Simplifying Flow Networks. - Therese C. Biedl; Brona Brejová; Tomás Vinar (MFCS, 2000)

Searching for the center of a circle. - Therese Biedl; Masud Hasan; Joseph Douglas Horton; Alejandro López-Ortiz; Tomás Vinar (CCCG, 2002)

A Better Method for Length Distribution Modeling in HMMs and Its Application to Gene Finding. - Brona Brejová; Tomás Vinar (CPM, 2002)

Optimal Spaced Seeds for Hidden Markov Models, with Application to Homologous Coding Regions. - Brona Brejová; Daniel G. Brown 001; Tomás Vinar (CPM, 2003)

Vector Seeds: An Extension to Spaced Seeds Allows Substantial Improvements in Sensitivity and Specifity. - Brona Brejová; Daniel G. Brown 001; Tomás Vinar (WABI, 2003)

Optimal DNA Signal Recognition Models with a Fixed Amount of Intrasignal Dependency. - Brona Brejová; Daniel G. Brown 001; Tomás Vinar (WABI, 2003)

Palindrome recognition using a multidimensional tape. - Therese Biedl; Jonathan F. Buss; Erik D. Demaine; Martin L. Demaine; Mohammad Taghi Hajiaghayi; Tomás Vinar (Theor. Comput. Sci., 2003)

The Most Probable Labeling Problem in HMMs and Its Application to Bioinformatics. - Brona Brejová; Daniel G. Brown 001; Tomás Vinar (WABI, 2004)

Optimal Spaced Seeds for Homologous Coding Regions. - Brona Brejová; Daniel G. Brown 001; Tomás Vinar (J. Bioinform. Comput. Biol., 2004)

Finding hidden independent sets in interval graphs. - Therese Biedl; Brona Brejová; Erik D. Demaine; Angèle M. Hamel; Alejandro López-Ortiz; Tomás Vinar (Theor. Comput. Sci., 2004)

Sharper Upper and Lower Bounds for an Approximation Scheme for Consensus-Pattern. - Brona Brejová; Daniel G. Brown 001; Ian M. Harrower; Alejandro López-Ortiz; Tomás Vinar (CPM, 2005)

ExonHunter: a comprehensive approach to gene finding. - Brona Brejová; Daniel G. Brown 001; Ming Li 001; Tomás Vinar (ISMB (Supplement of Bioinformatics), 2005)

Vector seeds: An extension to spaced seeds. - Brona Brejová; Daniel G. Brown 001; Tomás Vinar (J. Comput. Syst. Sci., 2005)

Enhancements to Hidden Markov Models for Gene Finding and Other Biological Applications. - Tomás Vinar (2005)

New Bounds for Motif Finding in Strong Instances. - Brona Brejová; Daniel G. Brown 001; Ian M. Harrower; Tomás Vinar (CPM, 2006)

Homology search for genes. - Xuefeng Cui; Tomás Vinar; Brona Brejová; Dennis E. Shasha; Ming Li 001 (ISMB/ECCB (Supplement of Bioinformatics), 2007)

On-Line Viterbi Algorithm for Analysis of Long Biological Sequences. - Rastislav Srámek; Brona Brejová; Tomás Vinar (WABI, 2007)

On-line Viterbi Algorithm and Its Relationship to Random Walks - Rastislav Srámek; Brona Brejová; Tomás Vinar (CoRR, 2007)

The most probable annotation problem in HMMs and its application to bioinformatics. - Brona Brejová; Daniel G. Brown 001; Tomás Vinar (J. Comput. Syst. Sci., 2007)

Reconstructing the Evolutionary History of Complex Human Gene Clusters. - Yu Zhang 002; Giltae Song; Tomás Vinar; Eric D. Green; Adam C. Siepel; Webb Miller (RECOMB, 2008)

Inferring the Recent Duplication History of a Gene Cluster. - Giltae Song; Louxin Zhang; Tomás Vinar; Webb Miller (RECOMB-CG, 2009)

Predicting Gene Structures from Multiple RT-PCR Tests. - Jakub Kovác; Tomás Vinar; Brona Brejová (WABI, 2009)

Bayesian History Reconstruction of Complex Human Gene Clusters on a Phylogeny - Tomás Vinar; Brona Brejová; Giltae Song; Adam C. Siepel (CoRR, 2009)

Evolutionary History Reconstruction for Mammalian Complex Gene Clusters. - Yu Zhang 002; Giltae Song; Tomás Vinar; Eric D. Green; Adam C. Siepel; Webb Miller (J. Comput. Biol., 2009)

The Highest Expected Reward Decoding for HMMs with Application to Recombination Detection. - Michal Nánási; Tomás Vinar; Brona Brejová (CPM, 2010)

Estimating effective DNA database size via compression. - Martina Visnovská; Michal Nánási; Tomás Vinar; Brona Brejová (ITAT, 2010)

CAGE: Combinatorial Analysis of Gene-Cluster Evolution. - Giltae Song; Louxin Zhang; Tomás Vinar; Webb Miller (J. Comput. Biol., 2010)

Reconstructing Histories of Complex Gene Clusters on a Phylogeny. - Tomás Vinar; Brona Brejová; Giltae Song; Adam C. Siepel (J. Comput. Biol., 2010)

Routing in Carrier-Based Mobile Networks. - Bronislava Brejová; Stefan Dobrev; Rastislav Královic; Tomás Vinar (SIROCCO, 2011)

Fast Computation of a String Duplication History under No-Breakpoint-Reuse - (Extended Abstract). - Brona Brejová; Gad M. Landau; Tomás Vinar (SPIRE, 2011)

Automated Segmentation of DNA Sequences with Complex Evolutionary Histories. - Brona Brejová; Michal Burger; Tomás Vinar (WABI, 2011)

A Practical Algorithm for Ancestral Rearrangement Reconstruction. - Jakub Kovác; Brona Brejová; Tomás Vinar (WABI, 2011)

Aligning sequences with repetitive motifs. - Peter Kovác; Brona Brejová; Tomás Vinar (ITAT, 2012)

Variants of Genes from the Next Generation Sequencing Data. - Martin Kravec; Martin Bobák 002; Brona Brejová; Tomás Vinar (ITAT, 2013)

DNA Sequence Segmentation Based on Local Similarity. - Martina Visnovská; Tomás Vinar; Brona Brejová (ITAT, 2013)

Efficient routing in carrier-based mobile networks. - Brona Brejová; Stefan Dobrev; Rastislav Královic; Tomás Vinar (Theor. Comput. Sci., 2013)

Probabilistic approaches to alignment with tandem repeats. - Michal Nánási; Tomás Vinar; Brona Brejová (Algorithms Mol. Biol., 2014)

Fishing in Read Collections: Memory Efficient Indexing for Sequence Assembly. - Vladimír Boza; Jakub Jursa; Brona Brejová; Tomás Vinar (SPIRE, 2015)

How Big is that Genome? Estimating Genome Size and Coverage from k-mer Abundance Spectra. - Michal Hozza; Tomás Vinar; Brona Brejová (SPIRE, 2015)

GAML: genome assembly by maximum likelihood. - Vladimír Boza; Brona Brejová; Tomás Vinar (Algorithms Mol. Biol., 2015)

Sequence annotation with HMMs: New problems and their complexity. - Michal Nánási; Tomás Vinar; Brona Brejová (Inf. Process. Lett., 2015)

OB-Fold Recognition Combining Sequence and Structural Motifs. - Martin Macko; Martin Králik; Brona Brejová; Tomás Vinar (ITAT, 2016)

RNA motif search with data-driven element ordering. - Ladislav Rampásek; Randi M. Jimenez; Andrej Lupták; Tomás Vinar; Brona Brejová (BMC Bioinform., 2016)

Approximate Abundance Histograms and Their Use for Genome Size Estimation. - Mário Lipovský; Tomás Vinar; Brona Brejová (ITAT, 2017)

Using Sequence Ensembles for Seeding Alignments of MinION Sequencing Data. - Rastislav Rabatin; Brona Brejová; Tomás Vinar (ITAT, 2017)

Isometric gene tree reconciliation revisited. - Brona Brejová; Askar Gafurov; Dana Pardubská; Michal Sabo; Tomás Vinar (Algorithms Mol. Biol., 2017)

DeepNano-blitz: a fast base caller for MinION nanopore sequencers. - Vladimír Boza; Peter Peresíni; Brona Brejová; Tomás Vinar (Bioinform., 2020)

Probabilistic Models of k-mer Frequencies (Extended Abstract). - Askar Gafurov; Tomás Vinar; Brona Brejová (CiE, 2021)

Time-adjusted Analysis Shows Weak Associations Between BCG Vaccination Policy and COVID-19 Disease Progression. - Katarína Bodová; Vladimír Boza; Brona Brejová; Richard Kollár; Katarína Mikusová; Tomás Vinar (ITAT, 2021)

Alternative Base Callers Aid Real-time Analysis of SARS-CoV-2 Sequencing Runs. - Vladimír Boza; Matej Fedor; Kristína Borsová; Viktória Cabanová; Jana Cerníková; Viktória Hodorová; Peter Peresíni; Klára Sládecková; Boris Klempa; Jozef Nosek; Brona Brejová; Tomás Vinar (ITAT, 2021)

Sequencing SARS-CoV-2 in Slovakia: An Unofficial Genomic Surveillance Report. - Brona Brejová; Viktória Hodorová; Kristína Borsová; Viktória Cabanová; Tomás Szemes; Matej Misík; Boris Klempa; Jozef Nosek; Tomás Vinar (ITAT, 2021)

Estimation of Proportions of SARS-CoV-2 Variants in a Mixed Sequencing Sample. - Askar Gafurov; Andrej Baláz; Tomás Vinar; Brona Brejová (ITAT, 2021)

SnakeLines Workflow for SARS-CoV-2 Variant Detection from Next-Generation Sequencing Reads. - Adrian Goga; Miroslav Böhmer; Rastislav Hekel; Werner Krampl; Bronislava Brejová; Tomás Vinar; Jaroslav Budis; Tomás Szemes (ITAT, 2021)

Nanopore base calling on the edge. - Peter Peresíni; Vladimír Boza; Brona Brejová; Tomás Vinar (Bioinform., 2021)

Dynamic Pooling Improves Nanopore Base Calling Accuracy. - Vladimír Boza; Peter Peresíni; Brona Brejová; Tomás Vinar (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

VirPool: model-based estimation of SARS-CoV-2 variant proportions in wastewater samples. - Askar Gafurov; Andrej Baláz; Fabian Amman; Kristína Borsová; Viktória Cabanová; Boris Klempa; Andreas Bergthaler; Tomás Vinar; Brona Brejová (BMC Bioinform., 2022)

Precise Nanopore Signal Modeling Improves Unsupervised Single-Molecule Methylation Detection. - Vladimír Boza; Eduard Batmendijn; Peter Peresíni; Viktória Hodorová; Hana Lichancová; Rastislav Rabatin; Brona Brejová; Jozef Nosek; Tomás Vinar (ITAT, 2023)

PlasBin-flow: a flow-based MILP algorithm for plasmid contigs binning. - Aniket C. Mane; Mahsa Faizrahnemoon; Tomás Vinar; Brona Brejová; Cédric Chauve (Bioinform., 2023)

Efficient Analysis of Annotation Colocalization Accounting for Genomic Contexts. - Askar Gafurov; Tomás Vinar; Paul Medvedev; Brona Brejová (RECOMB, 2024)

Bioinformatics of Pathogens (Invited Talk). - Tomás Vinar (WABI, 2024)

Maximum-scoring path sets on pangenome graphs of constant treewidth. - Brona Brejová; Travis Gagie; Eva Herencsárová; Tomás Vinar (Frontiers Bioinform., 2024)

Fast Context-Aware Analysis of Genome Annotation Colocalization. - Askar Gafurov; Tomás Vinar; Paul Medvedev; Brona Brejová (J. Comput. Biol., 2024)

RECOMB Satellite Conference on Comparative Genomics(RECOMB-CG 2023). - Tomás Vinar (J. Comput. Biol., 2024)