Published in Genome Biol on January 20, 2011
Epigenome-wide association studies for common human diseases. Nat Rev Genet (2011) 7.96
DNA methylation age of human tissues and cell types. Genome Biol (2013) 7.48
Genome-wide methylation profiles reveal quantitative views of human aging rates. Mol Cell (2012) 6.50
DNase I sensitivity QTLs are a major determinant of human expression variation. Nature (2012) 6.17
Epigenome-wide scans identify differentially methylated regions for age and age-related phenotypes in a healthy ageing population. PLoS Genet (2012) 4.05
Analysing and interpreting DNA methylation data. Nat Rev Genet (2012) 3.77
Factors underlying variable DNA methylation in a human community cohort. Proc Natl Acad Sci U S A (2012) 3.20
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Passive and active DNA methylation and the interplay with genetic variation in gene regulation. Elife (2013) 2.70
Dissecting the regulatory architecture of gene expression QTLs. Genome Biol (2012) 2.51
Global analysis of DNA methylation variation in adipose tissue from twins reveals links to disease-associated variants in distal regulatory elements. Am J Hum Genet (2013) 2.40
DNA methylation profiling identifies epigenetic dysregulation in pancreatic islets from type 2 diabetic patients. EMBO J (2012) 2.21
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Population-specificity of human DNA methylation. Genome Biol (2012) 2.04
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Systems genetics approaches to understand complex traits. Nat Rev Genet (2013) 1.97
Batch effect correction for genome-wide methylation data with Illumina Infinium platform. BMC Med Genomics (2011) 1.84
Enrichment of cis-regulatory gene expression SNPs and methylation quantitative trait loci among bipolar disorder susceptibility variants. Mol Psychiatry (2012) 1.84
Genomic impact of transient low-dose decitabine treatment on primary AML cells. Blood (2013) 1.80
Tissue-specific effects of genetic and epigenetic variation on gene regulation and splicing. PLoS Genet (2015) 1.78
A subset of methylated CpG sites differentiate psoriatic from normal skin. J Invest Dermatol (2011) 1.73
Epigenetic analysis leads to identification of HNF1B as a subtype-specific susceptibility gene for ovarian cancer. Nat Commun (2013) 1.73
A coherent approach for analysis of the Illumina HumanMethylation450 BeadChip improves data quality and performance in epigenome-wide association studies. Genome Biol (2015) 1.71
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Novel genetic variants associated with lumbar disc degeneration in northern Europeans: a meta-analysis of 4600 subjects. Ann Rheum Dis (2012) 1.66
DNA methylation contributes to natural human variation. Genome Res (2013) 1.66
Lymphoblastoid cell lines in pharmacogenomic discovery and clinical translation. Pharmacogenomics (2012) 1.63
Relationship of DNA methylation and gene expression in idiopathic pulmonary fibrosis. Am J Respir Crit Care Med (2014) 1.63
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Epigenetic variation during the adult lifespan: cross-sectional and longitudinal data on monozygotic twin pairs. Aging Cell (2012) 1.55
Genetic background drives transcriptional variation in human induced pluripotent stem cells. PLoS Genet (2014) 1.53
Integrative analysis of DNA methylation and gene expression data identifies EPAS1 as a key regulator of COPD. PLoS Genet (2015) 1.52
Cigarette smoking and DNA methylation. Front Genet (2013) 1.48
Environmental epigenetics: prospects for studying epigenetic mediation of exposure-response relationships. Hum Genet (2012) 1.47
Guthrie card methylomics identifies temporally stable epialleles that are present at birth in humans. Genome Res (2012) 1.45
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Epigenomic association analysis identifies smoking-related DNA methylation sites in African Americans. Hum Genet (2013) 1.43
CpGassoc: an R function for analysis of DNA methylation microarray data. Bioinformatics (2012) 1.41
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The PsychENCODE project. Nat Neurosci (2015) 1.39
Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels. PLoS Genet (2014) 1.39
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SNPs located at CpG sites modulate genome-epigenome interaction. Epigenetics (2013) 1.37
Genetic architecture of microRNA expression: implications for the transcriptome and complex traits. Am J Hum Genet (2012) 1.36
Differentially methylated regions of imprinted genes in prenatal, perinatal and postnatal human tissues. PLoS One (2012) 1.36
DNA methylation and gene expression changes in monozygotic twins discordant for psoriasis: identification of epigenetically dysregulated genes. PLoS Genet (2012) 1.35
Methylation quantitative trait loci (meQTLs) are consistently detected across ancestry, developmental stage, and tissue type. BMC Genomics (2014) 1.34
Differences in smoking associated DNA methylation patterns in South Asians and Europeans. Clin Epigenetics (2014) 1.33
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Genome-wide variation of cytosine modifications between European and African populations and the implications for complex traits. Genetics (2013) 1.31
DNA hydroxymethylation profiling reveals that WT1 mutations result in loss of TET2 function in acute myeloid leukemia. Cell Rep (2014) 1.31
Statistical approaches for the analysis of DNA methylation microarray data. Hum Genet (2011) 1.31
The effect of genotype and in utero environment on interindividual variation in neonate DNA methylomes. Genome Res (2014) 1.29
Differential methylation in glucoregulatory genes of offspring born before vs. after maternal gastrointestinal bypass surgery. Proc Natl Acad Sci U S A (2013) 1.28
DNA methylation and healthy human aging. Aging Cell (2015) 1.27
Accounting for population stratification in DNA methylation studies. Genet Epidemiol (2014) 1.25
The presence of methylation quantitative trait loci indicates a direct genetic influence on the level of DNA methylation in adipose tissue. PLoS One (2013) 1.25
The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels. PLoS Genet (2012) 1.25
Prenatal famine and genetic variation are independently and additively associated with DNA methylation at regulatory loci within IGF2/H19. PLoS One (2012) 1.24
A methylome-wide study of aging using massively parallel sequencing of the methyl-CpG-enriched genomic fraction from blood in over 700 subjects. Hum Mol Genet (2013) 1.24
DNA methylation profiling in breast cancer discordant identical twins identifies DOK7 as novel epigenetic biomarker. Carcinogenesis (2012) 1.22
The interaction of genetic variants and DNA methylation of the interleukin-4 receptor gene increase the risk of asthma at age 18 years. Clin Epigenetics (2013) 1.22
Genetic and epigenetic variations in inducible nitric oxide synthase promoter, particulate pollution, and exhaled nitric oxide levels in children. J Allergy Clin Immunol (2011) 1.21
Characterizing the genetic basis of methylome diversity in histologically normal human lung tissue. Nat Commun (2014) 1.20
Whole-genome bisulfite sequencing of multiple individuals reveals complementary roles of promoter and gene body methylation in transcriptional regulation. Genome Biol (2014) 1.19
Long-range epigenetic regulation is conferred by genetic variation located at thousands of independent loci. Nat Commun (2015) 1.18
Epigenetics: the link between nature and nurture. Mol Aspects Med (2012) 1.18
Is epidemiology ready for epigenetics? Int J Epidemiol (2012) 1.17
Allelic methylation levels of the noncoding VTRNA2-1 located on chromosome 5q31.1 predict outcome in AML. Blood (2011) 1.17
Genetic and environmental exposures constrain epigenetic drift over the human life course. Genome Res (2014) 1.13
DNA methylation differences at growth related genes correlate with birth weight: a molecular signature linked to developmental origins of adult disease? BMC Med Genomics (2012) 1.11
Patterns of methylation heritability in a genome-wide analysis of four brain regions. Nucleic Acids Res (2013) 1.11
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Prenatal arsenic exposure and the epigenome: identifying sites of 5-methylcytosine alterations that predict functional changes in gene expression in newborn cord blood and subsequent birth outcomes. Toxicol Sci (2014) 1.10
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COHCAP: an integrative genomic pipeline for single-nucleotide resolution DNA methylation analysis. Nucleic Acids Res (2013) 1.08
Intermediate DNA methylation is a conserved signature of genome regulation. Nat Commun (2015) 1.07
Dynamics of DNA methylation in recent human and great ape evolution. PLoS Genet (2013) 1.07
DNA methylation and childhood asthma in the inner city. J Allergy Clin Immunol (2015) 1.07
Synthesis of 53 tissue and cell line expression QTL datasets reveals master eQTLs. BMC Genomics (2014) 1.06
Epigenetic epidemiology: promises for public health research. Environ Mol Mutagen (2014) 1.06
Sex-biased methylome and transcriptome in human prefrontal cortex. Hum Mol Genet (2013) 1.06
Widespread natural variation of DNA methylation within angiosperms. Genome Biol (2016) 1.06
Genome-wide associations between genetic and epigenetic variation influence mRNA expression and insulin secretion in human pancreatic islets. PLoS Genet (2014) 1.06
Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic data. Genome Biol (2015) 1.05
Relating human genetic variation to variation in drug responses. Trends Genet (2012) 1.05
Novel region discovery method for Infinium 450K DNA methylation data reveals changes associated with aging in muscle and neuronal pathways. Aging Cell (2013) 1.05
Identification of DNA methylation biomarkers from Infinium arrays. Front Genet (2012) 1.05
Epigenome-wide Association Studies and the Interpretation of Disease -Omics. PLoS Genet (2016) 1.05
Hypermethylation of repeat expanded C9orf72 is a clinical and molecular disease modifier. Acta Neuropathol (2014) 1.04
Predicting genome-wide DNA methylation using methylation marks, genomic position, and DNA regulatory elements. Genome Biol (2015) 1.03
Integrated analysis of genome-wide DNA methylation and gene expression profiles in molecular subtypes of breast cancer. Nucleic Acids Res (2013) 1.03
Aberrant DNA methylation profiles in the premature aging disorders Hutchinson-Gilford Progeria and Werner syndrome. Epigenetics (2012) 1.03
Global properties and functional complexity of human gene regulatory variation. PLoS Genet (2013) 1.02
CpG methylation regulates allelic expression of GDF5 by modulating binding of SP1 and SP3 repressor proteins to the osteoarthritis susceptibility SNP rs143383. Hum Genet (2014) 1.01
The role of longitudinal cohort studies in epigenetic epidemiology: challenges and opportunities. Genome Biol (2012) 1.00
Systematic identification of genetic influences on methylation across the human life course. Genome Biol (2016) 1.00
DNA methylation studies using twins: what are they telling us? Genome Biol (2012) 0.99
Making sense of GWAS: using epigenomics and genome engineering to understand the functional relevance of SNPs in non-coding regions of the human genome. Epigenetics Chromatin (2015) 0.99
Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res (2008) 157.44
BLAT--the BLAST-like alignment tool. Genome Res (2002) 126.78
A second generation human haplotype map of over 3.1 million SNPs. Nature (2007) 85.39
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics (2003) 82.89
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
Human DNA methylomes at base resolution show widespread epigenomic differences. Nature (2009) 34.27
Population genomics of human gene expression. Nat Genet (2007) 24.49
Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature (2009) 24.41
Origins and functional impact of copy number variation in the human genome. Nature (2009) 23.63
CpG islands in vertebrate genomes. J Mol Biol (1987) 23.16
Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet (2007) 20.22
The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet (2009) 18.90
DNA methylation profiling of human chromosomes 6, 20 and 22. Nat Genet (2006) 18.08
Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature (2010) 16.86
Imputation-based analysis of association studies: candidate regions and quantitative traits. PLoS Genet (2007) 15.55
Transcriptome genetics using second generation sequencing in a Caucasian population. Nature (2010) 14.85
Capturing heterogeneity in gene expression studies by surrogate variable analysis. PLoS Genet (2007) 12.08
Linking DNA methylation and histone modification: patterns and paradigms. Nat Rev Genet (2009) 12.08
Common regulatory variation impacts gene expression in a cell type-dependent manner. Science (2009) 11.28
Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat Biotechnol (2009) 11.18
High-resolution mapping of expression-QTLs yields insight into human gene regulation. PLoS Genet (2008) 9.68
Variation in transcription factor binding among humans. Science (2010) 9.33
Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain. PLoS Genet (2010) 8.74
Parental origin of sequence variants associated with complex diseases. Nature (2009) 7.21
Practical issues in imputation-based association mapping. PLoS Genet (2008) 6.76
Intra-individual change over time in DNA methylation with familial clustering. JAMA (2008) 6.17
Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer. Genome Res (2010) 6.03
DNA methylation profiles in monozygotic and dizygotic twins. Nat Genet (2009) 5.99
Heritable individual-specific and allele-specific chromatin signatures in humans. Science (2010) 5.94
Genomic surveys by methylation-sensitive SNP analysis identify sequence-dependent allele-specific DNA methylation. Nat Genet (2008) 5.66
Mapping global histone acetylation patterns to gene expression. Cell (2004) 5.57
Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Genome Res (2010) 5.40
Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains. Genome Res (2010) 5.08
Genetic analysis of human traits in vitro: drug response and gene expression in lymphoblastoid cell lines. PLoS Genet (2008) 5.08
CpG islands influence chromatin structure via the CpG-binding protein Cfp1. Nature (2010) 4.86
Sex-specific genetic architecture of human disease. Nat Rev Genet (2008) 4.01
Genetic control of individual differences in gene-specific methylation in human brain. Am J Hum Genet (2010) 3.91
Accurate discovery of expression quantitative trait loci under confounding from spurious and genuine regulatory hotspots. Genetics (2008) 3.66
The relationship of DNA methylation with age, gender and genotype in twins and healthy controls. PLoS One (2009) 3.41
Allelic skewing of DNA methylation is widespread across the genome. Am J Hum Genet (2010) 3.17
Heritable rather than age-related environmental and stochastic factors dominate variation in DNA methylation of the human IGF2/H19 locus. Hum Mol Genet (2007) 3.06
The imprinted gene and parent-of-origin effect database. Nucleic Acids Res (2001) 2.96
Distinct effects on gene expression of chemical and genetic manipulation of the cancer epigenome revealed by a multimodality approach. Cancer Cell (2004) 2.73
Genetic analysis of variation in transcription factor binding in yeast. Nature (2010) 2.69
CpG island methylation in human lymphocytes is highly correlated with DNA sequence, repeats, and predicted DNA structure. PLoS Genet (2006) 2.66
EBV transformation and cell culturing destabilizes DNA methylation in human lymphoblastoid cell lines. Genomics (2009) 2.26
An association between variants in the IGF2 gene and Beckwith-Wiedemann syndrome: interaction between genotype and epigenotype. Hum Mol Genet (2003) 1.85
Allele-specific chromatin immunoprecipitation studies show genetic influence on chromatin state in human genome. PLoS Genet (2007) 1.71
Profound flanking sequence preference of Dnmt3a and Dnmt3b mammalian DNA methyltransferases shape the human epigenome. J Mol Biol (2005) 1.65
Comparison of the DNA methylation profiles of human peripheral blood cells and transformed B-lymphocytes. Hum Genet (2010) 1.31
Differences in DNA methylation patterns between humans and chimpanzees. Curr Biol (2004) 1.24
Genomic predictors of interindividual differences in response to DNA damaging agents. Genes Dev (2008) 1.20
Hypermethylation of Fads2 and altered hepatic fatty acid and phospholipid metabolism in mice with hyperhomocysteinemia. J Biol Chem (2007) 1.18
DNA methyltransferase 1 and 3B activate BAG-1 expression via recruitment of CTCFL/BORIS and modulation of promoter histone methylation. Cancer Res (2008) 1.17
Prediction of methylated CpGs in DNA sequences using a support vector machine. FEBS Lett (2005) 1.16
Gatm, a creatine synthesis enzyme, is imprinted in mouse placenta. Proc Natl Acad Sci U S A (2003) 1.09
The MTHFR 1298A>C polymorphism and genomic DNA methylation in human lymphocytes. Cancer Epidemiol Biomarkers Prev (2005) 1.08
CGG-repeat expansion in the DIP2B gene is associated with the fragile site FRA12A on chromosome 12q13.1. Am J Hum Genet (2006) 1.01
A systematic search for DNA methyltransferase polymorphisms reveals a rare DNMT3L variant associated with subtelomeric hypomethylation. Hum Mol Genet (2009) 0.98
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Gene expression in early expanded parthenogenetic and in vitro fertilized bovine blastocysts. J Reprod Dev (2009) 0.86
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A map of recent positive selection in the human genome. PLoS Biol (2006) 29.19
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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
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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
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
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DNase I sensitivity QTLs are a major determinant of human expression variation. Nature (2012) 6.17
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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
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Completing the map of human genetic variation. Nature (2007) 4.38
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Sex-specific and lineage-specific alternative splicing in primates. Genome Res (2009) 3.61
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Clonal origin and evolution of a transmissible cancer. Cell (2006) 3.60
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Noisy splicing drives mRNA isoform diversity in human cells. PLoS Genet (2010) 3.19
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Adaptations to climate in candidate genes for common metabolic disorders. PLoS Genet (2008) 2.68
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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
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Inferring admixture histories of human populations using linkage disequilibrium. Genetics (2013) 2.51
Evolutionary dynamics of human Toll-like receptors and their different contributions to host defense. PLoS Genet (2009) 2.35
Ancient DNA reveals key stages in the formation of central European mitochondrial genetic diversity. Science (2013) 2.23
Absence of the TAP2 human recombination hotspot in chimpanzees. PLoS Biol (2004) 2.22
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
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Functional constraints and frequency of deleterious mutations in noncoding DNA of rodents. Proc Natl Acad Sci U S A (2003) 1.98
A genome-wide study of DNA methylation patterns and gene expression levels in multiple human and chimpanzee tissues. PLoS Genet (2011) 1.92
Gene regulation in primates evolves under tissue-specific selection pressures. PLoS Genet (2008) 1.86
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
Dense fine-mapping study identifies new susceptibility loci for primary biliary cirrhosis. Nat Genet (2012) 1.85
Comparative studies of gene expression and the evolution of gene regulation. Nat Rev Genet (2012) 1.79
Gene expression and isoform variation analysis using Affymetrix Exon Arrays. BMC Genomics (2008) 1.76
Efficient counting of k-mers in DNA sequences using a bloom filter. BMC Bioinformatics (2011) 1.76
The effects of EBV transformation on gene expression levels and methylation profiles. Hum Mol Genet (2011) 1.74
Deciphering the genetic architecture of variation in the immune response to Mycobacterium tuberculosis infection. Proc Natl Acad Sci U S A (2012) 1.73
Genomic-scale capture and sequencing of endogenous DNA from feces. Mol Ecol (2010) 1.71