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BRL publications

Peer reviewed contributions

Papers published in peer reviewed international journals

  • Pavlopoulos GA, Promponas VJ, Ouzounis CA, Iliopoulos I. Biological information extraction and co-occurrence analysis. Methods Mol Biol. 2014;1159:77-92. doi: 10.1007/978-1-4939-0709-0_5.
  • Papanikolaou N, Pavlopoulos GA, Pafilis E, Theodosiou T, Schneider R, Satagopam VP, Ouzounis CA, Eliopoulos AG, Promponas VJ, Iliopoulos I. BioTextQuest+: a knowledge integration platform for literature mining and concept discovery. Bioinformatics. 2014 Aug 6. pii: btu524. [Epub ahead of print]
  • Katsani KR, Irimia M, Karapiperis C, Scouras ZG, Blencowe BJ, Promponas VJ, Ouzounis CA. Functional Genomics Evidence Unearths New Moonlighting Roles of Outer Ring Coat Nucleoporins. Sci Rep. 2014 Apr 11;4:4655. doi: 10.1038/srep04655. PMID:24722254; [Open access full text at the publisher's web site]; [Supplementary Data at Figshare]; [A short summary in Greek]
  • Kalvari I, Tsompanis S, Mulakkal NC, Osgood R, Johansen T, Nezis IP, Promponas VJ. iLIR: A web resource for prediction of Atg8-family interacting proteins. Autophagy 10:166 - 178, 2014PMID: 24589857; [Open access full text at the publisher's web site]; [Access the iLIR server]
  • Samara P., Kalbacher H., Ioannou K., Radu D.L., Livaniou E., Promponas V.J., Voelter W., Tsitsilonis O. Development of an ELISA for the quantification of the C-terminal decapeptide prothymosin α(100-109) in sera of mice infected with bacteria. J Immunol Methods 395(1-2):54-62, 2013.
  • Papadopoulos A., Kirmitzoglou I., Promponas V.J., Theocharides T. FPGA-based hardware acceleration for local complexity analysis of massive genomic data. INTEGRATION, the VLSI journal  46, 230–239, 2013.
  • Promponas V.J., Ouzounis C.A., Iliopoulos I. Experimental evidence validating the computational inference of functional associations from gene fusion events: a critical survey. Briefings in Bioinformatics 2012 [Publisher's website].
  • Ouzounis C.A., Promponas V.J., Iliopoulos I. The quest for an upper limit in systems biology. Journal of Biological Research-Thessaloniki. 2012.
  • Psomopoulos F.E., Siarkou V.I., Papanikolaou N., Iliopoulos I., Tsaftaris A.S., Promponas V.J., Ouzounis C.A. The Chlamydiales Pangenome Revisited: Structural Stability and Functional Coherence. Genes,  3(2):291-319, 2012. [Publisher's web site] [Supplementary Data]
  • Kountouris P, Agathocleous M, Promponas VJ, Christodoulou G,  Hadjicostas S, Vassiliades V. and Christodoulou C. A comparative study on filtering protein secondary structure prediction. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2012. [Publisher's web site]
  • Theodosiou A. and Promponas VJ*. LaTcOm: a web server for visualizing rare codon clusters in coding sequences. Bioinformatics 28(4):591-2, 2012. [Publisher's web site]
  • Papanikolaou N., Pafilis E.,  Nikolaou S., Ouzounis CA, Iliopoulos I*, and Promponas VJ*. BioTextQuest: A Web-based Biomedical Text Mining Suite for Concept Discovery. Bioinformatics27(23):3327-8, 2011. [Publisher's website]
  • Fokianos K. and Promponas VJ. Biological Applications of Time Series Frequency Domain Clustering. 2011 (accepted  - Journal of Time Series Analysis) [Publisher's website].
  • Kirschel, A. N. G., Cody, M. L., Harlow, Z. T., Promponas, V., Vallejo, E. E., and Taylor, C. E. Territorial dynamics of Mexican Antthrushes ( Formicarius moniliger) revealed by individual recognition of their songs. Ibis, 153(2), 255-268, 2011.[Publisher's website]
  • Ioannou A, Fokianos K, and Promponas VJ.  Spectral Density Ratio Based Clustering Methods for the Binary Segmentation of Protein Sequences: a Comparative Study,  Biosystems, 100, 132--143, 2010. [Publisher's website]
  • Papanikolaou N, Trachana K, Theodosiou T, Promponas VJ, and Iliopoulos I. Gene socialization: gene order, GC content and gene silencing in Salmonella, BMC Genomics, 10:597, doi:10.1186/1471-2164-10-597, 2009. [Publisher's website]
  • Savvides A, Promponas VJ, and Fokianos K. Clustering of biological time series by cepstral coefficients based distances, Pattern Recognition, doi:10.1016/j.patcog.2008.01.002, 2008. [Publisher's website].
  • Bagos PG, Liakopoulos TD, Promponas VJ, and Hamodrakas SJ. Prediction of β-barrel Outer Membrane Proteins", Proceedings of the Indian National Academy of Sciences - Part B (Biological Sciences), 71:1, 2005.
  • Papasaikas, PK, Bagos, PG, Litou, ZI, Promponas VJ, and Hamodrakas, SJ. PRED-GPCR: GPCR recognition and family classification server., Nucleic Acids Research, W380-382, 2004. [PUBMED]
  • Vernikos G, Gkogkas C, Promponas VJ, and Hamodrakas SJ. GeneViTo: Visualizing gene-product functional and structural features in genomic datasets. BMC Bioinformatics, 4:53, 2003. [PUBMED]
  • Iliopoulos I, Tsoka S, Andrade MA, Enright AJ, Carroll M, Poullet P, Promponas VJ, Liakopoulos T, Palaios G, Pasquier C, Hamodrakas S, Tamames J, Yagnik AT, Tramontano A, Devos D, Blaschke C, Valencia A, Brett D, Martin D, Leroy C, Rigoutsos I, Sander C, Ouzounis CA. Evaluation of annotation strategies using an entire genome sequence. Bioinformatics, 19(6), 717-726, 2003. [PUBMED] [Evaluated as a "Must Read" article by the F1000,  F1000.com/1013800]
  • Pasquier C, Promponas VJ, and Hamodrakas SJ. PRED-CLASS: cascading neural networks for generalized protein classification and genome-wide applications. Proteins: Structure Function, and Genetics, 44(3), 361-369, 2001. [PUBMED]
  • Promponas, VJ, Enright, A.J., Tsoka, S., Kreil, D., Leroy, C., Hamodrakas, S.J., Sander, C., and Ouzounis, CA. CAST: an iterative algorithm for the Complexity Analysis of Sequence Tracts. Bioinformatics, 16(10), 915-922, 2000. [PUBMED]
  • Tsoka, S., Promponas, V., and Ouzounis, C. Reproducibility in genome sequence annotation: The Plasmodium falciparum chromosome 2 case. FEBS Letters, 451, 354-355, 1999. [PUBMED]
  • Promponas, V.J., Palaios, G., Pasquier, C.M., Hamodrakas, J.S., and Hamodrakas SJ. CoPreTHi: A Web tool which combines transmembrane protein segment prediction methods. In Silico Biology, 01(0014), 1999. [PUBMED]
  • Pasquier, C.M., Promponas, V.J., Palaios, G., Hamodrakas, J.S., and Hamodrakas, S.J. A novel method for predicting transmembrane segments in proteins based on a statistical analysis of the SwissProt database: the PRED-TMR algorithm. Protein Engineering, 12(5), 381-385, 1999. [PUBMED]
  • Pasquier, C.M., Promponas, V.J., Varvayannis, N.J., and Hamodrakas, S.J. A Web server to locate periodicities in a sequence. Bioinformatics, 14(8), 749-750, 1998. [PUBMED]

Papers published in peer reviewed international conferences

  • Papadopoulos A., Kirmitzoglou I., Promponas V.J., Theocharides T. GPU technology as a platform for accelerating local complexity analysis of protein sequences. 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society - EMBC2013, Osaka, Japan, July 2013.
  • Chrysos G., Sotiriades E., Rousopoulos C., Dollas A., Papadopoulos A., Kirmitzoglou I., Promponas V., Theocharides T., Petihakis G., Lagnel J., Vavylis P., Kotoulas G. Opportunities from the Use of FPGAs as Platforms for Bioinformatics Algorithms. 12th IEEE International Conference on Bioinformatics and Bioengineering - BIBE2012, Larnaca, Cyprus,  November 2012.
  • Papadopoulos  A., Promponas V.J., Theocharides T. Towards systolic hardware acceleration for local complexity analysis of massive genomic data. ACM/IEEE Great Lakes Symposium on VLSI - GLSVLSI 2012, Salt Lake City, May 2012.
  • Agathocleous M.,  Christodoulou G.,  Promponas V.,  Christodoulou C.,  Vassiliades V., and Antoniou A.. Protein Secondary Structure Prediction with Bidirectional Recurrent Neural Nets: Can Weight Updating for Each Residue Enhance Performance? Artificial Intelligence Applications and Innovations, IFIP Advances in Information and Communication Technology, 2010, Volume 339/2010, 128-137. [Publisher's website]
  • Nikos Nikolaou, Pantelis Sampaziotis, Marilena Aplikioti, Andreas Drakos, Ioannis Kirmitzoglou, Marina Argyrou, Nikos Papamarkos, Vasilis J. Promponas * "VeSTIS: A Versatile Semi-Automatic Taxon Identification System from Digital Images", in Nimis P. L., Vignes Lebbe R. (eds.), Tools for Identifying Biodiversity: Progress and Problems – pp. 231-236. ISBN 978-88-8303-295-0. EUT, 2010.
  • Vasilis J. Promponas * "A simple clustering approach for pathogenic strain identification based on local and global amino acid compositional signatures from genomic sequences: the Escherichia genus case" In Proceedings of the 9th International Conference on Information Technology and Applications in Biomedicine, ITAB 2009.  

Conference/Workshop abstracts    

Poster Presentations in International Conferences 

  • Tamana S, Kirmitzoglou I, and Promponas VJ. “Accessibility of Compositionally Biased Regions in PDB structures”. 19th International Conference on Intelligent Systems for Molecular Biology and 10th European Conference on Computational Biology, Vienna, Austria, 17-19/07/2011. 
  • Xenophontos M, Theodosiou A, Kirmitzoglou I, and Promponas VJ. “Evaluation of transmembrane helix (TMH) packing prediction methods on successive in sequence TMHs”. 19th International Conference on Intelligent Systems for Molecular Biology and 10th European Conference on Computational Biology, Vienna, Austria, 17-19/07/2011. 
  • Theodosiou A, and Promponas VJ. “LaTcOm: A web server for visualizing rare codon clusters”. 19th International Conference on Intelligent Systems for Molecular Biology and 10th European Conference on Computational Biology, Vienna, Austria, 17-19/07/2011. 
  • Hamodrakas SJ, Iliopoulos I, Ouzounis CA, Bagos PG, and Promponas VJ. “The Hellenic Society for Computational Biology and Bioinformatics”. 19th International Conference on Intelligent Systems for Molecular Biology and 10th European Conference on Computational Biology, Vienna, Austria, 17-19/07/2011. 
  • Kountouris P, Agathocleous M, Promponas VJ, Christodoulou G, Hadjicostas S, Vassiliades V, and Christodoulou C. “A comparative study on filtering protein secondary structure prediction”. 19th International Conference on Intelligent Systems for Molecular Biology and 10th European Conference on Computational Biology, Vienna, Austria, 17-19/07/2011. 
  • Agathocleous M, Kountouris P, Promponas VJ, Christodoulou G, Hadjicostas S, Vassiliades V, and Christodoulou C. “Training bidirectional recurrent neural networks with Conjugate gradient-type algorithms for protein secondary structure prediction”. 19th International Conference on Intelligent Systems for Molecular Biology and 10th European Conference on Computational Biology, Vienna, Austria, 17-19/07/2011.
  • Kirmitzoglou I and Promponas VJ. “On the quality of established datasets for benchmarking sequence database search and low-complexity handling tools: the ASTRAL compendium test case”. 17th International Conference on Intelligent Systems for Molecular Biology and 8th European Conference on Computational Biology, Stockholm, Sweden, 27/06-02/07/2009. 
  • Promponas VJ and Mytilineou E. “Comparative analysis of local compositional complecity in plant encoded proteins”. 17th International Conference on Intelligent Systems for Molecular Biology and 8th European Conference on Computational Biology, Stockholm, Sweden, 27/06-02/07/2009.
  • Kirmitzoglou I and Promponas VJ. “Effects of different masking strategies on protein sequence database searches with BLASTP”. 15th International Conference on Intelligent Systems for Molecular Biology and 6th European Conference on Computational Biology, Vienna, Austria, 21-25/07/2007.
  • Tsirigos C., Bagos P, Promponas VJ Hamodrakas SJ. “Enhancing Transmembrane β -Barrel Topology Prediction by Information Encoded in Multiple Sequence Alignments”. 5th European Conference on Computational Biology, Eilat, Israel, 21-24/01/2007.
  • Promponas VJ, Papanikolaou N, Iliopoulos I. “Conservation of genomic neighbourhood is related to the rate by which intraparalogous proteins evolve in two bacterial species”. 14th International Conference on Intelligent Systems for Molecular Biology, Fortaleza, Brazil, 06-10/08/2006. 
  • Promponas VJ, Limitsiou O. “Computational identification and analysis of paralogous gene families encoding α-helical transmembrane proteins in two complete bacterial genomes”, In silico analysis of proteins - celebrating the 20th anniversary of Swiss-Prot 20, Fortaleza, Brazil, 30/07-04/08/2006. 

Oral Presentations  

  • Nikolaou N, Sampaziotis P, Aplikioti M, Drakos A, Kirmitzoglou I, Argyrou M, Papamarkos N, Promponas VJ∗ . VeSTIS: A Versatile Semi-Automatic Taxon Identification System from Digital Images, 2010, In BioIdentify Conference, Tools for identifying biodiversity: progress and problems, National Mus´eum of Natural History, Paris.
  • Nikolaou N, Sampaziotis P, Aplikioti M, Drakos A, Kirmitzoglou I, Argyrou M, Papamarkos N, Promponas VJ∗ . An Open Source system for semi-automatic species identification from digital images, 2010, In the 5th Conference of the Hellenic Society for Computational Biology, Thraki Palace Hotel, Alexandroupolis. 
  • Promponas VJ and Hamodrakas SJ. Structural analysis and an instance-based learning approach for the prediction of tightly interacting, successive in sequence, transmembrane α-helices in polytopic transmembrane proteins, 2009, In the 4th Conference of the Hellenic Society for Computational Biology, NHRF, Athens.
  • Promponas VJ. “Browsing the proceedings of the HSCBB08 conference”, 2008, In the 1st National MikroBioKosmos Society Conference. MikroBioKosmos: Our Unexplored National Wealth, National Center of Scientific Research ”Demokritos”, Athens. 
  • Kirmitzoglou I, Mitilinaiou E, Promponas VJ. “Local compositional extremes in protein sequences: definitions, algorithms and biological relevance”, 2008, In the 3rd Conference of the Hellenic Society for Computational Biology, CERTH, Thessaloniki, Greece. 
  • Promponas VJ, Rodakis, GC, and Hamodrakas SJ. “A comprehensive study on the performance of progressive multiple sequence alignment methods based on reference alignment sets and phylogenetic criteria”, 2005, In the Proceedings of the 27th Annual Meeting of the Hellenic Society for Biological Sciences, Nafplio.
  • Promponas VJ, and Hamodrakas SJ. “Biologically Inspired Computations: Principles, Methods and Bioinformatics Applications”, 2004, In the Proceedings of the 26th Annual Meeting of the Hellenic Society for Biological Sciences, Volos. 
  • Promponas VJ, and Hamodrakas SJ. “Machine Learning Computational Techniques for protein Fold Class prediction solely from aminoacid sequence”, 2003, In the Proceedings of the 25th Annual Meeting of the Hellenic Society for Biological Sciences, Mytelene.
  • Promponas VJ, Pasquier C, and Hamodrakas SJ. “PRED-CLASS: Bioinformatics software for the classification of protein sequences: Genome-wide applications”, 2001, In the Proceedings of the 23rd Annual Meeting of the Hellenic Society for Biological Sciences, Chios. 
  • Pasquier C, Promponas VJ, Palaios GA, Hamodrakas JS, and Hamodrakas SJ. “PRED-TMR2: An hierarchical neural network to classify proteins as transmembrane and a novel method to predict transmembrane segments”, 1999, In the Proceedings of the 21st Annual Meeting of the Hellenic Society for Biological Sciences, Syros.
  • Promponas VJ, Palaios G, Pasquier, CM, Hamodrakas JS, and Hamodrakas SJ. “CoPreTHi: A program to combine the results of transmembrane protein segment prediction methods, freely available through the Internet”, 1998, In the Proceedings of the 20th Annual Meeting of the Hellenic Society for Biological Sciences, Samos.

Invited Presentations     

  • Promponas VJ et al. “Computing local and global descriptors for infering gene/genomic fuctional features in prokaryotes”, 27-30/9/2011, 15th Evolutionary Biology Meeting, Marseilles, France.
  • Promponas VJ “From protein sequence to structure and function”, 15/04/2011, in 1st Course in Next Generation Sequencing for Rare and Common Genetic Disorders, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.
  • Promponas VJ. “Sequence database search with compositionally biased amino acid sequences”, Second Workshop of the ERCIM Working Group on Computing and Statistics 29-31 October 2009, Grand Resort Hotel, Limassol, Cyprus.
  • Promponas VJ. “Computing Some Secrets of Life: Computational Biology and Bioinformatics Research in the BRL@UCY.AC.CY”. LinkSCEEM Meeting: High Performance Computing Applications in Life Sciences. 05/11/2009, Larnaca, Cyprus.
  • Promponas VJ. “Computational Biology and Bioinformatics Research at BRL@UCY.AC.CY”, 12/12/2008, National Hellenic Research Foundation, Athens.
  • Promponas VJ. “Biologically Inspired Computation: Selected Bioinformatics Applications”, at the ’Biologically Inspired Computation’ Workshop, Aristotle University of Thessaloniki, 19/12/2003.


by Dr. Radut.