Published in Genome Biol Evol on January 01, 2013
Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment. Gigascience (2014) 1.00
Dynamic evolution of the alpha (α) and beta (β) keratins has accompanied integument diversification and the adaptation of birds into novel lifestyles. BMC Evol Biol (2014) 0.96
Feather development genes and associated regulatory innovation predate the origin of Dinosauria. Mol Biol Evol (2014) 0.91
Genomic organization, transcriptomic analysis, and functional characterization of avian α- and β-keratins in diverse feather forms. Genome Biol Evol (2014) 0.89
Topographical mapping of α- and β-keratins on developing chicken skin integuments: Functional interaction and evolutionary perspectives. Proc Natl Acad Sci U S A (2015) 0.83
Comparative Genomics Identifies Epidermal Proteins Associated with the Evolution of the Turtle Shell. Mol Biol Evol (2015) 0.82
Deciphering principles of morphogenesis from temporal and spatial patterns on the integument. Dev Dyn (2015) 0.81
Review: cornification, morphogenesis and evolution of feathers. Protoplasma (2016) 0.76
BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol (2007) 74.13
EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet (2000) 69.26
New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol (2010) 53.37
PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol (2007) 45.68
jModelTest: phylogenetic model averaging. Mol Biol Evol (2008) 44.78
MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol (2012) 40.23
Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol (1999) 33.07
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature (2004) 21.40
The genome of a songbird. Nature (2010) 5.90
The evolution of gene duplications: classifying and distinguishing between models. Nat Rev Genet (2010) 5.75
Modulating Hox gene functions during animal body patterning. Nat Rev Genet (2005) 5.10
Assessing concordance of fossil calibration points in molecular clock studies: an example using turtles. Am Nat (2004) 4.45
The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan. Nat Genet (2013) 4.40
Biased gene conversion and the evolution of mammalian genomic landscapes. Annu Rev Genomics Hum Genet (2009) 4.12
An ancestral turtle from the Late Triassic of southwestern China. Nature (2008) 3.68
Recombination drives the evolution of GC-content in the human genome. Mol Biol Evol (2004) 3.50
The genome of the green anole lizard and a comparative analysis with birds and mammals. Nature (2011) 3.32
The chemoreceptor superfamily in the honey bee, Apis mellifera: expansion of the odorant, but not gustatory, receptor family. Genome Res (2006) 3.15
A mitogenomic timescale for birds detects variable phylogenetic rates of molecular evolution and refutes the standard molecular clock. Mol Biol Evol (2006) 2.06
Evolution of the turtle body plan by the folding and creation of new muscle connections. Science (2009) 1.99
The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biol (2013) 1.87
Major taste loss in carnivorous mammals. Proc Natl Acad Sci U S A (2012) 1.81
Evolutionary rate analyses of orthologs and paralogs from 12 Drosophila genomes. Genome Res (2007) 1.71
The effect of gene conversion on the divergence between duplicated genes. Genetics (2004) 1.68
Morphogenesis of the turtle shell: the development of a novel structure in tetrapod evolution. Evol Dev (2001) 1.47
Rapid evolution of smell and taste receptor genes during host specialization in Drosophila sechellia. Proc Natl Acad Sci U S A (2007) 1.44
Identification of reptilian genes encoding hair keratin-like proteins suggests a new scenario for the evolutionary origin of hair. Proc Natl Acad Sci U S A (2008) 1.29
Divergent and convergent evolution of NK-cell receptors. Trends Immunol (2001) 1.28
Evolution of hard proteins in the sauropsid integument in relation to the cornification of skin derivatives in amniotes. J Anat (2009) 1.25
On the carapacial ridge in turtle embryos: its developmental origin, function and the chelonian body plan. Development (2007) 1.23
OPTIC: orthologous and paralogous transcripts in clades. Nucleic Acids Res (2007) 1.20
Comprehensive survey of carapacial ridge-specific genes in turtle implies co-option of some regulatory genes in carapace evolution. Evol Dev (2005) 1.17
Extensive and continuous duplication facilitates rapid evolution and diversification of gene families. Mol Biol Evol (2012) 1.17
A thin-shelled reptile from the Late Triassic of North America and the origin of the turtle shell. Proc Biol Sci (2009) 1.04
Genomic organization and molecular phylogenies of the beta (beta) keratin multigene family in the chicken (Gallus gallus) and zebra finch (Taeniopygia guttata): implications for feather evolution. BMC Evol Biol (2010) 1.03
Opsin gene duplication and divergence in ray-finned fish. Mol Phylogenet Evol (2011) 1.03
How the turtle forms its shell: a paracrine hypothesis of carapace formation. J Exp Zool B Mol Dev Evol (2005) 1.02
The leukocyte receptor complex in chicken is characterized by massive expansion and diversification of immunoglobulin-like Loci. PLoS Genet (2006) 1.01
Radiation and functional diversification of alpha keratins during early vertebrate evolution. Mol Biol Evol (2011) 0.98
Hard cornification in reptilian epidermis in comparison to cornification in mammalian epidermis. Exp Dermatol (2007) 0.96
Evolution of the turtle bauplan: the topological relationship of the scapula relative to the ribcage. Biol Lett (2012) 0.95
Origin and evolution of the chicken leukocyte receptor complex. Proc Natl Acad Sci U S A (2005) 0.95
Palaeontology: Turtle origins out to sea. Nature (2008) 0.95
Linking the molecular evolution of avian beta (β) keratins to the evolution of feathers. J Exp Zool B Mol Dev Evol (2011) 0.95
Hard (Beta-)keratins in the epidermis of reptiles: composition, sequence, and molecular organization. J Proteome Res (2007) 0.94
Evolutionary origin of the feather epidermis. Dev Dyn (2005) 0.93
Beta-keratins of the crocodilian epidermis: composition, structure, and phylogenetic relationships. J Exp Zool B Mol Dev Evol (2009) 0.92
Beta-keratins of turtle shell are glycine-proline-tyrosine rich proteins similar to those of crocodilians and birds. J Anat (2009) 0.85
The evolutionary history of the SAL1 gene family in eutherian mammals. BMC Evol Biol (2011) 0.81
The structure of the carapace and plastron of juvenile turtles, Chelonia mydas (the green turtle) and Caretta caretta (the loggerhead turtle). J Anat (1986) 0.81
Contrasting modes of evolution of the visual pigments in Heliconius butterflies. Mol Biol Evol (2010) 0.81
Immunocytochemical observations on the cornification of soft and hard epidermis in the turtle Chrysemys picta. Zoology (Jena) (2002) 0.79
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
Recent improvements to the SMART domain-based sequence annotation resource. Nucleic Acids Res (2002) 25.06
The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res (2003) 24.72
Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature (2004) 24.40
Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature (2005) 23.04
SMART 4.0: towards genomic data integration. Nucleic Acids Res (2004) 19.37
Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01
InterPro, progress and status in 2005. Nucleic Acids Res (2005) 17.53
Functional impact of global rare copy number variation in autism spectrum disorders. Nature (2010) 14.66
Mouse genomic variation and its effect on phenotypes and gene regulation. Nature (2011) 10.66
The obesity-associated FTO gene encodes a 2-oxoglutarate-dependent nucleic acid demethylase. Science (2007) 9.86
Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature (2007) 7.91
Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs. Genome Res (2007) 7.34
The genome of a songbird. Nature (2010) 5.90
Genome analysis of the platypus reveals unique signatures of evolution. Nature (2008) 5.74
Lineage-specific biology revealed by a finished genome assembly of the mouse. PLoS Biol (2009) 5.45
Mutations in genes encoding ribonuclease H2 subunits cause Aicardi-Goutières syndrome and mimic congenital viral brain infection. Nat Genet (2006) 5.26
A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature (2004) 5.24
The Tudor domain 'Royal Family': Tudor, plant Agenet, Chromo, PWWP and MBT domains. Trends Biochem Sci (2003) 5.19
A ChIP-seq defined genome-wide map of vitamin D receptor binding: associations with disease and evolution. Genome Res (2010) 4.77
Highly efficient targeted mutagenesis of Drosophila with the CRISPR/Cas9 system. Cell Rep (2013) 4.72
Bias of selection on human copy-number variants. PLoS Genet (2006) 4.44
EMSY links the BRCA2 pathway to sporadic breast and ovarian cancer. Cell (2003) 4.33
Insights into hominid evolution from the gorilla genome sequence. Nature (2012) 4.12
Comparative and demographic analysis of orang-utan genomes. Nature (2011) 3.83
Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes. Proc Natl Acad Sci U S A (2003) 3.73
Accelerated evolution of the Prdm9 speciation gene across diverse metazoan taxa. PLoS Genet (2009) 3.60
Systematic identification of novel protein domain families associated with nuclear functions. Genome Res (2002) 3.50
The reality of pervasive transcription. PLoS Biol (2011) 3.41
Genomic and transcriptional co-localization of protein-coding and long non-coding RNA pairs in the developing brain. PLoS Genet (2009) 3.38
Coordination of structure-specific nucleases by human SLX4/BTBD12 is required for DNA repair. Mol Cell (2009) 3.38
The genome of the green anole lizard and a comparative analysis with birds and mammals. Nature (2011) 3.32
The protein composition of mitotic chromosomes determined using multiclassifier combinatorial proteomics. Cell (2010) 3.26
Genome-wide identification of human functional DNA using a neutral indel model. PLoS Comput Biol (2006) 3.16
Phylogenetic reconstruction of orthology, paralogy, and conserved synteny for dog and human. PLoS Comput Biol (2006) 3.07
Natural genetic variation caused by small insertions and deletions in the human genome. Genome Res (2011) 3.00
The African coelacanth genome provides insights into tetrapod evolution. Nature (2013) 2.78
Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness. Genome Biol (2009) 2.70
InterPro: an integrated documentation resource for protein families, domains and functional sites. Brief Bioinform (2002) 2.66
Elevated rates of protein secretion, evolution, and disease among tissue-specific genes. Genome Res (2004) 2.58
The bonobo genome compared with the chimpanzee and human genomes. Nature (2012) 2.49
EYS, encoding an ortholog of Drosophila spacemaker, is mutated in autosomal recessive retinitis pigmentosa. Nat Genet (2008) 2.46
Positional cloning of a quantitative trait locus on chromosome 13q14 that influences immunoglobulin E levels and asthma. Nat Genet (2003) 2.21
Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes. Genome Biol (2010) 2.20
Positional cloning of a novel gene influencing asthma from chromosome 2q14. Nat Genet (2003) 2.16
A transcriptomic atlas of mouse neocortical layers. Neuron (2011) 2.08
Rapid turnover of long noncoding RNAs and the evolution of gene expression. PLoS Genet (2012) 2.05
Evolutionary conservation and selection of human disease gene orthologs in the rat and mouse genomes. Genome Biol (2004) 2.05
KDM2B links the Polycomb Repressive Complex 1 (PRC1) to recognition of CpG islands. Elife (2012) 1.99
Predicting protein cellular localization using a domain projection method. Genome Res (2002) 1.98
Common ancestry of the CENP-A chaperones Scm3 and HJURP. Cell (2009) 1.96
Homology explains the functional similarities of Treslin/Ticrr and Sld3. Curr Biol (2010) 1.94
Massive turnover of functional sequence in human and other mammalian genomes. Genome Res (2010) 1.89
The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biol (2013) 1.87
Mutations in BMP4 cause eye, brain, and digit developmental anomalies: overlap between the BMP4 and hedgehog signaling pathways. Am J Hum Genet (2008) 1.86
Comparison of the genomes of human and mouse lays the foundation of genome zoology. Hum Mol Genet (2003) 1.83
Stc1: a critical link between RNAi and chromatin modification required for heterochromatin integrity. Cell (2010) 1.82
Accurate distinction of pathogenic from benign CNVs in mental retardation. PLoS Comput Biol (2010) 1.75
Occurrence and consequences of coding sequence insertions and deletions in Mammalian genomes. Genome Res (2004) 1.73
Evolutionary rate analyses of orthologs and paralogs from 12 Drosophila genomes. Genome Res (2007) 1.71
Identification and properties of 1,119 candidate lincRNA loci in the Drosophila melanogaster genome. Genome Biol Evol (2012) 1.69
High levels of RNA-editing site conservation amongst 15 laboratory mouse strains. Genome Biol (2012) 1.68
Genome assembly quality: assessment and improvement using the neutral indel model. Genome Res (2010) 1.64
The genomic landscape shaped by selection on transposable elements across 18 mouse strains. Genome Biol (2012) 1.63
Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates. Elife (2013) 1.63
Death of PRDM9 coincides with stabilization of the recombination landscape in the dog genome. Genome Res (2011) 1.62
Regulation of DNA replication through Sld3-Dpb11 interaction is conserved from yeast to humans. Curr Biol (2011) 1.54
Reduced purifying selection prevails over positive selection in human copy number variant evolution. Genome Res (2008) 1.54
Hotspots of mutation and breakage in dog and human chromosomes. Genome Res (2005) 1.54
Vitamin K epoxide reductase: homology, active site and catalytic mechanism. Trends Biochem Sci (2004) 1.52
Structural and mechanistic insights into ras association domains of phospholipase C epsilon. Mol Cell (2006) 1.48
UIF, a New mRNA export adaptor that works together with REF/ALY, requires FACT for recruitment to mRNA. Curr Biol (2009) 1.45
Repo-Man coordinates chromosomal reorganization with nuclear envelope reassembly during mitotic exit. Dev Cell (2011) 1.43
Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs. Genome Biol (2013) 1.41
Defensins and the convergent evolution of platypus and reptile venom genes. Genome Res (2008) 1.37
Mutations in TOPORS cause autosomal dominant retinitis pigmentosa with perivascular retinal pigment epithelium atrophy. Am J Hum Genet (2007) 1.33
Sexual selection and the adaptive evolution of mammalian ejaculate proteins. Mol Biol Evol (2007) 1.28
GAT: a simulation framework for testing the association of genomic intervals. Bioinformatics (2013) 1.27
TRAM, LAG1 and CLN8: members of a novel family of lipid-sensing domains? Trends Biochem Sci (2002) 1.24
Preparation of high-quality next-generation sequencing libraries from picogram quantities of target DNA. Genome Res (2011) 1.24
Meisetz and the birth of the KRAB motif. Bioinformatics (2006) 1.24
Forging links between human mental retardation-associated CNVs and mouse gene knockout models. PLoS Genet (2009) 1.23
Evc2 is a positive modulator of Hedgehog signalling that interacts with Evc at the cilia membrane and is also found in the nucleus. BMC Biol (2011) 1.21
Identification of the MMS22L-TONSL complex that promotes homologous recombination. Mol Cell (2010) 1.21
OPTIC: orthologous and paralogous transcripts in clades. Nucleic Acids Res (2007) 1.20
The long non-coding RNA Paupar regulates the expression of both local and distal genes. EMBO J (2014) 1.19
Ontogeny and phylogeny: molecular signatures of selection, constraint, and temporal pleiotropy in the development of Drosophila. BMC Biol (2009) 1.17
Cdc45: the missing RecJ ortholog in eukaryotes? Bioinformatics (2011) 1.14
Evolution and comparative genomics of odorant- and pheromone-associated genes in rodents. Genome Res (2004) 1.14
Molecular evolution of genes in avian genomes. Genome Biol (2010) 1.12
An analysis of the gene complement of a marsupial, Monodelphis domestica: evolution of lineage-specific genes and giant chromosomes. Genome Res (2007) 1.11
Insights into the evolution of Darwin's finches from comparative analysis of the Geospiza magnirostris genome sequence. BMC Genomics (2013) 1.09