Bayesian History Reconstruction of Complex Human Gene Clusters on a Phylogeny (2009)
Vinař, Tomáš, Brejová, Broňa, Song, Giltae, Siepel, Adam
Clusters of genes that have evolved by repeated segmental duplication present difficult challenges throughout genomic analysis, from sequence assembly to functional analysis. Improved understanding...
On-line Viterbi Algorithm for Analysis of Long Biological Sequences (2009)
Rastislav ˇ Srámek, Broňa Brejová
Abstract. Hidden Markov models (HMMs) are routinely used for analysis of long genomic sequences to identify various features such as genes, CpG islands, and conserved elements. A commonly used...
Broňa Brejová, Chrysanne Dimarco, Gina Holguin, Cheryl Patten, Sandra Romero Hidalgo
In this report we provide an overview of known techniques for discovery of patterns of biological sequences (DNA and proteins). We also provide biological motivation, and methods of biological...
Advances in Hidden Markov Models for Sequence Annotation (2008)
Broňa Brejová, Daniel G. Brown, Tomas Vinar
One of the most basic tasks of bioinformatics is to identify features in a biological sequence. Whether those features are the binding sites of a protein, the regions of a DNA sequence that are most...
Ziv Bar-joseph, Therese Biedl, Broňa Brejová, Erik D. Demaine, David K. Gifford, Angèle M. Hamel, ...
Abstract. In this paper, we study how to present gene expression data to display similarities by trying to find a linear ordering of genes such that genes with similar expression profiles will be...
Xuefeng Cui, Broňa Brejová, Dennis Shasha, Ming Li
Motivation: Life science researchers often require an exhaustive list of protein coding genes similar to a given query gene. To find such genes, homology search tools, such as BLAST or PatternHunter,...
New Bounds for Motif Finding in Strong Instances (2008)
Broňa Brejová, Daniel G. Brown, Ian M. Harrower
Abstract. Many algorithms for motif finding that are commonly used in bioinformatics start by sampling r potential motif occurrences from n input sequences. The motif is derived from these samples...
Broňa Brejová, Chrysanne Dimarco, Gina Holguin, Cheryl Patten, Sandra Romero Hidalgo
In this report we provide an overview of known techniques for discovery of patterns of biological sequences (DNA and proteins). We also provide biological motivation, and methods of biological...
On-line Viterbi Algorithm and Its Relationship to Random Walks (2007)
Šrámek, Rastislav, Brejová, Broňa, Vinař, Tomáš
In this paper, we introduce the on-line Viterbi algorithm for decoding hidden Markov models (HMMs) in much smaller than linear space. Our analysis on two-state HMMs suggests that the expected maximum...
Sharper upper and lower bounds for an approximation scheme for Consensus-Pattern (2005)
Broňa Brejová, Daniel G. Brown, Ian M. Harrower, Ro López-ortiz
Abstract. We present sharper upper and lower bounds for a known polynomial-time approximation scheme due to Li, Ma and Wang [7] for the Consensus-Pattern problem. This NP-hard problem is an...
T.: Vector seeds: An extension to spaced seeds (2005)
Broňa Brejová, Daniel G. Brown
We present improved techniques for finding homologous regions in DNA and protein sequences. Our approach focuses on the core regions of a local pairwise alignment; we suggest new ways to characterize...
ExonHunter: a comprehensive approach to gene finding (2005)
Broňa Brejová, Daniel G. Brown, Ming Li
We present ExonHunter, a new and comprehensive gene finder system that outperforms existing systems, featuring several new ideas and approaches. Our system combines numerous sources of information...
ExonHunter: a comprehensive approach to gene finding (2005)
Broňa Brejová, Daniel G. Brown, Ming Li
We present ExonHunter, a new and comprehensive gene finder system that outperforms existing systems, featuring several new ideas and approaches. Our system combines numerous sources of information...
Finding hidden independent sets in interval graphs. Theoretical Computer Science (2004)
Therese Biedl, Broňa Brejová, Erik D. Demaine, Angèle M. Hamel, Ro López-ortiz
We design efficient competitive algorithms for discovering hidden information using few queries. Specifically, consider a game in a given set of intervals (and their implied interval graph G) in...
Therese Biedl, Broňa Brejová, Erik D. Demaine, Angèle M. Hamel
Abstract. In this paper, we study how to present gene expression data to display similarities by trying to find a linear ordering of genes such that genes with similar expression profiles will be...
Simplifying flow networks (2000)
Therese C. Biedl, Broňa Brejová
Abstract. Maximum flow problems appear in many practical applications. In this paper, we study how to simplify a given directed flow network by finding edges that can be removed without changing the...
Targeted discovery of novel human exons by comparative genomics
Siepel, Adam, Diekhans, Mark, Brejová, Broňa, Langton, Laura, Stevens, Michael, Comstock, Charles L.G., ...
A complete and accurate set of human protein-coding gene annotations is perhaps the single most important resource for genomic research after the human-genome sequence itself, yet the major gene...
Finding genes in Schistosoma japonicum: annotating novel genomes with help of extrinsic evidence
Brejová, Broňa, Vinař, Tomáš, Chen, Yangyi, Wang, Shengyue, Zhao, Guoping, Brown, Daniel G., ...
We have developed a novel method for estimating the parameters of hidden Markov models for gene finding in newly sequenced species. Our approach does not rely on curated training data sets, but...