Published in Trends Genet on October 02, 2009
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Transcriptome-based exon capture enables highly cost-effective comparative genomic data collection at moderate evolutionary scales. BMC Genomics (2012) 1.28
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A hierarchical Bayesian model for next-generation population genomics. Genetics (2011) 1.17
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Targeted enrichment of the black cottonwood (Populus trichocarpa) gene space using sequence capture. BMC Genomics (2012) 1.06
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Heart transcriptome of the bank vole (Myodes glareolus): towards understanding the evolutionary variation in metabolic rate. BMC Genomics (2010) 0.96
Quantifying whole transcriptome size, a prerequisite for understanding transcriptome evolution across species: an example from a plant allopolyploid. Genome Biol Evol (2010) 0.96
A second generation framework for the analysis of microsatellites in expressed sequence tags and the development of EST-SSR markers for a conifer, Cryptomeria japonica. BMC Genomics (2012) 0.95
Using blood informative transcripts in geographical genomics: impact of lifestyle on gene expression in fijians. Front Genet (2012) 0.94
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The Population Genomics of Sunflowers and Genomic Determinants of Protein Evolution Revealed by RNAseq. Biology (Basel) (2012) 0.89
New approaches to Prunus transcriptome analysis. Genetica (2011) 0.88
The possibility of de novo assembly of the genome and population genomics of the mangrove rivulus, Kryptolebias marmoratus. Integr Comp Biol (2012) 0.88
Performance assessment of copy number microarray platforms using a spike-in experiment. Bioinformatics (2011) 0.88
De novo transcriptome characterization of Lilium 'Sorbonne' and key enzymes related to the flavonoid biosynthesis. Mol Genet Genomics (2014) 0.85
Key questions in the genetics and genomics of eco-evolutionary dynamics. Heredity (Edinb) (2013) 0.85
Genomic resources for a model in adaptation and speciation research: characterization of the Poecilia mexicana transcriptome. BMC Genomics (2012) 0.84
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The diverse applications of RNA-seq for functional genomic studies in Aspergillus fumigatus. Ann N Y Acad Sci (2012) 0.79
Mining transcriptomic data to study the origins and evolution of a plant allopolyploid complex. PeerJ (2014) 0.77
Transcriptome analysis of a petal anthocyanin polymorphism in the arctic mustard, Parrya nudicaulis. PLoS One (2014) 0.76
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Phylogeny and historical demography of endemic fishes in Lake Biwa: the ancient lake as a promoter of evolution and diversification of freshwater fishes in western Japan. Ecol Evol (2016) 0.75
Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res (2008) 157.44
Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods (2008) 126.81
Accurate whole human genome sequencing using reversible terminator chemistry. Nature (2008) 90.20
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SOAP: short oligonucleotide alignment program. Bioinformatics (2008) 68.13
RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res (2008) 62.07
RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet (2009) 58.77
The complete genome of an individual by massively parallel DNA sequencing. Nature (2008) 52.81
The transcriptional landscape of the yeast genome defined by RNA sequencing. Science (2008) 48.99
The diploid genome sequence of an Asian individual. Nature (2008) 46.29
DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature (2008) 38.13
Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nat Rev Genet (2008) 30.94
A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science (2008) 29.99
A map of recent positive selection in the human genome. PLoS Biol (2006) 29.19
Evolution at two levels in humans and chimpanzees. Science (1975) 21.07
The impact of next-generation sequencing technology on genetics. Trends Genet (2008) 21.07
Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature (2008) 18.84
High-resolution mapping and characterization of open chromatin across the genome. Cell (2008) 15.93
Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res (2009) 15.15
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Evo-devo and an expanding evolutionary synthesis: a genetic theory of morphological evolution. Cell (2008) 9.47
The evolutionary significance of cis-regulatory mutations. Nat Rev Genet (2007) 9.35
Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Res (2008) 8.89
Transcript length bias in RNA-seq data confounds systems biology. Biol Direct (2009) 8.53
Sequencing of natural strains of Arabidopsis thaliana with short reads. Genome Res (2008) 8.44
Single-molecule sequencing of an individual human genome. Nat Biotechnol (2009) 8.35
Rapid whole-genome mutational profiling using next-generation sequencing technologies. Genome Res (2008) 8.01
The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group. Genome Res (2009) 7.87
De novo fragment assembly with short mate-paired reads: Does the read length matter? Genome Res (2008) 7.66
Natural selection has driven population differentiation in modern humans. Nat Genet (2008) 7.48
An RNA gene expressed during cortical development evolved rapidly in humans. Nature (2006) 7.23
Variation in gene expression within and among natural populations. Nat Genet (2002) 7.19
The allele frequency spectrum in genome-wide human variation data reveals signals of differential demographic history in three large world populations. Genetics (2004) 7.00
Tissue-specific transcriptional regulation has diverged significantly between human and mouse. Nat Genet (2007) 6.92
Reliability and reproducibility issues in DNA microarray measurements. Trends Genet (2005) 6.79
Ascertainment bias in studies of human genome-wide polymorphism. Genome Res (2005) 6.63
The locus of evolution: evo devo and the genetics of adaptation. Evolution (2007) 6.24
Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees. Science (2005) 5.68
Insights from genomic profiling of transcription factors. Nat Rev Genet (2009) 5.57
Identification of deleterious mutations within three human genomes. Genome Res (2009) 5.42
A gene expression map for the euchromatic genome of Drosophila melanogaster. Science (2004) 5.38
Repetitive and non-repetitive DNA sequences and a speculation on the origins of evolutionary novelty. Q Rev Biol (1971) 5.18
Patterns of positive selection in six Mammalian genomes. PLoS Genet (2008) 4.69
Transcriptome-wide identification of novel imprinted genes in neonatal mouse brain. PLoS One (2008) 4.03
Species-specific transcription in mice carrying human chromosome 21. Science (2008) 4.03
Large-scale turnover of functional transcription factor binding sites in Drosophila. PLoS Comput Biol (2006) 4.01
Differential allelic expression in the human genome: a robust approach to identify genetic and epigenetic cis-acting mechanisms regulating gene expression. PLoS Genet (2008) 3.92
Human-specific gain of function in a developmental enhancer. Science (2008) 3.84
Massively parallel sequencing of the polyadenylated transcriptome of C. elegans. Genome Res (2009) 3.83
The transcriptional consequences of mutation and natural selection in Caenorhabditis elegans. Nat Genet (2005) 3.58
Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation lines. Genome Res (2009) 3.47
Functional genomics and the study of development, variation and evolution. Nat Rev Genet (2001) 3.46
Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles. Genome Res (2005) 3.23
The evolution of gene regulation underlies a morphological difference between two Drosophila sister species. Cell (2008) 3.10
Global survey of genomic imprinting by transcriptome sequencing. Curr Biol (2008) 2.80
Population genetic analysis of ascertained SNP data. Hum Genomics (2004) 2.41
Neutral and adaptive variation in gene expression. Proc Natl Acad Sci U S A (2006) 2.37
A catalog of neutral and deleterious polymorphism in yeast. PLoS Genet (2008) 2.28
A mutation accumulation assay reveals a broad capacity for rapid evolution of gene expression. Nature (2005) 2.08
Global analysis of alternative splicing differences between humans and chimpanzees. Genes Dev (2007) 2.00
Natural selection on gene expression. Trends Genet (2006) 1.90
Gene regulation in primates evolves under tissue-specific selection pressures. PLoS Genet (2008) 1.86
Progress and prospects in mapping recent selection in the genome. Heredity (Edinb) (2007) 1.71
The genomics of speciation in Drosophila: diversity, divergence, and introgression estimated using low-coverage genome sequencing. PLoS Genet (2009) 1.63
Using DNA microarrays to study gene expression in closely related species. Bioinformatics (2007) 1.50
Independent effects of cis- and trans-regulatory variation on gene expression in Drosophila melanogaster. Genetics (2008) 1.45
Positive selection in the human genome: from genome scans to biological significance. Annu Rev Genomics Hum Genet (2008) 1.38
High-throughput multiplex sequencing to discover copy number variants in Drosophila. Genetics (2009) 1.31
Using DNA microarrays to study natural variation. Curr Opin Genet Dev (2006) 1.28
Intra-tumor heterogeneity of MLH1 promoter methylation revealed by deep single molecule bisulfite sequencing. Nucleic Acids Res (2009) 1.26
Positive selection in the human genome inferred from human-chimp-mouse orthologous gene alignments. Cold Spring Harb Symp Quant Biol (2003) 1.07
Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics (2003) 53.11
Genetic structure of human populations. Science (2002) 30.91
A map of recent positive selection in the human genome. PLoS Biol (2006) 29.19
A high-resolution survey of deletion polymorphism in the human genome. Nat Genet (2005) 16.99
Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature (2010) 16.86
A systematic survey of loss-of-function variants in human protein-coding genes. Science (2012) 12.25
Traces of human migrations in Helicobacter pylori populations. Science (2003) 11.92
Inferring weak population structure with the assistance of sample group information. Mol Ecol Resour (2009) 10.81
Inference of population structure using multilocus genotype data: dominant markers and null alleles. Mol Ecol Notes (2007) 10.11
High-resolution mapping of expression-QTLs yields insight into human gene regulation. PLoS Genet (2008) 9.68
Convergent adaptation of human lactase persistence in Africa and Europe. Nat Genet (2006) 9.44
A worldwide survey of haplotype variation and linkage disequilibrium in the human genome. Nat Genet (2006) 8.46
Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. Genome Res (2005) 8.38
Signals of recent positive selection in a worldwide sample of human populations. Genome Res (2009) 8.38
Sequencing and analysis of Neanderthal genomic DNA. Science (2006) 8.06
Overcoming the winner's curse: estimating penetrance parameters from case-control data. Am J Hum Genet (2007) 6.99
Informativeness of genetic markers for inference of ancestry. Am J Hum Genet (2003) 6.90
Clines, clusters, and the effect of study design on the inference of human population structure. PLoS Genet (2005) 6.73
DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines. Genome Biol (2011) 6.48
DNase I sensitivity QTLs are a major determinant of human expression variation. Nature (2012) 6.17
The origin of new genes: glimpses from the young and old. Nat Rev Genet (2003) 6.14
Revealing the architecture of gene regulation: the promise of eQTL studies. Trends Genet (2008) 5.78
Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data. Bioinformatics (2009) 5.62
Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Genome Res (2010) 5.40
Coalescent-based association mapping and fine mapping of complex trait loci. Genetics (2004) 5.26
Haplotype blocks and linkage disequilibrium in the human genome. Nat Rev Genet (2003) 5.16
High-resolution mapping of crossovers reveals extensive variation in fine-scale recombination patterns among humans. Science (2008) 5.02
Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet (2012) 4.85
Statistical tests for admixture mapping with case-control and cases-only data. Am J Hum Genet (2004) 4.52
Retroposed new genes out of the X in Drosophila. Genome Res (2002) 4.46
Completing the map of human genetic variation. Nature (2007) 4.38
Confounding from cryptic relatedness in case-control association studies. PLoS Genet (2005) 3.61
Clonal origin and evolution of a transmissible cancer. Cell (2006) 3.60
The role of geography in human adaptation. PLoS Genet (2009) 3.41
Noisy splicing drives mRNA isoform diversity in human cells. PLoS Genet (2010) 3.19
Identification of genetic variants that affect histone modifications in human cells. Science (2013) 3.11
Comment on "Widespread RNA and DNA sequence differences in the human transcriptome". Science (2012) 2.79
Adaptations to climate in candidate genes for common metabolic disorders. PLoS Genet (2008) 2.68
Genomics: ENCODE explained. Nature (2012) 2.62
Assessing the performance of the haplotype block model of linkage disequilibrium. Am J Hum Genet (2003) 2.59
Using environmental correlations to identify loci underlying local adaptation. Genetics (2010) 2.52
Dissecting the regulatory architecture of gene expression QTLs. Genome Biol (2012) 2.51
DNA sequence-dependent compartmentalization and silencing of chromatin at the nuclear lamina. Cell (2012) 2.20
Primate transcript and protein expression levels evolve under compensatory selection pressures. Science (2013) 2.18
Adaptations to climate-mediated selective pressures in humans. PLoS Genet (2011) 2.15
Controls of nucleosome positioning in the human genome. PLoS Genet (2012) 2.14
A genome-wide study of DNA methylation patterns and gene expression levels in multiple human and chimpanzee tissues. PLoS Genet (2011) 1.92
Evidence for extensive transmission distortion in the human genome. Am J Hum Genet (2003) 1.86
False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions. Bioinformatics (2011) 1.85
Efficient counting of k-mers in DNA sequences using a bloom filter. BMC Bioinformatics (2011) 1.76
Gene expression levels are a target of recent natural selection in the human genome. Mol Biol Evol (2008) 1.63
Identification by full-coverage array CGH of human DNA copy number increases relative to chimpanzee and gorilla. Genome Res (2005) 1.51
Extensive introgression of mitochondrial DNA relative to nuclear genes in the Drosophila yakuba species group. Evolution (2006) 1.50
Adaptive evolution of conserved noncoding elements in mammals. PLoS Genet (2007) 1.45
The genetic architecture of adaptations to high altitude in Ethiopia. PLoS Genet (2012) 1.38
Comparative RNA sequencing reveals substantial genetic variation in endangered primates. Genome Res (2011) 1.36
Kinetic analysis of a high-affinity antibody/antigen interaction performed by multiple Biacore users. Anal Biochem (2006) 1.31
Nucleotide variation along the Drosophila melanogaster fourth chromosome. Science (2002) 1.30
The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels. PLoS Genet (2012) 1.25
Haplotype variation and genotype imputation in African populations. Genet Epidemiol (2011) 1.10
Haplotypic background of a private allele at high frequency in the Americas. Mol Biol Evol (2009) 1.08
A genome sequence resource for the aye-aye (Daubentonia madagascariensis), a nocturnal lemur from Madagascar. Genome Biol Evol (2011) 1.07
Exon-specific QTLs skew the inferred distribution of expression QTLs detected using gene expression array data. PLoS One (2012) 0.98
The effects of genotype-dependent recombination, and transmission asymmetry, on linkage disequilibrium. Genetics (2005) 0.91
Whole-genome sequencing data offer insights into human demography. Nat Genet (2011) 0.90
Nucleotide variation and recombination along the fourth chromosome in Drosophila simulans. Genetics (2004) 0.90
Epigenetic modifications are associated with inter-species gene expression variation in primates. Genome Biol (2014) 0.90
The chromatin architectural proteins HMGD1 and H1 bind reciprocally and have opposite effects on chromatin structure and gene regulation. BMC Genomics (2014) 0.85
Experiments with the site frequency spectrum. Bull Math Biol (2010) 0.81
Adaptive drool in the gene pool. Nat Genet (2007) 0.79
Read all about it: The Lancet's Paper of the Year, 2003. Lancet (2003) 0.79
Association mapping and fine mapping with TreeLD. Bioinformatics (2005) 0.78
Breed differences in humoral and cellular responses of lambs to experimental infection with the gastrointestinal nematode Teladorsagia circumcincta. Vet Res (2015) 0.77
Intensive care unit providers more quickly and accurately assess risk of multiple harms using an engineered safety display. Health Informatics J (2018) 0.75