Publications of Brona Brejova

Journal articles | Conference articles | Book chapters | Theses | Technical reports

Articles downloadable on this page are pre-print versions for your personal use. They may differ from the final version avaliable from the publisher. If you are interested in a pre-print not available on this page, please contact me by e-mail.

Journal articles

• 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.
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• 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.
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• Vladimír Boža, Broňa Brejová, Tomáš Vinař. DeepNano: Deep recurrent neural networks for base calling in MinION nanopore reads. PLoS One, 12(6):e0178751. 2017.
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• 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.
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• Vladimír Boža, Broňa Brejová, Tomáš Vinař. GAML: genome assembly by maximum likelihood. Algorithms for Molecular Biology, 10:18. 2015. Early version at WABI 2014.
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• Michal Nánási, Tomáš Vinař, Broňa Brejová. Sequence annotation with HMMs: New problems and their complexity. Information Processing Letters, 115(6):635-639. 2015.
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• Marmoset Genome Sequencing and Analysis Consortium. The common marmoset genome provides insight into primate biology and evolution. Nature Genetics, 46(8):850-857. 2014.
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• 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.
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• 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.
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• Michal Nanasi, Tomas Vinar, Brona Brejova. Probabilistic approaches to alignment with tandem repeats. Algorithms for Molecular Biology, 9(1):3. 2014.
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• Eva Hegedusova, Brona Brejova, Lubomir Tomaska, Matthias Sipiczki, Jozef Nosek. Mitochondrial genome of the basidiomycetous yeast Jaminaea angkorensis. Current Genetics, 60(1):49-59. 2014.
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• Brona Brejova, Stefan Dobrev, Rastislav Kralovic, Tomas Vinar. Efficient routing in carrier-based mobile networks. Theoretical Computer Science, 509:113-121. 2013.
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• 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):1168-75. 2013.
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• 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.
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• Orangutan Genome Sequencing and Analysis Consortium. Comparative and demographic analysis of orang-utan genomes. Nature, 469(7331):529-533. 2011.
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• 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.
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• 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.
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• Matej Vesteg, Rostislav Vacula, Jurgen M. Steiner, Bianka Mateasikova, Wolfgang Loffelhardt, Brona Brejova, Juraj Krajcovic. A possible role for short introns in the acquisition of stroma-targeting peptides in the flagellate Euglena gracilis. DNA Research, 17(4):223-231. 2010.
  Abstract | Preprint, 191Kb | Download from publisher | BibTeX | PubMed
• The MGC Project Team. The Completion of the Mammalian Gene Collection (MGC). Genome Research, 2009.
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• Schistosoma japonicum Genome Sequencing and Functional Analysis Consortium, F. Liu, Y. Zhou, Z.Q. Wang, G. Lu, H. Zheng, P.J. Brindley, D.P. McManus, D. Blair, Q.H. Zhang, Y. Zhong, S. Wang, Z.G. Han, Z. Chen. The Schistosoma japonicum genome reveals features of host-parasite interplay. Nature, 460(7253):345-351. 2009.
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• 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. April 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.
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• Adam Siepel, Mark Diekhans, Brona Brejová, Laura Langton, Michael Stevens, Charles L.G. Comstock, Colleen Davis, Brent Ewing, Shelly Oommen, Christopher Lau, Hung-Chun Yu, Jianfeng Li, Bruce A. Roe, Phil Green, Daniela S. Gerhard, Gary Temple, David Haussler, and Michael R. Brent. Targeted discovery of novel human exons by comparative genomics. Genome Research, 17(12):1763-73. 2007. .
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• Xuefeng Cui, Tomas Vinar, Brona Brejova, Dennis Shasha and Ming Li. Homology Search for Genes. Bioinformatics, 23(13):i97-103. 2007. Intelligent Systems for Molecular Biology and European Conference on Computational Biology (ISMB/ECCB 2007).
  Abstract | Preprint, 159Kb | Download from publisher | BibTeX | PubMed
• Brona Brejova, Daniel G. Brown, Tomas Vinar. The most probable annotation 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 | Webpage | BibTeX | MathSciNet
• 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 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 in COCOON 2003.
  Abstract | Preprint, 216Kb | Download from publisher | BibTeX | MathSciNet
• Bronislava Brejova. Analyzing variants of Shellsort. Information Processing Letters, 79(5):223-227. September 2001.
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Conference articles (not published elsewhere)

• 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.
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• 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.
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• 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.
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• Vladimír Boža, Jakub Jursa, Tomáš Vinař, Broňa Brejová. Fishing in Read Collections: Memory Efficient Indexing for Sequence Assembly. In Costas S. Iliopoulos, Simon J. Puglisi, Emine Yilmaz, ed., String Processing and Information Retrieval (SPIRE), 9309 volume of Lecture Notes in Computer Science, pp. 188-198, London, UK, September 2015. Springer.
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• Michal Hozza, Tomáš Vinař, Broňa Brejová. How Big is That Genome? Estimating Genome Size and Coverage from k-mer Abundance Spectra. In Costas S. Iliopoulos, Simon J. Puglisi, Emine Yilmaz, ed., String Processing and Information Retrieval (SPIRE), 9309 volume of Lecture Notes in Computer Science, pp. 199-209, London, UK, September 2015. Springer.
  Abstract | BibTeX
• Andrej Ridzik, Broňa Brejová. Neuropeptide Recognition by Machine Learning Methods. In V. Kurkova, L. Bajer, V. Svatek, ed., Information Technologies - Applications and Theory (ITAT), number 1003 in CEUR-WS, pp. 72-78, Jasna, Slovakia, 2014.
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• Albert Herencsár, Broňa Brejová . An Improved Algorithm for Ancestral Gene Order Reconstruction. In V. Kurkova, L. Bajer, V. Svatek, ed., Information Technologies - Applications and Theory (ITAT), number 1003 in CEUR-WS, pp. 46-53, Jasna, Slovakia, 2014.
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• Martina Višňovská, Tomáš Vinař, Broňa Brejová. DNA Sequence Segmentation Based on Local Similarity. In Tomáš Vinař, ed., Information Technologies - Applications and Theory (ITAT), 1003 volume of CEUR-WS, pp. 36-43, 2013.
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• Martin Kravec, Martin Bobák, Broňa Brejová, Tomáš Vinař. Variants of Genes from the Next Generation Sequencing Data. In Tomáš Vinař, ed., Information Technologies - Applications and Theory (ITAT), 1003 volume of CEUR-WS, pp. 44-51, 2013.
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• Peter Kovac, Brona Brejova, Tomas Vinar. Aligning Sequences with Repetitive Motifs. In Information Technologies - Applications and Theory (ITAT), pp. 41-48, 2012. Best paper award.
  Abstract | Preprint, 618Kb | Download from publisher | BibTeX
• Marcel Kucharik, Jakub Kovac, Brona Brejova. Gene finding with complex external information. In Markéta Lopatková, ed., Information Technologies - Applications and Theory (ITAT), 788 volume of CEUR-WS, pp. 39-46, Vrátna dolina, Slovakia, September 2011. Best paper award.
  Abstract | Preprint, 320Kb | 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.
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• 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 | Preprint, 450Kb | Download from publisher | Webpage | BibTeX
• Martina Visnovska, Michal Nanasi, Tomas Vinar, Brona Brejova. Estimating effective DNA database size via compression. In Information Technologies, Applications and Theory (ITAT), 683 volume of pp. 63-70, Smrekovica, Slovakia, 2010. CEUR-WS. Best paper award.
  Abstract | Preprint, 109Kb | Download from publisher | BibTeX
• Michal Nanasi, Tomas Vinar, Brona Brejova. The Highest Expected Reward Decoding for HMMs with Application to Recombination Detection. In A. Amir and L. Parida, ed., Combinatorial Pattern Matching, 21th Annual Symposium (CPM 2010), 6129 volume of Lecture Notes in Computer Science, pp. 164-176, Brooklyn, New York, USA, 2010. Springer.
  Abstract | Preprint, 167Kb | Download from publisher | Webpage | BibTeX
• Jakub Kovac, Tomas Vinar, Brona Brejova. Predicting Gene Structures from Multiple RT-PCR Tests. In S.L. Salzberg, T. Warnow, ed., Workshop on Algorithms in Bioinformatics (WABI 2009), 5724 volume of Lecture Notes in Bioinformatics, pp. 181-193, Philadelphia, PA, USA, 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 | MathSciNet
• 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
• 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 2002. Springer.
  Abstract | Preprint, 209Kb | Download from publisher | BibTeX | MathSciNet
• Therese C. Biedl, Brona Brejova, and Tomas Vinar. Simplifying flow networks. In M. Nielsen, B. 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

Book chapters

• Jozef Nosek, Brona Brejova, Martina Nebohacova, Peter Barath, Ingrid Bhatia-Kissova, Ivan Valent, Richard Kollar, Lubomir Tomaska. Genomika. 2013. CreateSpace. Textbook in Slovak language.
  Abstract | Webpage | BibTeX
• 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.
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• Brona Brejova, Daniel G. Brown, Tomas Vinar. Advances in hidden Markov models for sequence annotation. In I. Mandoiu, A. Zelikovski, ed., Bioinformatics Algorithms: Techniques and Applications, chapter 3, pp. 55-92, 2008. Wiley.
  Abstract | Webpage | 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 | Webpage | BibTeX

Theses

• Bronislava Brejova. Evidence Combination in Hidden Markov Models for Gene Prediction. PhD thesis, University of Waterloo, November 2005.
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• Bronislava Brejova. Dva problemy z teorie komunikacnej zlozitosti (Two open problems in communication complexity). Master thesis, Comenius University, Bratislava, April 1999.
  Abstract | Preprint, 630Kb | BibTeX

Technical reports

• Rastislav Rabatin, Broňa Brejová, Tomáš Vinař. Using Sequence Ensembles for Seeding Alignments of MinION Sequencing Data. Technical Report arXiv:1606.08719, arXiv, 2016.
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• 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, Dept. of Computer Science, University of Waterloo, April 2001.
  Abstract | Preprint, 556Kb | Download from publisher | 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 | Download from publisher | BibTeX