Browsing by Author "Promponas, Vasilis J."

Now showing items 21-35 of 35

    • Article  

      An intrinsically disordered proteins community for ELIXIR 

      Davey, Norman E.; Babu, M. Madan; Blackledge, Martin; Bridge, Alan; Capella-Gutierrez, Salvador; Dosztanyi, Zsuzsanna; Drysdale, Rachel; Edwards, Richard J.; Elofsson, Arne; Felli, Isabella C.; Gibson, Toby J.; Gutmanas, Aleksandras; Hancock, John M.; Harrow, Jen; Higgins, Desmond; Jeffries, Cy M.; Le Mercier, Philippe; Mészáros, Balint; Necci, Marco; Notredame, Cedric; Orchard, Sandra; Ouzounis, Christos A.; Pancsa, Rita; Papaleo, Elena; Pierattelli, Roberta; Piovesan, Damiano; Promponas, Vasilis J.; Ruch, Patrick; Rustici, Gabriella; Romero, Pedro; Sarntivijai, Sirarat; Saunders, Gary; Schuler, Benjamin; Sharan, Malvika; Shields, Denis C.; Sussman, Joel L.; Tedds, Jonathan A.; Tompa, Peter; Turewicz, Michael; Vondrasek, Jiri; Vranken, Wim F.; Wallace, Bonnie Ann; Wichapong, Kanin; Tosatto, Silvio C. E. (2019)
      Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) are now recognised as major determinants in cellular regulation. This white paper presents a roadmap for future e-infrastructure developments ...
    • Article  

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

      Kirmitzoglou, Ioannis K.; Promponas, Vasilis J. (2015)
    • Article  

      LiSIs: An online scientific workflow system for virtual screening 

      Kannas, Christos C.; Kalvari, Ioanna; Lambrinidis, George; Neophytou, Christiana M.; Savva, Christiana G.; Kirmitzoglou, Ioannis K.; Antoniou, Zinonas C.; Achilleos, Kleo G.; Scherf, D.; Pitta, Chara A.; Nicolaou, Christos A.; Mikros, Emmanuel; Promponas, Vasilis J.; Gerhauser, C.; Mehta, R. G.; Constantinou, Andreas I.; Pattichis, Constantinos S. (2015)
      Modern methods of drug discovery and development in recent years make a wide use of computational algorithms. These methods utilise Virtual Screening (VS), which is the computational counterpart of experimental screening. ...
    • Article  

      LiSIs: An online scientific workflow system for virtual screeningAAA 

      Kannas, Christos C.; Kalvari, Ioanna; Lambrinidis, George; Neophytou, Christiana M.; Savva, Christiana G.; Kirmitzoglou, Ioannis K.; Antoniou, Zinonas C.; Achilleos, Kleo G.; Scherf, D.; Pitta, Chara A.; Nicolaou, Christos A.; Mikros, Emmanuel; Promponas, Vasilis J.; Gerhauser, C.; Mehta, R. G.; Constantinou, Andreas I.; Pattichis, Constantinos S. (2015)
      Modern methods of drug discovery and development in recent years make a wide use of computational algorithms. These methods utilise Virtual Screening (VS), which is the computational counterpart of experimental screening. ...
    • Conference Object  

      Open source workflow systems in life sciences informatics 

      Achilleos, Kleo G.; Kannas, Christos C.; Nicolaou, Christos A.; Pattichis, Constantinos S.; Promponas, Vasilis J. (2012)
      A simple yet powerful programming tool enabling in silico experimentation, end-to-end data management through web services as well as use of grid and cloud processing power is scientific workflows. This technology is ...
    • Article  

      Protein secondary structure prediction with bidirectional recurrent neural nets: Can weight updating for each residue enhance performance? 

      Agathocleous, Michalis; Christodoulou, Georgia; Promponas, Vasilis J.; Christodoulou, Chris C.; Vassiliades, Vassilis; Antoniou, Antonis (2010)
      Successful protein secondary structure prediction is an important step towards modelling protein 3D structure, with several practical applications. Even though in the last four decades several PSSP algorithms have been ...
    • Article  

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

      Panayidou, Stavria; Georgiades, Kaliopi; Christofi, Theodoulakis; Tamana, Stella; Promponas, Vasilis J.; Apidianakis, Yiorgos (2020)
      To assess the role of core metabolism genes in bacterial virulence - independently of their effect on growth - we correlated the genome, the transcriptome and the pathogenicity in flies and mice of 30 fully sequenced ...
    • Article  

      Sequence evidence for common ancestry of eukaryotic endomembrane coatomers 

      Promponas, Vasilis J.; Katsani, K. R.; Blencowe, B. J.; Ouzounis, Christos A. (2016)
      Eukaryotic cells are defined by compartments through which the trafficking of macromolecules is mediated by large complexes, such as the nuclear pore, transport vesicles and intraflagellar transport. The assembly and ...
    • Article  

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

      Ioannou, Androulla; Fokianos, Konstantinos; Promponas, Vasilis J. (2010)
      We compare several spectral domain based clustering methods for partitioning protein sequence data. The main instrument for this exercise is the spectral density ratio model, which specifies that the logarithmic ratio of ...
    • Article  

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

      Tørresen, Ole K.; Star, Bastiaan; Mier, Pablo; Andrade-Navarro, Miguel A.; Bateman, Alex; Jarnot, Patryk; Gruca, Aleksandra; Grynberg, Marcin; Kajava, Andrey V.; Promponas, Vasilis J.; Anisimova, Maria; Jakobsen, Kjetill S.; Linke, Dirk (2019)
      Abstract. The widespread occurrence of repetitive stretches of DNA in genomes of organisms across the tree of life imposes fundamental challenges for sequencin
    • Article  

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

      Kirschel, A. N. G.; Cody, M. L.; Harlow, Z. T.; Promponas, Vasilis J.; Vallejo, E. E.; Taylor, C. E. (2011)
      The ability to monitor interactions between individuals over time can provide us with information on life histories, mating systems, behavioural interactions between individuals and ecological interactions with the ...
    • Article  

      Training bidirectional recurrent neural network architectures with the scaled conjugate gradient algorithm 

      Agathocleous, Michalis; Christodoulou, Chris C.; Promponas, Vasilis J.; Kountouris, P.; Vassiliades, Vassilis (2016)
      Predictions on sequential data, when both the upstream and downstream information is important, is a difficult and challenging task. The Bidirectional Recurrent Neural Network (BRNN) architecture has been designed to deal ...
    • Article  

      An updated view of the oligosaccharyltransferase complex in Plasmodium 

      Tamana, Stella; Promponas, Vasilis J. (2019)
      Abstract. Despite the controversy regarding the importance of protein N-linked glycosylation in species of the genus Plasmodium, genes potentially encoding cor
    • Conference Object  

      Welcome address 

      Bourbakis, Nikolaos G.; Pattichis, Constantinos S.; Schneider, R.; Kyriacou, Efthyvoulos C.; Andrade, M.; Promponas, Vasilis J.; Schizas, Christos N. (2012)
      Conference proceedings front matter may contain various advertisements, welcome messages, committee or program information, and other miscellaneous conference information. This may in some cases also include the cover art, ...
    • Conference Object  

      A workflow system for virtual screening in cancer chemoprevention 

      Kannas, Christos C.; Achilleos, Kleo G.; Antoniou, Zinonas C.; Nicolaou, Christos A.; Pattichis, Constantinos S.; Kalvari, Ioanna; Kirmitzoglou, Ioannis K.; Promponas, Vasilis J. (2012)
      Computer-aided drug discovery techniques have been widely used in recent years to support the development of new pharmaceuticals. Virtual screening, the computational counterpart of experimental screening, attempts to ...