Publications

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Conferences/Workshops

MirPub v2: Towards Ranking and Refining miRNA Publication Search Results. Ilias Kanellos, Vasiliki Vlachokyriakou, Thanasis Vergoulis, Georgios Georgakilas, Yannis Vassiliou, Artemis K. Hatzigeorgiou, Theodore Dalamagas. TPDL 15, 2015 Full text
TarMiner: automatic extraction of miRNA targets from literature. Rodothea-Myrsini Tsoupidi, Ilias Kanellos, Thanasis Vergoulis, Ioannis S Vlachos, Artemis G Hatzigeorgiou, Theodore Dalamagas. SSDBM 2015, article No 12, 2015 Full text
Publishing Diachronic Life Science Linked Data. Katerina Gkirtzou, Thanasis Vergoulis, Artemis Hatzigeorgiou, Timos Sellis, Theodore Dalamagas. SWAT4LS 2014, 2014 Full text
MR-microT: A MapReduce-based MicroRNA Target Prediction Method. Ilias Kanellos, Thanasis Vergoulis, Dimitris Sacharidis, Theodore Dalamagas, Artemis Hatzigeorgiou, Stelios Sartzetakis, Timos Sellis. SSDBM ’14, Article No. 47, 2014 Full text
TARCLOUD: A Cloud-Based Platform to Support miRNA Target Prediction. Thanasis Vergoulis, Michail Alexakis, Theodore Dalamagas, Manolis Maragkakis, Artemis G. Hatzigeorgiou, Timos Sellis. SSDBM 2012: 628-633, 2012

Journals

DIANA-TarBase v8: a decade-long collection of experimentally supported miRNA–gene interactions. 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. Nucleic Acids Research, gkx1141, https://doi.org/10.1093/nar/gkx1141. Epub 201 November 16, 2017 Full text
BUFET: boosting the unbiased miRNA functional enrichment analysis using bitsets.. Konstantinos Zagganas, Thanasis Vergoulis, Maria D. Paraskevopoulou, Ioannis S. Vlachos, Spiros Skiadopoulos, Theodore Dalamagas. BMC Bioinformatics. 2017 Sep 6;18(1):399, 2017 Full text
DIANA-mirExTra v2.0: Uncovering microRNAs and transcription factors with crucial roles in NGS expression data. Ioannis S. Vlachos, Thanasis Vergoulis, Maria D. Paraskevopoulou, Filopoimin Lykokanellos, Georgios Georgakilas, Penny Georgiou, Serafeim Chatzopoulos, Dimitra Karagkouni, Foteini Christodoulou, Theodore Dalamagas, Artemis G Hatzigeorgiou. Nucl. Acids Res. , 2016 Full text
DIANA-miRGen v3.0: accurate characterization of microRNA promoters and their regulators. Georgios Georgakilas, Ioannis S. Vlachos, Konstantinos Zagganas, Thanasis Vergoulis, Maria D. Paraskevopoulou, Ilias Kanellos, Panayiotis Tsanakas, Dimitris Dellis, Athanasios Fevgas, Theodore Dalamagas, Artemis G. Hatzigeorgiou. Nucl. Acids Res. 44 (D1): D190-D195, 2016 Full text
DIANA-LncBase v2: indexing microRNA targets on non-coding transcripts. Maria D. Paraskevopoulou, Ioannis S. Vlachos, Dimitra Karagkouni, Georgios Georgakilas, Ilias Kanellos, Thanasis Vergoulis, Konstantinos Zagganas, Panayiotis Tsanakas, Evangelos Floros, Theodore Dalamagas, and Artemis Hatzigeorgiou. Nucl. Acids Res. 44 (D1): D231-D238, 2016 Full text
DIANA-miRPath v3.0: deciphering microRNA function with experimental support. Vlachos IS, Zagganas K, Paraskevopoulou MD, Georgakilas G, Karagkouni D, Vergoulis T, Dalamagas T, Hatzigeorgiou AG. Nucleic Acids Res. 2015 Jul 1;43(W1):W460-6. doi: 10.1093/nar/gkv403. Epub 2015 May 14, 2015 Full text
DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions. Ioannis S. Vlachos, Maria D. Paraskevopoulou, Dimitra Karagkouni, Georgios Georgakilas, Thanasis Vergoulis, Ilias Kanellos, Ioannis-Laertis Anastasopoulos, Sofia Maniou, Konstantina Karathanou, Despina Kalfakakou, Athanasios Fevgas, Theodore Dalamaga. Nucl. Acids Res. 43 (D1): D153-D159, 2015 Full text
mirPub: a database for searching microRNA publications. Thanasis Vergoulis, Ilias Kanellos, Nikos Kostoulas, Georgios Georgakilas, Timos Sellis, Artemis Hatzigeorgiou, Theodore Dalamagas. Bioinformatics 31 (9): 1502-1504, 2014 Full text
DIANA-LncBase: experimentally verified and computationally predicted microRNA targets on long non-coding RNAs. Paraskevopoulou MD, Georgakilas G, Kostoulas N, Reczko M, Maragkakis M, Dalamagas T, Hatzigeorgiou AG . Nucleic Acids Research 41(Database Issue):D239-D245, 2013 Full text
DIANA-microT web server v5.0: service integration into miRNA functional analysis workflows. Maria D. Paraskevopoulou, Georgios Georgakilas, Nikos Kostoulas, Ioannis S. Vlachos, Thanasis Vergoulis, Martin Reczko, Christos Filippidis, Theodore Dalamagas and A.G. Hatzigeorgiou. Nucl. Acids Res. 41(W1):W169-W173, 2013 Full text
DIANA miRPath v.2.0: investigating the combinatorial effect of microRNAs in pathways. I. S. Vlachos, N. Kostoulas, T. Vergoulis, G. Georgakilas, M. Reczko, M. Maragkakis, M. D. Paraskevopoulou, K. Prionidis, T. Dalamagas, A. G. Hatzigeorgiou. Nucl. Acids Res. 40(W1): W498-W504, 2012 Full text
Approximate Regional Sequence Matching for Genomic Databases. T. Vergoulis, T. Dalamagas, D. Sacharidis, T. Sellis. Volume 21, Issue 6, pp 779-795, 2012 Full text
Tarbase 6.0: Capturing the Exponential Growth of miRNA Targets with Experimental Support. T. Vergoulis, I. Vlachos, P. Alexiou, G. Georgakilas, M. Maragkakis, M. Reczko, S. Gerangelos, N. Koziris, T. Dalamagas, AG Hatzigeorgiou. Nucleic Acids Research, 40 (Database Issue), 2012 Full text
DIANA-microT Web server upgrade supports Fly and Worm miRNA target prediction and bibliographic miRNA to disease association. M. Maragkakis, T. Vergoulis, P. Alexiou, M. Reczko, K. Plomaritou, M. Gousis, K. Kourtis, N. Koziris, T. Dalamagas, A. Hatzigeorgiou. Nucleic Acids Research, 39, 2011 Full text
miRGen 2.0 a database of microRNA genomic information and regulation. P. Alexiou, T. Vergoulis, M. Gleditzsch, G. Prekas, T. Dalamagas, M. Megraw, I. Grosse, T. Sellis, A.G. Hatzigeorgiou. Nucleic Acid Research (NAR), 38, 2010 Full text
Accurate microRNA target prediction correlates with protein repression levels. Manolis Maragkakis, Panagiotis Alexiou, Giorgio L Papadopoulos, Martin Reczko, Theodore Dalamagas, George Giannopoulos, George Goumas, Evangelos Koukis, Kornilios Kourtis, Victor A Simossis, Praveen Sethupathy, Thanasis Vergoulis, Nectarios Koziris, . BMC Bioinformatics, 10, 2009 Full text
DIANA-microT web server: elucidating microRNA functions through target prediction. 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. Nucleic Acids Research (NAR) volume 37, 2009 Full text

Technical Reports

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PhD Theses

Advanced search and data management services in Life Sciences. Thanasis Vergoulis. National Technical University of Athens, Greece, 2014 Full text

Diploma Theses

Υλοποίηση μηχανισμού κατάταξης δημοσιεύσεων σχετικών με βιομόρια micro-RNA. Βασιλική Βλαχοκυριάκου. Department of Informatics and Telecommunications, National and Kapodistrian University of Athens, Greece, 2015 Full text
Approximate string matching for spam management in email servers. Christos Kopsidas. Department of Informatics and Telecommunications, National and Kapodistrian University of Athens, Greece, 2012
Querying scientific databases, considering the historic evolution of data. Ilias Kanellos. Department of Computer Engineering and Informatics, National Technical University of Athens, Greece, 2012 Full text
Term suggestion techniques for Scientific Databases. Petsios Theofilos. School of Electrical and Computer Engineering, NTUA, 2011 Full text
Advanced Web Application for Management of Biosciences Data. Γιώργος Πρέκας. Σχολή Ηλεκτρολόγων Μηχανικών και Μηχανικών Υπολογιστών, ΕΜΠ, 2010 Full text
Approximate Sequence Matching with MapReduce. Δανάη Κούτρα. Σχολή Ηλεκτρολόγων Μηχανικών και Μηχανικών Υπολογιστών, ΕΜΠ, 2010 Full text
Implementation of suffix tree construction using Hadoop MapReduce. Alexandros Konstantinakis - Karmis. Σχολή Ηλεκτρολόγων Μηχανικών και Μηχανικών Υπολογιστών, ΕΜΠ, 2010 Full text
DIANA 2.0: Advanced web application for the management of bioscience data. Γεωργία Φωτοπούλου. Σχολή Ηλεκτρολόγων Μηχανικών και Μηχανικών Υπολογιστών, ΕΜΠ, 2010 Full text

Books

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