| 2022 | DASFAA | Hierarchical Bitmap Indexing for Range Queries on Multidimensional Arrays. | Lubos Krcl, Shen-Shyang Ho, Jan Holub |
| 2021 | ALENEX | PFP Compressed Suffix Trees. | Christina Boucher, Ondrej Cvacho, Travis Gagie, Jan Holub, Giovanni Manzini, Gonzalo Navarro, Massimiliano Rossi |
| 2018 | DCC | Filtering Invalid Off-Targets in CRISPR/Cas9 Design Tools. | Ondrej Cvacho, Jan Holub |
| 2017 | HCI | Stress Measurement and Inducement in Experiments with Low Cost Flight Simulator for Testing of General Aviation Pilots. | Ondrej Bruna, Toms Levora, Jan Holub |
| 2017 | WABI | Byte-Aligned Pattern Matching in Encoded Genomic Sequences. | Petr Prochzka, Jan Holub |
| 2016 | DCC | Approximate String Matching for Self-Indexes. | Lukas Hrbek, Jan Holub |
| 2016 | DCC | Positional Inverted Self-index. | Petr Prochzka, Jan Holub |
| 2015 | DCC | Incremental Locality and Clustering-Based Compression. | Lubos Krcl, Jan Holub |
| 2014 | DCC | Compressing Similar Biological Sequences Using FM-Index. | Petr Prochzka, Jan Holub |
| 2013 | DCC | Natural Language Compression Optimized for Large Set of Files. | Petr Prochzka, Jan Holub |
| 2013 | IWOCA | Suffix Tree of Alignment: An Efficient Index for Similar Data. | Joong Chae Na, Heejin Park, Maxime Crochemore, Jan Holub, Costas S. Iliopoulos, Laurent Mouchard, Kunsoo Park |
| 2011 | DCC | Lossless Data Compression Testbed: ExCom and Prague Corpus. | Jan Holub, Jakub Reznicek, Filip Simek |
| 2011 | DCC | Block-Oriented Dense Compressor. | Petr Prochzka, Jan Holub |
| 2009 | ALENEX | Tuning BNDM with q-Grams. | Branislav Durian, Jan Holub, Hannu Peltola, Jorma Tarhio |
| 2009 | IWOCA | New Word-Based Adaptive Dense Compressors. | Petr Prochzka, Jan Holub |
| 2008 | DCC | DCA Using Suffix Arrays. | Martin Fiala, Jan Holub |