Publications

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Conferences/Workshops

ArtSim: Improved estimation of current impact for recent articles. Serafeim Chatzopoulos, Thanasis Vergoulis, Ilias Kanellos, Theodore Dalamagas, Christos Tryfonopoulos. AIMinScience 2020, 2020 Full text
VeTo: Expert Set Expansion in Academia. Thanasis Vergoulis, Serafeim Chatzopoulos, Theodore Dalamagas, Christos Tryfonopoulos. TPDL 2020, 2020 Full text
Efficient Calculation of Empirical P-values for AssociationTesting of Binary Classifications. Kostis Zagganas, Thanasis Vergoulis, Spiros Skiadopoulos, Theodore Dalamagas. SSDBM 2020, 2020 Full text
BIP! Finder: Facilitating scientific literature search by exploiting impact-based ranking. Thanasis Vergoulis, Serafeim Chatzopoulos, Ilias Kanellos, Panagiotis Deligiannis, Christos Tryfonopoulos, Theodore Dalamagas. CIKM 2019, 2019 Full text
A study on the readability of scientific publications. Thanasis Vergoulis, Ilias Kanellos, Anargiros Tzerefos, Serafeim Chatzopoulos, Theodore Dalamagas, Spiros Skiadopoulos. TPDL 2019, 2019 Full text
SciTo trends: visualising scientific topic trends. Serafeim Chatzopoulos, Panagiotis Deligiannis, Thanasis Vergoulis, Ilias Kanellos, Christos Tryfonopoulos, Theodore Dalamagas. TPDL 2019, 2019 Full text
RDF Keyword Search based on Keywords-To-SPARQL Translation. Katerina Gkirtzou, George Papastefanatos, Theodore Dalamagas. 1st International Workshop on Novel Web Search Interfaces and Systems, NWSearch 2015 (with CIKM15), Melbourne, Australia, October 23, 2015. , 2015 Full text
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
RDF Resource Search and Exploration with LinkZoo. Marios Meimaris, George Alexiou, Katerina Gkirtzou, George Papastefanatos, Theodore Dalamagas. In DATA 2015 pp. 232-239, 2015 Full text
Keywords-To-SPARQL translation for RDF data search and exploration. Katerina Gkirtzou, Kostis Karozos, Vassilis Vassalos and Theodore Dalamagas. TPDL 2015, 2015
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
RDivF: Diversifying Keyword Search on RDF Graphs. • Nikos Bikakis, Giorgos Giannopoulos, John Liagouris, Dimitrios Skoutas, Theodore Dalamagas, and Timos Sellis. 17th International Conference on Theory and Practice of Digital Libraries (TPDL '13), 2013 Full text
Publishing Census as Linked Open Data. A Case Study. Irene Petrou , George Papastefanatos, Theodore Dalamagas . 2nd International Workshop on Open Data (WOD13), 2013
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
Diachronic Linked Data: Towards Long-Term Preservation of Structured Interrelated Information. Yannis Stavrakas, George Papastefanatos, Theodore Dalamagas and Vassilis Christophides. International Workshop on Open Data (WOD 2012), Nantes, France, May 25 2012, 2012
Publishing Life Science Data as Linked Open Data: the Case Study of miRBase. Theodore Dalamagas, Nikos Bikakis, George Papastefanatos, Yannis Stavrakas and Artemis Hatzigeorgiou. International Workshop on Open Data (WOD 2012), Nantes, France, May 25 2012, 2012
Learning to rank user intent. Giorgos Giannopoulos, Ulf Brefeld, Theodore Dalamagas, and Timos Sellis. Proceedings of the 20th ACM International Conference on Information and Knowledge Management (CIKM’11), 2011 Full text
Search behavior-driven training for result re-ranking. Giorgos Giannopoulos, Theodore Dalamagas, and Timos Sellis. Proceedings of the International Conference on Theory and Practice of Digital Libraries (TPDL’11), 2011 Full text
Dynamic pickup and delivery with transfers. Panagiotis Bouros, Dimitris Sacharidis, Theodore Dalamagas, and Timos Sellis. Proceedings of the 12th International Symposium on Spatial and Temporal Databases (SSTD’11), 2011 Full text
FreePub: Collecting and Organizing Scientic Material Using Mindmaps. Theodore Dalamagas, Tryfon Farmakakis, Manolis Maragkakis and Artemis G. Hatzigeorgiou. SWAT4LS Workshop: Semantic Web Applications and Tools for Life Sciences, 2010
GoNTogle: a Tool for Semantic Annotation and Search. Giorgos Giannopoulos, Nikos Bikakis, Theodore Dalamagas, Timos Sellis. ESWC 2010 (demo paper), 2010
Integrating Keywords and Semantics on Document Annotation and Search. Nikos Bikakis, Giorgos Giannopoulos, Theodore Dalamagas, Timos Sellis. ODBASE 2010, 2010
Collaborative information spaces: Research directions at IMIS. George Papastefanatos, Yannis Stavrakas, Christos Papatheodorou, Theodore Dalamagas, Dieter Pfoser, Timos Sellis. 2nd ERCIM DIS Workshop on large scale and federated information spaces, Amsterdam, 2010 Full text
Evolution of Interrelated Data: Users, Problems, and Systems. Yannis Stavrakas, Theodore Dalamagas, Timos Sellis. 1st ERCIM DIS Workshop on large scale and federated information spaces, Paris, 2009 Full text
Collaborative Ranking Function Training for Web Search Personalization. Giorgos Giannopoulos, Theodore Dalamagas and Timos Sellis. PersDB 2009 : 13 - 18, 2009 Full text
Efficient Evaluation of Generalized Tree-Pattern Queries with Same-Path Constraints. Xiaoying Wu, Dimitri Theodoratos, Stefanos Souldatos, Theodore Dalamagas, Timos Sellis. SSDBM 2009: 361-379, 2009 Full text
Evaluating Reachability Queries over Path Collections. Panagiotis Bouros, Spiros Skiadopoulos, Theodore Dalamagas, Dimitris Sacharidis, Timos Sellis. SSDBM 2009: 398-416, 2009 Full text
Boosting the ranking function learning process using clustering. Giorgos Giannopoulos, Theodore Dalamagas, Magdalini Eirinaki, Timos Sellis. WIDM 2008: 125-132, 2008 Full text
A heuristic approach for checking containment of generalized tree-pattern queries. Pawel Placek, Stefanos Souldatos, Dimitri Theodoratos, Xiaoying Wu, Theodore Dalamagas, Timos Sellis. CIKM 2008: 551-560, 2008 Full text

Journals

Impact-Based Ranking of Scientific Publications: A Survey and Experimental Evaluation. Ilias Kanellos, Thanasis Vergoulis, Dimitris Sacharidis, Theodore Dalamagas, Yannis Vassiliou. TKDE, DOI: 10.1109/TKDE.2019.2941206 (early access), 2019 Full text
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
Classifying and comparing community innovation in Idea Management Systems. Adam Westerski, Theodore Dalamagas, Carlos A Iglesias. Decision Support Systems, 54(3): 1316-1326, 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
Processing and evaluating partial tree pattern queries on xml data. Xiaoying Wu, Stefanos Souldatos, Dimitri Theodoratos, Theodore Dalamagas, Yannis Vassiliou, and Timos Sellis. IEEE Transactions on Knowledge and Data Engineering (TKDE), 2011 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
Evaluating Path Queries over Frequently Updated Route Collections. P. Bouros, D. Sacharidis, T. Dalamagas, S. Skiadopoulos, T. Sellis. TKDE, 2011
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
Containment of Partially Specified Tree-Pattern Queries in the Presence of Dimension Graphs. Dimitri Theodoratos, Pawel Placek, Theodore Dalamagas, Stefanos Souldatos, Timos Sellis. VLDB Journal 18 (1): 233-254, 2009 Full text
Indexing Views to Route Queries in a PDMS. Lefteris Sidirourgos, Giorgos Kokkinidis, Theodore Dalamagas, Vassilis Christophides, Timos Sellis. Distributed and Parallel Databases 23(1): 45-68, 2008 Full text

Technical Reports

BIP4COVID19: Releasing impact measures forarticles relevant to COVID-19. Thanasis Vergoulis, Ilias Kanellos, Serafeim Chatzopoulos, Danae Pla Karidi, Theodore Dalamagas. bioRxiv 2020.04.11.037093; doi: https://doi.org/10.1101/2020.04.11.037093, 2020 Full text

PhD Theses

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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
Ανάκτηση Πληροφορίας Στον Ιστό με Χρήση Ταξινόμησης Όψεων και Συσταδοποίησης. Παναγιώτα Γεωργίου . Σχολή Ηλεκτρολόγων Μηχανικών και Μηχανικών Υπολογιστών, ΕΜΠ, 2009 Full text
Τεχνικές ταξινόμησης αποτελεσμάτων μηχανών αναζήτησης με βάση την ιστορία του χρήστη. Αντώνιος Νικολαΐδης . Σχολή Ηλεκτρολόγων Μηχανικών και Μηχανικών Υπολογιστών, ΕΜΠ, 2009 Full text
Εργαλείο Συλλογής και Οργάνωσης Γνώσης με Μηχανισμούς Μετα-Αναζήτησης στον Ιστό. Αργύρης Κόλλιας. Σχολή Ηλεκτρολόγων Μηχανικών και Μηχανικών Υπολογιστών, ΕΜΠ, 2009 Full text

Books

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