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Phylogenetic Simulation of Promoter Evolution: Estimation and Modeling of Binding Site Turnover Events and Assessing Their Impact on Alignment Tools

by: Weichun Huang, Joseph R Nevins, Uwe Ohler

Genome Biology, Vol. 8 (24 October 2007), R225.

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alignment, alignment_accuracy, binding_site, cis-regulatory, cis_regulatory_elements, conservation, evolution, genome, model, promotor, promotors, simulation, tf, tools, turnover

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3utr ab_initio accuracy acid adaptation adaptive adaptive_evolution affinity affy_array alignment alignment_accuracy allele-specific americana amino amino_acid angela_presented annotation anterior_posterior antisense antiviral ap_x_dv argonaute array assembly association association_mapping background_selection bacteria base bee binding binding_site binding_site_alignment biophysical_model body bootstrap brain brant_presented bristle browser c_elegans chimp chimpanzee chip_chip chromatin chromatin_modification cis cis_regulatory_elements cis_vs_trans clustering cnv coactivator co_dominance codon_usage coevolution coexpression cofactor colin_presented comparative comparative_genomics complex_trait composition computational concatonation concordance conservation conserved constraint convergent corepression correlation crm cutoff dan_presented danr_presented data database degredation demography detection development devin_presented diffusion discovery disease divergence_estimation dnasei dn_ds_ratio domain domains domestication dominance dosage_compensation drosophila duplication dynamics eisen_journal_club embryo embryonic_patterning emily_presented encode energy_landscape enhanceosome enhancer environment epistasis eqtl eukaryote even-skipped evo_devo evolution experimental experimental_evolution experssion_pattern expression expression_divergence expression_pattern expression_polymorphism extension extrinsic fitness formation ftz gc_content gene genealogy gene_expression gene-expression gene_family gene_function_evolution gene_prediction genetic genetic_interactions genetic_screen gene_tree gene_vs_species_tree genome genome_architecture genome_sequence genome_size genome_wide genomic germ germline gradient grammar haplotype_inference heart helical_phasing heterotachy histone hitchhiking hox human hybrid hypersensitive illumina_beads imprinting indel indels in_depth in-depth in_depth_suggestion insect insects in_situ insulators integration intergenic interval_mapping intron intron_evolution inversion karyotype kenetics lab_library length lenny_presented lethality life lineage lineage_specific linkage loss mammal markov massively_parallel_signature_sequencing maternal matrix matt_presented mechanism metazoan method micro_array microrna model modeling modularity morphological_evolution morphology motif motif_detection mouse multi-copy multiple_alignment multiple_testing mutation mutational_load natural_selection natural_variation nematode neo-y nervous network neural neuro neutral noise noncoding noncoding_dna noncoding_transcription non-essential non-neutral nonstationary not_recommended nucleosome odorant paleoecology paralog paralog_divergence parameter_estimation pattern phenotype phylogeny physical pigmentation placticity plan plants polymorphism population_genetics population_structure positive_selection post_transcriptional_modification prediction promoter properties protein protein_function_evolution proteomics pseudogene purifying pwm qtl range rapid rate recombination reconstruction regular_expressions regulation regulatory_evolution regulatory_network regulatory_polymorphism regulatory_sequence regulatory_sequence_evolution repression response review rich_presented rna rnai rockman_journal_club round_robin rules scaling sechellia segmentation selection semi_dominance seminal_paper sequence_properties sequence_specificity sequencing_error sequencing_technology sex short similarity simulation slightly_deleterious_mutations small_rnas snp snps sorting spacing specialization speciation specific sperm splicing steric_repression stew_presented strains structural_variation structure stuart_presented symbiont synteny system targets te test_for_selection theory threshold timing tissue_specific tissue-specific trait_covariance transcription transcription_factor translation_rate transposable_elements tree tree_topology tribolium turnover variation venky_presented vertebrate vertibrates virilis weak website whole_genome worms x_inactivation x_vs_autosomes yeast zygotic