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ORCIDTomás Vinar
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- affiliation: Comenius University, Bratislava, Slovakia
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2020 – today
- 2024
[j22]Brona Brejová, Travis Gagie, Eva Herencsárová, Tomás Vinar:
Maximum-scoring path sets on pangenome graphs of constant treewidth. Frontiers Bioinform. 4 (2024)- [j21]Tomás Vinar:
RECOMB Satellite Conference on Comparative Genomics(RECOMB-CG 2023). J. Comput. Biol. 31(4): 275-276 (2024) - [j20]Askar Gafurov, Tomás Vinar, Paul Medvedev, Brona Brejová
:
Fast Context-Aware Analysis of Genome Annotation Colocalization. J. Comput. Biol. 31(10): 946-964 (2024) - [c43]Askar Gafurov, Tomás Vinar, Paul Medvedev, Brona Brejová:
Efficient Analysis of Annotation Colocalization Accounting for Genomic Contexts. RECOMB 2024: 38-53 - [c42]Tomás Vinar:
Bioinformatics of Pathogens (Invited Talk). WABI 2024: 1:1-1:2 - 2023
- [j19]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): 288-296 (2023) - [c41]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: 223-231 - [e3]Katharina Jahn, Tomás Vinar:
Comparative Genomics - 20th International Conference, RECOMB-CG 2023, Istanbul, Turkey, April 14-15, 2023, Proceedings. Lecture Notes in Computer Science 13883, Springer 2023, ISBN 978-3-031-36910-0 [contents] - 2022
- [j18]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): 551 (2022) - [j17]Vladimír Boza, Peter Peresíni, Brona Brejová, Tomás Vinar:
Dynamic Pooling Improves Nanopore Base Calling Accuracy. IEEE ACM Trans. Comput. Biol. Bioinform. 19(6): 3416-3424 (2022) - 2021
- [j16]Peter Peresíni, Vladimír Boza, Brona Brejová, Tomás Vinar:
Nanopore base calling on the edge. Bioinform. 37(24): 4661-4667 (2021) - [c40]Askar Gafurov, Tomás Vinar, Brona Brejová:
Probabilistic Models of k-mer Frequencies (Extended Abstract). CiE 2021: 227-236 - [c39]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: 229-239 - [c38]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: 255-262 - [c37]Adrian Goga, Miroslav Böhmer, 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: 293-300 - [c36]Askar Gafurov, Andrej Baláz, Tomás Vinar, Brona Brejová:
Estimation of Proportions of SARS-CoV-2 Variants in a Mixed Sequencing Sample. ITAT 2021: 301-307 - [c35]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: 308-313 - [e2]Brona Brejová, Lucie Ciencialová, Martin Holena, Frantisek Mráz, Dana Pardubská, Martin Plátek, Tomás Vinar:
Proceedings of the 21st Conference Information Technologies - Applications and Theory (ITAT 2021), Hotel Heľpa, Nízke Tatry and Muránska planina, Slovakia, September 24-28, 2021. CEUR Workshop Proceedings 2962, CEUR-WS.org 2021 [contents] - [i7]Vladimír Boza, Peter Peresíni, Brona Brejová, Tomás Vinar:
Dynamic Pooling Improves Nanopore Base Calling Accuracy. CoRR abs/2105.07520 (2021) - 2020
- [j15]Vladimír Boza, Peter Peresíni, Brona Brejová, Tomás Vinar:
DeepNano-blitz: a fast base caller for MinION nanopore sequencers. Bioinform. 36(14): 4191-4192 (2020) - [i6]Peter Peresíni, Vladimír Boza, Brona Brejová, Tomás Vinar:
Nanopore Base Calling on the Edge. CoRR abs/2011.04312 (2020)
2010 – 2019
- 2017
- [j14]Brona Brejová, Askar Gafurov, Dana Pardubská, Michal Sabo, Tomás Vinar:
Isometric gene tree reconciliation revisited. Algorithms Mol. Biol. 12(1): 17:1-17:16 (2017) - [c34]Mário Lipovský, Tomás Vinar, Brona Brejová:
Approximate Abundance Histograms and Their Use for Genome Size Estimation. ITAT 2017: 27-34 - [c33]Rastislav Rabatin, Brona Brejová, Tomás Vinar:
Using Sequence Ensembles for Seeding Alignments of MinION Sequencing Data. ITAT 2017: 48-54 - 2016
- [j13]Ladislav Rampásek, Randi M. Jimenez, Andrej Lupták, Tomás Vinar, Brona Brejová:
RNA motif search with data-driven element ordering. BMC Bioinform. 17: 216 (2016) - [c32]Martin Macko, Martin Králik, Brona Brejová, Tomás Vinar:
OB-Fold Recognition Combining Sequence and Structural Motifs. ITAT 2016: 18-25 - [c31]Brona Brejová, Askar Gafurov, Dana Pardubská, Michal Sabo, Tomás Vinar:
Isometric Gene Tree Reconciliation Revisited. WABI 2016: 40-51 - [i5]Rastislav Rabatin, Brona Brejová, Tomás Vinar:
Using Sequence Ensembles for Seeding Alignments of MinION Sequencing Data. CoRR abs/1606.08719 (2016) - 2015
- [j12]Vladimír Boza, Brona Brejová, Tomás Vinar:
GAML: genome assembly by maximum likelihood. Algorithms Mol. Biol. 10: 18 (2015) - [j11]Michal Nánási, Tomás Vinar, Brona Brejová:
Sequence annotation with HMMs: New problems and their complexity. Inf. Process. Lett. 115(6-8): 635-639 (2015) - [c30]Vladimír Boza, Jakub Jursa, Brona Brejová, Tomás Vinar:
Fishing in Read Collections: Memory Efficient Indexing for Sequence Assembly. SPIRE 2015: 188-198 - [c29]Michal Hozza, Tomás Vinar, Brona Brejová:
How Big is that Genome? Estimating Genome Size and Coverage from k-mer Abundance Spectra. SPIRE 2015: 199-209 - 2014
- [j10]Michal Nánási, Tomás Vinar, Brona Brejová:
Probabilistic approaches to alignment with tandem repeats. Algorithms Mol. Biol. 9: 3 (2014) - [c28]Vladimír Boza, Brona Brejová, Tomás Vinar:
GAML: Genome Assembly by Maximum Likelihood. WABI 2014: 122-134 - 2013
- [j9]Brona Brejová, Stefan Dobrev, Rastislav Královic, Tomás Vinar:
Efficient routing in carrier-based mobile networks. Theor. Comput. Sci. 509: 113-121 (2013) - [c27]Martina Visnovská, Tomás Vinar, Brona Brejová:
DNA Sequence Segmentation Based on Local Similarity. ITAT 2013: 36-43 - [c26]Martin Kravec, Martin Bobák, Brona Brejová, Tomás Vinar:
Variants of Genes from the Next Generation Sequencing Data. ITAT 2013: 44-51 - [c25]Michal Nánási, Tomás Vinar, Brona Brejová:
Probabilistic Approaches to Alignment with Tandem Repeats. WABI 2013: 287-299 - [e1]Tomás Vinar:
Proceedings of the Conference on Information Technologies - Applications and Theory, Donovaly, Slovakia, September 11-15, 2013. CEUR Workshop Proceedings 1003, CEUR-WS.org 2013 [contents] - 2012
- [c24]Peter Kovác, Brona Brejová, Tomás Vinar:
Aligning sequences with repetitive motifs. ITAT 2012: 41-48 - [i4]Michal Nánási, Tomás Vinar, Brona Brejová:
Sequence Annotation with HMMs: New Problems and Their Complexity. CoRR abs/1210.2587 (2012) - 2011
- [c23]Bronislava Brejová, Stefan Dobrev, Rastislav Královic, Tomás Vinar:
Routing in Carrier-Based Mobile Networks. SIROCCO 2011: 222-233 - [c22]Brona Brejová, Gad M. Landau, Tomás Vinar:
Fast Computation of a String Duplication History under No-Breakpoint-Reuse - (Extended Abstract). SPIRE 2011: 144-155 - [c21]Brona Brejová, Michal Burger, Tomás Vinar:
Automated Segmentation of DNA Sequences with Complex Evolutionary Histories. WABI 2011: 1-13 - [c20]Jakub Kovác, Brona Brejová, Tomás Vinar:
A Practical Algorithm for Ancestral Rearrangement Reconstruction. WABI 2011: 163-174 - 2010
- [j8]Giltae Song, Louxin Zhang, Tomás Vinar, Webb Miller:
CAGE: Combinatorial Analysis of Gene-Cluster Evolution. J. Comput. Biol. 17(9): 1227-1242 (2010) - [j7]Tomás Vinar, Brona Brejová, Giltae Song, Adam C. Siepel:
Reconstructing Histories of Complex Gene Clusters on a Phylogeny. J. Comput. Biol. 17(9): 1267-1279 (2010) - [c19]Michal Nánási, Tomás Vinar, Brona Brejová:
The Highest Expected Reward Decoding for HMMs with Application to Recombination Detection. CPM 2010: 164-176 - [c18]Martina Visnovská, Michal Nánási, Tomás Vinar, Brona Brejová:
Estimating effective DNA database size via compression. ITAT 2010: 63-70 - [i3]Michal Nánási, Tomás Vinar, Brona Brejová:
The Highest Expected Reward Decoding for HMMs with Application to Recombination Detection. CoRR abs/1001.4499 (2010)
2000 – 2009
- 2009
- [j6]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): 1051-1070 (2009) - [c17]Giltae Song, Louxin Zhang, Tomás Vinar, Webb Miller:
Inferring the Recent Duplication History of a Gene Cluster. RECOMB-CG 2009: 111-125 - [c16]Tomás Vinar, Brona Brejová, Giltae Song, Adam C. Siepel:
Reconstructing Histories of Complex Gene Clusters on a Phylogeny. RECOMB-CG 2009: 150-163 - [c15]Jakub Kovác, Tomás Vinar, Brona Brejová:
Predicting Gene Structures from Multiple RT-PCR Tests. WABI 2009: 181-193 - [i2]Tomás Vinar, Brona Brejová, Giltae Song, Adam C. Siepel:
Bayesian History Reconstruction of Complex Human Gene Clusters on a Phylogeny. CoRR abs/0906.2635 (2009) - 2008
- [c14]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: 29-49 - 2007
- [j5]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): 1060-1077 (2007) - [c13]Xuefeng Cui, Tomás Vinar, Brona Brejová, Dennis E. Shasha, Ming Li:
Homology search for genes. ISMB/ECCB (Supplement of Bioinformatics) 2007: 97-103 - [c12]Rastislav Srámek, Brona Brejová, Tomás Vinar:
On-Line Viterbi Algorithm for Analysis of Long Biological Sequences. WABI 2007: 240-251 - [i1]Rastislav Srámek, Brona Brejová, Tomás Vinar:
On-line Viterbi Algorithm and Its Relationship to Random Walks. CoRR abs/0704.0062 (2007) - 2006
- [c11]Brona Brejová, Daniel G. Brown, Ian M. Harrower, Tomás Vinar:
New Bounds for Motif Finding in Strong Instances. CPM 2006: 94-105 - 2005
- [b1]Tomás Vinar:
Enhancements to Hidden Markov Models for Gene Finding and Other Biological Applications. University of Waterloo, Ontario, Canada, 2005 - [j4]Brona Brejová, Daniel G. Brown, Tomás Vinar:
Vector seeds: An extension to spaced seeds. J. Comput. Syst. Sci. 70(3): 364-380 (2005) - [c10]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: 1-10 - [c9]Brona Brejová, Daniel G. Brown, Ming Li, Tomás Vinar:
ExonHunter: a comprehensive approach to gene finding. ISMB (Supplement of Bioinformatics) 2005: 57-65 - 2004
- [j3]Brona Brejová, Daniel G. Brown, Tomás Vinar:
Optimal Spaced Seeds for Homologous Coding Regions. J. Bioinform. Comput. Biol. 1(4): 595-610 (2004) - [j2]Therese 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): 287-307 (2004) - [c8]Brona Brejová, Daniel G. Brown, Tomás Vinar:
The Most Probable Labeling Problem in HMMs and Its Application to Bioinformatics. WABI 2004: 426-437 - 2003
- [j1]Therese 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): 475-480 (2003) - [c7]Therese Biedl, Brona Brejová, Erik D. Demaine, Angèle M. Hamel, Alejandro López-Ortiz, Tomás Vinar:
Finding Hidden Independent Sets in Interval Graphs. COCOON 2003: 182-191 - [c6]Brona Brejová, Daniel G. Brown, Tomás Vinar:
Optimal Spaced Seeds for Hidden Markov Models, with Application to Homologous Coding Regions. CPM 2003: 42-54 - [c5]Brona Brejová, Daniel G. Brown, Tomás Vinar:
Vector Seeds: An Extension to Spaced Seeds Allows Substantial Improvements in Sensitivity and Specifity. WABI 2003: 39-54 - [c4]Brona Brejová, Daniel G. Brown, Tomás Vinar:
Optimal DNA Signal Recognition Models with a Fixed Amount of Intrasignal Dependency. WABI 2003: 78-94 - 2002
- [c3]Therese Biedl, Masud Hasan, Joseph Douglas Horton, Alejandro López-Ortiz, Tomás Vinar:
Searching for the center of a circle. CCCG 2002: 137-141 - [c2]Brona Brejová, Tomás Vinar:
A Better Method for Length Distribution Modeling in HMMs and Its Application to Gene Finding. CPM 2002: 190-202 - 2000
- [c1]Therese C. Biedl, Brona Brejová, Tomás Vinar:
Simplifying Flow Networks. MFCS 2000: 192-201
Coauthor Index
aka: Bronislava Brejová
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