Publications

2016 2015 2014 2013 2012 2011 2010 2009 2008 2007

2016

Refereed (journals/proceedings) (8)

  • [Journal (without IF)]Eliáš R., Hoksza D.: RNA Secondary Structure Visualization Using Tree Edit Distance, in International Journal of Bioscience, Biochemistry and Bioinformatics, Vol. 6, Num. 1, ISSN: 2010-3638, pp. 9-17, 2016 - text
  • Galvánek R., Hoksza D., Pánek J.: Template-based prediction of RNA tertiary structure, in 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Shenzhen, China, IEEE, ISBN: 978-1-5090-1610-5, pp. 1897-1900, 2016
  • Hoksza D., Jelínek J.: Using Neo4j for mining protein graphs: a case study, in 2015 26th International Workshop on Database and Expert Systems Applications (DEXA), Valencia, IEEE, ISBN: 978-1-4673-7581-8, ISSN: 1529-4188, pp. 230-234, 2016 - text
  • Hoksza D., Škoda P.: Using Bayesian Modeling on Molecular Fragments Features for Virtual Screening, in 2016 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), Chiang Mai, Thailand, IEEE, ISBN: 978-1-4673-9472-7, pp. nestránkováno, 2016
  • Jelínek J., Hoksza D., Škoda P.: Utilizing knowledge base of amino acids structural neighborhoods to predict protein-protein interaction sites, in 2016 IEEE 6th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), Atlanta, GA, USA, IEEE, ISBN: 978-1-5090-4199-2, pp. nestránkováno, 2016
  • [Journal (without IF)]Pešek J., Hoksza D.: Large RNA secondary structure conservation annotation using secondary structure-based MSA, in International Journal of Bioscience, Biochemistry and Bioinformatics, Vol. 6, Num. 1, ISSN: 2010-3638, pp. 18-25, 2016 - text
  • Škoda P., Hoksza D.: Benchmarking Platform for Ligand-Based Virtual Screening, in 2016 IEEE International Conference on Bioinformatics and Biomedicine, Shenzhen, IEEE (The Institute of Electrical and Electronics Engineers), ISBN: 978-1-5090-1611-2, pp. 1225-1232, 2016 - text
  • [Journal (without IF)]Velkoborský J., Hoksza D.: Scaffold analysis of PubChem database as background for hierarchical scaffold-based visualization, in Journal of Cheminformatics, Vol. 8, Num. 12, ISSN: 1758-2946, pp. nestránkováno, 2016

2015

Refereed (journals/proceedings) (6)

  • [IF Journal]Čech P., Hoksza D., Svozil D.: MultiSETTER: web server for multiple RNA structure comparison, in BMC BIOINFORMATICS, Vol. 16, Num. 1, ISSN: 1471-2105, pp. 1-8, 2015 - text
  • [IF Journal]Hoksza D., Krivák R.: Improving protein-ligand binding site prediction accuracy by classification of inner pocket points using local features, in Journal of Cheminformatics, Vol. 7, Num. 12, ISSN: 1758-2946, pp. 1-13, 2015 - text
  • [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
  • Krivák R., Hoksza D.: P2RANK: knowledge-based ligand binding site prediction using aggregated local features, in Algorithms for Computational Biology, Mexico City, Mexico, Springer International Publishing, ISBN: 978-3-319-21232-6, ISSN: 0302-9743, pp. 41-52, 2015 - text
  • Šícho M., Hoksza D., Svozil D.: Activity-driven exploration of chemical space with morphing, in Bioinformatics and Biomedicine (BIBM), 2015 IEEE International Conference on, Washington, DC, IEEE, ISBN: 978-1-4673-6798-1, pp. 1024-1031, 2015 - text
  • Škoda P., Hoksza D.: Exploration of topological torsion fingerprints, in 2015 IEEE International Conference on Bioinformatics and Biomedicine, Washington DC, IEEE (The Institute of Electrical and Electronics Engineers), ISBN: 978-1-4673-6799-8, pp. 822-828, 2015 - text

2014

Refereed (journals/proceedings) (4)

  • 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
  • Hoksza D., Škoda P.: Scaffold-based chemical space exploration, in Bioinformatics and Biomedicine (BIBM), 2014 IEEE International Conference on, Belfast, UK, IEEE, ISBN: 978-1-4799-5669-2, pp. 1-3, 2014
  • Pánek J., Hajič J., Hoksza D.: Template-based prediction of ribosomal RNA secondary structure, in Bioinformatics and Biomedicine (BIBM), 2014 IEEE International Conference on, Belfast, UK, IEEE, ISBN: 978-1-4799-5669-2, pp. 17-20, 2014
  • Škoda P., Hoksza D.: Target-Oriented Generic Fingerprint-Based Molecular Representation, in Computer Science & Information Technology, Sydney, Australia, AIRCC Publishing, ISBN: 978-1-921987-18-2, pp. 231-244, 2014

2013

Refereed (journals/proceedings) (7)

  • 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
  • Hoksza D., Škoda P., Vorsilak M., Svozil D.: Molpher: a software framework for systematic chemical space exploration, in Journal of Cheminformatics, Vol. 6, Num. 1, ISSN: 1758-2946, pp. nestránkováno, 2013
  • Novák J., Sachsenberg T., Hoksza D., Skopal T., Kohlbacher O.: A Statistical Comparison of SimTandem with State-of-the-Art Peptide Identification Tools, in Advances in Intelligent Systems and Computing, Vol. 2013, Num. 222, ISSN: 1867-5662, pp. 101-109, 2013
  • Novák J., Sachsenberg T., Hoksza D., Skopal T., Kohlbacher O.: On Comparison of SimTandem with State-of-the-Art Peptide Identification Tools, Efficiency of Precursor Mass Filter and Dealing with Variable Modifications, in Journal of Integrative Bioinformatics, Vol. 2013, Num. 10/3, ISSN: 1613-4516, pp. nestránkováno, 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

2012

Refereed (journals/proceedings) (5)

  • 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., Hoksza D., Lokoč J., Skopal T.: On Optimizing the Non-metric Similarity Search in Tandem Mass Spectra by Clustering, in Lecture Notes in Computer Science, Vol. 2012, Num. 7292, ISSN: 0302-9743, pp. 189-200, 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

2011

Refereed (journals/proceedings) (5)

  • Galgonek J., Hoksza D.: On Metric Approximations of the SProt Measure, in Fourth International Conference on Similarity Search and Applications 2011, Lipari, Italy, ACM, ISBN: 978-1-4503-0795-6, pp. 119-120, 2011
  • 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
  • Novák J., Skopal T., Hoksza D., Lokoč J., Galgonek J.: Protein Sequences Identification using NM-tree, in Fourth International Conference on Similarity Search and Applications 2011, Lipari, Italy, ACM, ISBN: 978-1-4503-0795-6, pp. 125-126, 2011 - On-line verze

2010

Refereed (journals/proceedings) (5)

  • 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
  • Novák J., Hoksza D.: Parametrised Hausdorff Distance as a Non-Metric Similarity Model for Tandem Mass Spectrometry, accepted for publication in Proceedings of the Dateso 2010 Annual International Workshop on DAtabases, TExts, Specifications and Objects, Stedronin-Plazy, Czech Republic, MATFYZPRESS, ISSN: 1613-0073, pp. 1-12, 2010 - On-line PDF verze
  • Novák J., Hoksza D.: Similarity Search and Posttranslational Modifications in Tandem Mass Spectra, in Bioinformatics and Biomedicine Workshops, Hong Kong, China, IEEE, ISBN: 978-1-4244-8302-0, pp. 845-846, 2010
  • Novák J., Skopal T., Hoksza D., Lokoč J.: Improving the Similarity Search of Tandem Mass Spectra using Metric Access Methods, in Third International Conference on Similarity Search and Applications, Istanbul, Turkey, ACM, ISBN: 978-1-4503-0420-7, pp. 85-92, 2010 - On-line PDF verze

2009

Refereed (journals/proceedings) (4)

  • Galgonek J., Hoksza D.: On the Effectiveness of Distances Measuring Protein Structure Similarity, in SISAP 2009: Second international workshop on similarity search and applications, Prague, Czech Republic, IEEE, ISBN: 978-0-7695-3765-8, pp. 165-166, August 2009
  • 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
  • Novák J., Hoksza D.: An Application of the Metric Access Methods to the Mass Spectrometry Data, 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

2008

Refereed (journals/proceedings) (3)

  • 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.: Methods of Protein Structure Alignment, in DATAKON 2008, Hotel Santon, Brno, Czech Republic, ISBN: 978-80-7355-081-3, pp. 187-196, October 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

2007

Refereed (journals/proceedings) (4)

  • Hoksza D.: Metric indexing of protein databases and promising approaches, in Proceedings of WDS'07, ISBN: 978-80-7378-023-4, pp. 91-98, May 2007
  • Hoksza D., Skopal T.: Index-based approach to similarity search in protein and nucleotide databases, in DATESO 2007, Desna, Czech Republic, Matfyz Press, Praha, ISBN: 978-80-7378-002-9, ISSN: 1613-0073, pp. 67-80, April 2007
  • 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
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