David Hoksza, Ph.D.

assistant professor

Research groups


Research topics

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


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

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
Using tree edit distance to model structural similarity of RNA moleculesTomáš HromadaMS20172017
Utilizing simulated annealing for molecular fingerprints optimization for virtual screeningAdam FilandrBS20172017
Utilization of latent semantic analysis in virtual screeningJiří KolářBS20162017
Application for monitoring and analysis of vascular reconstructionsJan DrozenMS20162016
Machine learning-based identification of separating features in molecular fragmentsAakash RaviBS20152017
Template-based RNA tertiary structure predictionRastislav GalvánekBS20152016
Utiliziation of uncorrelated multi-point pharmacophores in virtual screeningOndřej MičkaBS20152016
Hierarchical visualization of the chemical spaceJakub VelkoborskýMS20152016
RNA secondary structure conservation identification module for rPredictorJan PešekMS20152015
Database prediction of small molecules side effectsMichal KrkavecMS2014
RNA secondary structure visualization using existing structuresRichard EliášBS20142016
Representation of chemical compounds and its utilization in similarity searchPetr ŠkodaPh.D.2014
Artificial intelligence module – Expert system for differential and predictive diagnosticsJiří KorchňákMS2013
Efficient molecular representation designPetr ŠkodaMS20132014
Exploratin of chemical and protein space structureRadoslav KrivákPh.D.2013
Atomix for Microsoft Kinect for WindowsVladimír MachMS20132014
DEBRA - Derscriptor BarnKhanh Chuong LeBS20132013
Algorithm for true positives identification of protein-ligand complexesJakub ZáhumenskýMS2013
BiobankTomáš PolákBS20132013
Visual Querying in Chemical Databases using SMARTS PatternsVojtěch ŠípekBS20132014
Data Generator for Microsoft SQL ServerJan DrozenBS20122013
Scaffold hopping-based exploration of chemical spaceMarek MikešMS20122014
Visualisation of secondary structure of RNA moleculesTomáš KadlecBS20122013
Multiple RNA Structure SimilarityPeter SzépeMS20112013
Visualization of the Chemical SpacePetr ŠkodaBS20112012
Munis InstantLukáš TomasyBS20112011
Importing simple-structured data into DBFrantišek HaškoBS2010
IS for organizaton's production monitoringTomáš DzurenkoBS20102011
Protein Structure Similarity Using Genetic ProgrammingMiroslav ŠiagiBS20102013
RNA Secondary Structure PredictionRobert GoldweinMS2009
GroupeasMiroslav HrivíkBS20092010
WESNA - program for creation html presentations with php componentsJiří MizeraBS20092010
Oracle Visual ToolsEva OndráškováBS20092009
Oracle Visual ToolsEva OndráškováBS20092010
PExplorer (Protein Explorer) - Supporting Library for Proteins' ManipulationsEvžen ŠindelářBS2009
Database of students and their paymentsMarie KonárováBS20082009
Internal IS for travel agencyPavel SelementBS20072009
Internal IS for travel agencyPavel SelementBS20072010
Visual Graph ToolAleš VýmolaBS2007

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


Molpher, P3S, PGRTree, SETTER


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