Genome sequence, comparative analysis and haplotype structure of the domestic dog

No abstract is available for this paper.

• Publication year

  2005

• Venue

  Nature

• Publication date

  2005-12-08

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1038/nature04338PMID 16341006
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Comparative Genomics

  2020cited by this paper
• An evaluation of the molecular clock hypothesis using mammalian DNA sequences

  2007cited by this paper
• Finishing of

  2007cited by this paper
• Correspondence and requests for materials should be addressed to:

  2006cited by this paper
• Hotspots of mutation and breakage in dog and human chromosomes.

  2005cited by this paper
• The rate of DNA evolution: effects of body size and temperature on the molecular clock.

  2005cited by this paper
• SINE exonic insertion in the PTPLA gene leads to multiple splicing defects and segregates with the autosomal recessive centronuclear myopathy in dogs.

  2005cited by this paper
• An initial strategy for the systematic identification of functional elements in the human genome by low-redundancy comparative sequencing.

  2005cited by this paper
• Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets.

  2005cited by this paper
• Initial sequence of the chimpanzee genome and comparison with the human genome

  2005cited by this paper
• Short interspersed elements (SINEs) are a major source of canine genomic diversity.

  2005cited by this paper
• Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals

  2005cited by this paper
• [International HapMap project].

  2005cited by this paper
• Facilitating genome navigation: survey sequencing and dense radiation-hybrid gene mapping

  2005cited by this paper
• Striking nucleotide frequency pattern at the borders of highly conserved vertebrate non-coding sequences.

  2005cited by this paper
• A molecular phylogeny of the Canidae based on six nuclear loci.

  2005cited by this paper
• Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.

  2005cited by this paper
• A Model of the Statistical Power of Comparative Genome Sequence Analysis

  2005cited by this paper
• Maternal inheritance, sexual conflict and the maladapted male.

  2005cited by this paper
• Chromosomal rearrangements are associated with higher rates of molecular evolution in mammals.

  2005cited by this paper
• Evolution and functional classification of vertebrate gene deserts.

  2005cited by this paper
• Haploview: analysis and visualization of LD and haplotype maps

  2005cited by this paper
• Toward genome-wide SNP genotyping

  2005cited by this paper
• Isolation and molecular evolution of the selenocysteine tRNA (Cf TRSP) and RNase P RNA (Cf RPPH1) genes in the dog family, Canidae.

  2005influential reference
• Selective sweep mapping of genes with large phenotypic effects.

  2005cited by this paper
• A functional survey of the enhancer activity of conserved non-coding sequences from vertebrate Iroquois cluster gene deserts.

  2005cited by this paper
• Whole-genome experimental identification of insertion/deletion polymorphisms of interspersed repeats by a new general approach

  2005cited by this paper
• Genes of domestic mammals augmented by backcrossing with wild ancestors.

  2005cited by this paper
• Genome sequence of the Brown Norway rat yields insights into mammalian evolution

  2004cited by this paper
• Finishing the euchromatic sequence of the human genome

  2004cited by this paper
• [Dog as a mammalian genetic model].

  2004cited by this paper
• Highly Conserved Non-Coding Sequences Are Associated with Vertebrate Development

  2004influential reference
• Accelerated evolution of nervous system genes in the origin of Homo sapiens.

  2004cited by this paper
• Hotspots of mammalian chromosomal evolution

  2004cited by this paper
• Genetic Structure of the Purebred Domestic Dog

  2004influential reference
• An integrated 4249 marker FISH/RH map of the canine genome

  2004cited by this paper
• Aligning multiple genomic sequences with the threaded blockset aligner.

  2004cited by this paper
• Detailed four-way comparative mapping and gene order analysis of the canine ctvm locus reveals evolutionary chromosome rearrangements.

  2004cited by this paper
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  2004cited by this paper
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  2004cited by this paper
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  2004cited by this paper
• Rate of molecular evolution of the seminal protein gene SEMG2 correlates with levels of female promiscuity

  2004cited by this paper
• From wild wolf to domestic dog: gene expression changes in the brain.

  2004cited by this paper
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  2004cited by this paper
• IDID: Inherited Diseases in Dogs: Web-based information for canine inherited disease genetics

  2004cited by this paper
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  2004cited by this paper
• Extensive and breed-specific linkage disequilibrium in Canis familiaris.

  2004cited by this paper
• Molecular origins of rapid and continuous morphological evolution

  2004cited by this paper
• Evidence for turnover of functional noncoding DNA in mammalian genome evolution.

  2004cited by this paper
• Comparative genomics.

  2004cited by this paper
• Comparison of human chromosome 21 conserved nongenic sequences (CNGs) with the mouse and dog genomes shows that their selective constraint is independent of their genic environment.

  2004cited by this paper
• Ultraconserved Elements in the Human Genome

  2004cited by this paper
• Genome sequence of the Brown Norway rat yields insights into mammalian evolution

  2004cited by this paper
• Inaugural Article: Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution

  2004cited by this paper
• Dog star rising: the canine genetic system

  2004cited by this paper
• Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

  2004cited by this paper
• The biology and conservation of wild canids

  2004cited by this paper
• Le chien, un modèle pour la génétique des mammifères

  2004cited by this paper
• Metagenes and molecular pattern discovery using matrix factorization

  2004cited by this paper
• Genetic Structure of the Purebred Domestic Dog

  2004cited by this paper
• Accelerated evolution of the electron transport chain in anthropoid primates.

  2004cited by this paper
• Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

  2004cited by this paper
• Comparative analyses of multi-species sequences from targeted genomic regions

  2003cited by this paper
• Molecular evolution meets the genomics revolution

  2003cited by this paper
• Human-mouse alignments with BLASTZ.

  2003cited by this paper
• Quantitative estimates of sequence divergence for comparative analyses of mammalian genomes.

  2003cited by this paper
• Sequence divergence, functional constraint, and selection in protein evolution.

  2003cited by this paper
• Scanning Human Gene Deserts for Long-Range Enhancers

  2003cited by this paper
• The International HapMap Project

  2003cited by this paper
• Comparison of the genomes of human and mouse lays the foundation of genome zoology.

  2003cited by this paper
• Using haplotype blocks to map human complex trait loci.

  2003cited by this paper
• Prospects for whole genome linkage disequilibrium mapping in domestic dog breeds

  2003cited by this paper
• PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes

  2003cited by this paper
• Single nucleotide polymorphisms (SNPs) that map to gaps in the human SNP map.

  2003cited by this paper
• An Alu transposition model for the origin and expansion of human segmental duplications.

  2003cited by this paper
• Whole-genome sequence assembly for mammalian genomes: Arachne 2.

  2003influential reference
• Phylogenetic Shadowing of Primate Sequences to Find Functional Regions of the Human Genome

  2003cited by this paper
• The Dog Genome: Survey Sequencing and Comparative Analysis

  2003influential reference
• The extent and distribution of linkage disequilibrium in a multi-hierarchic outbred canine pedigree

  2003cited by this paper
• Power of a Labrador Retriever-Greyhound pedigree for linkage analysis of hip dysplasia and osteoarthritis.

  2003cited by this paper
• Functional analysis of chicken Sox2 enhancers highlights an array of diverse regulatory elements that are conserved in mammals.

  2003cited by this paper
• The International HapMap Consortium. The International HapMap Project (Co-PI of Hong Kong Centre which responsible for 2.5% of genome)

  2003cited by this paper
• Canine CNGB3 mutations establish cone degeneration as orthologous to the human achromatopsia locus ACHM3.

  2002cited by this paper
• Initial sequencing and comparative analysis of the mouse genome.

  2002cited by this paper
• Genetic Evidence for an East Asian Origin of Domestic Dogs

  2002cited by this paper
• Initial sequencing and comparative analysis of the mouse genome

  2002influential reference
• PatternHunter: faster and more sensitive homology search

  2002cited by this paper
• Evolution of sex: Postcopulatory sexual selection

  2002cited by this paper
• Ancient DNA Evidence for Old World Origin of New World Dogs

  2002cited by this paper
• Genetic basis for systems of skeletal quantitative traits: Principal component analysis of the canid skeleton

  2002cited by this paper
• The Structure of Haplotype Blocks in the Human Genome

  2002cited by this paper
• The Ka/Ks ratio: diagnosing the form of sequence evolution.

  2002cited by this paper
• Near-neutrality in evolution of genes and gene regulation

  2002cited by this paper
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  2001cited by this paper
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  2001cited by this paper
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  2001cited by this paper
• A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms

  2001cited by this paper
• Molecular phylogenetics and the origins of placental mammals

  2001cited by this paper
• Initial sequencing and analysis of the human genome

  2001influential reference
• SSAHA: a fast search method for large DNA databases.

  2001cited by this paper

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