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Phylogenetic hidden Markov model detects CNEEs using Phastcons
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Wings, Feathers, Flight - The PhyloG2P Approach to Understanding Bird Biology
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- 1 Intro
- 2 Using phylogenies to connect genotype to phenotype
- 3 Matching human regulatory regions to independently lost mammalian traits
- 4 Taste receptors in mammals
- 5 Birds inherited only the umami (meat) receptor from their dinosaur ancestors
- 6 Hummingbirds can taste sugar due to changes in the gene other binds use to taste meat (or insects)
- 7 Non-coding 'Dark matter of the genome: a regulatory network?
- 8 CNEEs: evolutionarily conserved non-coding enhancer regions
- 9 Noncoding enhancers: long-range control of gene expression
- 10 Phylogenetic hidden Markov model detects CNEEs using Phastcons
- 11 A role for gene regulation in the origin of feathers
- 12 Conserved non-exonic elements (CNEES) act as enhancers for feather genes
- 13 High origination rates of feather CNEEs, but not feather genes, when feathers evolved
- 14 Bird-specific regulatory evolution: what makes a bird a bird?
- 15 Bird-specific CNEEs associated with genes for limb and body size evolution
- 16 CNEEs and the convergent evolution of flightlessness in Palaeognathae
- 17 Skeletal modifications for flightlessness
- 18 11 new palaeognath genomes
- 19 42-species whole genome alignment for birds using ProgressiveCactus
- 20 Relationships of rheas unclear
- 21 Coalescent analyses resolve the position of rheas and reveal an ancient rapid radiation
- 22 Gene tree distribution suggests a near polytomy at base of ratites
- 23 Anomaly zone: most common gene tree does not match the species tree
- 24 Evolutionary change: genes or gene regulation? Evolution at Two Levels in Humans and Chimpanzees
- 25 A convergently accelerated CNEE detected with a novel Bayesian method
- 26 Additional examples of convergently accelerated CNEES
- 27 Rapid regulatory evolution near 1000 developmental genes
- 28 Genes showing convergent regulatory evolution in 3 lineages of ratites
- 29 Assay for Transposase-Accessible Chromatin
- 30 Differences in ATAC-se peaks between thea and chicken suggest changes in limb gene regulation
- 31 Combined information from multiple sources suggests candidate enhancers for flightlessness phenotypes
- 32 Volant version of CNEE drives gene expression in the developing forelimb of chicken but flightless version does not
- 33 Measuring gene expression and open chromatin across fore- and hindlimbs of paleognath embryos
