| 2023 | CHIRA | Visual Representations for Data Analytics: User Study. | Ladislav Peska, Ivan Sixtova, David Hoksza, David Bernhauer, Toms Skopal |
| 2016 | CIBCB | Using Bayesian modeling on molecular fragments features for virtual screening. | David Hoksza, Petr Skoda |
| 2013 | PACBB | A Statistical Comparison of SimTandem with State-of-the-Art Peptide Identification Tools. | Jir Novk, Timo Sachsenberg, David Hoksza, Toms Skopal, Oliver Kohlbacher |
| 2012 | EuroPar | On the Parallelization of the SProt Measure and the TM-Score Algorithm. | Jakub Galgonek, Martin Krulis, David Hoksza |
| 2012 | EuroPar | P3S: Protein Structure Similarity Search. | Jakub Galgonek, Toms Skopal, David Hoksza |
| 2012 | SISAP | SimTandem: Similarity Search in Tandem Mass Spectra. | Jir Novk, Jakub Galgonek, David Hoksza, Toms Skopal |
| 2011 | BIBE | Exploration of Chemical Space by Molecular Morphing. | David Hoksza, Daniel Svozil |
| 2011 | SISAP | On metric approximations of the SProt measure. | Jakub Galgonek, David Hoksza |
| 2011 | SISAP | Protein sequences identification using NM-tree. | Jir Novk, Toms Skopal, David Hoksza, Jakub Lokoc, Jakub Galgonek |
| 2010 | SISAP | Improving the similarity search of tandem mass spectra using metric access methods. | Jir Novk, Toms Skopal, David Hoksza, Jakub Lokoc |
| 2009 | CIBCB | DDPIn - Distance and density based protein indexing. | David Hoksza |
| 2009 | CIBCB | An application of the metric access methods to the mass spectrometry data. | Jir Novk, David Hoksza |
| 2009 | SISAP | On the Effectiveness of Distances Measuring Protein Structure Similarity. | Jakub Galgonek, David Hoksza |
| 2008 | COMAD | Native Multidimensional Indexing in Relational Databases. | David Hoksza, Toms Skopal |
| 2007 | ADBIS | Improving the Performance of M-Tree Family by Nearest-Neighbor Graphs. | Toms Skopal, David Hoksza |
| 2007 | DASFAA | Construction of Tree-Based Indexes for Level-Contiguous Buffering Support. | Toms Skopal, David Hoksza, Jaroslav Pokorn |