Tomás Vinar

According to our database, Tomás Vinar authored at least 63 papers between 2000 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

RECOMB Satellite Conference on Comparative Genomics(RECOMB-CG 2023).

Tomás Vinar

J. Comput. Biol., 2024

Fast Context-Aware Analysis of Genome Annotation Colocalization.

Askar Gafurov, Tomás Vinar, Paul Medvedev, Brona Brejová

J. Comput. Biol., 2024

Maximum-scoring path sets on pangenome graphs of constant treewidth.

Brona Brejová, Travis Gagie, Eva Herencsárová, Tomás Vinar

Frontiers Bioinform., 2024

Bioinformatics of Pathogens (Invited Talk).

Tomás Vinar

Proceedings of the 24th International Workshop on Algorithms in Bioinformatics, 2024

Efficient Analysis of Annotation Colocalization Accounting for Genomic Contexts.

Askar Gafurov, Tomás Vinar, Paul Medvedev, Brona Brejová

Proceedings of the Research in Computational Molecular Biology, 2024

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

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

Proceedings of the 23rd Conference Information Technologies, 2023

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., December, 2022

Dynamic Pooling Improves Nanopore Base Calling Accuracy.

Vladimír Boza, Peter Peresíni, Brona Brejová, Tomás Vinar

IEEE ACM Trans. Comput. Biol. Bioinform., 2022

2021

Nanopore base calling on the edge.

Peter Peresíni, Vladimír Boza, Brona Brejová, Tomás Vinar

Bioinform., 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

Proceedings of the 21st Conference Information Technologies, 2021

Estimation of Proportions of SARS-CoV-2 Variants in a Mixed Sequencing Sample.

Askar Gafurov, Andrej Baláz, Tomás Vinar, Brona Brejová

Proceedings of the 21st Conference Information Technologies, 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

Proceedings of the 21st Conference Information Technologies, 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

Proceedings of the 21st Conference Information Technologies, 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

Proceedings of the 21st Conference Information Technologies, 2021

Probabilistic Models of k-mer Frequencies (Extended Abstract).

Askar Gafurov, Tomás Vinar, Brona Brejová

Proceedings of the Connecting with Computability, 2021

2020

DeepNano-blitz: a fast base caller for MinION nanopore sequencers.

Vladimír Boza, Peter Peresíni, Brona Brejová, Tomás Vinar

Bioinform., 2020

2017

Isometric gene tree reconciliation revisited.

Brona Brejová, Askar Gafurov, Dana Pardubská, Michal Sabo, Tomás Vinar

Algorithms Mol. Biol., 2017

Using Sequence Ensembles for Seeding Alignments of MinION Sequencing Data.

Rastislav Rabatin, Brona Brejová, Tomás Vinar

Proceedings of the 17th Conference on Information Technologies, 2017

Approximate Abundance Histograms and Their Use for Genome Size Estimation.

Mário Lipovský, Tomás Vinar, Brona Brejová

Proceedings of the 17th Conference on Information Technologies, 2017

2016

RNA motif search with data-driven element ordering.

Ladislav Rampásek, Randi M. Jimenez, Andrej Lupták, Tomás Vinar, Brona Brejová

BMC Bioinform., 2016

OB-Fold Recognition Combining Sequence and Structural Motifs.

Martin Macko, Martin Králik, Brona Brejová, Tomás Vinar

Proceedings of the 16th ITAT Conference Information Technologies, 2016

2015

Sequence annotation with HMMs: New problems and their complexity.

Michal Nánási, Tomás Vinar, Brona Brejová

Inf. Process. Lett., 2015

GAML: genome assembly by maximum likelihood.

Vladimír Boza, Brona Brejová, Tomás Vinar

Algorithms Mol. Biol., 2015

How Big is that Genome? Estimating Genome Size and Coverage from k-mer Abundance Spectra.

Michal Hozza, Tomás Vinar, Brona Brejová

Proceedings of the String Processing and Information Retrieval, 2015

Fishing in Read Collections: Memory Efficient Indexing for Sequence Assembly.

Vladimír Boza, Jakub Jursa, Brona Brejová, Tomás Vinar

Proceedings of the String Processing and Information Retrieval, 2015

2014

Probabilistic approaches to alignment with tandem repeats.

Michal Nánási, Tomás Vinar, Brona Brejová

Algorithms Mol. Biol., 2014

2013

Efficient routing in carrier-based mobile networks.

Brona Brejová, Stefan Dobrev, Rastislav Královic, Tomás Vinar

Theor. Comput. Sci., 2013

DNA Sequence Segmentation Based on Local Similarity.

Martina Visnovská, Tomás Vinar, Brona Brejová

Proceedings of the Conference on Information Technologies, 2013

Variants of Genes from the Next Generation Sequencing Data.

Martin Kravec, Martin Bobák, Brona Brejová, Tomás Vinar

Proceedings of the Conference on Information Technologies, 2013

2012

Aligning sequences with repetitive motifs.

Peter Kovác, Brona Brejová, Tomás Vinar

Proceedings of the Conference on Theory and Practice of Information Technologies, 2012

2011

A Practical Algorithm for Ancestral Rearrangement Reconstruction.

Jakub Kovác, Brona Brejová, Tomás Vinar

Proceedings of the Algorithms in Bioinformatics - 11th International Workshop, 2011

Automated Segmentation of DNA Sequences with Complex Evolutionary Histories.

Brona Brejová, Michal Burger, Tomás Vinar

Proceedings of the Algorithms in Bioinformatics - 11th International Workshop, 2011

Fast Computation of a String Duplication History under No-Breakpoint-Reuse - (Extended Abstract).

Brona Brejová, Gad M. Landau, Tomás Vinar

Proceedings of the String Processing and Information Retrieval, 2011

Routing in Carrier-Based Mobile Networks.

Bronislava Brejová, Stefan Dobrev, Rastislav Královic, Tomás Vinar

Proceedings of the Structural Information and Communication Complexity, 2011

2010

Reconstructing Histories of Complex Gene Clusters on a Phylogeny.

Tomás Vinar, Brona Brejová, Giltae Song, Adam C. Siepel

J. Comput. Biol., 2010

CAGE: Combinatorial Analysis of Gene-Cluster Evolution.

Giltae Song, Louxin Zhang, Tomás Vinar, Webb Miller

J. Comput. Biol., 2010

Estimating effective DNA database size via compression.

Martina Visnovská, Michal Nánási, Tomás Vinar, Brona Brejová

Proceedings of the Conference on Theory and Practice of Information Technologies, 2010

The Highest Expected Reward Decoding for HMMs with Application to Recombination Detection.

Michal Nánási, Tomás Vinar, Brona Brejová

Proceedings of the Combinatorial Pattern Matching, 21st Annual Symposium, 2010

2009

Evolutionary History Reconstruction for Mammalian Complex Gene Clusters.

Yu Zhang, Giltae Song, Tomás Vinar, Eric D. Green, Adam C. Siepel, Webb Miller

J. Comput. Biol., 2009

Bayesian History Reconstruction of Complex Human Gene Clusters on a Phylogeny

Tomás Vinar, Brona Brejová, Giltae Song, Adam C. Siepel

CoRR, 2009

Predicting Gene Structures from Multiple RT-PCR Tests.

Jakub Kovác, Tomás Vinar, Brona Brejová

Proceedings of the Algorithms in Bioinformatics, 9th International Workshop, 2009

Inferring the Recent Duplication History of a Gene Cluster.

Giltae Song, Louxin Zhang, Tomás Vinar, Webb Miller

Proceedings of the Comparative Genomics, International Workshop, 2009

2008

Reconstructing the Evolutionary History of Complex Human Gene Clusters.

Yu Zhang, Giltae Song, Tomás Vinar, Eric D. Green, Adam C. Siepel, Webb Miller

Proceedings of the Research in Computational Molecular Biology, 2008

2007

The most probable annotation problem in HMMs and its application to bioinformatics.

Brona Brejová, Daniel G. Brown, Tomás Vinar

J. Comput. Syst. Sci., 2007

On-line Viterbi Algorithm and Its Relationship to Random Walks

Rastislav Srámek, Brona Brejová, Tomás Vinar

CoRR, 2007

On-Line Viterbi Algorithm for Analysis of Long Biological Sequences.

Rastislav Srámek, Brona Brejová, Tomás Vinar

Proceedings of the Algorithms in Bioinformatics, 7th International Workshop, 2007

Homology search for genes.

Xuefeng Cui, Tomás Vinar, Brona Brejová, Dennis E. Shasha, Ming Li

Proceedings of the Proceedings 15th International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), 2007

2006

New Bounds for Motif Finding in Strong Instances.

Brona Brejová, Daniel G. Brown, Ian M. Harrower, Tomás Vinar

Proceedings of the Combinatorial Pattern Matching, 17th Annual Symposium, 2006

2005

Enhancements to Hidden Markov Models for Gene Finding and Other Biological Applications.

Tomás Vinar

PhD thesis, 2005

Vector seeds: An extension to spaced seeds.

Brona Brejová, Daniel G. Brown, Tomás Vinar

J. Comput. Syst. Sci., 2005

ExonHunter: a comprehensive approach to gene finding.

Brona Brejová, Daniel G. Brown, Ming Li, Tomás Vinar

Proceedings of the Proceedings Thirteenth International Conference on Intelligent Systems for Molecular Biology 2005, 2005

Sharper Upper and Lower Bounds for an Approximation Scheme for Consensus-Pattern.

Brona Brejová, Daniel G. Brown, Ian M. Harrower, Alejandro López-Ortiz, Tomás Vinar

Proceedings of the Combinatorial Pattern Matching, 16th Annual Symposium, 2005

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

Optimal Spaced Seeds for Homologous Coding Regions.

Brona Brejová, Daniel G. Brown, Tomás Vinar

J. Bioinform. Comput. Biol., 2004

The Most Probable Labeling Problem in HMMs and Its Application to Bioinformatics.

Brona Brejová, Daniel G. Brown, Tomás Vinar

Proceedings of the Algorithms in Bioinformatics, 4th International Workshop, 2004

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

Optimal DNA Signal Recognition Models with a Fixed Amount of Intrasignal Dependency.

Brona Brejová, Daniel G. Brown, Tomás Vinar

Proceedings of the Algorithms in Bioinformatics, Third International Workshop, 2003

Vector Seeds: An Extension to Spaced Seeds Allows Substantial Improvements in Sensitivity and Specifity.

Brona Brejová, Daniel G. Brown, Tomás Vinar

Proceedings of the Algorithms in Bioinformatics, Third International Workshop, 2003

Optimal Spaced Seeds for Hidden Markov Models, with Application to Homologous Coding Regions.

Brona Brejová, Daniel G. Brown, Tomás Vinar

Proceedings of the Combinatorial Pattern Matching, 14th Annual Symposium, 2003

2002

A Better Method for Length Distribution Modeling in HMMs and Its Application to Gene Finding.

Brona Brejová, Tomás Vinar

Proceedings of the Combinatorial Pattern Matching, 13th Annual Symposium, 2002

Searching for the center of a circle.

Therese Biedl, Masud Hasan, Joseph Douglas Horton, Alejandro López-Ortiz, Tomás Vinar

Proceedings of the 14th Canadian Conference on Computational Geometry, 2002

2000

Simplifying Flow Networks.

Therese C. Biedl, Brona Brejová, Tomás Vinar

Proceedings of the Mathematical Foundations of Computer Science 2000, 2000