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Curriculum Vitae

e-mail:   galgonek (at) ksi (dot) mff (dot) cuni (dot) cz
www: http://siret.cz/galgonek

  • Ph.D. degree in Computer Science (2012)
    Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic
    thesis: Similarity Search in Protein Structure Databases
    supervisor: Tomáš Skopal
    consultant: David Hoksza
  • Master degree in Computer Science (2008)
    Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic
    thesis: Query Languages for the Semantic Web
    supervisor: Jakub Yaghob
  • databases : metric indexing, non-metric indexing
  • bioinformatics : structural bioinformatics, protein structure databases, rna sequence and structure databases
  • cheminformatics : chemical databases

Lecturer (2009 - 2011)
Department of Software Engineering
Faculty of Mathematics and Physics

Charles University in Prague

Lecturer (2009 - 2010)
Department of Computer Science and Mathematics
The University of Finance and Administration

Similarity retrieval in protein structure databases
AG Porto, Institute for Theoretical Physics, University of Cologne, 9.1. - 9.4.2012
funded by the Federation of European Biochemical Societies (FEBS)

D. Hoksza, J. Galgonek. Alignment-Based Extension to DDPIn Feature Extraction, International Journal of Computational Bioscience, Acta Press, (1), ISSN: 1918-3909, 2010
D. Hoksza, J. Galgonek. Density-Based Classification of Protein Structures Using Iterative TM-score, CSBW 2009 (workshop at BIBM 2009), IEEE, ISBN: 978-1-4244-5121-0, 2009
J. Galgonek, D. Hoksza. On Metric Approximations of the SProt Measure, SISAP 2011: Fourth International Conference on Similarity Search and Applications, ACM, ISBN: 978-1-4503-0795-6, 2011
J. Galgonek, D. Hoksza. On the Effectiveness of Distances Measuring Protein Structure Similarity, SISAP 2009: Second international workshop on similarity search and applications, IEEE, ISBN: 978-0-7695-3765-8, 2009
J. Galgonek, M. Kruliš, D. Hoksza. On the Parallelization of the SProt Measure and the TM-score Algorithm, 3rd International Workshop on High Performance Bioinformatics and Biomedicine (HiBB), Lecture Notes in Computer Science, Springer, 7640 , ISSN: 0302-9743, 2013
J. Galgonek, T. Skopal, D. Hoksza. P3S: Protein Structure Similarity Search, 3rd International Workshop on High Performance Bioinformatics and Biomedicine (HiBB), Lecture Notes in Computer Science, Springer, 7640 , ISSN: 0302-9743, 2013
J. Novák, T. Skopal, D. Hoksza, J. Lokoč, J. Galgonek. Protein Sequences Identification using NM-tree, SISAP, ACM, ISBN: 978-1-4503-0795-6, 2011
J. Galgonek. Query languages for the Semantic web, , , 2008
J. Novák, J. Galgonek, D. Hoksza, T. Skopal. SimTandem: Similarity Search in Tandem Mass Spectra, SISAP, Springer, LNCS 7404 , 2012
J. Galgonek, T. Knap, M. Kruliš, M. Nečaský. SMILE - A Framework for Semantic Applications, On the Move to Meaningful Internet Systems Workshops, Springer, ISBN: 978-3-642-16960-1, 2010
J. Galgonek, D. Hoksza. SProt - From Local to Global Protein Structure Similarity, BIBM'10 International Workshop on Computational Proteomics, IEEE, ISBN: 978-1-4244-8302-0, 2010
J. Galgonek, D. Hoksza, T. Skopal. SProt: sphere-based protein structure similarity algorithm, Proteome Science, BioMed Central, 9(Supplment 1), ISSN: 1477-5956, 2011
J. Galgonek. Tequila - a query language for the Semantic Web, DATESO 2009, Czech Technical University in Prague, ISBN: 978-80-01-04323-3, ISSN: 1613-0073, 2009
  • member of SIRET Research Group
  • member of CSBMB (Czech Society For Biochemistry and Molecular Biology)
  • member of FOBIA (Czech Free & Open BioInformatic Association)

Charles University in Prague, Prague, Czech Republic
Lecturer (2009 – 2011)

  • Data organisation and processing I
  • Data organisation and processing II

The University of Finance and Administration, Prague, Czech Rebpulic
Lecturer (2009 – 2010)

  • Introduction to Unix

Programming Languages:

  • C, C++, Java, UNIX shell scripting, Fortran, R

Frameworks:

  • CORBA, GWT, RDF, Jena