Published in PLoS One on February 17, 2010
Sequencing technologies and genome sequencing. J Appl Genet (2011) 2.52
Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads--a baiting and iterative mapping approach. Nucleic Acids Res (2013) 2.08
Next Generation Sequencing of Ancient DNA: Requirements, Strategies and Perspectives. Genes (Basel) (2010) 1.22
Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle. Genome Biol (2015) 1.10
The enigmatic origin of bovine mtDNA haplogroup R: sporadic interbreeding or an independent event of Bos primigenius domestication in Italy? PLoS One (2010) 1.09
The complete mitochondrial genome of an 11,450-year-old aurochsen (Bos primigenius) from Central Italy. BMC Evol Biol (2011) 1.02
Unraveling bovin phylogeny: accomplishments and challenges. BMC Biol (2010) 0.85
Paging through history: parchment as a reservoir of ancient DNA for next generation sequencing. Philos Trans R Soc Lond B Biol Sci (2015) 0.83
The de novo assembly of mitochondrial genomes of the extinct passenger pigeon (Ectopistes migratorius) with next generation sequencing. PLoS One (2013) 0.83
Hunting the Extinct Steppe Bison (Bison priscus) Mitochondrial Genome in the Trois-Frères Paleolithic Painted Cave. PLoS One (2015) 0.82
Temporal genetic variation of the red fox, Vulpes vulpes, across western Europe and the British Isles. Quat Sci Rev (2012) 0.82
Definition of the cattle killer cell Ig-like receptor gene family: comparison with aurochs and human counterparts. J Immunol (2014) 0.79
Accurate determination of phenotypic information from historic thoroughbred horses by single base extension. PLoS One (2010) 0.77
Microsatellite genotyping of medieval cattle from central Italy suggests an old origin of Chianina and Romagnola cattle. Front Genet (2015) 0.76
Genetic origin, admixture and population history of aurochs (Bos primigenius) and primitive European cattle. Heredity (Edinb) (2016) 0.75
Mitogenomes from Egyptian Cattle Breeds: New Clues on the Origin of Haplogroup Q and the Early Spread of Bos taurus from the Near East. PLoS One (2015) 0.75
Resequencing and comparison of whole mitochondrial genome to gain insight into the evolutionary status of the Shennongjia golden snub-nosed monkey (SNJ R. roxellana). Ecol Evol (2017) 0.75
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31
MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol (2007) 168.76
Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res (2008) 157.44
Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res (2008) 26.36
MEGAN analysis of metagenomic data. Genome Res (2007) 25.29
Complete sequence of bovine mitochondrial DNA. Conserved features of the mammalian mitochondrial genome. J Mol Biol (1982) 11.71
The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science (2009) 8.23
Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA. Science (2005) 8.14
Sequencing and analysis of Neanderthal genomic DNA. Science (2006) 8.06
Rise and fall of the Beringian steppe bison. Science (2004) 7.91
A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell (2008) 6.98
Analysis of one million base pairs of Neanderthal DNA. Nature (2006) 6.17
Patterns of damage in genomic DNA sequences from a Neandertal. Proc Natl Acad Sci U S A (2007) 6.12
Targeted retrieval and analysis of five Neandertal mtDNA genomes. Science (2009) 5.79
Mitochondrial diversity and the origins of African and European cattle. Proc Natl Acad Sci U S A (1996) 5.55
Evidence for two independent domestications of cattle. Proc Natl Acad Sci U S A (1994) 4.70
Widespread origins of domestic horse lineages. Science (2001) 4.42
Sequencing the nuclear genome of the extinct woolly mammoth. Nature (2008) 4.31
Multiplex amplification of the mammoth mitochondrial genome and the evolution of Elephantidae. Nature (2005) 3.74
Genetic evidence for Near-Eastern origins of European cattle. Nature (2001) 3.60
Investigation of heteroplasmy in the human mitochondrial DNA control region: a synthesis of observations from more than 5000 global population samples. J Mol Evol (2009) 3.47
Novel high-resolution characterization of ancient DNA reveals C > U-type base modification events as the sole cause of post mortem miscoding lesions. Nucleic Acids Res (2007) 3.41
Patterns of nucleotide misincorporations during enzymatic amplification and direct large-scale sequencing of ancient DNA. Proc Natl Acad Sci U S A (2006) 3.40
Technical note: improved DNA extraction from ancient bones using silica-based spin columns. Am J Phys Anthropol (1998) 3.10
The origin of European cattle: evidence from modern and ancient DNA. Proc Natl Acad Sci U S A (2006) 3.09
A complete mtDNA genome of an early modern human from Kostenki, Russia. Curr Biol (2009) 3.09
DNA markers reveal the complexity of livestock domestication. Nat Rev Genet (2003) 3.07
Whole-genome shotgun sequencing of mitochondria from ancient hair shafts. Science (2007) 2.85
Mitochondrial DNA analysis shows a Near Eastern Neolithic origin for domestic cattle and no indication of domestication of European aurochs. Proc Biol Sci (2007) 2.61
The thermal history of human fossils and the likelihood of successful DNA amplification. J Hum Evol (2003) 2.47
The Neandertal genome and ancient DNA authenticity. EMBO J (2009) 2.46
The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus). Genome Res (2009) 2.30
Paleo-Eskimo mtDNA genome reveals matrilineal discontinuity in Greenland. Science (2008) 2.19
Mitochondrial genomes of extinct aurochs survive in domestic cattle. Curr Biol (2008) 2.14
Complete mitochondrial genome and phylogeny of Pleistocene mammoth Mammuthus primigenius. PLoS Biol (2006) 2.13
A read-ahead function in archaeal DNA polymerases detects promutagenic template-strand uracil. Proc Natl Acad Sci U S A (1999) 2.03
Cattle domestication in the Near East was followed by hybridization with aurochs bulls in Europe. Proc Biol Sci (2005) 2.01
Large-scale mitochondrial DNA analysis of the domestic goat reveals six haplogroups with high diversity. PLoS One (2007) 1.72
Identification of ancient remains through genomic sequencing. Genome Res (2008) 1.72
Independent mitochondrial origin and historical genetic differentiation in North Eastern Asian cattle. Mol Phylogenet Evol (2004) 1.65
Ancient DNA suggests a recent expansion of European cattle from a diverse wild progenitor species. Proc Biol Sci (1996) 1.64
Analysis of mitochondrial DNA indicates that domestic sheep are derived from two different ancestral maternal sources: no evidence for contributions from urial and argali sheep. J Hered (1998) 1.59
The multifaceted origin of taurine cattle reflected by the mitochondrial genome. PLoS One (2009) 1.58
Complete mitochondrial genome sequence of the Tyrolean Iceman. Curr Biol (2008) 1.55
Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes. Proc Natl Acad Sci U S A (2008) 1.53
Neanderthal DNA. Not just old but old and cold? Nature (2001) 1.42
Five ovine mitochondrial lineages identified from sheep breeds of the near East. Genetics (2006) 1.35
New insights from old bones: DNA preservation and degradation in permafrost preserved mammoth remains. Nucleic Acids Res (2009) 1.32
Y-SNPs do not indicate hybridisation between European aurochs and domestic cattle. PLoS One (2008) 1.13
Zebu cattle are an exclusive legacy of the South Asia neolithic. Mol Biol Evol (2010) 1.11
Cytochrome b sequences of ancient cattle and wild ox support phylogenetic complexity in the ancient and modern bovine populations. Anim Genet (2009) 1.07
Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution. BMC Evol Biol (2009) 1.07
Complete nucleotide sequence of pig (Sus scrofa) mitochondrial genome and dating evolutionary divergence within Artiodactyla. Gene (1999) 0.98
Paleogenomics in a temperate environment: shotgun sequencing from an extinct Mediterranean caprine. PLoS One (2009) 0.96
A partial african ancestry for the creole cattle populations of the Caribbean. J Hered (2003) 0.94
Early medieval cattle remains from a Scandinavian settlement in Dublin: genetic analysis and comparison with extant breeds. Philos Trans R Soc Lond B Biol Sci (1999) 0.80
Genome sequences from extinct relatives. Cell (2008) 0.79
Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences. Mol Biol Evol (2005) 8.42
The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science (2009) 8.23
Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA. Science (2005) 8.14
Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science (2009) 7.64
Correcting for purifying selection: an improved human mitochondrial molecular clock. Am J Hum Genet (2009) 5.37
Diverse plant and animal genetic records from Holocene and Pleistocene sediments. Science (2003) 4.48
Measuring European population stratification with microarray genotype data. Am J Hum Genet (2007) 4.03
Comprehensive analysis of the gene encoding filaggrin uncovers prevalent and rare mutations in ichthyosis vulgaris and atopic eczema. Nat Genet (2007) 3.94
African pastoralism: genetic imprints of origins and migrations. Science (2002) 3.66
Ancient DNA, pig domestication, and the spread of the Neolithic into Europe. Proc Natl Acad Sci U S A (2007) 3.45
Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature (2013) 3.45
Documenting domestication: the intersection of genetics and archaeology. Trends Genet (2006) 3.27
Accommodating the effect of ancient DNA damage on inferences of demographic histories. Mol Biol Evol (2008) 3.07
DNA markers reveal the complexity of livestock domestication. Nat Rev Genet (2003) 3.07
Cognitive and clinical characteristics of patients with amyotrophic lateral sclerosis carrying a C9orf72 repeat expansion: a population-based cohort study. Lancet Neurol (2012) 3.04
A genome-wide association study of sporadic ALS in a homogenous Irish population. Hum Mol Genet (2007) 2.84
The archaeogenetics of Europe. Curr Biol (2010) 2.71
A common MYBPC3 (cardiac myosin binding protein C) variant associated with cardiomyopathies in South Asia. Nat Genet (2009) 2.67
Mitochondrial DNA analysis shows a Near Eastern Neolithic origin for domestic cattle and no indication of domestication of European aurochs. Proc Biol Sci (2007) 2.61
Species-specific responses of Late Quaternary megafauna to climate and humans. Nature (2011) 2.60
Genetic evidence for the convergent evolution of light skin in Europeans and East Asians. Mol Biol Evol (2006) 2.54
The thermal history of human fossils and the likelihood of successful DNA amplification. J Hum Evol (2003) 2.47
A genome scan for positive selection in thoroughbred horses. PLoS One (2009) 2.42
The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium. Proc Natl Acad Sci U S A (2012) 2.39
SD-208, a novel transforming growth factor beta receptor I kinase inhibitor, inhibits growth and invasiveness and enhances immunogenicity of murine and human glioma cells in vitro and in vivo. Cancer Res (2004) 2.35
Gene-culture coevolution between cattle milk protein genes and human lactase genes. Nat Genet (2003) 2.35
Ancient hybridization and an Irish origin for the modern polar bear matriline. Curr Biol (2011) 2.33
Evidence for time dependency of molecular rate estimates. Syst Biol (2007) 2.26
Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics. PLoS Comput Biol (2007) 2.25
Genomic evidence of geographically widespread effect of gene flow from polar bears into brown bears. Mol Ecol (2015) 2.19
The global spread of hepatitis C virus 1a and 1b: a phylodynamic and phylogeographic analysis. PLoS Med (2009) 2.06
The earliest evidence for anatomically modern humans in northwestern Europe. Nature (2011) 2.03
Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci. Mol Biol Evol (2012) 2.02
Inhibition of growth and metastasis of mouse mammary carcinoma by selective inhibitor of transforming growth factor-beta type I receptor kinase in vivo. Clin Cancer Res (2006) 2.01
A spliceosomal intron in Giardia lamblia. Proc Natl Acad Sci U S A (2002) 1.95
Skyline-plot methods for estimating demographic history from nucleotide sequences. Mol Ecol Resour (2011) 1.90
True single-molecule DNA sequencing of a pleistocene horse bone. Genome Res (2011) 1.88
High-resolution mtDNA evidence for the late-glacial resettlement of Europe from an Iberian refugium. Genome Res (2005) 1.85
Using time-structured data to estimate evolutionary rates of double-stranded DNA viruses. Mol Biol Evol (2010) 1.80
The Expansion of mtDNA Haplogroup L3 within and out of Africa. Mol Biol Evol (2011) 1.78
tRNAHis maturation: an essential yeast protein catalyzes addition of a guanine nucleotide to the 5' end of tRNAHis. Genes Dev (2003) 1.78
Ancient papillomavirus-host co-speciation in Felidae. Genome Biol (2007) 1.75
Recombination confounds the early evolutionary history of human immunodeficiency virus type 1: subtype G is a circulating recombinant form. J Virol (2007) 1.74
Climate change and postglacial human dispersals in southeast Asia. Mol Biol Evol (2008) 1.74
Bioinformatic discovery of novel bioactive peptides. Nat Chem Biol (2007) 1.72
Mycobacterial lineages causing pulmonary and extrapulmonary tuberculosis, Ethiopia. Emerg Infect Dis (2013) 1.72
Methicillin resistance alters the biofilm phenotype and attenuates virulence in Staphylococcus aureus device-associated infections. PLoS Pathog (2012) 1.72
The effect of inappropriate calibration: three case studies in molecular ecology. PLoS One (2008) 1.67
Progressive transforming growth factor beta1-induced lung fibrosis is blocked by an orally active ALK5 kinase inhibitor. Am J Respir Crit Care Med (2004) 1.66
Ancient voyaging and Polynesian origins. Am J Hum Genet (2011) 1.65
Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling. Genome Biol (2013) 1.62
Ancient DNA analyses exclude humans as the driving force behind late Pleistocene musk ox (Ovibos moschatus) population dynamics. Proc Natl Acad Sci U S A (2010) 1.55
Genetic signatures of a Mediterranean influence in Iberian Peninsula sheep husbandry. Mol Biol Evol (2006) 1.55
Complete mitochondrial genome sequence of the Tyrolean Iceman. Curr Biol (2008) 1.55
Polycomb PHF19 binds H3K36me3 and recruits PRC2 and demethylase NO66 to embryonic stem cell genes during differentiation. Nat Struct Mol Biol (2012) 1.52
The peopling of Europe and the cautionary tale of Y chromosome lineage R-M269. Proc Biol Sci (2011) 1.52
The intestinal protozoan parasite Entamoeba histolytica contains 20 cysteine protease genes, of which only a small subset is expressed during in vitro cultivation. Eukaryot Cell (2003) 1.51
Mitochondrial DNA signals of late glacial recolonization of Europe from near eastern refugia. Am J Hum Genet (2012) 1.49
Microsatellite diversity suggests different histories for Mediterranean and Northern European cattle populations. Proc Biol Sci (2005) 1.49
Genetic structure and extinction of the woolly mammoth, Mammuthus primigenius. Curr Biol (2007) 1.47
Population genetic structure in Indian Austroasiatic speakers: the role of landscape barriers and sex-specific admixture. Mol Biol Evol (2010) 1.46
Ancient DNA chronology within sediment deposits: are paleobiological reconstructions possible and is DNA leaching a factor? Mol Biol Evol (2007) 1.44
Inhibition of transforming growth factor beta signaling reduces pancreatic adenocarcinoma growth and invasiveness. Mol Pharmacol (2007) 1.44
The origin of the 'Mycoplasma mycoides cluster' coincides with domestication of ruminants. PLoS One (2012) 1.42
Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry". Science (2008) 1.41
Runs of homozygosity and population history in cattle. BMC Genet (2012) 1.40
Genetic and archaeological perspectives on the initial modern human colonization of southern Asia. Proc Natl Acad Sci U S A (2013) 1.40
Sequencing and analysis of an Irish human genome. Genome Biol (2010) 1.39
Role of the TGF-beta/Alk5 signaling pathway in monocrotaline-induced pulmonary hypertension. Am J Respir Crit Care Med (2008) 1.37
Temporal change in gene expression in the rat dentate gyrus following passive avoidance learning. J Neurochem (2007) 1.37
Phylogeography of lions (Panthera leo ssp.) reveals three distinct taxa and a late Pleistocene reduction in genetic diversity. Mol Ecol (2009) 1.34
The Longue Durée of genetic ancestry: multiple genetic marker systems and Celtic origins on the Atlantic facade of Europe. Am J Hum Genet (2004) 1.33
Genomic evidence for island population conversion resolves conflicting theories of polar bear evolution. PLoS Genet (2013) 1.31
A Y-chromosome signature of hegemony in Gaelic Ireland. Am J Hum Genet (2005) 1.31
A sequence polymorphism in MSTN predicts sprinting ability and racing stamina in thoroughbred horses. PLoS One (2010) 1.27
Bayesian estimation of substitution rates from ancient DNA sequences with low information content. Syst Biol (2011) 1.25
Molecular basis for the specification of floral organs by APETALA3 and PISTILLATA. Proc Natl Acad Sci U S A (2012) 1.23
The diversity of Rab GTPases in Entamoeba histolytica. Exp Parasitol (2005) 1.23
Unique organisation of tRNA genes in Entamoeba histolytica. Mol Biochem Parasitol (2005) 1.22
Evidence for lateral transfer of genes encoding ferredoxins, nitroreductases, NADH oxidase, and alcohol dehydrogenase 3 from anaerobic prokaryotes to Giardia lamblia and Entamoeba histolytica. Eukaryot Cell (2002) 1.21
Discovery of lost diversity of paternal horse lineages using ancient DNA. Nat Commun (2011) 1.20
Revealing the maternal demographic history of Panthera leo using ancient DNA and a spatially explicit genealogical analysis. BMC Evol Biol (2014) 1.20
Delineating the genetic heterogeneity of ALS using targeted high-throughput sequencing. J Med Genet (2013) 1.20
Insights into the evolutionary history of an emerging livestock pathogen: porcine circovirus 2. J Virol (2009) 1.19
Ancient mitochondrial DNA from hair. Curr Biol (2004) 1.19
Sequencing illustrates the transcriptional response of Legionella pneumophila during infection and identifies seventy novel small non-coding RNAs. PLoS One (2011) 1.18
The Arabian cradle: mitochondrial relicts of the first steps along the southern route out of Africa. Am J Hum Genet (2012) 1.16
Genome-wide associations for milk production and somatic cell score in Holstein-Friesian cattle in Ireland. BMC Genet (2012) 1.16
Control of reproductive floral organ identity specification in Arabidopsis by the C function regulator AGAMOUS. Plant Cell (2013) 1.15
Partial genetic turnover in neandertals: continuity in the East and population replacement in the West. Mol Biol Evol (2012) 1.14
DNA sequence polymorphisms in a panel of eight candidate bovine imprinted genes and their association with performance traits in Irish Holstein-Friesian cattle. BMC Genet (2010) 1.14
Correlating Bayesian date estimates with climatic events and domestication using a bovine case study. Biol Lett (2008) 1.14