| 2026 | WABI | Efficient Algorithms for Pangenome Personalization. | Denys Andrukhovskyi, Martin Madzin, Luca Denti, Toms Vinar, Brona Brejov |
| 2024 | RECOMB | Efficient Analysis of Annotation Colocalization Accounting for Genomic Contexts. | Askar Gafurov, Toms Vinar, Paul Medvedev, Brona Brejov |
| 2021 | CiE | Probabilistic Models of k-mer Frequencies (Extended Abstract). | Askar Gafurov, Toms Vinar, Brona Brejov |
| 2016 | WABI | Isometric Gene Tree Reconciliation Revisited. | Brona Brejov, Askar Gafurov, Dana Pardubsk, Michal Sabo, Toms Vinar |
| 2015 | SPIRE | Fishing in Read Collections: Memory Efficient Indexing for Sequence Assembly. | Vladimr Boza, Jakub Jursa, Brona Brejov, Toms Vinar |
| 2015 | SPIRE | How Big is that Genome? Estimating Genome Size and Coverage from k-mer Abundance Spectra. | Michal Hozza, Toms Vinar, Brona Brejov |
| 2014 | WABI | GAML: Genome Assembly by Maximum Likelihood. | Vladimr Boza, Brona Brejov, Toms Vinar |
| 2013 | WABI | Probabilistic Approaches to Alignment with Tandem Repeats. | Michal Nnsi, Toms Vinar, Brona Brejov |
| 2011 | SPIRE | Fast Computation of a String Duplication History under No-Breakpoint-Reuse - (Extended Abstract). | Brona Brejov, Gad M. Landau, Toms Vinar |
| 2011 | WABI | Automated Segmentation of DNA Sequences with Complex Evolutionary Histories. | Brona Brejov, Michal Burger, Toms Vinar |
| 2011 | WABI | A Practical Algorithm for Ancestral Rearrangement Reconstruction. | Jakub Kovc, Brona Brejov, Toms Vinar |
| 2010 | CPM | The Highest Expected Reward Decoding for HMMs with Application to Recombination Detection. | Michal Nnsi, Toms Vinar, Brona Brejov |
| 2009 | RECOMB | Reconstructing Histories of Complex Gene Clusters on a Phylogeny. | Toms Vinar, Brona Brejov, Giltae Song, Adam C. Siepel |
| 2009 | WABI | Predicting Gene Structures from Multiple RT-PCR Tests. | Jakub Kovc, Toms Vinar, Brona Brejov |
| 2007 | ISMB | Homology search for genes. | Xuefeng Cui, Toms Vinar, Brona Brejov, Dennis E. Shasha, Ming Li |
| 2007 | WABI | On-Line Viterbi Algorithm for Analysis of Long Biological Sequences. | Rastislav Srmek, Brona Brejov, Toms Vinar |
| 2006 | CPM | New Bounds for Motif Finding in Strong Instances. | Brona Brejov, Daniel G. Brown, Ian M. Harrower, Toms Vinar |
| 2005 | CPM | Sharper Upper and Lower Bounds for an Approximation Scheme for Consensus-Pattern. | Brona Brejov, Daniel G. Brown, Ian M. Harrower, Alejandro Lpez-Ortiz, Toms Vinar |
| 2005 | ISMB | ExonHunter: a comprehensive approach to gene finding. | Brona Brejov, Daniel G. Brown, Ming Li, Toms Vinar |
| 2004 | WABI | The Most Probable Labeling Problem in HMMs and Its Application to Bioinformatics. | Brona Brejov, Daniel G. Brown, Toms Vinar |
| 2003 | COCOON | Finding Hidden Independent Sets in Interval Graphs. | Therese Biedl, Brona Brejov, Erik D. Demaine, Angle M. Hamel, Alejandro Lpez-Ortiz, Toms Vinar |
| 2003 | CPM | Optimal Spaced Seeds for Hidden Markov Models, with Application to Homologous Coding Regions. | Brona Brejov, Daniel G. Brown, Toms Vinar |
| 2003 | WABI | Vector Seeds: An Extension to Spaced Seeds Allows Substantial Improvements in Sensitivity and Specifity. | Brona Brejov, Daniel G. Brown, Toms Vinar |
| 2003 | WABI | Optimal DNA Signal Recognition Models with a Fixed Amount of Intrasignal Dependency. | Brona Brejov, Daniel G. Brown, Toms Vinar |
| 2002 | CPM | A Better Method for Length Distribution Modeling in HMMs and Its Application to Gene Finding. | Brona Brejov, Toms Vinar |
| 2000 | MFCS | Simplifying Flow Networks. | Therese C. Biedl, Brona Brejov, Toms Vinar |