BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC

[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.