David Hoksza, Ph.D.

hoksza<at>ksi.mff.cuni.cz
assistant professor

Research groups

Siret

Research topics

  • bioinformatics
  • structural bioinformatics
  • cheminformatics
  • protein and RNA databases

Teachingtop

CodeTitleLinks
NDBI007Data Organisation and Processing I
NDBI039Microsoft SQL Server Administration
NDBI042Data Visualization Techniques
NDBI044Algorithms, databases and tools in bioinformatics
NPRG045Individual Software Project
NPRG061Project in bioinformatics
NSWI122Dissertation Thesis Preparation

Ph.D. studentstop

Current: Petr Škoda, M.Sc.

Former: Radoslav Krivák, M.Sc.

Supervised thesestop

TitleStudentTypeStartedDefended
Web-based tool for RNA secondary structure visualizationJakub SaksaBS2017
Protein secondary structure prediction using deep neural networksMichal FilippiMS20172017
Development of web-based interface for visualization of protein-ligand interaction sites and their conservationLukáš JendeleBS20172017
Graph-based molecular representation and its utilization in virtual screeningAneta ŠťastnáBS20172017
(show all)

Research grantstop

  • Similarity Searching in Very Large Multimedia Databases (GACR 201/09/0683) 2009-2011 cooperant
  • Modern methods and applications of software engineering (GAUK SVV-2010-261312) 2010-2010 cooperant
  • Similarity Search in Biological Databases (GAUK 57907) 2007-2008 head investigator

Selected publications (complete list)top

  • [Journal (without IF)]Hoksza D., Svozil D.: Multiple 3D RNA Structure Superposition Using Neighbor Joining, in IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. PP, Num. 99, ISSN: 1545-5963, pp. nestránkováno, 2015 - text
  • Hoksza D., Škoda P.: 2D Pharmacophore Query Generation, in Lecture Notes in Computer Science, Zhangjiajie, China, Springer International Publishing, ISBN: 978-3-319-08170-0, ISSN: 0302-9743, pp. 289-300, 2014
  • Galgonek J., Kruliš M., Hoksza D.: On the Parallelization of the SProt Measure and the TM-score Algorithm, in Euro-Par 2012: Parallel Processing Workshops, Rhodes Island, Greece, Springer Berlin Heidelberg, ISBN: 978-3-642-36948-3, ISSN: 0302-9743, pp. 238-247, 2013
  • Galgonek J., Skopal T., Hoksza D.: P3S: Protein Structure Similarity Search, in Euro-Par 2012: Parallel Processing Workshops, Rhodes Islands, Greece, Springer Berlin Heidelberg, ISBN: 978-3-642-36948-3, ISSN: 0302-9743, pp. 228-237, 2013
  • Hoksza D., Szepe P., Svozil D.: MultiSETTER - Multiple RNA Structure Similarity Algorithm, in Advances in Bioinformatics and Computational Biology, Recife, Springer, ISBN: 978-3-319-02623-7, ISSN: 0302-9743, pp. 59-70, 2013
  • Škoda P., Hoksza D.: Chemical Space Visualization Using ViFrame, in 2013 IEEE/ACIS 12th International Conference on Computer and Information Science (ICIS), Niigata, Japan, IEEE, ISBN: 978-1-4799-0174-6, pp. 541-546, 2013
  • Cech P., Svozil D., Hoksza D.: SETTER: web server for RNA structure comparison, in NUCLEIC ACIDS RESEARCH, Vol. 40, Num. W1, ISSN: 0305-1048, pp. W42-W48, 2012
  • Hoksza D., Svozil D.: Efficient RNA pairwise structure comparison by SETTER method, in BIOINFORMATICS, Vol. 28, Num. 14, ISSN: 1367-4803, pp. 1858-1864, 2012
  • Novák J., Galgonek J., Hoksza D., Skopal T.: SimTandem: Similarity Search in Tandem Mass Spectra, in Lecture Notes in Computer Science, Vol. 2012, Num. 7404, ISSN: 0302-9743, pp. 242-243, 2012
  • Novák J., Skopal T., Hoksza D., Lokoč J.: Non-metric Similarity Search of Tandem Mass Spectra Including Posttranslational Modifications, in Journal of Discrete Algorithms, Vol. 2012, Num. 13, ISSN: 1570-8667, pp. 19-31, 2012 - On-line verze
  • Galgonek J., Hoksza D., Skopal T.: SProt: sphere-based protein structure similarity algorithm, in Proteome Science, Vol. 9, Num. Suppl. 1, ISSN: 1477-5956, pp. nestránkováno, 2011
  • Hoksza D., Svozil D.: Exploration of Chemical Space by Molecular Morphing, in Proceedings of the 2011 11th IEEE International Conference on Bioinformatics and Bioengineering (BIBE 2011), Taichung, Taiwan, IEEE Computer Society, ISBN: 978-0-7695-4391-8, pp. 201-208, 2011
  • Hoksza D., Svozil D.: SETTER - RNA SEcondary sTructure-based TERtiary Structure Similarity Algorithm, in Lecture Notes in Bioinformatics, Vol. 6674, Num. 5, ISSN: 0302-9743, pp. 37-48, 2011
  • Galgonek J., Hoksza D.: SProt - From Local to Global Protein Structure Similarity, in 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshop, Hong Kong, China, IEEE, ISBN: 978-1-4244-8302-0, pp. 124-129, 2010 - článek v PDF
  • Hoksza D., Galgonek J.: Alignment-Based Extension to DDPIn Feature Extraction, in International Journal of Computational Bioscience, Vol. 1, Num. 1, ISSN: 1918-3909, pp. 79-87, 2010 - článek v PDF
  • Hoksza D.: DDPIn - Distance and Density Based Protein Indexing, in 2009 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, Nashville, Tennessee, USA, IEEE, ISBN: 978-1-4244-2756-7 , pp. 1-8, March 2009
  • Hoksza D., Galgonek J.: Density-Based Classification of Protein Structures Using Iterative TM-score, in 2009 IEEE International Conference on Bioinformatics and Biomedicine Workshops, Wahsington, D.C., USA, IEEE, ISBN: 978-1-4244-5121-0, pp. 87-93, 2009
  • Hoksza D.: Improved Alignment of Protein Sequences Based on Common Parts, in ISBRA 2008: Bioinformatics Research and Applications, Atlanta, GA, USA, Springer, ISBN: 978-3-540-79449-3, pp. 87-99, May 2008
  • Hoksza D., Skopal T.: Native Multidimensional Indexing in Relational Databases, in COMAD 2008, Bombay, India, Computer Society of India, ACM SIGMOD online, ISBN: 978-81-8424-370-3, pp. 251-261, December 2008
  • Skopal T., Hoksza D.: Improving the Performance of M-tree Family by Nearest-Neighbor Graphs, in 11th East-European Conference on Advances in Databases and Information Systems ADBIS 2007, Springer, ISBN: 978-3-540-75184-7, ISSN: 0302-9743, pp. 172-188, 2007
  • Skopal T., Hoksza D., Pokorný J.: Construction of Tree-based Indexes for Level-Contiguous Buffering Support, in 13th International Conference on Database Systems for Advance Applications, New Delhi, India, Springer, ISBN: 978-3-540-78567-5, ISSN: 0302-9743, pp. 361-373, March 2007

Software

Molpher, P3S, PGRTree, SETTER

Contactstop

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