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
- The MGC Project Team.
The Completion of the Mammalian Gene Collection (MGC).
Genome Research,
2009.
Abstract | Download from publisher | BibTeX | PubMed - 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.
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.
April 2009.
Abstract | 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 - 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.
.
Abstract | Download from publisher | Webpage | BibTeX | PubMed - 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.
Abstract | Download from publisher | BibTeX | MathSciNet
Conference articles (not published elsewhere)
- Tomas Vinar, Brona Brejova, Giltae Song, Adam Siepel.
Reconstructing Histories of Complex Gene Clusters on a Phylogeny.
In F. D. Ciccarelli, I. Miklos, ed.,
Comparative Genomics, International Workshop (RECOMB-CG),
5817 volume of Lecture Notes in Bioinformatics,
pp. 150-163, Budapest, 2009. Springer.
Abstract | Preprint, 310Kb | 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
- 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.
Abstract | Preprint, 2409Kb | Download from publisher | BibTeX - 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
- 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
