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.", Front Genet. 2011;2:103. Epub 2012 Jan 18. , 2011;2:103. Epub 2012 Jan 18. [PubMed].

Reczko M, Maragkakis M, Alexiou P, Grosse I, Hatzigeorgiou AG. 2012, "Functional microRNA targets in protein coding sequences.", Bioinformatics. , 2012 Jan 27. [Epub ahead of print] [PubMed].

Vergoulis T, Vlachos IS, Alexiou P, Georgakilas G, Maragkakis M, Reczko M, Gerangelos S, Koziris N, Dalamagas T, Hatzigeorgiou AG. 2012, "TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support.", Nucleic Acids Res. , 2012 Jan;40(Database issue):D222-9. Epub 2011 Dec 1. [PubMed].

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. , 2011 May 6. [Epub ahead of print] [PubMed].

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. , 2011 Feb 1; , 71(3):779-89. Epub 2011 Jan 25 [PubMed].

Iizasa H, Wulff BE, Alla NR, Maragkakis M, Megraw M, Hatzigeorgiou A, Iwakiri D, Takada K, Wiedmer A, Showe L, Lieberman P, Nishikura K. 2010, "Editing of EBV-encoded BART6 microRNAs controls their dicer targeting and consequently affects viral latency.", J Biol Chem. , 2010 Aug 17. , [Epub ahead of print] [PubMed].

Megraw M, Sethupathy P, Gumireddy K, Jensen ST, Huang Q, Hatzigeorgiou AG. 2010, "Isoform specific gene auto-regulation via miRNAs: a case study on miR-128b and ARPP-21", Theoretical Chemistry Accounts. , 2010 Mar; , 125(3-6): 593-598.

Riback J, Hatzigeorgiou AG, Reczko 2010, "M Computational classification of microRNAs in next-generation sequencing data.", Theoretical Chemistry Accounts. , 2010 Mar; , 125(3-6): 637-642.

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. , 2010 Feb 11; , 5(2):e9171. [PubMed].

Alexiou P, Vergoulis T, Gleditzsch M, Prekas G, Dalamagas T, Megraw M, Grosse I, Sellis T, Hatzigeorgiou AG. 2010, "miRGen 2.0: a database of microRNA genomic information and regulation.", Nucleic Acids Res. , 2010 Jan;38(Database issue) , :D137-41. Epub 2009 Oct 22. [PubMed].

Megraw M, Hatzigeorgiou AG. 2010, "MicroRNA promoter analysis.", Methods Mol Biol. , 2010;592, :149-61. [PubMed].

Alexiou P, Maragkakis M, Papadopoulos GL, Reczko M Hatzigeorgiou AG. 2009, "Lost in translation: an assessment and perspective for computational microRNA target identification.", Bioinformatics. , 2009 Dec 1 , ;25(23):3049-55. Epub 2009 Sep 29. Review. [PubMed].

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. [PubMed].

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. Epub 2009 May 12. [PubMed].

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. , 2009 Jul 1;37(Web Server issue): , W273-6. Epub 2009 Apr 30. [PubMed].

Megraw M, Pereira F, Jensen ST, Ohler U, Hatzigeorgiou AG. 2009, "A transcription factor affinity-based code for mammalian transcription initiation.", Genome Res. , 2009 Apr;19(4): , 644-56. Epub 2009 Jan 13. [PubMed].

Papadopoulos GL, Reczko M, Simossis VA, Sethupathy P, Hatzigeorgiou AG. 2009, "The database of experimentally supported targets: a functional update of TarBase.", Nucleic Acids Res. , 2009 Jan;37(Database issue): , D155-8. Epub 2008 Oct 27. [PubMed].

Kawahara Y, Megraw M, Kreider E, Iizasa H, Valente L, Hatzigeorgiou AG, Nishikura K. 2008, "Frequency and fate of microRNA editing in human brain.", Nucleic Acids Res. , 2008 Aug 6. [Epub ahead of print], [PubMed].

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., 2008 May 13;105(19):7004-9. Epub 2008 May 5., [PubMed].

Giannakakis A, Coukos G, Hatzigeorgiou A, Sandaltzopoulos R, Zhang L. 2007, "miRNA genetic alterations in human cancers.", Expert Opin Biol Ther. , 2007 Sep; , 7(9):1375-86. [PubMed].

Sethupathy P, Borel C, Gagnebin M, Grant GR, Deutsch S, Elton TS, Hatzigeorgiou AG, Antonarakis SE 2007, "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.", Am J Hum Genet. , 2007 Aug; , 81(2):405-13. Epub 2007 Jul 12. [PubMed].

Bernal A, Crammer K, Hatzigeorgiou A, Pereira F 2007, "Global discriminative learning for higher-accuracy computational gene prediction.", PLoS Comput Biol. , 2007 Mar 16;, 3(3):e54. Epub 2007 Feb 2. [PubMed].

Kawahara Y, Zinshteyn B, Sethupathy P, Iizasa H, Hatzigeorgiou AG, Nishikura K. 2007, "Redirection of silencing targets by adenosine-to-inosine editing of miRNAs.", Science. , 2007 Feb 23; , 315(5815):1137-40. [PubMed].

Megraw M, Sethupathy P, Corda B, Hatzigeorgiou AG. 2007, "miRGen: a database for the study of animal microRNA genomic organization and function.", Nucleic Acids Res. , 2007 Jan; , 35(Database issue):D149-55. Epub 2006 Nov 15. [PubMed].

Sethupathy P, Megraw M, Hatzigeorgiou AG. 2006, "A guide through present computational approaches for the identification of mammalian microRNA targets.", Nat Methods. , 2006 Nov; , 3(11):881-6. [PubMed].

Kang W, Mukerjee R, Gartner JJ, Hatzigeorgiou AG, Sandri-Goldin RM, Fraser NW. 2006, "Characterization of a spliced exon product of herpes simplex type-1 latency-associated transcript in productively infected cells.", Virology. , 2006 Dec 5-20; , 356(1-2):106-14. Epub 2006 Aug 30. [PubMed].

Megraw M, Baev V, Rusinov V, Jensen ST, Kalantidis K, Hatzigeorgiou AG. 2006, "MicroRNA promoter element discovery in Arabidopsis.", RNA. , 2006 Sep;12(9): , 1612-9. Epub 2006 Aug 3. [PubMed].

Zhang L, Huang J, Yang N, Greshock J, Megraw MS, Giannakakis A, Liang S, Naylor TL, Barchetti A, Ward MR, Yao G, Medina A, O'brien-Jenkins A, Katsaros D, Hatzigeorgiou A, Gimotty PA, Weber BL, Coukos G. 2006, "microRNAs exhibit high frequency genomic alterations in human cancer..", Proc Natl Acad Sci U S A. , 2006 Jun 13; , 103(24):9136-41. Epub 2006 Jun 5. [PubMed].

Sethupathy P, Corda B, Hatzigeorgiou AG. 2006, "TarBase: A comprehensive database of experimentally supported animal microRNA targets.", RNA. , 2006 Feb; , 12(2):192-7. Epub 2005 Dec 22. [PubMed].

Reczko M, Hatzigeorgiou A. 2004, " Prediction of the subcellular localization of eukaryotic proteins using sequence signals and composition.", Proteomics. , 2004 Jun, 4(6):1591-6. [PubMed].

Kiriakidou M, Nelson PT, Kouranov A, Fitziev P, Bouyioukos C, Mourelatos Z, Hatzigeorgiou A, 2004, "A combined computational-experimental approach predicts human microRNA targets.", Genes Dev. , 2004 May 15; , 18(10):1165-78. Epub 2004 May 6. [PubMed].

Yousef M, Kouranov A, Mourelatos Z, Hatzigeorgiou A, 2004, " Prediction of Human microRNA Targets using Parallel Computing.", WSEAS Trans. on Inf. Science and Appl. , 1(1): , 581-586. [PubMed].

Hillier LW, Miller W, Birney E, Warren W, Hardison RC, Ponting CP, Bork P, Burt DW, Groenen MAM, Delany ME, Dodgson JB, Chinwalla AT, Cliften PF, Clifton SW, Delehaunty KD, Fronick C, Fulton RS, Graves TA, Kremitzki C, Layman D, Magrini V, McPherson JD, Miner TL, Minx P, Nash WE, Nhan MN, Nelson JO, Oddy LG, Pohl CS, Randall-Maher J, Smith SM, Wallis JW, Yang SP, Romanov MN, Rondelli CM, Paton B, Smith J, Morrice D, Daniels L, Tempest HG, Robertson L, Masabanda JS, Griffin DK, Vignal A, Fillon V, Jacobbson L, Kerje S, Andersson L, Crooijmans RPM, Aerts J, van der Poel JJ, Ellegren H, Caldwell RB, Hubbard SJ, Grafham DV, Kierzek AM, McLaren SR, Overton IM, Arakawa H, Beattie KJ, Bezzubov Y, Boardman PE, Bonfield JK, Croning MDR, Davies RM, Francis MD, Humphray SJ, Scott CE, Taylor RG, Tickle C, Brown WRA, Rogers J, Buerstedde JM, Wilson SA, Stubbs L, Ovcharenko I, Gordon L, Lucas S, Miller MM, Inoko H, Shiina T, Kaufman J, Salomonsen J, Skjoedt K, Wong GKS, Wang J, Liu B, Wang J, Yu J, Yang HM, Nefedov M, Koriabine M, deJong PJ, Goodstadt L, Webber C, Dickens NJ, Letunic I, Suyama M, Torrents D, von Mering C, Zdobnov EM, Makova K, Nekrutenko A, Elnitski L, Eswara P, King DC, Yang S, Tyekucheva S, Radakrishnan A, Harris RS, Chiaromonte F, Taylor J, He JB, Rijnkels M, Griffiths-Jones S, Ureta-Vidal A, Hoffman MM, Severin J, Searle SMJ, Law AS, Speed D, Waddington D, Cheng Z, Tuzun E, Eichler E, Bao ZR, Flicek P, Shteynberg DD, Brent MR, Bye JM, Huckle EJ, Chatterji S, Dewey C, Pachter L, Kouranov A, Mourelatos Z, Hatzigeorgiou APaterson AH, Ivarie R, Brandstrom M, Axelsson E, Backstrom N, Berlin S, Webster MT, Pourquie O, Reymond A, Ucla C, Antonarakis SE, Long MY, Emerson JJ, Betran E, Dupanloup I, Kaessmann H, Hinrichs AS, Bejerano G, Furey TS, Harte RA, Raney B, Siepel A, Kent WJ, Haussler D, Eyras E, Castelo R, Abril JF, Castellano S, Camara F, Parra G, Guigo R, Bourque G, Tesler G, Pevzner PA, Smit A, Fulton LA, Mardis ER, Wilson RK, 2004, "Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution .", Nature, 432(7018): , 695-716. [PubMed].

Nelson PT, Hatzigeorgiou AG, Mourelatos Z. 2004, "miRNP:mRNA association in polyribosomes in a human neuronal cell line.", RNA. , 2004 Mar; , 10(3):387-94. [PubMed].

Bajic VB, Tang S, Han H, Brusic V, Hatzigeorgiou AG. 2002, "Artificial Neural Networks based systems for recognition of genomic signals and regions.", Informatica. , 26:, 389-400

Hatzigeorgiou AG. 2002, "Translation initiation start prediction in human cDNAs with high accuracy.", Bioinformatics. , 2002 Feb; , 18(2):343-50. [PubMed].

Hatzigeorgiou AG, Fiziev P, Reczko M. 2001, "DIANA-EST: a statistical analysis.", Bioinformatics. , 2001 Oct; , 17(10):913-9. [PubMed].

Hannenhalli SS, Hayes WS, Hatzigeorgiou AG, Fickett JW. 1999, "Bacterial start site prediction.", Nucleic Acids Res. , 1999 Sep 1; , 27(17):3577-82. [PubMed].

Fickett JW, Hatzigeorgiou AG. 1997, "Eukaryotic promoter recognition.", Genome Res. , 1997 Sep; , 7(9):861-78 [PubMed].

Bucher P, Fickett JW, Hatzigeorgiou A. 1996, "Computational analysis of transcriptional regulatory elements.", Comput. Appl. Biosci. , 1996 Oct; , 12(5):361-2. [PubMed].

Botz J, Zerfass-Thome K, Spitkovsky D, Delius H, Vogt B, Eilers M, Hatzigeorgiou A, Jansen-Dürr P. 1996, "Cell cycle regulation of the murine Cylin E gene depends on an E2F binding cite in the promoter.", Mol. Cell. Biol. , 1996 Jul;, 16(7):3401-9 [PubMed].

Reczko M, Hatzigeorgiou A, Mache N, Zell A, Suhai S. 1995, "A Parallel Neural Network Simulator on the Connection Machine CM-5", Comput. Appl. Biosci. , 1995 Jun; , 11(3):309-15. [PubMed].