Tomás Vinar

Publication Activity (10 Years)

Years Active: 2000-2024
Publications (10 Years): 25

Top Topics

Efficient Indexing

Structural Motifs

Disease Progression

Top Venues

Publications

Brona Brejová, Travis Gagie, Eva Herencsárová, Tomás Vinar
Maximum-scoring path sets on pangenome graphs of constant treewidth. Frontiers Bioinform. 4 (2024)
Askar Gafurov, Tomás Vinar, Paul Medvedev, Brona Brejová
Efficient Analysis of Annotation Colocalization Accounting for Genomic Contexts. RECOMB (2024)
Tomás Vinar
Bioinformatics of Pathogens (Invited Talk). WABI (2024)
Tomás Vinar
RECOMB Satellite Conference on Comparative Genomics(RECOMB-CG 2023). J. Comput. Biol. 31 (4) (2024)
Aniket C. Mane, Mahsa Faizrahnemoon, Tomás Vinar, Brona Brejová, Cédric Chauve
PlasBin-flow: a flow-based MILP algorithm for plasmid contigs binning. Bioinform. 39 (Supplement-1) (2023)
Vladimír Boza, Eduard Batmendijn, Peter Peresíni, Viktória Hodorová, Hana Lichancová, Rastislav Rabatin, Brona Brejová, Jozef Nosek, Tomás Vinar
Precise Nanopore Signal Modeling Improves Unsupervised Single-Molecule Methylation Detection. ITAT (2023)
Askar Gafurov, Andrej Baláz, Fabian Amman, Kristína Borsová, Viktória Cabanová, Boris Klempa, Andreas Bergthaler, Tomás Vinar, Brona Brejová
VirPool: model-based estimation of SARS-CoV-2 variant proportions in wastewater samples. BMC Bioinform. 23 (1) (2022)
Vladimír Boza, Peter Peresíni, Brona Brejová, Tomás Vinar
Dynamic Pooling Improves Nanopore Base Calling Accuracy. IEEE ACM Trans. Comput. Biol. Bioinform. 19 (6) (2022)
Adrian Goga, Miroslav Bohmer, Rastislav Hekel, Werner Krampl, Bronislava Brejová, Tomás Vinar, Jaroslav Budis, Tomás Szemes
SnakeLines Workflow for SARS-CoV-2 Variant Detection from Next-Generation Sequencing Reads. ITAT (2021)
Vladimír Boza, Peter Peresíni, Brona Brejová, Tomás Vinar
Dynamic Pooling Improves Nanopore Base Calling Accuracy. CoRR (2021)
Vladimír Boza, Matej Fedor, Kristína Borsová, Viktória Cabanová, Jana Cerníková, Viktória Hodorová, Peter Peresíni, Klára Sládecková, Boris Klempa, Jozef Nosek, Brona Brejová, Tomás Vinar
Alternative Base Callers Aid Real-time Analysis of SARS-CoV-2 Sequencing Runs. ITAT (2021)
Askar Gafurov, Andrej Baláz, Tomás Vinar, Brona Brejová
Estimation of Proportions of SARS-CoV-2 Variants in a Mixed Sequencing Sample. ITAT (2021)
Peter Peresíni, Vladimír Boza, Brona Brejová, Tomás Vinar
Nanopore base calling on the edge. Bioinform. 37 (24) (2021)
Askar Gafurov, Tomás Vinar, Brona Brejová
Probabilistic Models of k-mer Frequencies (Extended Abstract). CiE (2021)
Katarína Bodová, Vladimír Boza, Brona Brejová, Richard Kollár, Katarína Mikusová, Tomás Vinar
Time-adjusted Analysis Shows Weak Associations Between BCG Vaccination Policy and COVID-19 Disease Progression. ITAT (2021)
Brona Brejová, Viktória Hodorová, Kristína Borsová, Viktória Cabanová, Tomás Szemes, Matej Misík, Boris Klempa, Jozef Nosek, Tomás Vinar
Sequencing SARS-CoV-2 in Slovakia: An Unofficial Genomic Surveillance Report. ITAT (2021)
Vladimír Boza, Peter Peresíni, Brona Brejová, Tomás Vinar
DeepNano-blitz: a fast base caller for MinION nanopore sequencers. Bioinform. 36 (14) (2020)
Peter Peresíni, Vladimír Boza, Brona Brejová, Tomás Vinar
Nanopore Base Calling on the Edge. CoRR (2020)
Mário Lipovský, Tomás Vinar, Brona Brejová
Approximate Abundance Histograms and Their Use for Genome Size Estimation. ITAT (2017)
Brona Brejová, Askar Gafurov, Dana Pardubská, Michal Sabo, Tomás Vinar
Isometric gene tree reconciliation revisited. Algorithms Mol. Biol. 12 (1) (2017)
Rastislav Rabatin, Brona Brejová, Tomás Vinar
Using Sequence Ensembles for Seeding Alignments of MinION Sequencing Data. ITAT (2017)
Rastislav Rabatin, Brona Brejová, Tomás Vinar
Using Sequence Ensembles for Seeding Alignments of MinION Sequencing Data. CoRR (2016)
Martin Macko, Martin Králik, Brona Brejová, Tomás Vinar
OB-Fold Recognition Combining Sequence and Structural Motifs. ITAT (2016)
Brona Brejová, Askar Gafurov, Dana Pardubská, Michal Sabo, Tomás Vinar
Isometric Gene Tree Reconciliation Revisited. WABI (2016)
Ladislav Rampásek, Randi M. Jimenez, Andrej Lupták, Tomás Vinar, Brona Brejová
RNA motif search with data-driven element ordering. BMC Bioinform. 17 (2016)
Michal Nánási, Tomás Vinar, Brona Brejová
Sequence annotation with HMMs: New problems and their complexity. Inf. Process. Lett. 115 (6-8) (2015)
Vladimír Boza, Jakub Jursa, Brona Brejová, Tomás Vinar
Fishing in Read Collections: Memory Efficient Indexing for Sequence Assembly. SPIRE (2015)
Michal Hozza, Tomás Vinar, Brona Brejová
How Big is that Genome? Estimating Genome Size and Coverage from k-mer Abundance Spectra. SPIRE (2015)
Vladimír Boza, Brona Brejová, Tomás Vinar
GAML: genome assembly by maximum likelihood. Algorithms Mol. Biol. 10 (2015)
Vladimír Boza, Brona Brejová, Tomás Vinar
GAML: Genome Assembly by Maximum Likelihood. WABI (2014)
Michal Nánási, Tomás Vinar, Brona Brejová
Probabilistic approaches to alignment with tandem repeats. Algorithms Mol. Biol. 9 (2014)
Martin Kravec, Martin Bobák, Brona Brejová, Tomás Vinar
Variants of Genes from the Next Generation Sequencing Data. ITAT (2013)
Michal Nánási, Tomás Vinar, Brona Brejová
Probabilistic Approaches to Alignment with Tandem Repeats. WABI (2013)
Brona Brejová, Stefan Dobrev, Rastislav Královic, Tomás Vinar
Efficient routing in carrier-based mobile networks. Theor. Comput. Sci. 509 (2013)
Martina Visnovská, Tomás Vinar, Brona Brejová
DNA Sequence Segmentation Based on Local Similarity. ITAT (2013)
Michal Nánási, Tomás Vinar, Brona Brejová
Sequence Annotation with HMMs: New Problems and Their Complexity CoRR (2012)
Peter Kovác, Brona Brejová, Tomás Vinar
Aligning sequences with repetitive motifs. ITAT (2012)
Bronislava Brejová, Stefan Dobrev, Rastislav Královic, Tomás Vinar
Routing in Carrier-Based Mobile Networks. SIROCCO (2011)
Jakub Kovác, Brona Brejová, Tomás Vinar
A Practical Algorithm for Ancestral Rearrangement Reconstruction. WABI (2011)
Brona Brejová, Michal Burger, Tomás Vinar
Automated Segmentation of DNA Sequences with Complex Evolutionary Histories. WABI (2011)
Brona Brejová, Gad M. Landau, Tomás Vinar
Fast Computation of a String Duplication History under No-Breakpoint-Reuse - (Extended Abstract). SPIRE (2011)
Michal Nánási, Tomás Vinar, Brona Brejová
The Highest Expected Reward Decoding for HMMs with Application to Recombination Detection. CPM (2010)
Giltae Song, Louxin Zhang, Tomás Vinar, Webb Miller
CAGE: Combinatorial Analysis of Gene-Cluster Evolution. J. Comput. Biol. 17 (9) (2010)
Michal Nánási, Tomás Vinar, Brona Brejová
The Highest Expected Reward Decoding for HMMs with Application to Recombination Detection CoRR (2010)
Martina Visnovská, Michal Nánási, Tomás Vinar, Brona Brejová
Estimating effective DNA database size via compression. ITAT (2010)
Tomás Vinar, Brona Brejová, Giltae Song, Adam C. Siepel
Reconstructing Histories of Complex Gene Clusters on a Phylogeny. J. Comput. Biol. 17 (9) (2010)
Tomás Vinar, Brona Brejová, Giltae Song, Adam C. Siepel
Bayesian History Reconstruction of Complex Human Gene Clusters on a Phylogeny CoRR (2009)
Yu Zhang, Giltae Song, Tomás Vinar, Eric D. Green, Adam C. Siepel, Webb Miller
Evolutionary History Reconstruction for Mammalian Complex Gene Clusters. J. Comput. Biol. 16 (8) (2009)
Jakub Kovác, Tomás Vinar, Brona Brejová
Predicting Gene Structures from Multiple RT-PCR Tests. WABI (2009)
Giltae Song, Louxin Zhang, Tomás Vinar, Webb Miller
Inferring the Recent Duplication History of a Gene Cluster. RECOMB-CG (2009)
Tomás Vinar, Brona Brejová, Giltae Song, Adam C. Siepel
Reconstructing Histories of Complex Gene Clusters on a Phylogeny. RECOMB-CG (2009)
Yu Zhang, Giltae Song, Tomás Vinar, Eric D. Green, Adam C. Siepel, Webb Miller
Reconstructing the Evolutionary History of Complex Human Gene Clusters. RECOMB (2008)
Rastislav Srámek, Brona Brejová, Tomás Vinar
On-line Viterbi Algorithm and Its Relationship to Random Walks CoRR (2007)
Xuefeng Cui, Tomás Vinar, Brona Brejová, Dennis E. Shasha, Ming Li
Homology search for genes. ISMB/ECCB (Supplement of Bioinformatics) (2007)
Brona Brejová, Daniel G. Brown, Tomás Vinar
The most probable annotation problem in HMMs and its application to bioinformatics. J. Comput. Syst. Sci. 73 (7) (2007)
Rastislav Srámek, Brona Brejová, Tomás Vinar
On-Line Viterbi Algorithm for Analysis of Long Biological Sequences. WABI (2007)
Brona Brejová, Daniel G. Brown, Ian M. Harrower, Tomás Vinar
New Bounds for Motif Finding in Strong Instances. CPM (2006)
Brona Brejová, Daniel G. Brown, Ming Li, Tomás Vinar
ExonHunter: a comprehensive approach to gene finding. ISMB (Supplement of Bioinformatics) (2005)
Brona Brejová, Daniel G. Brown, Ian M. Harrower, Alejandro López-Ortiz, Tomás Vinar
Sharper Upper and Lower Bounds for an Approximation Scheme for Consensus-Pattern. CPM (2005)
Brona Brejová, Daniel G. Brown, Tomás Vinar
Vector seeds: An extension to spaced seeds. J. Comput. Syst. Sci. 70 (3) (2005)
Therese C. Biedl, Brona Brejová, Erik D. Demaine, Angèle M. Hamel, Alejandro López-Ortiz, Tomás Vinar
Finding hidden independent sets in interval graphs. Theor. Comput. Sci. 310 (1-3) (2004)
Brona Brejová, Daniel G. Brown, Tomás Vinar
The Most Probable Labeling Problem in HMMs and Its Application to Bioinformatics. WABI (2004)
Brona Brejová, Daniel G. Brown, Tomás Vinar
Optimal Spaced Seeds for Homologous Coding Regions. J. Bioinform. Comput. Biol. 1 (4) (2004)
Therese C. Biedl, Brona Brejová, Erik D. Demaine, Angèle M. Hamel, Alejandro López-Ortiz, Tomás Vinar
Finding Hidden Independent Sets in Interval Graphs. COCOON (2003)
Brona Brejová, Daniel G. Brown, Tomás Vinar
Optimal DNA Signal Recognition Models with a Fixed Amount of Intrasignal Dependency. WABI (2003)
Brona Brejová, Daniel G. Brown, Tomás Vinar
Optimal Spaced Seeds for Hidden Markov Models, with Application to Homologous Coding Regions. CPM (2003)
Therese C. Biedl, Jonathan F. Buss, Erik D. Demaine, Martin L. Demaine, Mohammad Taghi Hajiaghayi, Tomás Vinar
Palindrome recognition using a multidimensional tape. Theor. Comput. Sci. 302 (1-3) (2003)
Brona Brejová, Daniel G. Brown, Tomás Vinar
Vector Seeds: An Extension to Spaced Seeds Allows Substantial Improvements in Sensitivity and Specifity. WABI (2003)
Therese C. Biedl, Masud Hasan, Joseph Douglas Horton, Alejandro López-Ortiz, Tomás Vinar
Searching for the center of a circle. CCCG (2002)
Brona Brejová, Tomás Vinar
A Better Method for Length Distribution Modeling in HMMs and Its Application to Gene Finding. CPM (2002)
Therese C. Biedl, Brona Brejová, Tomás Vinar
Simplifying Flow Networks. MFCS (2000)