2020-: Associate Professor in Bioinformatics, Department of Biological Sciences, University of Cyprus
2012-2019: Assistant Professor in Bioinformatics, Department of Biological Sciences, University of Cyprus
2005-2012: Lecturer in Bioinformatics, Department of Biological Sciences, University of Cyprus
2005-: Head, Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus
2004-2005: Post Doctorate Research Assistant, Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Greece
1997-2004 PhD in Biological Sciences: Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Greece.
Thesis title: “Prediction of protein function from aminoacid sequence”.
1991-1996 BSc in Physics: University of Athens, Greece.
Diploma thesis title: “Structural and Modeling studies of possible inhibitors of the enzyme Dihydrofolate Reductase (DHFR)”.
Understanding the principles of microbial genome structure, function and evolution through comparative genomics approaches. Large Scale Comparative Genomics and Computer Assisted Genome Annotation. Genomic data analysis and visualization.Sequence repeats, low complexity/compositionally biased regions: Investigation of their relation to protein structure and association to protein (mis)function. Study of the evolution of protein repeats. Development of new methods and algorithms.Evolution of transmembrane and membrane-associated proteins. Applications on classification, function, topology and structure preciction based on complete genomic data statistical and machine learning approaches. Simulation of native or ‘in silico engineered’ membrane proteins.Application of Statistical, Machine Learning and Data Mining techniques in Biological Sequence Analysis.Computational Approaches towards Systems and Synthetic Biology.
Structure-Function-Evolution of eukaryotic endomembrane systems (Autophagy, Nuclear Pore Complex)
Promponas, V. J., Katerina R. Katsani, Benjamin J. Blencowe, and Christos A. Ouzounis. "Sequence evidence for common ancestry of eukaryotic endomembrane coatomers." Scientific reports 6 (2016): 22311.
Jacomin, Anne-Claire, Siva Samavedam, V. J. Promponas, and Ioannis P. Nezis. "iLIR database: A web resource for LIR motif-containing proteins in eukaryotes." Autophagy 12, no. 10 (2016): 1945-1953.
Klionsky, Daniel J., K. Abdelmohsen, ..., V. J. Promponas, ..., and SM Zughaier. "Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)." Autophagy 12, no. 1 (2016): 1-222.
Kalvari, Ioanna, Stelios Tsompanis, Nitha C. Mulakkal, Richard Osgood, Terje Johansen, Ioannis P. Nezis, and V. J. Promponas. "iLIR: A web resource for prediction of Atg8-family interacting proteins." Autophagy 10, no. 5 (2014): 913-25.
Katsani, Katerina R., Manuel Irimia, Christos Karapiperis, Zacharias G. Scouras, Benjamin J. Blencowe, V. J. Promponas, and Christos A. Ouzounis. "Functional genomics evidence unearths new moonlighting roles of outer ring coat nucleoporins." Scientific reports 4 (2014): 4655.
Protein sequence analysis (Compositional bias, Intrinsically disorderedproteins,sequence repeats)
Hatos, András, Borbála Hajdu-Soltész, ..., V. J. Promponas, ..., Silvio C. E. Tosatto, and Damiano Piovesan. "DisProt: intrinsic protein disorder annotation in 2020." Nucleic Acids Res. (2020): 48(D1):D269-D276.
Ntountoumi, Chrysa, Panayotis Vlastaridis, Dimitris Mossialos, Constantinos Stathopoulos, Ioannis Iliopoulos, V. J. Promponas, Stephen G. Oliver, and Grigoris D. Amoutzias. "Low complexity regions in the proteins of prokaryotes perform important functional roles and are highly conserved." Nucleic Acids Res. 47, no. 19 (2019): 9998-10009.
Kirmitzoglou, Ioannis, and V. J. Promponas. "LCR-eXXXplorer: a web platform to search, visualize and share data for low complexity regions in protein sequences." Bioinformatics (Oxford, England) 31, no. 13 (2015): 2208-10.
Genome annotation
Tørresen, Ole K., Bastiaan Star, Pablo Mier, Miguel A. Andrade-Navarro, Alex Bateman, Patryk Jarnot, Aleksandra Gruca, Marcin Grynberg, Andrey V. Kajava, V. J. Promponas, Anisimova M, Jakobsen KS, Linke D. "Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases." Nucleic Acids Res. (2019) 47(21):10994-11006.
Promponas, V. J., Ioannis Iliopoulos, and Christos A. Ouzounis. "Annotation inconsistencies beyond sequence similarity-based function prediction - phylogeny and genome structure." Standards in genomic sciences 10 (2015): 108.
Promponas, V. J., Christos A. Ouzounis, and Ioannis Iliopoulos. "Experimental evidence validating the computational inference of functional associations from gene fusion events: a critical survey." Briefings in bioinformatics 15, no. 3 (2014): 443-54.
