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Thanasis Vergoulis

Artemidos 6 & Epidavrou · Marousi, 15125, Greece · vergoulis@athenarc.gr

I am the Development & Operation Director of OpenAIRE and a scientific associate at IMSI, "Athena" Research Center in Greece. In addition, I have been teaching courses in undergraduate and postgraduate level in academic institutions in Greece and Cyprus. Finally, I am the coordinating officer of the ELIXIR-GR Compute Platform.

I received my diploma in Computer Engineering & Informatics from the University of Patras and my PhD in Computer Science from the NTU of Athens, under the supervision of Prof. Timos Sellis (thesis title: "Advanced search and data managementservices in Life Sciences").

Research interests

I have been involved in several EU and national ICT projects related to big data, scientific data management, open science, and linked data. My research interests also involve bioinformatics, text mining & information retrieval for scientific publications, and research analytics.

Highlights

I am or was the co-organizer in the following events:

I have (co)edited the following books or journal special issues:

I am supervising or have supervised the following relevant projects:

Signatory of DORA

Publications

  •   T. Vergoulis, I. Kanellos, G. Giannopoulos, T. Dalamagas: Simplifying Impact Prediction for Scientific Articles. EDBT/ICDT Workshops 2021
  •   K. Zagganas, M. Lioli, T. Vergoulis, T. Dalamagas: Simplifying p-value calculation for the unbiased microRNAenrichment analysis, using ML-techniques. EDBT/ICDT Workshops 2021
  •   T. Vergoulis, K. Zagganas, L. Kavouras, M. Reczko, S. Sartzetakis, T. Dalamagas: SCHeMa: Scheduling Scientific Containers on a Cluster of Heterogeneous Machines. SSDBM 2021: 243-247
  •   T. Vergoulis, I. Kanellos, C. Atzori, A. Mannocci, S. Chatzopoulos, S. La Bruzzo, N. Manola, P. Manghi: BIP! DB: A Dataset of Impact Measures for Scientific Publications. WWW (Companion Volume) 2021: 456-460
  •   P. Deligiannis, T. Vergoulis, S. Chatzopoulos, C. Tryfonopoulos: Visualising Scientific Topic Evolution. WWW (Companion Volume) 2021: 468-472
  •   S. Chatzopoulos, T. Vergoulis, P. Deligiannis, D. Skoutas, T. Dalamagas, C. Tryfonopoulos: SciNeM: A Scalable Data Science Tool for Heterogeneous Network Mining. In Proceedings of EDBT 2021, 654-657 (demo)
  •   I. Kanellos, T. Vergoulis, D. Sacharidis, T. Dalamagas, Y. Vassiliou: Ranking Papers by their Short-Term Scientific Impact. In Proceedings of ICDE 2021, 1997-2002
  •   I. Kanellos, T. Vergoulis, D. Sacharidis, T. Dalamagas, Y. Vassiliou: Impact-Based Ranking of Scientific Publications: A Survey and Experimental Evaluation. TKDE 33(4), 2021 [full text]
  •   S. Chatzopoulos, K. Patroumpas, A. Zeakis, T. Vergoulis, D. Skoutas: SPHINX: A System for Metapath-based Entity Exploration in Heterogeneous Information Networks. In Proceedings of VLDB 2020 (demo)
  •   S. Chatzopoulos, T. Vergoulis, I. Kanellos, T. Dalamagas, C. Tryfonopoulos: ArtSim: Improved estimation of current impact for recent articles. In Proceedings of AIMinScience 2020
  •   T. Vergoulis, S. Chatzopoulos, T. Dalamagas, C. Tryfonopoulos: VeTo: Expert Set Expansion in Academia. In Proceedings of TPDL 2020
  •   K. Zagganas, T. Vergoulis, S. Skiadopoulos, T. Dalamagas: Efficient Calculation of Empirical P-values for AssociationTesting of Binary Classifications. In Proceedings of SSDBM 2020
  •   T. Vergoulis, I. Kanellos, S. Chatzopoulos, D. Pla Karidi, T. Dalamagas: BIP4COVID19: Releasing impact measures forarticles relevant to COVID-19. bioRxiv 2020.04.11.037093; doi: https://doi.org/10.1101/2020.04.11.037093
  •   T. Vergoulis, S. Chatzopoulos, I. Kanellos, P. Deligiannis, C. Tryfonopoulos, T. Dalamagas: BIP! Finder: Facilitating scientific literature search by exploiting impact-based ranking. CIKM 2019: 2937-2940
  •   T. Vergoulis, I. Kanellos, A. Tzerefos, S. Chatzopoulos, T. Dalamagas, S. Skiadopoulos: A study on the readability of scientific publications. In Proceedings of TPDL 2019 (Oslo, Norway): pp 136-144 [full text, slides]
  •   S. Chatzopoulos, P. Deligiannis, T. Vergoulis, I. Kanellos, C. Tryfonopoulos, T. Dalamagas: SciTo trends: visualising scientific topic trends. In Proceedings of TPDL 2019 (Oslo, Norway): pp 393-396 (demo) [full text, poster, slides]
  •   D. Karagkouni, M. D. Paraskevopoulou, S. Chatzopoulos, I. S. Vlachos, S. Tastsoglou, I. Kanellos, D. Papadimitriou, I. Kavakiotis, S. Maniou, G. Skoufos, T. Vergoulis, T. Dalamagas, A. G. Hatzigeorgiou: DIANA-TarBase v8: a decade-long collection of experimentally supported miRNA-gene interactions. Nucleic Acids Research 46(Database-Issue): D239-D245 (2018)
  •   K. Zagganas, T. Vergoulis, M. D. Paraskevopoulou, I. S. Vlachos, S. Skiadopoulos, T. Dalamagas: BUFET: boosting the unbiased miRNA functional enrichment analysis using bitsets. BMC Bioinformatics 18(1): 399:1-399:8 (2017)
  •   G. Georgakilas, I. S. Vlachos, K. Zagganas, T. Vergoulis, M. D. Paraskevopoulou, I. Kanellos, P. Tsanakas, D. Dellis, A. Fevgas, T. Dalamagas, A. G. Hatzigeorgiou: DIANA-miRGen v3.0: accurate characterization of microRNA promoters and their regulators. Nucleic Acids Research 44(Database-Issue): 190-195 (2016)
  •   M. D. Paraskevopoulou, I. S. Vlachos, D. Karagkouni, G. Georgakilas, I. Kanellos, T. Vergoulis, K. Zagganas, P. Tsanakas, E. Floros, T. Dalamagas, A. G. Hatzigeorgiou: DIANA-LncBase v2: indexing microRNA targets on non-coding transcripts. Nucleic Acids Research 44(Database-Issue): 231-238 (2016)
  •   I. S. Vlachos, T. Vergoulis, M. D. Paraskevopoulou, F. Lykokanellos, G. Georgakilas, P. Georgiou, S. Chatzopoulos, D. Karagkouni, F. Christodoulou, T. Dalamagas, A. G. Hatzigeorgiou: DIANA-mirExTra v2.0: Uncovering microRNAs and transcription factors with crucial roles in NGS expression data. Nucleic Acids Research 44(Webserver-Issue): W128-W134 (2016)
  •   I. Kanellos, V. Vlachokyriakou, T. Vergoulis, G. Georgakilas, Y. Vassiliou, A. G. Hatzigeorgiou, T. Dalamagas: MirPub v2: Towards Ranking and Refining miRNA Publication Search Results. TPDL 2015: 355-359
  •   T. Vergoulis, I. Kanellos, N. Kostoulas, G. Georgakilas, T. K. Sellis, A. G. Hatzigeorgiou, T. Dalamagas: mirPub: a database for searching microRNA publications. Bioinformatics 31(9): 1502-1504 (2015)
  •   I. S. Vlachos, M. D. Paraskevopoulou, D. Karagkouni, G. Georgakilas, T. Vergoulis, I. Kanellos, I-L. Anastasopoulos, S. Maniou, K. Karathanou, D. Kalfakakou, A. Fevgas, T. Dalamagas, A. G. Hatzigeorgiou: DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA: mRNA interactions. Nucleic Acids Research 43(Database-Issue): 153-159 (2015)
  •   I. S. Vlachos, K. Zagganas, M. D. Paraskevopoulou, G. Georgakilas, D. Karagkouni, T. Vergoulis, T. Dalamagas, A. G. Hatzigeorgiou: DIANA-miRPath v3.0: deciphering microRNA function with experimental support. Nucleic Acids Research 43(Webserver-Issue): W460-W466 (2015)
  •   R-M. Tsoupidi, I. Kanellos, T. Vergoulis, I. S. Vlachos, A. G. Hatzigeorgiou, T. Dalamagas: TarMiner: automatic extraction of miRNA targets from literature. SSDBM 2015: 12:1-12:5
  •   I. Kanellos, T. Vergoulis, D. Sacharidis, T. Dalamagas, A. G. Hatzigeorgiou, S. Sartzetakis, T. K. Sellis: MR-microT: a MapReduce-based MicroRNA target prediction method. SSDBM 2014: 47:1-47:4
  •   K. Gkirtzou, T. Vergoulis, A. G. Hatzigeorgiou, T. K. Sellis, T. Dalamagas: Publishing Diachronic Life Science Linked Data. SWAT4LS 2014
  •   M. D. Paraskevopoulou, G. Georgakilas, N. Kostoulas, I. S. Vlachos, T. Vergoulis, M. Reczko, C. Filippidis, T. Dalamagas, A. G. Hatzigeorgiou: DIANA-microT web server v5.0: service integration into miRNA functional analysis workflows. Nucleic Acids Research 41(Webserver-Issue): 169-173 (2013)
  •   T. Vergoulis, I. S. Vlachos, P. Alexiou, G. Georgakilas, M. Maragkakis, M. Reczko, S. Gerangelos, N. Koziris, T. Dalamagas, A. G. Hatzigeorgiou: TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support. Nucleic Acids Research 40(Database-Issue): 222-229 (2012)
  •   I. S. Vlachos, N. Kostoulas, T. Vergoulis, G. Georgakilas, M. Reczko, M. Maragkakis, M. D. Paraskevopoulou, K. Prionidis, T. Dalamagas, A. G. Hatzigeorgiou: DIANA miRPath v.2.0: investigating the combinatorial effect of microRNAs in pathways. Nucleic Acids Research 40(Web-Server-Issue): 498-504 (2012)
  •   T. Vergoulis, T. Dalamagas, D. Sacharidis, T. K. Sellis: Approximate regional sequence matching for genomic databases. VLDB J. 21(6): 779-795 (2012)
  •   T. Vergoulis, M. Alexakis, T. Dalamagas, M. Maragkakis, A. G. Hatzigeorgiou, T. K. Sellis: TARCLOUD: A Cloud-Based Platform to Support miRNA Target Prediction. SSDBM 2012: 628-633
  •   M. Maragkakis, T. Vergoulis, P. Alexiou, M. Reczko, K. Plomaritou, M. Gousis, K. Kourtis, N. Koziris, T. Dalamagas, A. G. Hatzigeorgiou: DIANA-microT Web server upgrade supports Fly and Worm miRNA target prediction and bibliographic miRNA to disease association. Nucleic Acids Research 39(Web-Server-Issue): 145-148 (2011)
  •   P. Alexiou, T. Vergoulis, M. Gleditzsch, G. Prekas, T. Dalamagas, M. Megraw, I. Grosse, T. K. Sellis, A. G. Hatzigeorgiou: miRGen 2.0: a database of microRNA genomic information and regulation. Nucleic Acids Research 38(Database-Issue): 137-141 (2010)
  •   M. Maragkakis, P. Alexiou, G. L. Papadopoulos, M. Reczko, T. Dalamagas, G. Giannopoulos, G. I. Goumas, E. Koukis, K. Kourtis, V. A. Simossis, P. Sethupathy, T. Vergoulis, N. Koziris, T. K. Sellis, P. Tsanakas, A. G. Hatzigeorgiou: Accurate microRNA target prediction correlates with protein repression levels. BMC Bioinformatics 10: 295 (2009)
  •   M. Maragkakis, M. Reczko, V. A. Simossis, P. Alexiou, G. L. Papadopoulos, T. Dalamagas, G. Giannopoulos, G. I. Goumas, E. Koukis, K. Kourtis, T. Vergoulis, N. Koziris, T. K. Sellis, P. Tsanakas, A. G. Hatzigeorgiou: DIANA-microT web server: elucidating microRNA functions through target prediction. Nucleic Acids Research 37(Web-Server-Issue): 273-276 (2009)

Open code & data

Code. The complete list of my open codes can be fount in my GitHub profile. In addition, I have the technical coordination of most software products of the DIWIS department (IMSI, ATHENA RC). An indicative list of my personal codes can be found below:

  •   GeSuTr: A C++ library for generalised suffix trees.
  •   koCodeJS: A Javascript Konami Code listener to integrate in webpages.

Data. Moreover, an indicative list of open access datasets in which I have contribution can be found below:

  •   Domain expert readability dataset DOI
  •   BIP4COVID19: Impact metrics and indicators for coronavirus related publications DOI
    •   Program Committees (PC) dataset DOI
  •   BIP! DB dataset DOI
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