Brona Brejová

75 papers B 7C 15Misc 1Journal 30Unranked 19

Year	Rank	Type	Title / Venue / Authors
2025	C	`ed.`	25th International Conference on Algorithms for Bioinformatics, WABI 2025, University of Maryland, College Park, MD, USA, August 20-22, 2025 WABI Brona Brejová, Rob Patro
2024	B	`conf`	Efficient Analysis of Annotation Colocalization Accounting for Genomic Contexts. RECOMB Askar Gafurov, Tomás Vinar, Paul Medvedev, Brona Brejová
2024	J	`jnl`	Fast Context-Aware Analysis of Genome Annotation Colocalization. J. Comput. Biol. Askar Gafurov, Tomás Vinar, Paul Medvedev, Brona Brejová
2024	J	`jnl`	Maximum-scoring path sets on pangenome graphs of constant treewidth. Frontiers Bioinform. Brona Brejová, Travis Gagie, Eva Herencsárová, Tomás Vinar
2023	—	`conf`	Identifying Clusters in Graph Representations of Genomes. ITAT Eva Herencsárová, Brona Brejová
2023	J	`jnl`	PlasBin-flow: a flow-based MILP algorithm for plasmid contigs binning. Bioinform. Aniket C. Mane, Mahsa Faizrahnemoon, Tomás Vinar, Brona Brejová, Cédric Chauve
2023	—	`conf`	Precise Nanopore Signal Modeling Improves Unsupervised Single-Molecule Methylation Detection. ITAT Vladimír Boza, Eduard Batmendijn, Peter Peresíni, Viktória Hodorová, Hana Lichancová, Rastislav Rabatin, Brona Brejová, Jozef Nosek, Tomás Vinar
2023	—	`ed.`	Proceedings of the 23rd Conference Information Technologies - Applications and Theory (ITAT 2023), Tatranské Matliare, Slovakia, September 22-26, 2023. ITAT Brona Brejová, Lucie Ciencialová, Martin Holena, Róbert Jajcay, Tatiana Jajcayová, Matej Lexa, Frantisek Mráz, Dana Pardubská, Martin Plátek
2023	J	`jnl`	WarpSTR: determining tandem repeat lengths using raw nanopore signals. Bioinform. Jozef Sitarcík, Tomás Vinar, Brona Brejová, Werner Krampl, Jaroslav Budis, Ján Radvánszky, Mária Lucká
2022	J	`jnl`	Dynamic Pooling Improves Nanopore Base Calling Accuracy. IEEE ACM Trans. Comput. Biol. Bioinform. Vladimír Boza, Peter Peresíni, Brona Brejová, Tomás Vinar
2022	J	`jnl`	Markov chains improve the significance computation of overlapping genome annotations. Bioinform. Askar Gafurov, Brona Brejová, Paul Medvedev
2022	J	`jnl`	VirPool: model-based estimation of SARS-CoV-2 variant proportions in wastewater samples. BMC Bioinform. Askar Gafurov, Andrej Baláz, Fabian Amman, Kristína Borsová, Viktória Cabanová, Boris Klempa, Andreas Bergthaler, Tomás Vinar, Brona Brejová
2021	—	`conf`	Alternative Base Callers Aid Real-time Analysis of SARS-CoV-2 Sequencing Runs. ITAT Vladimír Boza, Matej Fedor, Kristína Borsová, Viktória Cabanová, Jana Cerníková, Viktória Hodorová, Peter Peresíni, Klára Sládecková, Boris Klempa, Jozef Nosek, Brona Brejová, Tomás Vinar
2021	J	`jnl`	Dynamic Pooling Improves Nanopore Base Calling Accuracy. CoRR Vladimír Boza, Peter Peresíni, Brona Brejová, Tomás Vinar
2021	—	`conf`	Estimation of Proportions of SARS-CoV-2 Variants in a Mixed Sequencing Sample. ITAT Askar Gafurov, Andrej Baláz, Tomás Vinar, Brona Brejová
2021	J	`jnl`	Nanopore base calling on the edge. Bioinform. Peter Peresíni, Vladimír Boza, Brona Brejová, Tomás Vinar
2021	C	`conf`	Probabilistic Models of k-mer Frequencies (Extended Abstract). CiE Askar Gafurov, Tomás Vinar, Brona Brejová
2021	—	`ed.`	Proceedings of the 21st Conference Information Technologies - Applications and Theory (ITAT 2021), Hotel Heľpa, Nízke Tatry and Muránska planina, Slovakia, September 24-28, 2021. ITAT Brona Brejová, Lucie Ciencialová, Martin Holena, Frantisek Mráz, Dana Pardubská, Martin Plátek, Tomás Vinar
2021	—	`conf`	Sequencing SARS-CoV-2 in Slovakia: An Unofficial Genomic Surveillance Report. ITAT Brona Brejová, Viktória Hodorová, Kristína Borsová, Viktória Cabanová, Tomás Szemes, Matej Misík, Boris Klempa, Jozef Nosek, Tomás Vinar
2021	—	`conf`	Time-adjusted Analysis Shows Weak Associations Between BCG Vaccination Policy and COVID-19 Disease Progression. ITAT Katarína Bodová, Vladimír Boza, Brona Brejová, Richard Kollár, Katarína Mikusová, Tomás Vinar
2020	J	`jnl`	A Linear-Time Algorithm for the Isometric Reconciliation of Unrooted Trees. Algorithms Brona Brejová, Rastislav Královic
2020	J	`jnl`	DeepNano-blitz: a fast base caller for MinION nanopore sequencers. Bioinform. Vladimír Boza, Peter Peresíni, Brona Brejová, Tomás Vinar
2020	J	`jnl`	Nanopore Base Calling on the Edge. CoRR Peter Peresíni, Vladimír Boza, Brona Brejová, Tomás Vinar
2019	J	`jnl`	Dante: genotyping of known complex and expanded short tandem repeats. Bioinform. Jaroslav Budis, Marcel Kucharík, Frantisek Duris, Juraj Gazdarica, Michaela Zrubcová, Andrej Ficek, Tomás Szemes, Brona Brejová, Ján Radvánszky
2017	—	`conf`	Approximate Abundance Histograms and Their Use for Genome Size Estimation. ITAT Mário Lipovský, Tomás Vinar, Brona Brejová
2017	J	`jnl`	Isometric gene tree reconciliation revisited. Algorithms Mol. Biol. Brona Brejová, Askar Gafurov, Dana Pardubská, Michal Sabo, Tomás Vinar
2017	—	`conf`	Using Sequence Ensembles for Seeding Alignments of MinION Sequencing Data. ITAT Rastislav Rabatin, Brona Brejová, Tomás Vinar
2016	C	`conf`	Isometric Gene Tree Reconciliation Revisited. WABI Brona Brejová, Askar Gafurov, Dana Pardubská, Michal Sabo, Tomás Vinar
2016	—	`conf`	OB-Fold Recognition Combining Sequence and Structural Motifs. ITAT Martin Macko, Martin Králik, Brona Brejová, Tomás Vinar
2016	—	`ed.`	Proceedings of the 16th ITAT Conference Information Technologies - Applications and Theory, Tatranské Matliare, Slovakia, September 15-19, 2016. ITAT Brona Brejová
2016	J	`jnl`	RNA motif search with data-driven element ordering. BMC Bioinform. Ladislav Rampásek, Randi M. Jimenez, Andrej Lupták, Tomás Vinar, Brona Brejová
2016	J	`jnl`	Using Sequence Ensembles for Seeding Alignments of MinION Sequencing Data. CoRR Rastislav Rabatin, Brona Brejová, Tomás Vinar
2015	C	`conf`	Fishing in Read Collections: Memory Efficient Indexing for Sequence Assembly. SPIRE Vladimír Boza, Jakub Jursa, Brona Brejová, Tomás Vinar
2015	J	`jnl`	GAML: genome assembly by maximum likelihood. Algorithms Mol. Biol. Vladimír Boza, Brona Brejová, Tomás Vinar
2015	C	`conf`	How Big is that Genome? Estimating Genome Size and Coverage from k-mer Abundance Spectra. SPIRE Michal Hozza, Tomás Vinar, Brona Brejová
2015	J	`jnl`	Sequence annotation with HMMs: New problems and their complexity. Inf. Process. Lett. Michal Nánási, Tomás Vinar, Brona Brejová
2014	—	`conf`	An Improved Algorithm for Ancestral Gene Order Reconstruction. ITAT Albert Herencsár, Brona Brejová
2014	C	`conf`	GAML: Genome Assembly by Maximum Likelihood. WABI Vladimír Boza, Brona Brejová, Tomás Vinar
2014	—	`conf`	Neuropeptide Recognition by Machine Learning Methods. ITAT Andrej Ridzik, Brona Brejová
2014	J	`jnl`	Probabilistic approaches to alignment with tandem repeats. Algorithms Mol. Biol. Michal Nánási, Tomás Vinar, Brona Brejová
2013	—	`conf`	DNA Sequence Segmentation Based on Local Similarity. ITAT Martina Visnovská, Tomás Vinar, Brona Brejová
2013	J	`jnl`	Efficient routing in carrier-based mobile networks. Theor. Comput. Sci. Brona Brejová, Stefan Dobrev, Rastislav Královic, Tomás Vinar
2013	C	`conf`	Probabilistic Approaches to Alignment with Tandem Repeats. WABI Michal Nánási, Tomás Vinar, Brona Brejová
2013	—	`conf`	Variants of Genes from the Next Generation Sequencing Data. ITAT Martin Kravec, Martin Bobák, Brona Brejová, Tomás Vinar
2012	—	`conf`	Aligning sequences with repetitive motifs. ITAT Peter Kovác, Brona Brejová, Tomás Vinar
2012	J	`jnl`	Sequence Annotation with HMMs: New Problems and Their Complexity CoRR Michal Nánási, Tomás Vinar, Brona Brejová
2011	C	`conf`	A Practical Algorithm for Ancestral Rearrangement Reconstruction. WABI Jakub Kovác, Brona Brejová, Tomás Vinar
2011	C	`conf`	Automated Segmentation of DNA Sequences with Complex Evolutionary Histories. WABI Brona Brejová, Michal Burger, Tomás Vinar
2011	C	`conf`	Fast Computation of a String Duplication History under No-Breakpoint-Reuse - (Extended Abstract). SPIRE Brona Brejová, Gad M. Landau, Tomás Vinar
2011	—	`conf`	Gene finding with complex external information. ITAT Marcel Kucharík, Jakub Kovác, Brona Brejová
2010	—	`conf`	Estimating effective DNA database size via compression. ITAT Martina Visnovská, Michal Nánási, Tomás Vinar, Brona Brejová
2010	J	`jnl`	Reconstructing Histories of Complex Gene Clusters on a Phylogeny. J. Comput. Biol. Tomás Vinar, Brona Brejová, Giltae Song, Adam C. Siepel
2010	J	`jnl`	The Highest Expected Reward Decoding for HMMs with Application to Recombination Detection CoRR Michal Nánási, Tomás Vinar, Brona Brejová
2010	B	`conf`	The Highest Expected Reward Decoding for HMMs with Application to Recombination Detection. CPM Michal Nánási, Tomás Vinar, Brona Brejová
2009	J	`jnl`	Bayesian History Reconstruction of Complex Human Gene Clusters on a Phylogeny CoRR Tomás Vinar, Brona Brejová, Giltae Song, Adam C. Siepel
2009	C	`conf`	Predicting Gene Structures from Multiple RT-PCR Tests. WABI Jakub Kovác, Tomás Vinar, Brona Brejová
2009	—	`conf`	Reconstructing Histories of Complex Gene Clusters on a Phylogeny. RECOMB-CG Tomás Vinar, Brona Brejová, Giltae Song, Adam C. Siepel
2007	—	`conf`	Homology search for genes. ISMB/ECCB (Supplement of Bioinformatics) Xuefeng Cui, Tomás Vinar, Brona Brejová, Dennis E. Shasha, Ming Li
2007	C	`conf`	On-Line Viterbi Algorithm for Analysis of Long Biological Sequences. WABI Rastislav Srámek, Brona Brejová, Tomás Vinar
2007	J	`jnl`	On-line Viterbi Algorithm and Its Relationship to Random Walks CoRR Rastislav Srámek, Brona Brejová, Tomás Vinar
2007	J	`jnl`	The most probable annotation problem in HMMs and its application to bioinformatics. J. Comput. Syst. Sci. Brona Brejová, Daniel G. Brown, Tomás Vinar
2006	B	`conf`	New Bounds for Motif Finding in Strong Instances. CPM Brona Brejová, Daniel G. Brown, Ian M. Harrower, Tomás Vinar
2005	—	`conf`	ExonHunter: a comprehensive approach to gene finding. ISMB (Supplement of Bioinformatics) Brona Brejová, Daniel G. Brown, Ming Li, Tomás Vinar
2005	B	`conf`	Sharper Upper and Lower Bounds for an Approximation Scheme for Consensus-Pattern. CPM Brona Brejová, Daniel G. Brown, Ian M. Harrower, Alejandro López-Ortiz, Tomás Vinar
2005	J	`jnl`	Vector seeds: An extension to spaced seeds. J. Comput. Syst. Sci. Brona Brejová, Daniel G. Brown, Tomás Vinar
2004	J	`jnl`	Finding hidden independent sets in interval graphs. Theor. Comput. Sci. Therese Biedl, Brona Brejová, Erik D. Demaine, Angèle M. Hamel, Alejandro López-Ortiz, Tomás Vinar
2004	J	`jnl`	Optimal Spaced Seeds for Homologous Coding Regions. J. Bioinform. Comput. Biol. Brona Brejová, Daniel G. Brown, Tomás Vinar
2004	C	`conf`	The Most Probable Labeling Problem in HMMs and Its Application to Bioinformatics. WABI Brona Brejová, Daniel G. Brown, Tomás Vinar
2003	Misc	`conf`	Finding Hidden Independent Sets in Interval Graphs. COCOON Therese Biedl, Brona Brejová, Erik D. Demaine, Angèle M. Hamel, Alejandro López-Ortiz, Tomás Vinar
2003	C	`conf`	Optimal DNA Signal Recognition Models with a Fixed Amount of Intrasignal Dependency. WABI Brona Brejová, Daniel G. Brown, Tomás Vinar
2003	B	`conf`	Optimal Spaced Seeds for Hidden Markov Models, with Application to Homologous Coding Regions. CPM Brona Brejová, Daniel G. Brown, Tomás Vinar
2003	C	`conf`	Vector Seeds: An Extension to Spaced Seeds Allows Substantial Improvements in Sensitivity and Specifity. WABI Brona Brejová, Daniel G. Brown, Tomás Vinar
2002	B	`conf`	A Better Method for Length Distribution Modeling in HMMs and Its Application to Gene Finding. CPM Brona Brejová, Tomás Vinar
2001	J	`jnl`	Analyzing variants of Shellsort. Inf. Process. Lett. Brona Brejová
2000	B	`conf`	Simplifying Flow Networks. MFCS Therese C. Biedl, Brona Brejová, Tomás Vinar