BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC
暂无分享,去创建一个
[1] István Miklós,et al. StatAlign: an extendable software package for joint Bayesian estimation of alignments and evolutionary trees , 2008, Bioinform..
[2] Lior Pachter,et al. Combining statistical alignment and phylogenetic footprinting to detect regulatory elements , 2008, Bioinform..
[3] Alexandre Z. Caldeira,et al. Uncertainty in homology inferences: assessing and improving genomic sequence alignment. , 2008, Genome research.
[4] M. Suchard,et al. Alignment Uncertainty and Genomic Analysis , 2008, Science.
[5] David Haussler,et al. The UCSC Genome Browser Database: 2008 update , 2007, Nucleic Acids Res..
[6] István Miklós,et al. How reliably can we predict the reliability of protein structure predictions? , 2008, BMC Bioinformatics.
[7] Daniel J. Blankenberg,et al. 28-way vertebrate alignment and conservation track in the UCSC Genome Browser. , 2007, Genome research.
[8] Ian Holmes,et al. Transducers: an emerging probabilistic framework for modeling indels on trees , 2007, Bioinform..
[9] Colin N. Dewey,et al. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures , 2007, Nature.
[10] Melanie A. Huntley,et al. Evolution of genes and genomes on the Drosophila phylogeny , 2007, Nature.
[11] Jun Zhu,et al. Statistical power of phylo-HMM for evolutionarily conserved element detection , 2007, BMC Bioinformatics.
[12] Xin He,et al. MORPH: Probabilistic Alignment Combined with Hidden Markov Models of cis-Regulatory Modules , 2007, PLoS Comput. Biol..
[13] Gerton Lunter,et al. Probabilistic whole-genome alignments reveal high indel rates in the human and mouse genomes , 2007, ISMB/ECCB.
[14] Michael B. Eisen,et al. Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments , 2006, BMC Bioinformatics.
[15] D. Guhathakurta,et al. Computational identification of transcriptional regulatory elements in DNA sequence , 2006, Nucleic acids research.
[16] Long Li,et al. REDfly: a Regulatory Element Database for Drosophila , 2006, Bioinform..
[17] Lior Pachter,et al. Parametric Alignment of Drosophila Genomes , 2005, PLoS Comput. Biol..
[18] Chris P. Ponting,et al. Genome-Wide Identification of Human Functional DNA Using a Neutral Indel Model , 2005, PLoS Comput. Biol..
[19] D. Haussler,et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. , 2005, Genome research.
[20] S. Prabhakar,et al. Annotation of cis-regulatory elements by identification, subclassification, and functional assessment of multispecies conserved sequences. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[21] M. Suchard,et al. Joint Bayesian estimation of alignment and phylogeny. , 2005, Systematic biology.
[22] Casey M. Bergman,et al. Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster , 2005, Bioinform..
[23] István Miklós,et al. Bayesian coestimation of phylogeny and sequence alignment , 2005, BMC Bioinformatics.
[24] Ian Holmes,et al. Using evolutionary Expectation Maximization to estimate indel rates , 2005, Bioinform..
[25] S. Eddy. A Model of the Statistical Power of Comparative Genome Sequence Analysis , 2005, PLoS biology.
[26] J. Felsenstein,et al. An evolutionary model for maximum likelihood alignment of DNA sequences , 1991, Journal of Molecular Evolution.
[27] H. Kishino,et al. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA , 2005, Journal of Molecular Evolution.
[28] David Haussler,et al. Computational identification of evolutionarily conserved exons , 2004, RECOMB.
[29] I. Holmes,et al. A "Long Indel" model for evolutionary sequence alignment. , 2003, Molecular biology and evolution.
[30] J. Felsenstein,et al. Inching toward reality: An improved likelihood model of sequence evolution , 2004, Journal of Molecular Evolution.
[31] L. Fulton,et al. Finding Functional Features in Saccharomyces Genomes by Phylogenetic Footprinting , 2003, Science.
[32] I. Holmes,et al. Using guide trees to construct multiple-sequence evolutionary HMMs , 2003, ISMB.
[33] Jon D. McAuliffe,et al. Phylogenetic Shadowing of Primate Sequences to Find Functional Regions of the Human Genome , 2003, Science.
[34] Ian Holmes,et al. Evolutionary HMMs: a Bayesian approach to multiple alignment , 2001, Bioinform..
[35] C. Lawrence,et al. Human-mouse genome comparisons to locate regulatory sites , 2000, Nature Genetics.
[36] J. Hein,et al. Statistical alignment: computational properties, homology testing and goodness-of-fit. , 2000, Journal of molecular biology.
[37] Sean R. Eddy,et al. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids , 1998 .
[38] N. Patel,et al. Functional analysis of eve stripe 2 enhancer evolution in Drosophila: rules governing conservation and change. , 1998, Development.
[39] Ian Holmes,et al. Dynamic programming alignment accuracy , 1998, RECOMB '98.
[40] J. D. Engel,et al. GATA-1 transcription is controlled by distinct regulatory mechanisms during primitive and definitive erythropoiesis. , 1997, Proceedings of the National Academy of Sciences of the United States of America.
[41] M. Kreitman,et al. Tempo and mode ofeven-skippedstripe 2 enhancer evolution inDrosophila , 1996 .
[42] M. Levine,et al. Regulation of a segmentation stripe by overlapping activators and repressors in the Drosophila embryo. , 1991, Science.
[43] M. Goodman,et al. Embryonic ε and γ globin genes of a prosimian primate (Galago crassicaudatus): Nucleotide and amino acid sequences, developmental regulation and phylogenetic footprints , 1988 .
[44] M. Goodman,et al. Embryonic epsilon and gamma globin genes of a prosimian primate (Galago crassicaudatus). Nucleotide and amino acid sequences, developmental regulation and phylogenetic footprints. , 1988, Journal of molecular biology.
[45] M. Kimura. Estimation of evolutionary distances between homologous nucleotide sequences. , 1981, Proceedings of the National Academy of Sciences of the United States of America.
[46] S. Jeffery. Evolution of Protein Molecules , 1979 .
[47] W. K. Hastings,et al. Monte Carlo Sampling Methods Using Markov Chains and Their Applications , 1970 .
[48] T. Jukes. CHAPTER 24 – Evolution of Protein Molecules , 1969 .
[49] N. Metropolis,et al. Equation of State Calculations by Fast Computing Machines , 1953, Resonance.