 617–629 (2015). more…

  20. Maragkakis M*, Alexiou P*, Nakaya T, Mourelatos Z, CLIPSeqTools - A novel bioinformatics CLIP-Seq analysis suite. RNA 22, 1–9 (2016). more…

  21. Vourekas A, ALexiou P, Vrettos N, Maragkakis M, Mourelatos Z, Sequence-dependent but not sequence-specific piRNA adhesion traps mRNAs to the germ plasm. Nature 531, 390–394 (2016). more…

  22. Vrettos N*, Maragkakis M*, Alexiou P, Mourelatos Z, Kc167, a widely used Drosophila cell line, contains an active primary piRNA pathway. RNA 23, 108–118 (2016). more…

  23. Kortschak RD, Snyder JB, Maragkakis M, Adelson DL, bíogo: a simple high-performance bioinformatics toolkit for the Go language. JOSS, (2017). more…

  24. Ibrahim F*, Maragkakis M*, Alexiou P, Mourelatos Z, Ribothrypsis, a novel process of canonical mRNA decay, mediates ribosome-phased mRNA endonucleolysis. Nat. Struct. Mol. Biol., (2018). more…

Book chapters and preprints

  1. Maragkakis M, Alexiou P, Mourelatos Z, GenOO: A Modern Perl Framework for High Throughput Sequencing analysis. BioRxiv, (2015). more…

  2. Alexiou P, Maragkakis M, Mourelatos Z, Vourekas A, cCLIP-Seq: Retrieval of Chimeric Reads from HITS-CLIP (CLIP-Seq) Libraries. In: Okamura K., Nakanishi K. (eds) Argonaute Proteins. Methods in Molecular Biology, vol 1680. Humana Press, New York, NY (2018). more…