All Stories

  1. The bioinformatics wealth of nations

    Article • Bioinformatics, March 2020, Oxford University Press (OUP)

    Dr Vasilis J Promponas

  2. Establishment of computational biology in Greece and Cyprus: Past, present, and future

    Article • PLoS Computational Biology, December 2019, PLOS

    Dr Nikos C Kyrpides, Dr Vasilis J Promponas

  3. Pseudomonas aeruginosa core metabolism exerts a widespread growth-independent control on virulence

    Article • November 2019, Cold Spring Harbor Laboratory Press

    Dr Vasilis J Promponas

  4. DisProt: intrinsic protein disorder annotation in 2020

    Article • Nucleic Acids Research, November 2019, Oxford University Press (OUP)

    Dr Vasilis J Promponas, Dr Sandra Macedo-Ribeiro

  5. An intrinsically disordered proteins community for ELIXIR

    Article • F1000Research, October 2019, Faculty of 1000, Ltd.

    Cy Jeffries, Wim Vranken, Richard Edwards, Dr Vasilis J Promponas, Roberta Pierattelli, Dr John M Hancock

  6. Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases

    Article • Nucleic Acids Research, October 2019, Oxford University Press (OUP)

    Dr Vasilis J Promponas

  7. Low complexity regions in the proteins of prokaryotes perform important functional roles and are highly conserved

    Article • Nucleic Acids Research, September 2019, Oxford University Press (OUP)

    Dr Vasilis J Promponas

  8. An updated view of the oligosaccharyltransferase complex in Plasmodium

    Article • Glycobiology, March 2019, Oxford University Press (OUP)

    Dr Vasilis J Promponas

  9. Hypothesis, analysis and synthesis, it's all Greek to me

    Article • eLife, February 2019, eLife

    Dr Vasilis J Promponas, Antoine Danchin

  10. Convolutional Neural Networks in Combination with Support Vector Machines for Complex Sequential Data Classification

    Article • January 2018, Springer Science + Business Media

    Dr Vasilis J Promponas

  11. A fragment of the alarmin prothymosin α as a novel biomarker in murine models of bacteria-induced sepsis

    Article • Oncotarget, May 2017, Impact Journals, LLC

    Dr Vasilis J Promponas

  12. Functional characterisation of long intergenic non-coding RNAs through genetic interaction profiling in Saccharomyces cerevisiae

    Article • BMC Biology, December 2016, Springer Science + Business Media

    Dr Vasilis J Promponas

  13. iLIR database: A web resource for LIR motif-containing proteins in eukaryotes

    Article • Autophagy, August 2016, Taylor & Francis

    Dr Vasilis J Promponas

  14. Sequence evidence for common ancestry of eukaryotic endomembrane coatomers

    Article • Scientific Reports, March 2016, Springer Science + Business Media

    Dr Vasilis J Promponas

  15. Erratum

    Article • Autophagy, February 2016, Taylor & Francis

    Dr Janos KristonVizi, Juan Segura-Aguilar, Professor Nektarios Tavernarakis, Dr Reinhard Dechant, Dr Vasilis J Promponas, Professor Marc Lecuit, Professor Paula I. Moreira, Professor Mark Cragg, Executive Director, The Hormel Institute Robert Clarke, Dr Eleonora García Véscovi, Professor Jean-François Beaulieu, Shile Huang, Maria João Sousa

  16. Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

    Article • Autophagy, January 2016, Taylor & Francis

    Professor CIRO ISIDORO, Dr Akira Matsuura, Prof Hirokazu Arimoto, Professor Marc Diederich, Maria Vaccaro, Professor Abdel Halim Harrath, Professor Hyun Kyu Song, Dr Takeshi Noda, Dr Regina Menezes, Dr Janos KristonVizi, Cristina Muñoz-Pinedo, Professor Nektarios Tavernarakis, Juan Segura-Aguilar, Professor Marc Lecuit, Leonardo Travassos, Prof Robert Bryson-Richardson, Isabelle Dugail, PD Dipl.-Ing. Dr. techn. Werner J Kovacs, Dr Luca Galluzzi, Dr Reinhard Dechant, Dr. Sandra Moreno, Maurizio Molinari, Dr Vasilis J Promponas, Professor Günther Weindl, Dr Marc Etienne Poirot, Professor Paula I. Moreira, Maria João Sousa, Dr Janna Morrison, Professor Mark Cragg, Executive Director, The Hormel Institute Robert Clarke, Dr Eleonora García Véscovi, Paula Ludovico, Professor Jean-François Beaulieu, Shile Huang

  17. Training Bidirectional Recurrent Neural Network Architectures with the Scaled Conjugate Gradient Algorithm

    Article • January 2016, Springer Science + Business Media

    Dr Vasilis J Promponas

  18. H3ABioNet computational metagenomics workshop in Mauritius: training to analyse microbial diversity for Africa

    Article • Standards in Genomic Sciences, December 2015, Springer Science + Business Media

    Dr Vasilis J Promponas

  19. Annotation inconsistencies beyond sequence similarity-based function prediction – phylogeny and genome structure

    Article • Standards in Genomic Sciences, November 2015, Springer Science + Business Media

    Dr Vasilis J Promponas

  20. Sequence evidence for common ancestry of eukaryotic endomembrane coatomers

    Article • June 2015, Cold Spring Harbor Laboratory Press

    Dr Vasilis J Promponas

  21. LiSIs: An Online Scientific Workflow System for Virtual Screening

    Article • Combinatorial Chemistry & High Throughput Screening, April 2015, Bentham Science Publishers

    Dr Vasilis J Promponas

  22. LCR-eXXXplorer: a web platform to search, visualize and share data for low complexity regions in protein sequences

    Article • Bioinformatics, February 2015, Oxford University Press (OUP)

    Dr Vasilis J Promponas

  23. BioTextQuest+: a knowledge integration platform for literature mining and concept discovery

    Article • Bioinformatics, February 2015, Oxford University Press (OUP)

    Dr Vasilis J Promponas

  24. BioTextQuest + : a knowledge integration platform for literature mining and concept discovery

    Article • Bioinformatics, August 2014, Oxford University Press (OUP)

    Dr Vasilis J Promponas

  25. Editorial: Intelligent Biomedical Systems

    Article • International Journal on Artificial Intelligence Tools, May 2014, World Scientific Pub Co Pte Lt

    Dr Vasilis J Promponas

  26. Guest Editorial: Computational Solutions to Large-Scale Data Management and Analysis in Translational and Personalized Medicine

    Article • IEEE Journal of Biomedical and Health Informatics, May 2014, Institute of Electrical & Electronics Engineers (IEEE)

    Dr Vasilis J Promponas

  27. Functional Genomics Evidence Unearths New Moonlighting Roles of Outer Ring Coat Nucleoporins

    Article • Scientific Reports, April 2014, Springer Science + Business Media

    Christos Karapiperis, Dr Vasilis J Promponas

  28. iLIR

    Article • Autophagy, February 2014, Taylor & Francis

    Dr Vasilis J Promponas

  29. Reconfiguring the Bioinformatics Computational Spectrum: Challenges and Opportunities of FPGA-Based Bioinformatics Acceleration Platforms

    Article • IEEE Design and Test, February 2014, Institute of Electrical & Electronics Engineers (IEEE)

    Dr Vasilis J Promponas

  30. Biological Information Extraction and Co-occurrence Analysis

    Article • January 2014, Springer Science + Business Media

    Dr Vasilis J Promponas

  31. Development of an ELISA for the quantification of the C-terminal decapeptide prothymosin α(100–109) in sera of mice infected with bacteria

    Article • Journal of Immunological Methods, September 2013, Elsevier

    Dr Vasilis J Promponas, Evangelia Livaniou

  32. GPU technology as a platform for accelerating local complexity analysis of protein sequences

    Article • July 2013, Institute of Electrical & Electronics Engineers (IEEE)

    Dr Vasilis J Promponas

  33. FPGA-based hardware acceleration for local complexity analysis of massive genomic data

    Article • Integration, June 2013, Elsevier

    Dr Vasilis J Promponas

  34. MEETING REPORT: THE SEVENTH CONFERENCE OF THE HELLENIC SOCIETY FOR COMPUTATIONAL BIOLOGY AND BIOINFORMATICS

    Article • Computational and Structural Biotechnology Journal, March 2013, Elsevier

    Pantelis Bagos, Dr Vasilis J Promponas

  35. Experimental evidence validating the computational inference of functional associations from gene fusion events: a critical survey

    Article • Briefings in Bioinformatics, December 2012, Oxford University Press (OUP)

    Dr Vasilis J Promponas

  36. Opportunities from the use of FPGAs as platforms for bioinformatics algorithms

    Article • November 2012, Institute of Electrical & Electronics Engineers (IEEE)

    Dr Vasilis J Promponas

  37. Sequence features of Compositionally Biased regions in three dimensional protein structures

    Article • November 2012, Institute of Electrical & Electronics Engineers (IEEE)

    Dr Vasilis J Promponas

  38. A workflow system for virtual screening in cancer chemoprevention

    Article • November 2012, Institute of Electrical & Electronics Engineers (IEEE)

    Dr Vasilis J Promponas

  39. Open source workflow systems in life sciences informatics

    Article • November 2012, Institute of Electrical & Electronics Engineers (IEEE)

    Dr Vasilis J Promponas

  40. [Front matter]

    Article • November 2012, Institute of Electrical & Electronics Engineers (IEEE)

    Dr Vasilis J Promponas

  41. The Chlamydiales Pangenome Revisited: Structural Stability and Functional Coherence

    Article • Genes, May 2012, MDPI AG

    Dr Fotis E. Psomopoulos, Dr Vasilis J Promponas

  42. A Comparative Study on Filtering Protein Secondary Structure Prediction

    Article • IEEE/ACM Transactions on Computational Biology and Bioinformatics, May 2012, Institute of Electrical & Electronics Engineers (IEEE)

    Dr Vasilis J Promponas

  43. Towards systolic hardware acceleration for local complexity analysis of massive genomic data

    Article • January 2012, ACM (Association for Computing Machinery)

    Dr Vasilis J Promponas

  44. LaTcOm: a web server for visualizing rare codon clusters in coding sequences

    Article • Bioinformatics, December 2011, Oxford University Press (OUP)

    Dr Vasilis J Promponas

  45. BioTextQuest: a web-based biomedical text mining suite for concept discovery

    Article • Bioinformatics, October 2011, Oxford University Press (OUP)

    Dr Vasilis J Promponas

  46. Biological applications of time series frequency domain clustering

    Article • Journal of Time Series Analysis, September 2011, Wiley

    Dr Vasilis J Promponas

  47. Territorial dynamics of Mexican Ant-thrushes Formicarius moniliger revealed by individual recognition of their songs

    Article • Ibis, February 2011, Wiley

    Dr Vasilis J Promponas

  48. Spectral density ratio based clustering methods for the binary segmentation of protein sequences: A comparative study

    Article • Biosystems, May 2010, Elsevier

    Dr Vasilis J Promponas

  49. Protein Secondary Structure Prediction with Bidirectional Recurrent Neural Nets: Can Weight Updating for Each Residue Enhance Performance?

    Article • January 2010, Springer Science + Business Media

    Dr Vasilis J Promponas

  50. A simple clustering approach for pathogenic strain identification based on local and global amino acid compositional signatures from enomic sequences: the Escherichia genus case

    Article • November 2009, Institute of Electrical & Electronics Engineers (IEEE)

    Dr Vasilis J Promponas

  51. 2nd Combined Working Group and Management Committee Meeting of Urine and Kidney Proteomics COST Action 29-30 March 2009, Nafplio, Greece

    Article • PROTEOMICS - CLINICAL APPLICATIONS, August 2009, Wiley

    prof alberto ortiz , Dr Vasilis J Promponas, Gian Marco Ghiggeri

  52. Gene socialization: gene order, GC content and gene silencing in Salmonella

    Article • BMC Genomics, January 2009, Springer Science + Business Media

    Dr Vasilis J Promponas

  53. Clustering of biological time series by cepstral coefficients based distances

    Article • Pattern Recognition, July 2008, Elsevier

    Dr Vasilis J Promponas

  54. PRED-GPCR: GPCR recognition and family classification server

    Article • Nucleic Acids Research, July 2004, Oxford University Press (OUP)

    Pantelis Bagos, Panagiotis Papasaikas, Dr Vasilis J Promponas

  55. Evaluation of annotation strategies using an entire genome sequence

    Article • Bioinformatics, April 2003, Oxford University Press (OUP)

    Dr Vasilis J Promponas

  56. Article • BMC Bioinformatics, January 2003, Springer Science + Business Media

    Dr Vasilis J Promponas

  57. PRED-CLASS: Cascading neural networks for generalized protein classification and genome-wide applications

    Article • Proteins Structure Function and Bioinformatics, January 2001, Wiley

    Dr Vasilis J Promponas

  58. CAST: an iterative algorithm for the complexity analysis of sequence tracts

    Article • Bioinformatics, October 2000, Oxford University Press (OUP)

    Dr Vasilis J Promponas

  59. Reproducibility in genome sequence annotation: the Plasmodium falciparum chromosome 2 case

    Article • FEBS Letters, May 1999, Wiley

    Dr Vasilis J Promponas