Publications

2024

Ovsepian, A., Kardaras, F. S., Skoulakis, A., & Hatzigeorgiou, A. G. (2024). Microbial signatures in human periodontal disease: a metatranscriptome meta-analysis. Frontiers in Microbiology, 15, 1383404.

Nagandla, H., Tastsoglou, S., Cap, K. C., Phillips, A., Qian, W., Zhou, J., … & Thomas, C. (2024). Anti-metastatic effects of estrogen receptor β in inflammatory breast cancer. Cancer Research, 84(6_Supplement), 6270-6270.

Kim, K., Kim, M. M., Skoufos, G., Diffenderfer, E. S., Motlagh, S. A. O., Kokkorakis, M., … & Verginadis, I. I. (2024). FLASH proton radiotherapy mitigates inflammatory and fibrotic pathways and preserves cardiac function in a preclinical mouse model of radiation-induced heart disease. International Journal of Radiation Oncology* Biology* Physics.

Kotsira V, Skoufos G, Alexiou A, Zioga M, Tastsoglou S, Kardaras FS, Perdikopanis N, Elissavet Z, Gouzouasis V, Charitou T, Hatzigeorgiou AG. 2024. Agnodice: indexing experimentally supported bacterial sRNA-RNA interactions. mBio 15:e03010-23.

Skoufos, G., Kakoulidis, P., Tastsoglou, S., Zacharopoulou, E., Kotsira, V., Miliotis, M., … & Hatzigeorgiou, A. G. (2024). TarBase-v9. 0 extends experimentally supported miRNA–gene interactions to cell-types and virally encoded miRNAs. Nucleic Acids Research, 52(D1), D304-D310.

2023

Nikolaou, P. E., Mylonas, N., Miliotis, M., Kostopoulos, I., Georgoulis, A., Orologas, N., … & Andreadou, I. (2023). Empagliflozin restores the deregulated cardiac endothelial cell transcriptome in vivo upon myocardial ischemia reperfusion injury and reduces the infiltration of immune cells. European Heart Journal, 44(Supplement_2), ehad655-3119.

Amaral, P., Carbonell-Sala, S., De La Vega, F. M., Faial, T., Frankish, A., Gingeras, T., … & Salzberg, S. L. (2023). The status of the human gene catalogue. Nature, 622(7981), 41-47.

Gouzouasis, V., Tastsoglou, S., Giannakakis, A., & Hatzigeorgiou, A. G. (2023). Virus-derived small rnas and microRNAs in health and disease. Annual Review of Biomedical Data Science, 6, 275-298.

Tastsoglou, S., Skoufos, G., Miliotis, M., Karagkouni, D., Koutsoukos, I., Karavangeli, A., … & Hatzigeorgiou, A. G. (2023). DIANA-miRPath v4. 0: expanding target-based miRNA functional analysis in cell-type and tissue contexts. Nucleic Acids Research, 51(W1), W154-W159.

Spyros Tastsoglou, Athanasios Alexiou, Dimitra Karagkouni, Giorgos Skoufos, Elissavet Zacharopoulou, Artemis G Hatzigeorgiou, DIANA-microT 2023: including predicted targets of virally encoded miRNAs, Nucleic Acids Research, Volume 51, Issue W1, 5 July 2023, Pages W148–W153

Zikopoulos, A., Grigoriadis, S., Karagkouni, D., Maziotis, E., Tomara, P., Kotsifaki, A., … & Simopoulou, M. (2023). O-137 Mapping microRNA profiling and dysregulated pathways in non-obstructive azoospermia cases with maturation arrest: A systematic review and in-silico analysis of the affected pathways. Human Reproduction, 38(Supplement_1), dead093-164.

Grigoriadis, S., Sfakianoudis, K., Karagkouni, D., Maziotis, E., Tomara, P., Kotsifaki, A., … & Simopoulou, M. (2023). P-099 Alterations in microRNA expression profiles may be implicated in increased prevalence of cancer in Sertoli cell-only syndrome cases: A systematic review and in-silico analysis. Human Reproduction, 38(Supplement_1), dead093-463.

Papadimitriou, E., Koutsoudaki, P. N., Thanou, I., Karagkouni, D., Karamitros, T., Chroni-Tzartou, D., … & Thomaidou, D. (2023). A miR-124-mediated post-transcriptional mechanism controlling the cell fate switch of astrocytes to induced neurons. Stem Cell Reports, 18(4), 915-935.

Chitalia, R., Miliotis, M., Jahani, N., Tastsoglou, S., McDonald, E. S., Belenky, V., … & Kontos, D. (2023). Radiomic tumor phenotypes augment molecular profiling in predicting recurrence free survival after breast neoadjuvant chemotherapy. Communications medicine, 3(1), 46.

2022

Grigoriadis, D., Perdikopanis, N., Georgakilas, G. K., & Hatzigeorgiou, A. G. (2022). DeepTSS: multi-branch convolutional neural network for transcription start site identification from CAGE data. BMC bioinformatics, 23(Suppl 2), 395.

Madè, A., Greco, S., Vausort, M., Miliotis, M., Schordan, E., Baksi, S., … & Martelli, F. (2022). Association of miR-144 levels in the peripheral blood with COVID-19 severity and mortality. Scientific Reports, 12(1), 20048.

Kazerooni, A. F., Akbari, H., Toorens, E., Grigoriadis, D., Hu, X., Sako, C., … & Davatzikos, C. (2022). NIMG-82. RADIOGENOMIC SIGNATURES OF KEY DRIVER GENES IN GBM REVEAL MOLECULAR HETEROGENEITY OF THE TUMOR MICROENVIRONMENT LINKED TO SPATIAL DISTRIBUTION: IMPACT ON THE TRAJECTORY OF GLIOMA EVOLUTION. Neuro-Oncology, 24(Supplement_7), vii184-vii184.

Pantou, A., Grigoriadis, S., Karagkouni, D., Pantos, K., Maziotis, E., Tomara, P., … & Simopoulou, M. (2022). P-012 Investigating the potential role of microRNAs as biomarkers in idiopathic non-obstructive azoospermia: A systematic review and in-silico analysis of the affected pathways. Human Reproduction, 37(Supplement_1), deac107-011.

Margaroni, M., Agallou, M., Vasilakaki, A., Karagkouni, D., Skoufos, G., Hatzigeorgiou, A. G., & Karagouni, E. (2022). Transcriptional profiling of Leishmania infantum infected dendritic cells: Insights into the role of immunometabolism in host-parasite interaction. Microorganisms, 10(7), 1271.

Verginadis, I. I., Avgousti, H., Monslow, J., Skoufos, G., Chinga, F., Kim, K., … & Koumenis, C. (2022). A stromal Integrated Stress Response activates perivascular cancer-associated fibroblasts to drive angiogenesis and tumour progression. Nature cell biology, 24(6), 940-953.

Skoufos, G., Almodaresi, F., Zakeri, M. et al. AGAMEMNON: an Accurate metaGenomics And MEtatranscriptoMics quaNtificatiON analysis suite. Genome Biol 23, 39 (2022)

Ioannis Kavakiotis, Athanasios Alexiou, Spyros Tastsoglou, Ioannis S Vlachos, Artemis G Hatzigeorgiou, DIANA-miTED: a microRNA tissue expression database, Nucleic Acids Research, Volume 50, Issue D1, 7 January 2022, Pages D1055–D1061

2021

Velalopoulou, A., Karagounis, I. V., Cramer, G. M., Kim, M. M., Skoufos, G., Goia, D., … & Busch, T. M. (2021). FLASH proton radiotherapy spares normal epithelial and mesenchymal tissues while preserving sarcoma response. Cancer research, 81(18), 4808-4821.

Kavakiotis, I., Alexiou, A., Tastsoglou, S., Vlachos, I. S., & Hatzigeorgiou, A. G. (2021). DIANA-miTED: a microRNA tissue expression database. Nucleic Acids Research.

Laliotis, G. I., Chavdoula, E., Paraskevopoulou, M. D., Kaba, A., La Ferlita, A., Singh, S., … & Tsichlis, P. N. (2021). AKT3-mediated IWS1 phosphorylation promotes the proliferation of EGFR-mutant lung adenocarcinomas through cell cycle-regulated U2AF2 RNA splicing. Nature communications, 12(1), 1-25.

Perdikopanis, N., Georgakilas, G. K., Grigoriadis, D., Pierros, V., Kavakiotis, I., Alexiou, P., & Hatzigeorgiou, A. (2021). DIANA-miRGen v4: indexing promoters and regulators for more than 1500 microRNAs. Nucleic acids research, 49(D1), D151-D159.

RNAcentral 2021: secondary structure integration, improved sequence search and new member databases. Nucleic acids research, 2021, 49.D1: D212-D220.

Skoufos, G., Kardaras, F. S., Alexiou, A., Kavakiotis, I., Lambropoulou, A., Kotsira, V., … & Hatzigeorgiou, A. G. (2021). Peryton: a manual collection of experimentally supported microbe-disease associations. Nucleic acids research, 49(D1), D1328-D1333.

Karagkouni, D., Karavangeli, A., Paraskevopoulou, M. D., & Hatzigeorgiou, A. G. (2021). Characterizing miRNA–lncRNA Interplay. In Long Non-Coding RNAs (pp. 243-262). Humana, New York, NY.

Tastsoglou, S., Miliotis, M., Kavakiotis, I., Alexiou, A., Gkotsi, E. C., Lambropoulou, A., … & Hatzigeorgiou, A. G. (2021). PlasmiR: A Manual Collection of Circulating microRNAs of Prognostic and Diagnostic Value. Cancers, 13(15), 3680.

Alexiou, A., Zisis, D., Kavakiotis, I., Miliotis, M., Koussounadis, A., Karagkouni, D., & Hatzigeorgiou, A. G. (2021). DIANA-mAP: Analyzing miRNA from Raw NGS Data to Quantification. Genes, 12(1), 46.

2020

Perdikopanis N, Georgakilas GK, Grigoriadis D, Pierros V, Kavakiotis I, Alexiou P, Hatzigeorgiou A. DIANA-miRGen v4: indexing promoters and regulators for more than 1500 microRNAs. Nucleic Acids Research. 2020 Nov 27.

Skoufos G, Kardaras FS, Alexiou A, Kavakiotis I, Lambropoulou A, Kotsira V, Tastsoglou S, Hatzigeorgiou AG. Peryton: a manual collection of experimentally supported microbe-disease associations. Nucleic Acids Research. 2020 Oct 20.

RNAcentral Consortium. RNAcentral 2021: secondary structure integration, improved sequence search and new member databases. Nucleic acids research. 2020:gkaa921.

Prodromidou K, Vlachos IS, Gaitanou M, Kouroupi G, Hatzigeorgiou AG, Matsas R. MicroRNA-934 is a novel primate-specific small non-coding RNA with neurogenic function during early development. Elife. 2020 May 27;9:e50561.

Grigoriadis D, Perdikopanis N, Georgakilas GK, Hatzigeorgiou A. DiS-TSS: An Annotation Agnostic Algorithm for TSS Identification. InInternational Work-Conference on Bioinformatics and Biomedical Engineering 2020 May 6 (pp. 613-623). Springer, Cham.

Georgakilas GK, Perdikopanis N, Hatzigeorgiou A. Solving the transcription start site identification problem with ADAPT-CAGE: a Machine Learning algorithm for the analysis of CAGE data. Scientific reports. 2020 Jan 21;10(1):1-2.

Handzlik JE, Tastsoglou S, Vlachos IS, Hatzigeorgiou AG. Manatee: detection and quantification of small non-coding RNAs from next-generation sequencing data. Scientific reports. 2020 Jan 20;10(1):1-0.

Karagkouni D, Paraskevopoulou MD, Tastsoglou S, Skoufos G, Karavangeli A, Pierros V, Zacharopoulou E, Hatzigeorgiou AG. DIANA-LncBase v3: indexing experimentally supported miRNA targets on non-coding transcripts. Nucleic acids research. 2020 Jan 8;48(D1):D101-10.

2019

Kontizas E, Tastsoglou S, Karamitros T, Karayiannis Y, Kollia P, Hatzigeorgiou A, Mentis A, Sgouras DN. Putative impact of CagA protein on DNA damage repair modulation during Helicobacter pylori infection. In HELICOBACTER 2019 Sep 1 (Vol. 24). 111 RIVER ST, HOBOKEN 07030-5774, NJ USA: WILEY.

RNAcentral: a hub of information for non-coding RNA sequences. Nucleic acids research, 2018, 47.D1: D221-D229.

Agallou M, Athanasiou E, Kammona O, Tastsoglou S, Hatzigeorgiou AG, Kiparissides C, Karagouni E. Transcriptome analysis identifies immune markers related to visceral leishmaniasis establishment in the experimental model of BALB/c mice. Frontiers in Immunology. 2019;10:2749.

2018

ECCB 2018 Steering Committee, Hatzigeorgiou, A. G., Bagos, P., Benos, P. V., Nikolaou, C., Moreau, Y., & Kavakiotis, I. (2018). ECCB 2018: The 17th European Conference on Computational Biology. Bioinformatics, 34(17), i595-i598.

Paraskevopoulou MD, Karagkouni D, Vlachos IS, Tastsoglou S, Hatzigeorgiou AG. microCLIP super learning framework uncovers functional transcriptome-wide miRNA interactions. Nat Commun. 2018 Sep 6;9(1):3601. doi: 10.1038/s41467-018-06046-y. PubMed PMID: 30190538; PubMed Central PMCID: PMC6127135.

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. DIANA-TarBase v8: a decade-long collection of experimentally supported miRNA-gene interactions. Nucleic Acids Res. 2018 Jan 4;46(D1):D239-D245. doi: 10.1093/nar/gkx1141. PubMed PMID: 29156006; PubMed Central PMCID: PMC5753203.

Georgakilas G, Perdikopanis N, Hatzigeorgiou AG. Identifying Pri-miRNA Transcription Start Sites. Methods Mol Biol. 2018;1823:11-31. doi: 10.1007/978-1-4939-8624-8_2. PubMed PMID: 29959670.

2017

Athanasiou E, Agallou M, Tastsoglou S, Kammona O, Hatzigeorgiou A, Kiparissides C, Karagouni E. A Poly(Lactic-co-Glycolic) Acid Nanovaccine Based on Chimeric Peptides from Different Leishmania infantum Proteins Induces Dendritic Cells Maturation and Promotes Peptide-Specific IFNγ-Producing CD8(+) T Cells Essential for the Protection against Experimental Visceral Leishmaniasis. Front Immunol. 2017 Jun 13;8:684. doi: 10.3389/fimmu.2017.00684. eCollection 2017. PubMed PMID: 28659922; PubMed Central PMCID: PMC5468442.

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. Defective synaptic connectivity and axonal neuropathology in a human iPSC-based model of familial Parkinson’s disease. Proc Natl Acad Sci U S A. 2017 May 2;114(18):E3679-E3688. doi: 10.1073/pnas.1617259114. Epub 2017 Apr 17. PubMed PMID: 28416701; PubMed Central PMCID: PMC5422768.

Fragkouli A, Koukouraki P, Vlachos IS, Paraskevopoulou MD, Hatzigeorgiou AG, Doxakis E. Neuronal ELAVL proteins utilize AUF-1 as a co-partner to induce neuron-specific alternative splicing of APP. Sci Rep. 2017 Mar 14;7:44507. doi: 10.1038/srep44507. PubMed PMID: 28291226; PubMed Central PMCID: PMC5349543.

Vlachos IS, Hatzigeorgiou AG. Functional Analysis of miRNAs Using the DIANA Tools Online Suite. Methods Mol Biol. 2017;1517:25-50. PubMed PMID: 27924472.

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. 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. 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. PubMed PMID: 27659211; PubMed Central PMCID: PMC5034548.

2016

Paraskevopoulou MD, Vlachos IS, Hatzigeorgiou AG. DIANA-TarBase and DIANA Suite Tools: Studying Experimentally Supported microRNA Targets. Curr Protoc Bioinformatics. 2016 Sep 7;55:12.14.1-12.14.18. doi: 10.1002/cpbi.12. PubMed PMID: 27603020.

Vlachos IS, Vergoulis T, Paraskevopoulou MD, Lykokanellos F, Georgakilas G, Georgiou P, Chatzopoulos S, Karagkouni D, Christodoulou F, Dalamagas T, Hatzigeorgiou AG. DIANA-mirExTra v2.0: Uncovering microRNAs and transcription factors with crucial roles in NGS expression data. Nucleic Acids Res. 2016 Jul 8;44(W1):W128-34. doi: 10.1093/nar/gkw455. Epub 2016 May 20. PubMed PMID: 27207881; PubMed Central PMCID: PMC4987956.

Giakountis A, Moulos P, Zarkou V, Oikonomou C, Harokopos V, Hatzigeorgiou AG, Reczko M, Hatzis P. A Positive Regulatory Loop between a Wnt-Regulated Non-coding RNA and ASCL2 Controls Intestinal Stem Cell Fate. Cell Rep. 2016 Jun 21;15(12):2588-96. doi: 10.1016/j.celrep.2016.05.038. Epub 2016 Jun 9. PubMed PMID: 27292638.

Paraskevopoulou MD, Vlachos IS, Karagkouni D, Georgakilas G, Kanellos I, Vergoulis T, Zagganas K, Tsanakas P, Floros E, Dalamagas T, Hatzigeorgiou AG. DIANA-LncBase v2: indexing microRNA targets on non-coding transcripts. Nucleic Acids Res. 2016 Jan 4;44(D1):D231-8. doi: 10.1093/nar/gkv1270. Epub 2015 Nov 26. PubMed PMID: 26612864; PubMed Central PMCID: PMC4702897.

Georgakilas G, Vlachos IS, Zagganas K, Vergoulis T, Paraskevopoulou MD, Kanellos I, Tsanakas P, Dellis D, Fevgas A, Dalamagas T, Hatzigeorgiou AG. DIANA-miRGen v3.0: accurate characterization of microRNA promoters and their regulators. Nucleic Acids Res. 2016 Jan 4;44(D1):D190-5. doi: 10.1093/nar/gkv1254. Epub 2015 Nov 19. PubMed PMID: 26586797; PubMed Central PMCID: PMC4702888.

Paraskevopoulou MD, Hatzigeorgiou AG. Analyzing MiRNA-LncRNA Interactions. Methods Mol Biol. 2016;1402:271-286. doi: 10.1007/978-1-4939-3378-5_21. PubMed PMID: 26721498.

Vlachos IS, Zagganas K, Paraskevopoulou MD, Georgakilas G, Karagkouni D, Vergoulis T, Dalamagas T, Hatzigeorgiou AG. DIANA-miRPath v3.0: deciphering microRNA function with experimental support. Nucleic Acids Res. 2015 Jul 1;43(W1):W460-6. doi: 10.1093/nar/gkv403. Epub 2015 May 14. PubMed PMID: 25977294; PubMed Central PMCID: PMC4489228.

2015

Vergoulis T, Kanellos I, Kostoulas N, Georgakilas G, Sellis T, Hatzigeorgiou A, Dalamagas T. mirPub: a database for searching microRNA publications. Bioinformatics. 2015 May 1;31(9):1502-4. doi: 10.1093/bioinformatics/btu819. Epub 2014 Dec 20. PubMed PMID: 25527833; PubMed Central PMCID: PMC4410649.

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. DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions. Nucleic Acids Res. 2015 Jan;43(Database issue):D153-9. doi: 10.1093/nar/gku1215. Epub 2014 Nov 21. PubMed PMID: 25416803; PubMed Central PMCID: PMC4383989.

RNAcentral Consortium. RNAcentral: an international database of ncRNA sequences. Nucleic Acids Res. 2015 Jan;43(Database issue):D123-9. doi: 10.1093/nar/gku991. Epub 2014 Oct 28. PubMed PMID: 25352543; PubMed Central PMCID: PMC4384043.

2014

Georgakilas G, Vlachos IS, Paraskevopoulou MD, Yang P, Zhang Y, Economides AN, Hatzigeorgiou AG. microTSS: accurate microRNA transcription start site identification reveals a significant number of divergent pri-miRNAs. Nat Commun. 2014 Dec 10;5:5700. doi: 10.1038/ncomms6700. PubMed PMID: 25492647.

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. Integrated analysis of microRNA and mRNA expression and association with HIF binding reveals the complexity of microRNA expression regulation under hypoxia. Mol Cancer. 2014 Feb 11;13:28. doi: 10.1186/1476-4598-13-28. PubMed PMID: 24517586; PubMed Central PMCID: PMC3928101.

2013

Vlachos IS, Hatzigeorgiou AG. Online resources for miRNA analysis. Clin Biochem. 2013 Jul;46(10-11):879-900. doi: 10.1016/j.clinbiochem.2013.03.006. Epub 2013 Mar 18. Review. PubMed PMID: 23518312.

Paraskevopoulou MD, Georgakilas G, Kostoulas N, Vlachos IS, Vergoulis T, Reczko M, Filippidis C, Dalamagas T, Hatzigeorgiou AG. DIANA-microT web server v5.0: service integration into miRNA functional analysis workflows. Nucleic Acids Res. 2013 Jul;41(Web Server issue):W169-73. doi: 10.1093/nar/gkt393. Epub 2013 May 16. PubMed PMID: 23680784; PubMed Central PMCID: PMC3692048.

Papakonstantinou N, Ntoufa S, Chartomatsidou E, Papadopoulos G, Hatzigeorgiou A, Anagnostopoulos A, Chlichlia K, Ghia P, Muzio M, Belessi C, Stamatopoulos K. Differential microRNA profiles and their functional implications in different immunogenetic subsets of chronic lymphocytic leukemia. Mol Med. 2013 May 20;19:115-23. doi: 10.2119/molmed.2013.00005. PubMed PMID: 23615967; PubMed Central PMCID: PMC3667214.

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. 2013 Jan;41(Database issue):D239-45. doi: 10.1093/nar/gks1246. Epub 2012 Nov 28. PubMed PMID: 23193281; PubMed Central PMCID: PMC3531175.

2012

Pandis I, Ospelt C, Karagianni N, Denis MC, Reczko M, Camps C, Hatzigeorgiou AG, Ragoussis J, Gay S, Kollias G. Identification of microRNA-221/222 and microRNA-323-3p association with rheumatoid arthritis via predictions using the human tumour necrosis factor transgenic mouse model. Ann Rheum Dis. 2012 Oct;71(10):1716-23. doi: 10.1136/annrheumdis-2011-200803. Epub 2012 May 5. PubMed PMID: 22562984.

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. 2012 Jul;40(Web Server issue):W498-504. doi: 10.1093/nar/gks494. Epub 2012 May 30. PubMed PMID: 22649059; PubMed Central PMCID: PMC3394305.

Reczko M, Maragkakis M, Alexiou P, Grosse I, Hatzigeorgiou AG. Functional microRNA targets in protein coding sequences. Bioinformatics. 2012 Mar 15;28(6):771-6. doi: 10.1093/bioinformatics/bts043. Epub 2012 Jan 27. PubMed PMID: 22285563.

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. 2012 Jan 18;2:103. doi: 10.3389/fgene.2011.00103. eCollection 2011. PubMed PMID: 22303397; PubMed Central PMCID: PMC3265086.

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. 2012 Jan;40(Database issue):D222-9. doi: 10.1093/nar/gkr1161. Epub 2011 Dec 1. PubMed PMID: 22135297; PubMed Central PMCID: PMC3245116.

Paschou M, Paraskevopoulou MD, Vlachos IS, Koukouraki P, Hatzigeorgiou AG, Doxakis E. miRNA regulons associated with synaptic function. PLoS One. 2012;7(10):e46189. doi: 10.1371/journal.pone.0046189. Epub 2012 Oct 8. PubMed PMID: 23071543; PubMed Central PMCID: PMC3468272.

Kalajdzic P, Oehler S, Reczko M, Pavlidi N, Vontas J, Hatzigeorgiou AG, Savakis C. Use of mutagenesis, genetic mapping and next generation transcriptomics to investigate insecticide resistance mechanisms. PLoS One. 2012;7(6):e40296. doi: 10.1371/journal.pone.0040296. Epub 2012 Jun 29. PubMed PMID: 22768270; PubMed Central PMCID: PMC3386967.

2011

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. 2011 Jul;39(Web Server issue):W145-8. doi: 10.1093/nar/gkr294. Epub 2011 May 6. PubMed PMID: 21551220; PubMed Central PMCID: PMC3125744.

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. 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. doi: 10.1158/0008-5472.CAN-10-3061. Epub 2011 Jan 25. PubMed PMID: 21266355; PubMed Central PMCID: PMC3071295.

2010

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 microRNAs controls their dicer targeting and consequently affects viral latency. J Biol Chem. 2010 Oct 22;285(43):33358-70. doi: 10.1074/jbc.M110.138362. Epub 2010 Aug 17. PubMed PMID: 20716523; PubMed Central PMCID: PMC2963350.

Alexiou P, Maragkakis M, Papadopoulos GL, Simmosis VA, Zhang L, Hatzigeorgiou AG. The DIANA-mirExTra web server: from gene expression data to microRNA function. PLoS One. 2010 Feb 11;5(2):e9171. doi: 10.1371/journal.pone.0009171. PubMed PMID: 20161787; PubMed Central PMCID: PMC2820085.

Megraw M, Hatzigeorgiou AG. MicroRNA promoter analysis. Methods Mol Biol. 2010;592:149-61. doi: 10.1007/978-1-60327-005-2_11. PubMed PMID: 19802595.

Alexiou P, Vergoulis T, Gleditzsch M, Prekas G, Dalamagas T, Megraw M, Grosse I, Sellis T, Hatzigeorgiou AG. miRGen 2.0: a database of microRNA genomic information and regulation. Nucleic Acids Res. 2010 Jan;38(Database issue):D137-41. doi: 10.1093/nar/gkp888. Epub 2009 Oct 22. PubMed PMID: 19850714; PubMed Central PMCID: PMC2808909.

2009

Alexiou P, Maragkakis M, Papadopoulos GL, Reczko M, Hatzigeorgiou AG. Lost in translation: an assessment and perspective for computational microRNA target identification. Bioinformatics. 2009 Dec 1;25(23):3049-55. doi: 10.1093/bioinformatics/btp565. Epub 2009 Sep 29. Review. PubMed PMID: 19789267.

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 microRNA target prediction correlates with protein repression levels. BMC Bioinformatics. 2009 Sep 18;10:295. doi: 10.1186/1471-2105-10-295. PubMed PMID: 19765283; PubMed Central PMCID: PMC2752464.

Papadopoulos GL, Alexiou P, Maragkakis M, Reczko M, Hatzigeorgiou AG. DIANA-mirPath: Integrating human and mouse microRNAs in pathways. Bioinformatics. 2009 Aug 1;25(15):1991-3. doi: 10.1093/bioinformatics/btp299. Epub 2009 May 12. PubMed PMID: 19435746.

26. 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 microRNA functions through target prediction. Nucleic Acids Res. 2009 Jul;37(Web Server issue):W273-6. doi: 10.1093/nar/gkp292. Epub 2009 Apr 30. PubMed PMID: 19406924; PubMed Central PMCID: PMC2703977.

Megraw M, Pereira F, Jensen ST, Ohler U, Hatzigeorgiou AG. A transcription factor affinity-based code for mammalian transcription initiation. Genome Res. 2009 Apr;19(4):644-56. doi: 10.1101/gr.085449.108. Epub 2009 Jan 13. PubMed PMID: 19141595; PubMed Central PMCID: PMC2665783.

Papadopoulos GL, Reczko M, Simossis VA, Sethupathy P, Hatzigeorgiou AG. The database of experimentally supported targets: a functional update of TarBase. Nucleic Acids Res. 2009 Jan;37(Database issue):D155-8. doi: 10.1093/nar/gkn809. Epub 2008 Oct 27. PubMed PMID: 18957447; PubMed Central PMCID: PMC2686456.

2008

Kawahara Y, Megraw M, Kreider E, Iizasa H, Valente L, Hatzigeorgiou AG, Nishikura K. Frequency and fate of microRNA editing in human brain. Nucleic Acids Res. 2008 Sep;36(16):5270-80. doi: 10.1093/nar/gkn479. Epub 2008 Aug 6. PubMed PMID: 18684997; PubMed Central PMCID: PMC2532740.

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. 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. doi: 10.1073/pnas.0801615105. Epub 2008 May 5. PubMed PMID: 18458333; PubMed Central PMCID: PMC2383982.

Gartner JJ, Sethupathy P, Hatzigeorgiou AG, Fraser NW. Anti-apoptotic function of a microRNA encoded by the HSV-1 latency-associated transcript. Nature. 2008 Jan 31;451(7178):600. doi: 10.1038/nature06621. PubMed PMID: 18235505.

2007

Giannakakis A, Coukos G, Hatzigeorgiou A, Sandaltzopoulos R, Zhang L. miRNA genetic alterations in human cancers. Expert Opin Biol Ther. 2007 Sep;7(9):1375-86. Review. PubMed PMID: 17727327.

Sethupathy P, Borel C, Gagnebin M, Grant GR, Deutsch S, Elton TS, Hatzigeorgiou AG, Antonarakis SE. 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 PMID: 17668390; PubMed Central PMCID: PMC1950808.

Bernal A, Crammer K, Hatzigeorgiou A, Pereira F. Global discriminative learning for higher-accuracy computational gene prediction. PLoS Comput Biol. 2007 Mar 16;3(3):e54. Epub 2007 Feb 2. PubMed PMID: 17367206; PubMed Central PMCID: PMC1828702.

Kawahara Y, Zinshteyn B, Sethupathy P, Iizasa H, Hatzigeorgiou AG, Nishikura K. Redirection of silencing targets by adenosine-to-inosine editing of miRNAs. Science. 2007 Feb 23;315(5815):1137-40. PubMed PMID: 17322061; PubMed Central PMCID: PMC2953418.

Megraw M, Sethupathy P, Corda B, Hatzigeorgiou AG. 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 PMID: 17108354; PubMed Central PMCID: PMC1669779.

2006

Kang W, Mukerjee R, Gartner JJ, Hatzigeorgiou AG, Sandri-Goldin RM, Fraser NW. 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 PMID: 16938324.

Sethupathy P, Megraw M, Hatzigeorgiou AG. A guide through present computational approaches for the identification of mammalian microRNA targets. Nat Methods. 2006 Nov;3(11):881-6. PubMed PMID: 17060911.

Megraw M, Baev V, Rusinov V, Jensen ST, Kalantidis K, Hatzigeorgiou AG. MicroRNA promoter element discovery in Arabidopsis. RNA. 2006 Sep;12(9):1612-9. Epub 2006 Aug 3. PubMed PMID: 16888323; PubMed Central PMCID: PMC1557699.

Gupta A, Gartner JJ, Sethupathy P, Hatzigeorgiou AG, Fraser NW. Anti-apoptotic function of a microRNA encoded by the HSV-1 latency-associated transcript. 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. PubMed PMID: 16738545.

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. 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 PMID: 16754881; PubMed Central PMCID: PMC1474008.

Sethupathy P, Corda B, Hatzigeorgiou AG. TarBase: A comprehensive database of experimentally supported animal microRNA targets. RNA. 2006 Feb;12(2):192-7. Epub 2005 Dec 22. PubMed PMID: 16373484; PubMed Central PMCID: PMC1370898.

Up to 2005

Kiriakidou M, Nelson PT, Kouranov A, Fitziev P, Bouyioukos C, Mourelatos Z, Hatzigeorgiou A. A combined computational-experimental approach predicts human microRNA targets. Genes Dev. 2004 May 15;18(10):1165-78. Epub 2004 May 6. PubMed PMID: 15131085; PubMed Central PMCID: PMC415641.

Nelson PT, Hatzigeorgiou AG, Mourelatos Z. miRNP:mRNA association in polyribosomes in a human neuronal cell line. RNA. 2004 Mar;10(3):387-94. PubMed PMID: 14970384; PubMed Central PMCID: PMC1370934.

Hatzigeorgiou AG. Translation initiation start prediction in human cDNAs with high accuracy. Bioinformatics. 2002 Feb;18(2):343-50. PubMed PMID: 11847092.

Hatzigeorgiou AG, Fiziev P, Reczko M. DIANA-EST: a statistical analysis. Bioinformatics. 2001 Oct;17(10):913-9. PubMed PMID: 11673235.

Hannenhalli SS, Hayes WS, Hatzigeorgiou AG, Fickett JW. Bacterial start site prediction. Nucleic Acids Res. 1999 Sep 1;27(17):3577-82. PubMed PMID: 10446249; PubMed Central PMCID: PMC148603.

Fickett JW, Hatzigeorgiou AG. Eukaryotic promoter recognition. Genome Res. 1997 Sep;7(9):861-78. Review. PubMed PMID: 9314492.

Bucher P, Fickett JW, Hatzigeorgiou A. Computational analysis of transcriptional regulatory elements: a field in flux. Comput Appl Biosci. 1996 Oct;12(5):361-2. PubMed PMID: 8996783.

Botz J, Zerfass-Thome K, Spitkovsky D, Delius H, Vogt B, Eilers M, Hatzigeorgiou A, Jansen-Dürr P. Cell cycle regulation of the murine cyclin E gene depends on an E2F binding site in the promoter. Mol Cell Biol. 1996 Jul;16(7):3401-9. PubMed PMID: 8668155; PubMed Central PMCID: PMC231334.

Reczko M, Hatzigeorgiou A, Mache N, Zell A, Suhai S. A parallel neural network simulator on the connection machine CM-5. Comput Appl Biosci. 1995 Jun;11(3):309-15. PubMed PMID: 7583700.