Heterogeneity in DNA multiple alignments: modeling, inference, and applications in motif finding
HMMsegmentationmotif findingbackground modelingtranscription factor binding siteevolutionary conservationnucleotide base composition
Applications of Markov chains and discrete-time Markov processes on general state spaces (social mobility, learning theory, industrial processes, etc.) (60J20) Bayesian inference (62F15) Applications of statistics to biology and medical sciences; meta analysis (62P10) Applications of mathematical programming (90C90) Biochemistry, molecular biology (92C40) Genetics and epigenetics (92D10)
- A transdimensional Bayesian model for pattern recognition in DNA sequences
- Context dependent models for discovery of transcription factor binding sites
- Supervised Detection of Regulatory Motifs in DNA Sequences
- Finding transcription factor binding motifs for coregulated genes by combining sequence overrepresentation with cross-species conservation
- A Simple Hyper-Geometric Approach for Discovering Putative Transcription Factor Binding Sites
- A Bayesian Approach to DNA Sequence Segmentation
- Algorithms for the optimal identification of segment neighborhoods
- Bayesian Models for Multiple Local Sequence Alignment and Gibbs Sampling Strategies
- Computational Biology: Toward Deciphering Gene Regulatory Information in Mammalian Genomes
- Coupling hidden Markov models for the discovery of Cis-regulatory modules in multiple species
- Discovery of Conserved Sequence Patterns Using a Stochastic Dictionary Model
- Multiple changepoint fitting via quasilikelihood, with application to DNA sequence segmentation
- Reversible jump Markov chain Monte Carlo computation and Bayesian model determination
- Sampling motifs on phylogenetic trees
- Selecting Differentially Expressed Genes from Microarray Experiments
- Statistical methods for DNA sequence segmentation
- Stochastic models for heterogeneous DNA sequences
- Estimating the occurrence rate of DNA palindromes
- Context dependent models for discovery of transcription factor binding sites
- Estimating Motifs Under Order Restrictions
- \textsc{motifDiverge}: a model for assessing the statistical significance of gene regulatory motif divergence between two DNA sequences
- Flexible statistical modelling of the occurrences of transcription factor binding sites along a DNA sequence
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