Curriculum Vitae

Curriculum Vitae

Name Panagiotis Alexiou
Position Research Associate
Perelman School of Medicine, University of Pennsylvania, USA
Home Address 825 S St Bernard Str.
Philadelphia, PA 19143
USA
Work Address Department of Pathology and Laboratory Medicine
Division of Neuropathology
613B Stellar Chance Labs
422 Curie Boulevard
Philadelphia, PA 19104-6100
Phone: (+1) (267) 277-2661
E-mail: palexiou@mail.med.upenn.edu
Website: http://www.panalexiou.com/

Education & Research

1999 – 2004: University of Aberdeen, UK — BSc Genetics with Industrial Placement
2004 – 2006: Universiteit van Amsterdam, Netherlands — MSc Molecular Cell Biology and Bioinformatics
2007-2011: Aristotelian University of Thessaloniki, Greece — PhD
BSRC Alexander Fleming, Greece — PhD Research
2011 – 2016: University of Pennsylvania, USA — Postdoctoral Research
2016 – Present: University of Pennsylvania, USA — Research Associate

Grants and Scholarships

2007­ – 2010
BSRC Alexander Fleming PhD funding scholarship (3 years)

2010 – ­2012
IKYDA personel exchange program grant (Greece­Germany) in collaboration with Martin Luther University Halle­Wittenberg (2 years)

Teaching

2009 – ­2011
Graduate Teaching Assistant
University of Thessaly, Greece, Department of Electrical and Computer Engineering
Bioinformatics (HY501) Undergraduate Course

2009­- 2011
Substitute Lectures
National and Kapodistrian University of Athens, Department of Informatics and Communications, MSc Information Technologies in Medicine and Biology.

Publications in chronological order (* denotes equal contribution):

  1. 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 (2008) Genomic and Epigenetic Alterations Deregulate microRNA Expression in Human Epithelial Ovarian Cancer, Proc Natl Acad Sci U S A ,105(19) ,7004-9.
  2. 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. (2009) DIANA-microT web server: elucidating microRNA functions through target prediction., Nucleic Acids Res. ,37(Web Server issue):W273-6.
  3. Papadopoulos GL, Alexiou P, Maragkakis M, Reczko M, Hatzigeorgiou AG. (2009) DIANA-mirPath: Integrating human and mouse microRNAs in pathways., Bioinformatics. ,2009 Aug 1;25(15):1991-3.
  4. 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. (2009) Accurate microRNA target prediction correlates with protein repression levels. BMC Bioinformatics ,2009 Sep 18;10:295.
  5. Alexiou P, Maragkakis M, Papadopoulos GL, Reczko M, Hatzigeorgiou AG (2009) Lost in translation: an assessment and perspective for computational microRNA target identification., Bioinformatics , 25(23):3049-55
  6. Alexiou P, T. Vergoulis, M. Gleditzsch, G. Prekas, T. Dalamagas, M. Megraw, I. Grosse, T. Sellis, A.G. Hatzigeorgiou (2009) miRGen 2.0: a database of microRNA genomic information and regulation, Nucleic Acids Research ,Nucleic Acids Res. 2010 January; 38(Database issue): D137–D141.
  7. Alexiou P, Maragkakis M, Papadopoulos GL, Simmosis VA, Zhang L, Hatzigeorgiou AG (2010) The DIANA-mirExTra web server: from gene expression data to microRNA function., PLoS ONE ,5(2):e9171
  8. Marotta D, Karar J, Jenkins WT, Kumanova M, Jenkins KW, Tobias JW, Baldwin D, Hatzigeorgiou A, Alexiou P, Evans SM, Alarcon R, Maity A, Koch C, Koumenis C. (2011) In vivo profiling of hypoxic gene expression in gliomas using the hypoxia marker EF5 and laser-capture microdissection. Cancer Res ,71(3):779-89
  9. Alexiou P, Maragkakis M, Hatzigeorgiou AG (2011) Online resources for microRNA analysis. Journal of Nucleic Acid Investigation, 2(1)
  10. Maragkakis M, Vergoulis T, Alexiou P, Reczko M, Plomaritou K, Gousis M, Kourtis K, Koziris N, Dalamagas T, Hatzigeorgiou AG. (2011) DIANA-microT Web server upgrade supports Fly and Worm miRNA target prediction and bibliographic miRNA to disease association. Nucleic Acids Res. (Web Server issue)
  11. Vergoulis T, Vlachos IS, Alexiou P, Georgakilas G, Maragkakis M, Reczko M, Gerangelos S, Koziris N, Dalamagas T, Hatzigeorgiou AG. (2011) TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support. Nucleic Acids Res. 2011 Dec 1.
  12. Reczko M, Maragkakis M, Alexiou P, Papadopoulos GL, Hatzigeorgiou AG. (2012) Accurate microRNA target prediction using detailed binding site accessibility and machine learning on proteomics data. Frontiers in Bioinformatics and Computational Biology
  13. Vourekas A, Zheng Q, Alexiou P, Maragkakis M, Kirino Y, Gregory BD, Mourelatos Z. (2012) Mili and Miwi target RNA repertoire reveals piRNA biogenesis and function of Miwi in spermiogenesis. Nat Struct Mol Biol. 19(8):773-81
  14. Honda S, Kirino Y, Maragkakis M, Alexiou P, Ohtaki A, Murali R, Mourelatos Z, Kirino Y. (2013) Mitochondrial protein BmPAPI modulates the length of mature piRNAs. RNA.
  15. Ibrahim F, Maragkakis M, Alexiou P, Maronski MA, Dichter MA, Mourelatos Z. (2013) Identification of in vivo, conserved, TAF15 RNA binding sites reveals the impact of TAF15 on the neuronal transcriptome. Cell Rep. 3(2):301-8
  16. Nakaya T, Alexiou P, Maragkakis M, Chang A, Mourelatos Z. (2013) FUS regulates genes coding for RNA-binding proteins in neurons by binding to their highly conserved introns. RNA 19(4):498-509.
  17. Liu X, Zheng Q, Vrettos N, Maragkakis M, Alexiou P, Gregory BD, Mourelatos Z. (2014) A MicroRNA precursor surveillance system in quality control of MicroRNA synthesis. Mol Cell. 55(6):868-79.
  18. Vourekas A, Zheng K, Fu Q, Maragkakis M, Alexiou P, Ma J, Pillai RS, Mourelatos Z, Wang PJ. (2015) The RNA helicase MOV10L1 binds piRNA precursors to initiate piRNA processing. Genes Dev. 2015 Mar 15;29(6):617-29.
  19. Maragkakis M*, Alexiou P*, Mourelatos M. (2015) GenOO: A Modern Perl Framework for High Throughput Sequencing analysis.bioRxiv doi:http://dx.doi.org/10.1101/019265
  20. Maragkakis M*, Alexiou P*, Nakaya T, Mourelatos M. (2015) CLIPSeqTools—a novel bioinformatics CLIP-seq analysis suite. RNA 22(1)
  21. Vourekas A*, Alexiou P*, Vrettos N, Maragkakis M, Mourelatos Z. (2016) Sequence-dependent but not sequence-specific piRNA adhesion traps and anchors mRNAs to the germ plasm. Nature  531(7594)
  22. Vrettos N, Maragkakis M, Alexiou P, Mourelatos Z. (2016) Kc167, a widely used Drosophila cell line, contains an active primary piRNA pathway. RNA (in press)
  23. Alexiou P*, Maragkakis M, Mourelatos Z, Vourekas A* (2017). cCLIP-Seq: Retrieval of chimaeric reads from HITS-CLIP (CLIP-Seq) libraries. Methods in Molecular Biology (in press)