Publications


Things I've authored

Metrics

Citations:  3250
First author publications:  9
h-index:  18
Source:  Google Scholar

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., 2009, Nucleic Acids Res. (link)

  2. Papadopoulos GL, Alexiou P, Maragkakis M, Reczko M, Hatzigeorgiou AG, DIANA-mirPath: Integrating human and mouse miRNAs in pathways., 2009, Bioinformatics. (link)

  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., 2009, BMC Bioinformatics (link)

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

  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., 2010 PLoS One (link)

  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., 2010, Journal of Biological Chemistry. (link)

  7. Alexiou P, Maragkakis M, Hatzigeorgiou AG, Online resources for miRNA analysis., 2011 Journal of Nucleic Acids Investigation (link)

  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., 2011, Nucleic Acids Res. (link)

  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., 2011, Frontiers in genetics (link)

  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., 2012, Nucleic Acids Res. (link)

  11. Reczko M*, Maragkakis M*, Alexiou P, Grosse I, Hatzigeorgiou AG, Functional microRNA targets in protein coding sequences., 2012, Bioinformatics (link)

  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., 2012, Nucleic Acids Res. (link)

  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., 2012, Nature Structural Molecular Biology (link)

  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., 2013, Nucleic Acids Res. (link)

  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., 2013, Cell Reports (link)

  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., 2013, RNA (link)

  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., 2013, RNA (link)

  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., 2014, Molecular Cell (link)

  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., 2015, Genes & Development (link)

  20. Maragkakis M*, Alexiou P*, Nakaya T, Mourelatos Z, CLIPSeqTools - A novel bioinformatics CLIP-Seq analysis suite., 2015, RNA (link)

  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., 2016, Nature (link)

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

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

  24. Tadashi N, Maragkakis M, Amyotrophic Lateral Sclerosis associated FUS mutation shortens mitochondria and induces neurotoxicity., under review

  25. Ibrahim F*, Maragkakis M*, Alexiou P, Mourelatos Z, Ribothrypsis mediates canonical, ribosome-phased mRNA endonucleolytic decay., under review

Conferences and posters

  1. Dalamagas, T, Farmakakis, T, Maragkakis, M, Hatzigeorgiou, AG, FreePub: Collecting and Organizing Scientific Material Using Mindmaps., 3rd International Workshop on Semantic Web Applications and Tools for the Life Sciences, 2010.

  2. Grau J, Arend D, Grosse I, Hatzigeorgiou AG, Keilwagen J, Maragkakis M, Weinholdt C, Posch S, Predicting miRNA targets utilizing an extended profile HMM., 25th German Conference on Bioinformatics, 2010.

  3. Vergoulis T, Alexakis M, Dalamagas T, Maragkakis M, Hatzigeorgiou AG, Sellis T, Tarcloud: A cloud-based platform to support mirna target prediction., Lecture Notes in Computer Science, 2012.

  4. Maragkakis M, Alexiou P, Mourelatos Z, GenOO-HTS: A Modern Perl Framework for High Throughput Sequencing analysis., HiTSEQ 2013: High Throughput Sequencing Algorithms & Applications, 2013

  5. Maragkakis M, Alexiou P, Tadashi N, Mourelatos Z, CLIPSeqTools: A novel bioinformatics CLIP-Seq analysis suite applied on Human Brain Ago HITS-CLIP., HSCBB14, 2014

  6. Ibrahim F*, Maragkakis M*, Alexiou P, Mourelatos Z, Ribothrypsis mediates widespread, ribosome-phased, endonucleolytic decay of canonical mRNAs., RECOMB/ISCB, 2017

Archives

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