Tomas Vinar's publications
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- Janik Sielemann, Katharina Sielemann, Broňa Brejová, Tomáš Vinař, Cedric Chauve.
plASgraph2: using graph neural networks to detect plasmid contigs from an assembly graph.
Frontiers in Microbiology,
14:fmicb.2023.1267695.
2023.
[ Abstract ] [ Download from publisher ] [ BibTeX ]
- Vladimír Boža, Eduard Batmendijn, Peter Perešíni, Viktória Hodorová, Hana Lichancová, Rastislav Rabatin, Broňa Brejová, Jozef Nosek, Tomáš Vinař.
Precise Nanopore Signal Modeling Improves Unsupervised Single-Molecule Methylation Detection.
In Proceedings of the 23rd Conference Information Technologies – Applications and Theory (ITAT 2023),
3498 volume of CEUR Workshop Proceedings,
pp. 223-231, Tatranske Matliare, 2023.
[ Abstract ] [ Download from publisher ] [ BibTeX ]
- Aniket Mane, Mahsa Faizrahnemoon, Tomas Vinar, Brona Brejova, Cedric Chauve.
PlasBin-flow: a flow-based MILP algorithm for plasmid contigs binning.
Bioinformatics,
39(S1):i288-i296.
2023.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Jozef Sitarcik, Tomas Vinar, Brona Brejova, Werner Krampl, Jaroslav Budis, Jan Radvanszky, Maria Lucka.
WarpSTR: determining tandem repeat lengths using raw nanopore signals.
Bioinformatics,
39(6).
2023.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Bronislava Brejova, Veronika Vozarikova, Ivan Agarsky, Hana Derkova, Matej Fedor, Dominika Harmanova, Lukas Kiss, Andrej Korman, Martin Pasen, Filip Brazdovic, Tomas Vinar, Jozef Nosek, Lubomir Tomaska.
y-mtPTM: Yeast mitochondrial posttranslational modification database.
Genetics,
224(3):iyad087.
2023.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Janik Sielemann, Katharina Sielemann, Broňa Brejová, Tomáš Vinař, Cedric Chauve.
plASgraph2: using graph neural networks to detect plasmid contigs from an assembly graph.
Frontiers in Microbiology,
14:fmicb.2023.1267695.
2023.
[ Abstract ] [ Download from publisher ] [ BibTeX ]
- Aniket Mane, Mahsa Faizrahnemoon, Tomas Vinar, Brona Brejova, Cedric Chauve.
PlasBin-flow: a flow-based MILP algorithm for plasmid contigs binning.
Bioinformatics,
39(S1):i288-i296.
2023.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Jozef Sitarcik, Tomas Vinar, Brona Brejova, Werner Krampl, Jaroslav Budis, Jan Radvanszky, Maria Lucka.
WarpSTR: determining tandem repeat lengths using raw nanopore signals.
Bioinformatics,
39(6).
2023.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Bronislava Brejova, Veronika Vozarikova, Ivan Agarsky, Hana Derkova, Matej Fedor, Dominika Harmanova, Lukas Kiss, Andrej Korman, Martin Pasen, Filip Brazdovic, Tomas Vinar, Jozef Nosek, Lubomir Tomaska.
y-mtPTM: Yeast mitochondrial posttranslational modification database.
Genetics,
224(3):iyad087.
2023.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Brona Brejova, Viktoria Hodorova, Hana Lichancova, Eunika Perickova, Veronika Anna Soucova, Matthias Sipiczki, Tomas Vinar, Jozef Nosek.
Chromosome-Level Genome Assembly of the Yeast Candida verbasci.
Microbiology Resource Announcements,
12(3):e0000523.
2023.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Askar Gafurov, Andrej Balaz, Fabian Amman, Kristina Borsova, Viktoria Cabanova, Boris Klempa, Andreas Bergthaler, Tomas Vinar, Brona Brejova.
VirPool: model-based estimation of SARS-CoV-2 variant proportions in wastewater samples.
BMC Bioinformatics,
23(1):551.
2022.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Andrea Cillingova, Renata Toth, Anna Mojakova, Igor Zeman, Romana Vrzonova, Barbara Sivakova, Peter Barath, Martina Nebohacova, Zuzana Klepcova, Filip Brazdovic, Hana Lichancova, Viktoria Hodorova, Brona Brejova, Tomas Vinar, Sofia Mutalova, Veronika Vozarikova, Giacomo Mutti, Lubomir Tomaska, Atilla Gacser, Toni Gabaldon, Jozef Nosek.
Transcriptome and proteome profiling reveals complex adaptations of Candidaparapsilosis cells assimilating hydroxyaromatic carbon sources.
PLoS Genetics,
18(3):e1009815.
2022.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Branislav Kovacech, Lubica Fialova, Peter Filipcik, Rostislav Skrabana, Monika Zilkova, Natalia Paulenka-Ivanovova, Andrej Kovac, Denisa Palova, Gabriela Paulikova Rolkova, Katarina Tomkova, Natalia Turic Csokova, Karina Markova, Michaela Skrabanova, Kristina Sinska, Neha Basheer, Petra Majerova, Jozef Hanes, Vojtech Parrak, Michal Prcina, Ondrej Cehlar, Martin Cente, Juraj Piestansky, Michal Fresser, Michal Novak, Monika Slavikova, Kristina Borsova, Viktoria Cabanova, Bronislava Brejova, Tomas Vinar, Jozef Nosek, Boris Klempa, Ludek Eyer, Vaclav Honig, Martin Palus, Daniel Ruzek, Tereza Vyhlidalova, Petra Strakova, Blanka Mrazkova, Dagmar Zudova, Gizela Koubkova, Vendula Novosadova, Jan Prochazka, Radislav Sedlacek, Norbert Zilka, Eva Kontsekova.
Monoclonal antibodies targeting two immunodominant epitopes on the Spike protein neutralize emerging SARS-CoV-2 variants of concern.
EBioMedicine,
76:103818.
2022.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Vladimir Boza, Peter Peresini, Brona Brejova, Tomas Vinar.
Dynamic Pooling Improves Nanopore Base Calling Accuracy.
IEEE/ACM Trans Comput Biol Bioinform,
2022.
accepted, published on-line ahead of print.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Kristina Borsova, Evan D. Paul, Viera Kovacova, Monika Radvanszka, Roman Hajdu, Viktoria Cabanova, Monika Slavikova, Martina Lickova, Lubomira Lukacikova, Andrej Belak, Lucia Roussier, Michaela Kosticova, Anna Liskova, Lucia Madarova, Maria Stefkovicova, Lenka Reizigova, Elena Novakova, Peter Sabaka, Alena Koscalova, Brona Brejova, Edita Staronova, Matej Misik, Tomas Vinar, Jozef Nosek, Pavol Cekan, Boris Klempa.
Surveillance of SARS-CoV-2 lineage B.1.1.7 in Slovakia using a novel, multiplexedRT-qPCR assay.
Scientific Reports,
11(1):20494.
2021.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Brona Brejova, Kristina Borsova, Viktoria Hodorova, Viktoria Cabanova, Askar Gafurov, Dominika Fricova, Martina Nebohacova, Tomas Vinar, Boris Klempa, Jozef Nosek.
Nanopore sequencing of SARS-CoV-2: Comparison of short and long PCR-tilingamplicon protocols.
PLoS One,
16(10):e0259277.
2021.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Peter Peresini, Vladimir Boza, Brona Brejova, Tomas Vinar.
Nanopore Base Calling on the Edge.
Bioinformatics,
37(24):4661-4667.
2021.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Brona Brejova, Kristina Borsova, Viktoria Hodorova, Viktoria Cabanova, Lenka Reizigova, Evan D. Paul, Pavol Cekan, Boris Klempa, Jozef Nosek, Tomas Vinar.
A SARS-CoV-2 mutant from B.1.258 lineage with H69/V70 deletion in the Spike protein circulating in Central Europe in the fall 2020.
Virus genes,
57(6):556-560.
2021.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Vladimir Boza, Peter Peresini, Brona Brejova, Tomas Vinar.
DeepNano-blitz: a fast base caller for MinION nanopore sequencers.
Bioinformatics,
36(14):4191-4192.
2020.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Eva Zahradnikova, Andrej Ficek, Brona Brejova, Tomas Vinar, Karol Micieta.
Mosaicism in old trees and its patterns.
Trees,
34:357-370.
2020.
[ Abstract ] [ Download from publisher ] [ BibTeX ]
- Rute R. {da Fonseca}, Alvarina Couto, Andre M. Machado, Brona Brejova, Carolin B. Albertin, Filipe Silva, Paul Gardner, Tobias Baril, Alex Hayward, Alexandre Campos, Angela M. Ribeiro, Inigo Barrio-Hernandez, Henk-Jan Hoving, Ricardo Tafur-Jimenez, Chong Chu, Barbara Frazao, Bent Petersen, Fernando Penaloza, Francesco Musacchia, Graham C. Alexander, Hugo Osorio, Inger Winkelmann, Oleg Simakov, Simon Rasmussen, M. Ziaur Rahman, Davide Pisani, Jakob Vinther, Erich Jarvis, Guojie Zhang, Jan M. Strugnell, L. Filipe C. Castro, Olivier Fedrigo, Mateus Patricio, Qiye Li, Sara Rocha, Agostinho Antunes, Yufeng Wu, Bin Ma, Remo Sanges, Tomas Vinar, Blagoy Blagoev, Thomas Sicheritz-Ponten, Rasmus Nielsen, M. Thomas P. Gilbert.
A draft genome sequence of the elusive giant squid, Architeuthis dux.
Gigascience,
9(1).
2020.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Jerilyn A. Walker, Vallmer E. Jordan, Jessica M. Storer, Cody J. Steely, Paulina Gonzalez-Quiroga, Thomas O. Beckstrom, Lydia C. Rewerts, Corey P. {St Romain}, Catherine E. Rockwell, Jeffrey Rogers, Clifford J. Jolly, Miriam K. Konkel, {Baboon Genome Analysis Consortium}, Mark A. Batzer.
Alu insertion polymorphisms shared by Papio baboons and Theropithecus geladareveal an intertwined common ancestry.
Mobile DNA,
10:46.
2019.
Tomas Vinar is a member of the Baboon Genome Analysis Consortium.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Brona Brejova, Hana Lichancova, Viktoria Hodorova, Martina Nebohacova, Lubomir Tomaska, Tomas Vinar, Jozef Nosek.
Genome Sequence of an Arthroconidial Yeast, Saprochaete fungicola CBS 625.85.
Microbiology Resource Announcements,
8(15).
2019.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Hana Lichancová, Viktória Hodorová, Karolina Sienkiewicz, Sarah Mae U. Penir, Philipp Afanasyev, Dominic Boceck, Sarah Bonnin, Siras Hakobyan, Pawel S. Krawczyk, Urszula Smyczynska, Erik Zhivkoplias, Maryna Zlatohurska, Adrian Odrzywolski, Eugeniusz Tralle, Alina Frolova, Leszek P. Pryszcz, Broňa Brejová, Tomáš Vinař, Jozef Nosek.
Genome Sequence of Flavor-Producing Yeast Saprochaete suaveolens NRRL Y-17571.
Microbiology Resource Announcements,
8(9):e00094-19.
2019.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- {Baboon Genome Analysis Consortium}.
The Comparative Genomics and Complex Population History of Papio Baboons.
Science Advances,
5(1):eaau6947.
2019.
Tomas Vinar is a member of the Baboon Genome Analysis Consortium.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Bronislava Brejova, Hana Lichancova, Filip Brazdovic, Eva Hegedusova, Michaela {Forgacova Jakubkova}, Viktoria Hodorova, Vladimira Dzugasova, Andrej Balaz, Lucia Zeiselova, Andrea Cillingova, Martina Nebohacova, Vladislav Raclavsky, Lubomir Tomaska, B. Franz Lang, Tomas Vinar, Jozef Nosek.
Genome sequence of the opportunistic human pathogen Magnusiomyces capitatus.
Current Genetics,
65(2):539-560.
2019.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Jaroslav Budis, Marcel Kucharik, Frantisek Duris, Juraj Gazdarica, Michaela Zrubcova, Andrej Ficek, Tomas Szemes, Brona Brejova, Jan Radvanszky.
Dante: genotyping of known complex and expanded short tandem repeats.
Bioinformatics,
35(8):1310-1317.
2019.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Vallmer E. Jordan, Jerilyn A. Walker, Thomas O. Beckstrom, Cody J. Steely, Cullen L. McDaniel, Corey P. {St Romain}, {Baboon Genome Analysis Consortium}, Kim C. Worley, Jane Phillips-Conroy, Clifford J. Jolly, Jeffrey Rogers, Miriam K. Konkel, Mark A. Batzer.
A computational reconstruction of Papio phylogeny using Alu insertionpolymorphisms.
Mobile DNA,
9:13.
2018.
Tomas Vinar is a member of the Baboon Genome Analysis Consortium.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Cody J. Steely, Jasmine N. Baker, Jerilyn A. Walker, Charles D. 3rd Loupe, {Baboon Genome Analysis Consortium}, Mark A. Batzer.
Analysis of lineage-specific Alu subfamilies in the genome of the olive baboon,Papio anubis.
Mobile DNA,
9:10.
2018.
Tomas Vinar is a member of the Baboon Genome Analysis Consortium.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Jerilyn A. Walker, Vallmer E. Jordan, Cody J. Steely, Thomas O. Beckstrom, Cullen L. McDaniel, Corey P. {St Romain}, Emily C. Bennett, Arianna Robichaux, Brooke N. Clement, Miriam K. Konkel, {Baboon Genome Analysis Consortium}, Mark A. Batzer.
Papio Baboon Species Indicative Alu Elements.
Genome Biology and Evolution,
9(6):1788-1796.
2017.
Tomas Vinar is a member of the Baboon Genome Analysis Consortium.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Brona Brejova, Hana Lichancova, Filip Brazdovic, Andrea Cillingova, Martina Nebohacova, Lubomir Tomaska, Tomas Vinar, Jozef Nosek.
Draft Genome Sequence of an Obligate Psychrophilic Yeast, Candida psychrophila NRRL Y-17665T.
Genome Announc,
5(35).
2017.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Broňa Brejová, Askar Gafurov, Dana Pardubská, Michal Sabo, Tomáš Vinař.
Isometric gene tree reconciliation revisited.
Algorithms for Molecular Biology,
12:17.
2017.
Early version appeared at WABI 2016.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Vladimír Boža, Broňa Brejová, Tomáš Vinař.
DeepNano: Deep recurrent neural networks for base calling in MinION nanopore reads.
PLoS One,
12(6):e0178751.
2017.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Andrew D. Foote, Nagarjun Vijay, Maria C. Avila-Arcos, Robin W. Baird, John W. Durban, Matteo Fumagalli, Richard A. Gibbs, M. Bradley Hanson, Thorfinn S. Korneliussen, Michael D. Martin, Kelly M. Robertson, Vitor C. Sousa, Filipe G. Vieira, Tomas Vinar, Paul Wade, Kim C. Worley, Laurent Excoffier, Phillip A. Morin, M. Thomas P. Gilbert, Jochen B. W. Wolf.
Genome-culture coevolution promotes rapid divergence of killer whale ecotypes.
Nature Communications,
7:11693.
2016.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Ladislav Rampasek, Randi M. Jimenez, Andrej Luptak, Tomas Vinar, Brona Brejova.
RNA motif search with data-driven element ordering.
BMC Bioinformatics,
17(1):216.
2016.
[ Abstract ] [ Download from publisher ] [ Webpage ] [ BibTeX ] [ PubMed ]
- Vladimír Boža, Broňa Brejová, Tomáš Vinař.
GAML: genome assembly by maximum likelihood.
Algorithms for Molecular Biology,
10:18.
2015.
Early version at WABI 2014.
[ Abstract ] [ Download from publisher ] [ Webpage ] [ BibTeX ] [ PubMed ]
- Michal Nánási, Tomáš Vinař, Broňa Brejová.
Sequence annotation with HMMs: New problems and their complexity.
Information Processing Letters,
115(6):635-639.
2015.
[ Abstract ] [ Download from publisher ] [ BibTeX ]
- Andrew D. Foote, Yue Liu, Gregg W. C. Thomas, Tomas Vinar, Jessica Alfoldi, Jixin Deng, Shannon Dugan, Cornelis E. {van Elk}, Margaret E. Hunter, Vandita Joshi, Ziad Khan, Christie Kovar, Sandra L. Lee, Kerstin Lindblad-Toh, Annalaura Mancia, Rasmus Nielsen, Xiang Qin, Jiaxin Qu, Brian J. Raney, Nagarjun Vijay, Jochen B. W. Wolf, Matthew W. Hahn, Donna M. Muzny, Kim C. Worley, M. Thomas P. Gilbert, Richard A. Gibbs.
Convergent evolution of the genomes of marine mammals.
Nature Genetics,
47(3):272-275.
2015.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Marmoset Genome Sequencing and Analysis Consortium.
The common marmoset genome provides insight into primate biology and evolution.
Nature Genetics,
46(8):850-857.
2014.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Brona Brejova, Martin Kravec, Gad M. Landau, Tomas Vinar.
Fast computation of a string duplication history under no-breakpoint-reuse.
Philos Trans A Math Phys Eng Sci,
372(2016):20130133.
2014.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- B. Franz Lang, Michaela Jakubkova, Eva Hegedusova, Rachid Daoud, Lise Forget, Brona Brejova, Tomas Vinar, Peter Kosa, Dominika Fricova, Martina Nebohacova, Peter Griac, Lubomir Tomaska, Gertraud Burger, Jozef Nosek.
Massive programmed translational jumping in mitochondria.
Proceedings of the National Academy of Sciences of the United States of America,
111(16):5926-5931.
2014.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Michal Nanasi, Tomas Vinar, Brona Brejova.
Probabilistic approaches to alignment with tandem repeats.
2014.
Early version appeared in WABI 2013.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- R. Alan Harris, Suzette D. Tardif, Tomas Vinar, Derek E. Wildman, Julienne N. Rutherford, Jeffrey Rogers, Kim C. Worley, Kjersti M. Aagaard.
Evolutionary genetics and implications of small size and twinning incallitrichine primates.
Proceedings of the National Academy of Sciences of the United States of America,
111(4):1467-1472.
2014.
[ Abstract ] [ BibTeX ] [ PubMed ]
- Xin Ma, Joanna L. Kelley, Kirsten Eilertson, Shaila Musharoff, Jeremiah D. Degenhardt, Andre L. Martins, Tomas Vinar, Carolin Kosiol, Adam Siepel, Ryan N. Gutenkunst, Carlos D. Bustamante.
Population Genomic Analysis Reveals a Rich Speciation and Demographic History of Orang-utans (Pongo pygmaeus and Pongo abelii).
PLoS One,
8(10):e77175.
2013.
[ Abstract ] [ BibTeX ] [ PubMed ]
- Brona Brejova, Stefan Dobrev, Rastislav Kralovic, Tomas Vinar.
Efficient routing in carrier-based mobile networks.
2013.
Early version appeared in SIROCCO 2011.
[ Abstract ] [ Download from publisher ] [ BibTeX ]
- Huajun Zheng, Wenbao Zhang, Liang Zhang, Zhuangzhi Zhang, Jun Li, Gang Lu, Yongqiang Zhu, Yuezhu Wang, Yin Huang, Jing Liu, Hui Kang, Jie Chen, Lijun Wang, Aojun Chen, Shuting Yu, Zhengchao Gao, Lei Jin, Wenyi Gu, Zhiqin Wang, Li Zhao, Baoxin Shi, Hao Wen, Renyong Lin, Malcolm K. Jones, Brona Brejova, Tomas Vinar, Guoping Zhao, Donald P. McManus, Zhu Chen, Yan Zhou, Shengyue Wang.
The genome of the hydatid tapeworm Echinococcus granulosus.
Nature Genetics,
45(10):1168-1175.
2013.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- H. Bradley Shaffer et al..
The western painted turtle genome, a model for the evolution of extremephysiological adaptations in a slowly evolving lineage.
Genome Biology,
14(3):R28.
2013.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Sheng Zhu, You-Zhi Cao, Cong Jiang, Bi-Yue Tan, Zhong Wang, Sisi Feng, Liang Zhang, Xiao-Hua Su, Brona Brejova, Tomas Vinar, Meng Xu, Ming-Xiu Wang, Shou-Gong Zhang, Min-Ren Huang, Rongling Wu, Yan Zhou.
Sequencing the genome of Marssonina brunnea reveals fungus-poplar co-evolution.
BMC Genomics,
13:382.
2012.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Orangutan Genome Sequencing and Analysis Consortium.
Comparative and demographic analysis of orang-utan genomes.
Nature,
469(7331):529-533.
2011.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- M. Valach, Z. Farkas, D. Fricova, J. Kovac, B. Brejova, T. Vinar, I. Pfeiffer, J. Kucsera, L. Tomaska, B. F. Lang, J. Nosek.
Evolution of linear chromosomes and multipartite genomes in yeast mitochondria.
Nucleic Acids Research,
39(10):4202-4219.
2011.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Giltae Song, Luoxin Zhang, Tomas Vinar, Webb Miller.
CAGE: Combinatorial Analysis of Gene-Cluster Evolution.
Journal of Computational Biology,
17(9):1227-1232.
2010.
Early version appeared in RECOMB-CG 2009.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Tomas Vinar, Brona Brejova, Giltae Song, Adam C. Siepel.
Reconstructing Histories of Complex Gene Clusters on a Phylogeny.
Journal of Computational Biology,
17(9):1267-1279.
2010.
Early version appeared in RECOMB-CG 2009.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Rute R. {da Fonseca}, Carolin Kosiol, Tomas Vinar, Adam Siepel, Rasmus Nielsen.
Positive selection on apoptosis related genes.
FEBS letters,
584(3):469-476.
2010.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Panda Genome Sequencing and Analysis Consortium.
The sequence and de novo assembly of the giant panda genome.
Nature,
463(7279):269-392.
2010.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Yu Zhang, Giltae Song, Tomas Vinar, Eric D. Green, Adam Siepel, Webb Miller.
Evolutionary History Reconstruction for Mammalian Complex Gene Clusters.
Journal of Computational Biology,
16(8):1051-1070.
2009.
Early version appeared in RECOMB 2008.
[ Abstract ] [ Preprint, 965Kb ] [ Download from publisher ] [ BibTeX ]
- Schistosoma japonicum Genome Sequencing and Functional Analysis Consortium .
The Schistosoma japonicum genome reveals features of host-parasite interplay.
Nature,
460(7253):345-351.
2009.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Brona Brejova, Tomas Vinar, Yangyi Chen, Shengyue Wang, Guoping Zhao, Daniel G. Brown, Ming Li, Yan Zhou.
Finding genes in Schistosoma japonicum: annotating novel genomes with help of extrinsic evidence.
Nucleic Acids Research,
37(7):e52.
2009.
[ Abstract ] [ Preprint, 153Kb ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Avril Coghlan, Tristan J. Fiedler, Sheldon J. McKay, Paul Flicek, Todd W. Harris, Darin Blasiar, {The nGASP Consortium}, Lincoln D. Stein.
nGASP - the nematode genome annotation assessment project .
BMC Bioinformatics,
9:549.
2008.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Carolin Kosiol, Tomas Vinar, Rute R. {da Fonseca}, Melissa J. Hubisz, Carlos D. Bustamante, Rasmus Nielsen, Adam Siepel.
Patterns of positive selection in six Mammalian genomes.
PLoS Genetics,
4(8):e1000144.
2008.
[ Abstract ] [ Preprint, 538Kb ] [ Download from publisher ] [ Webpage ] [ BibTeX ] [ PubMed ]
- Xuefeng Cui, Tomas Vinar, Brona Brejova, Dennis Shasha, Ming Li.
Homology Search for Genes.
Bioinformatics,
23(13):i97-i103.
2007.
Intelligent Systems for Molecular Biology (ISMB 2007).
[ Abstract ] [ Preprint, 159Kb ] [ Download from publisher ] [ Webpage ] [ BibTeX ] [ PubMed ]
- Rhesus Macaque Genome Sequencing and Analysis Consortium.
Evolutionary and biomedical insights from the rhesus macaque genome.
Science,
316(5822):222-234.
April 2007.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Brona Brejova, Daniel G. Brown, Tomas Vinar.
The most probable labeling problem in HMMs and its application to bioinformatics.
Journal of Computer and System Sciences,
73(7):1060-1077.
2007.
Early version in WABI 2004.
[ Abstract ] [ Preprint, 335Kb ] [ Download from publisher ] [ BibTeX ]
- Brona Brejova, Daniel G. Brown, Ming Li, Tomas Vinar.
ExonHunter: A Comprehensive Approach to Gene Finding.
Bioinformatics,
21(S1):i57-i65.
2005.
Intelligent Systems for Molecular Biology (ISMB 2005).
[ Abstract ] [ Preprint, 144Kb ] [ Download from publisher ] [ Webpage ] [ BibTeX ] [ PubMed ]
- Brona Brejova, Daniel G. Brown, Tomas Vinar.
Vector seeds: an extension to spaced seeds.
Journal of Computer and System Sciences,
70(3):364-380.
May 2005.
Special issue on bioinformatics. Early version in WABI 2003.
[ Abstract ] [ Preprint, 406Kb ] [ Download from publisher ] [ BibTeX ]
- Brona Brejova, Daniel G. Brown, Tomas Vinar.
Optimal Spaced Seeds for Homologous Coding Regions.
Journal of Bioinformatics and Computational Biology,
1(4):595-610.
January 2004.
Early version appeared in CPM 2003.
[ Abstract ] [ Preprint, 2657Kb ] [ Download from publisher ] [ Webpage ] [ BibTeX ] [ PubMed ]
- Therese Biedl, Brona Brejova, Erik D. Demaine, Angele M. Hamel, Alejandro Lopez-Ortiz, Tomas Vinar.
Finding Hidden Independent Sets in Interval Graphs.
Theoretical Computer Science,
310(1-3):287-307.
January 2004.
Early version appeared in COCOON 2003.
[ Abstract ] [ Preprint, 216Kb ] [ Download from publisher ] [ BibTeX ] [ MathSciNet ]
- Therese Biedl, Jonathan F. Buss, Erik D. Demaine, Martin L. Demaine, Mohammadtaghi Hajiaghayi, Tomas Vinar.
Palindrome recognition using a multidimensional tape .
Theoretical Computer Science,
302(1-3):475-480.
13 June 2003.
[ Abstract ] [ Preprint, 79Kb ] [ Download from publisher ] [ BibTeX ] [ MathSciNet ]
- Vladimír Boža, Eduard Batmendijn, Peter Perešíni, Viktória Hodorová, Hana Lichancová, Rastislav Rabatin, Broňa Brejová, Jozef Nosek, Tomáš Vinař.
Precise Nanopore Signal Modeling Improves Unsupervised Single-Molecule Methylation Detection.
In Proceedings of the 23rd Conference Information Technologies – Applications and Theory (ITAT 2023),
3498 volume of CEUR Workshop Proceedings,
pp. 223-231, Tatranske Matliare, 2023.
[ Abstract ] [ Download from publisher ] [ BibTeX ]
- Vladimír Boža, Matej Fedor, Kristína Boršová, Viktória Čabanová, Jana Černíková, Viktória Hodorová, Peter Perešíni, Klára Sládečková, Boris Klempa, Jozef Nosek, Broňa Brejová, Tomáš Vinař.
Alternative Base Callers Aid Real-time Analysis of SARS-CoV-2 Sequencing Runs.
In Information Technologies: Applications and Theory (ITAT 2021),
2962 volume of CEUR Workshop Proceedings,
pp. 308-313, 2021.
[ Abstract ] [ Download from publisher ] [ BibTeX ]
- Askar Gafurov, Andrej Baláž, Tomáš Vinař, Broňa Brejová.
Estimation of Proportions of SARS-CoV-2 Variants in a Mixed Sequencing Sample.
In Information Technologies: Applications and Theory (ITAT 2021),
2962 volume of CEUR Workshop Proceedings,
pp. 301-307, 2021.
[ Abstract ] [ Download from publisher ] [ BibTeX ]
- Adrián Goga, Miroslav Böhmer, Rastislav Hekel, Werner Krampl, Bronislava Brejová, Tomáš Vinař, Jaroslav Budiš, Tomáš Szemes.
SnakeLines Workflow for SARS-CoV-2 Variant Detection from Next-Generation Sequencing Reads.
In Information Technologies: Applications and Theory (ITAT 2021),
2962 volume of CEUR Workshop Proceedings,
pp. 293-300, 2021.
[ Abstract ] [ Download from publisher ] [ BibTeX ]
- Katarína Boďová, Vladimír Boža, Broňa Brejová, Richard Kollár, Katarína Mikušová, Tomáš Vinař.
Time-adjusted Analysis Shows Weak Associations Between BCG Vaccination Policy and COVID-19 Disease Progression.
In Information Technologies: Applications and Theory (ITAT 2021),
2962 volume of CEUR Workshop Proceedings,
pp. 255-262, 2021.
[ Abstract ] [ Download from publisher ] [ BibTeX ]
- 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.
In Information Technologies: Applications and Theory (ITAT 2021),
2962 volume of CEUR Workshop Proceedings,
pp. 229-239, 2021.
[ Abstract ] [ Download from publisher ] [ BibTeX ]
- Askar Gafurov, Tomáš Vinař, Broňa Brejová.
Probabilistic Models of k-mer Frequencies.
In L. De Mol, A. Weiermann, F. Manea, D. Fernández-Duque, ed.,
Connecting with Computability (CiE 2021),
12813 volume of Lecture Notes in Computer Science,
pp. 227-236, Computability in Europe, 2021. Computational pangenomics special session.
[ Abstract ] [ Download from publisher ] [ BibTeX ]
- Rastislav Rabatin, Broňa Brejová, Tomáš Vinař.
Using Sequence Ensembles for Seeding Alignments of MinION Sequencing Data .
In J. Hlaváčová, ed.,
Information Technologies - Applications and Theory (ITAT),
number 1885 in CEUR-WS,
pp. 48-54, Martinské hole, Slovakia, 2017.
[ Abstract ] [ Download from publisher ] [ BibTeX ]
- Mário Lipovský, Tomáš Vinař, Broňa Brejová.
Approximate Abundance Histograms and Their Use for Genome Size Estimation.
In J. Hlaváčová, ed.,
Information Technologies - Applications and Theory (ITAT),
number 1885 in CEUR-WS,
pp. 27-34, Martinské hole, Slovakia, 2017.
[ Abstract ] [ Download from publisher ] [ BibTeX ]
- Martin Macko, Martin Králik, Broňa Brejová, Tomáš Vinař.
OB-Fold Recognition Combining Sequence and Structural Motifs.
In B. Brejová, ed.,
Information Technologies - Applications and Theory (ITAT),
number 1649 in CEUR-WS,
pp. 18-25, Tatranské Matliare, Slovakia, 2016.
[ Abstract ] [ Download from publisher ] [ Webpage ] [ BibTeX ]
- Martin Kravec, Martin Bobak, Brona Brejova, Tomas Vinar.
Variants of Genes from the Next Generation Sequencing Data.
In Proceedings of the Conference on Information Technologies - Applications and Theory (ITAT),
1003 volume of CEUR Workshop Proceedings,
pp. 44-51, Donovaly, Slovakia, September 2013.
[ Abstract ] [ Download from publisher ] [ BibTeX ]
- Martina Visnovska, Tomas Vinar, Brona Brejova.
DNA Sequence Segmentation Based on Local Similarity.
In Proceedings of the Conference on Information Technologies - Applications and Theory (ITAT),
1003 volume of CEUR Workshop Proceedings,
pp. 36-43, Donovaly, Slovakia, September 2013.
[ Abstract ] [ Download from publisher ] [ BibTeX ]
- Peter Kovac, Brona Brejova, Tomas Vinar.
Aligning Sequences with Repetitive Motifs.
In Proceedings of the Conference on Theory and Practice of Information Technologies (ITAT),
990 volume of CEUR Workshop Proceedings,
pp. 41-48, 2012. Best paper award.
[ Abstract ] [ Download from publisher ] [ BibTeX ]
- Brona Brejova, Michal Burger, Tomas Vinar.
Automated Segmentation of DNA Sequences with Complex Evolutionary Histories.
In Teresa M. Przytycka, Marie-France Sagot, ed.,
Algorithms in Bioinformatics, 11th International Workshop (WABI),
6833 volume of Lecture Notes in Computer Science,
pp. 1-13, Saarbrücken, Germany, September 2011. Springer.
[ Abstract ] [ Download from publisher ] [ Webpage ] [ BibTeX ]
- Jakub Kovac, Brona Brejova, Tomas Vinar.
A Practical Algorithm for Ancestral Rearrangement Reconstruction.
In Teresa M. Przytycka, Marie-France Sagot, ed.,
Algorithms in Bioinformatics, 11th International Workshop (WABI),
6833 volume of Lecture Notes in Computer Science,
pp. 163-174, Saarbrücken, Germany, September 2011. Springer.
[ Abstract ] [ Download from publisher ] [ Webpage ] [ BibTeX ]
- Martina Visnovska, Michal Nanasi, Tomas Vinar, Brona Brejova.
Estimating effective DNA database size via compression.
In Dana Pardubska, ed.,
Information Technologies, Applications and Theory (ITAT),
683 volume of CEUR Workshop Proceedings,
pp. 63-70, Smrekovica, 2010. Best paper award.
[ Abstract ] [ Preprint, 109Kb ] [ BibTeX ]
- Michal Nanasi, Tomas Vinar, Brona Brejova.
The Highest Expected Reward Decoding for HMMs with Application to Recombination Detection .
In Amihood Amir, Laxmi Parida, ed.,
Combinatorial Pattern Matching, 21st Annual Symposium (CPM 2010),
6129 volume of Lecture Notes in Computer Science,
pp. 164-176, New York, NY, June 2010. Springer.
[ Abstract ] [ Download from publisher ] [ BibTeX ]
- Jakub Kovac, Tomas Vinar, Brona Brejova.
Predicting Gene Structures from Multiple RT-PCR Tests.
In Steven L. Salzberg, Tandy Warnow, ed.,
Algorithm in Bioinformatics, 9th International Workshop (WABI),
5724 volume of Lecture Notes in Bioinformatics,
pp. 181-193, Philadelphia, PA, September 2009. Springer.
[ Abstract ] [ Preprint, 325Kb ] [ Download from publisher ] [ BibTeX ]
- Rastislav Sramek, Brona Brejova, Tomas Vinar.
On-line Viterbi Algorithm for Analysis of Long Biological Sequences.
In Raffaele Giancarlo, Sridhar Hannenhalli, ed.,
Algorithms in Bioinformatics: 7th International Workshop (WABI),
4645 volume of Lecture Notes in Computer Science,
pp. 240-251, Philadelphia, PA, USA, September 2007. Springer.
[ Abstract ] [ Preprint, 243Kb ] [ Download from publisher ] [ BibTeX ]
- Brona Brejova, Daniel G. Brown, Ian M. Harrower, Tomas Vinar.
New bounds for motif finding in strong instances.
In Combinatorial Pattern Matching, 17th Annual Symposium (CPM 2006),
4009 volume of Lecture Notes in Computer Science,
pp. 94-105, Barcelona, Spain, July 2006.
[ Abstract ] [ Preprint, 410Kb ] [ Download from publisher ] [ BibTeX ]
- Brona Brejova, Daniel G. Brown, Ian M. Harrower, Alejandro Lopez-Ortiz, Tomas Vinar.
Sharper Upper and Lower Bounds for an Approximation Scheme for CONSENSUS-PATTERN.
In Alberto Apostolico, Maxime Crochemore, Kunsoo Park, ed.,
Combinatorial Pattern Matching, 16th Annual Symposium (CPM),
3537 volume of Lecture Notes in Computer Science,
pp. 1-10, Jeju Island, Korea, June 19-22 2005. Springer.
[ Abstract ] [ Preprint, 143Kb ] [ Download from publisher ] [ BibTeX ]
- Brona Brejova, Daniel G. Brown, Tomas Vinar .
Optimal DNA signal recognition models with a fixed amount of intrasignal dependency.
In G. Benson, R. Page, ed.,
Algorithms and Bioinformatics: 3rd International Workshop (WABI),
2812 volume of Lecture Notes in Bioinformatics,
pp. 78-94, Budapest, Hungary, September 2003. Springer.
[ Abstract ] [ Preprint, 111Kb ] [ Download from publisher ] [ BibTeX ]
- Therese Biedl, Masud Hasan, Joe D. Horton, Alejandro Lopez-Ortiz, Tomas Vinar.
Searching for the centre of a circle.
In S. Wismath, ed.,
Proceedings of the 14th Canadian Conference on Computational Geometry,
pp. 137-141, August 12-14 2002. University of Lethbridge.
[ Abstract ] [ Preprint, 88Kb ] [ BibTeX ]
- Brona Brejova, Tomas Vinar.
A Better Method for Length Distribution Modeling in HMMs and Its Application to Gene Finding .
In A. Apostolico, M. Takeda, ed.,
Combinatorial Pattern Matching, 13th Annual Symposium (CPM),
2373 volume of Lecture Notes in Computer Science,
pp. 190-202, Fukuoka, Japan, July 3-5 2002. Springer.
[ Abstract ] [ Preprint, 209Kb ] [ Download from publisher ] [ BibTeX ] [ MathSciNet ]
- Therese C. Biedl, Brona Brejova, and Tomas Vinar.
Simplifying Flow Networks.
In Mogens Nielsen, Branislav Rovan, ed.,
Mathematical Foundations of Computer Science 2000 (MFCS),
1893 volume of Lecture Notes in Computer Science,
pp. 192-201, Bratislava, August 2000. Springer.
[ Abstract ] [ Preprint, 163Kb ] [ Download from publisher ] [ BibTeX ] [ MathSciNet ]
- Randi M. Jimenez, Ladislav Rampášek, Broňa Brejová, Tomáš Vinař, Andrej Lupták.
Discovery of RNA Motifs Using a Computational Pipeline that Allows Insertions in Paired Regions and Filtering of Candidate Sequences .
In Jörg S. Hartig, ed.,
Ribozymes: Methods and Protocols,
848 volume of Methods in Molecular Biology,
chapter 10, pp. 145-158, 2012. Springer.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Broňa Brejová, Tomáš Vinař.
Metódy v bioinformatike [Methods in Bioinformatics].
2011. Knižničné a edičné centrum FMFI UK.
Lecture notes.
[ Abstract ] [ Preprint, 1688Kb ] [ BibTeX ]
- Brona Brejova, Daniel G. Brown, Tomas Vinar.
Advances in hidden Markov models for sequence annotation.
In I. I. Mandoiu, A. Zelikovski, ed.,
Bioinformatics Algorithms: Techniques and Applications,
chapter 4, pp. 55-92, 2008. Wiley.
[ Abstract ] [ Preprint, 369Kb ] [ BibTeX ]
- Brona Brejova, Tomas Vinar, Ming Li.
Pattern Discovery: Methods and Software.
In Stephen A. Krawetz, David D. Womble, ed.,
Introduction to Bioinformatics,
chapter 29, pp. 491-522, 2003. Humana Press.
[ Abstract ] [ Preprint, 365Kb ] [ BibTeX ]
- Tomas Vinar.
Enhancements to Hidden Markov Models for Gene Finding and Other Biological Applications.
PhD thesis, University of Waterloo, October 2005.
[ Abstract ] [ Preprint, 1474Kb ] [ BibTeX ]
- Tomas Vinar.
Privatne vypocitatelne funkcie (Privately Computable Functions).
Master thesis, Comenius University Bratislava, April 1999.
[ Abstract ] [ Preprint, 498Kb ] [ BibTeX ]
- Janik Sielemann, Katharina Sielemann, Broňa Brejová, Tomas Vinar, Cedric Chauve.
plASgraph-using graph neural networks to detect plasmid contigs from an assembly graph.
Technical Report 2022.05.24.493339, bioRxiv,
2022.
[ Abstract ] [ Download from publisher ] [ BibTeX ]
- Broňa Brejová, Viktória Hodorová, Kristína Boršová, Viktória Čabanová, Tomáš Szemes, Matej Mišík, Boris Klempa, Jozef Nosek, Tomáš Vinař.
Sequencing SARS-CoV-2 in Slovakia: An Unofficial Genomic Surveillance Report.
Technical Report 2021.07.13.21260431, medRxiv,
2021.
[ Abstract ] [ Download from publisher ] [ BibTeX ]
- Matus Medo, Martin Suster, Katarina Bodova, Alexandra Brazinova, Brona Brejova, Richard Kollar, Vladimir Leksa, Jana Lindbloom, Jozef Nosek, Tomas Vinar.
Technical comment on The impact of population-wide rapid antigen testing on SARS-CoV-2 prevalence in Slovakia.
Technical Report arXiv:2105.13633, arXiv preprint,
2021.
[ Abstract ] [ Download from publisher ] [ BibTeX ]
- Vladimír Boža, Broňa Brejová, Tomáš Vinař.
Improving Nanopore Reads Raw Signal Alignment.
Technical Report arXiv:1705.01620, arXiv,
2017.
[ Abstract ] [ Download from publisher ] [ BibTeX ]
- Rastislav Rabatin, Broňa Brejová, Tomáš Vinař.
Using Sequence Ensembles for Seeding Alignments of MinION Sequencing Data.
Technical Report arXiv:1606.08719, arXiv,
2016.
[ Abstract ] [ Download from publisher ] [ BibTeX ]
- Therese Biedl, Brona Brejova, Erik D. Demaine, Angele M. Hamel, Tomas Vinar.
Optimal Arrangement of Leaves in the Tree Representing Hierarchical Clustering of Gene Expression Data.
Technical Report CS-2001-14, University of Waterloo,
April 2001.
[ Abstract ] [ Preprint, 556Kb ] [ Webpage ] [ BibTeX ]
- Brona Brejova, Chrysanne DiMarco, Tomas Vinar, Sandra Romero Hidalgo, Gina Holguin, Cheryl Patten.
Finding Patterns in Biological Sequences.
Technical Report CS-2000-22, University of Waterloo,
December 2000.
[ Abstract ] [ Preprint, 605Kb ] [ Webpage ] [ BibTeX ]
- Tomas Vinar.
Using suffix trees to find the most specific substring.
Unpublished manuscript, University of Waterloo,
August 2000.
[ Abstract ] [ Preprint, 252Kb ] [ BibTeX ]
- Brona Brejova, Tomas Vinar.
Weihe's algorithm for maximum flow in planar graphs.
Unpublished manuscript, University of Waterloo,
December 1999.
[ Abstract ] [ Preprint, 632Kb ] [ Webpage ] [ BibTeX ]
- Martin Pal, Tomas Vinar.
On Multiplicity of Permutation Graphs.
Unpublished manuscript, Comenius University Bratislava,
December 1996.
[ Abstract ] [ Preprint, 128Kb ] [ BibTeX ]
Last update: 08/14/2019