Combining Phylogenetic and Hidden Markov Models in Biosequence Analysis
By Adam C. Siepel, David Haussler. Annual International Conference on Research in Computational Molecular Biology, 2003
313 citations recorded by the source corpus.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/1c0d6bfe82bfadc76c22c3e604545ff9c91d7a7b
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In Molecular Biology
- David Haussler
- W. James Kent
- Adam C. Siepel
- Donna Karolchik
- A. Hinrichs
- Gregory M. Cooper
- Serafim Batzoglou
- Manolis Kellis
Citations in the corpus
- Efficient approximations for learning phylogenetic HMM models from data (2004, methodology): “The same inconsistency is present and noted in Siepel and Haussler (2003).”
- Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm (2008, background): “simulans, and (2) PhastCons scores measuring constraint across 12 sequenced, closely and distantly related Drosophila species [57,58].”
- Distribution and intensity of constraint in mammalian genomic sequence. (2005, methodology): “…and characterization of constrained elements (Gumucio et al. 1992; Dubchak et al. 2000; Mayor et al. 2000; Sumiyama et al. 2001; Boffelli et al. 2003; Margulies et al. 2003; Cooper et al. 2004a; Shah et al. 2004; Siepel and Haussler 2004a) suffer from one, or multiple, of several general drawbacks.”
- The UCSC Table Browser data retrieval tool (2004, background): “The group has been active in the analysis of evolutionary conservation and divergence among species (3,4), phylogenetic analysis of rates of substitution (5) and multiple species alignments.”
- Clustering and conservation patterns of human microRNAs (2005, methodology): “In this study, we used the UCSC phastCons conservation scores (22,23) (http://genome.”
- PhyLAT: a phylogenetic local alignment tool (2012, background): “This theory can be extended to allow the query to contain bases that are not homologous to any reference position or vice versa; for example, Siepel and Haussler describe such an approach for phylogenetic HMMs (Siepel and Haussler, 2004).”