Published in Bioinformatics on June 19, 2011
Signatures of mutational processes in human cancer. Nature (2013) 21.63
Therapeutic targeting of BET bromodomain proteins in castration-resistant prostate cancer. Nature (2014) 5.45
Locus-specific editing of histone modifications at endogenous enhancers. Nat Biotechnol (2013) 3.82
Analysing and interpreting DNA methylation data. Nat Rev Genet (2012) 3.77
Seventy-five genetic loci influencing the human red blood cell. Nature (2012) 2.77
Controls of nucleosome positioning in the human genome. PLoS Genet (2012) 2.14
Cooperativity and rapid evolution of cobound transcription factors in closely related mammals. Cell (2013) 1.52
Identifying and mitigating bias in next-generation sequencing methods for chromatin biology. Nat Rev Genet (2014) 1.44
Using population admixture to help complete maps of the human genome. Nat Genet (2013) 1.35
Transcription factor binding dynamics during human ES cell differentiation. Nature (2015) 1.30
A genome-wide analysis of Cas9 binding specificity using ChIP-seq and targeted sequence capture. Nucleic Acids Res (2015) 1.20
Differential methylation of the TRPA1 promoter in pain sensitivity. Nat Commun (2014) 1.19
Maps of open chromatin highlight cell type-restricted patterns of regulatory sequence variation at hematological trait loci. Genome Res (2013) 1.10
Active promoters give rise to false positive 'Phantom Peaks' in ChIP-seq experiments. Nucleic Acids Res (2015) 1.02
Mapping the human reference genome's missing sequence by three-way admixture in Latino genomes. Am J Hum Genet (2013) 1.01
Fine-mapping cellular QTLs with RASQUAL and ATAC-seq. Nat Genet (2015) 0.98
Simultaneous SNP identification and assessment of allele-specific bias from ChIP-seq data. BMC Genet (2012) 0.96
Noninvasive prenatal testing using a novel analysis pipeline to screen for all autosomal fetal aneuploidies improves pregnancy management. Eur J Hum Genet (2015) 0.95
BayMeth: improved DNA methylation quantification for affinity capture sequencing data using a flexible Bayesian approach. Genome Biol (2014) 0.93
Epigenetic coordination of signaling pathways during the epithelial-mesenchymal transition. Epigenetics Chromatin (2013) 0.91
Increased H3K9me3 drives dedifferentiated phenotype via KLF6 repression in liposarcoma. J Clin Invest (2015) 0.86
New insights from existing sequence data: generating breakthroughs without a pipette. Mol Cell (2013) 0.84
A dynamic CTCF chromatin binding landscape promotes DNA hydroxymethylation and transcriptional induction of adipocyte differentiation. Nucleic Acids Res (2014) 0.84
Relationship between nucleosome positioning and progesterone-induced alternative splicing in breast cancer cells. RNA (2015) 0.83
A comparison of control samples for ChIP-seq of histone modifications. Front Genet (2014) 0.83
Computational methodology for ChIP-seq analysis. Quant Biol (2013) 0.82
Detrimental effects of duplicate reads and low complexity regions on RNA- and ChIP-seq data. BMC Bioinformatics (2015) 0.81
Constrained transcription factor spacing is prevalent and important for transcriptional control of mouse blood cells. Nucleic Acids Res (2014) 0.79
A haplotype-based normalization technique for the analysis and detection of allele specific expression. BMC Bioinformatics (2016) 0.77
CNV-guided multi-read allocation for ChIP-seq. Bioinformatics (2014) 0.77
Interplay between PREX2 mutations and the PI3K pathway and its effect on epigenetic regulation of gene expression in NRAS-mutant melanoma. Small GTPases (2016) 0.75
Novel H3K4me3 marks are enriched at human- and chimpanzee-specific cytogenetic structures. Genome Res (2014) 0.75
HMCan-diff: a method to detect changes in histone modifications in cells with different genetic characteristics. Nucleic Acids Res (2017) 0.75
ChIP-BIT: Bayesian inference of target genes using a novel joint probabilistic model of ChIP-seq profiles. Nucleic Acids Res (2015) 0.75
Estimating genome-wide regulatory activity from multi-omics data sets using mathematical optimization. BMC Syst Biol (2017) 0.75
Selected heterozygosity at cis-regulatory sequences increases the expression homogeneity of a cell population in humans. Genome Biol (2016) 0.75
BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes. Genome Biol (2017) 0.75
A map of human genome variation from population-scale sequencing. Nature (2010) 121.13
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
Genome-wide mapping of in vivo protein-DNA interactions. Science (2007) 64.92
Model-based analysis of ChIP-Seq (MACS). Genome Biol (2008) 51.63
Origins and functional impact of copy number variation in the human genome. Nature (2009) 23.63
Recent segmental duplications in the human genome. Science (2002) 21.30
Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet (2008) 18.28
High-resolution mapping and characterization of open chromatin across the genome. Cell (2008) 15.93
Dynamic regulation of nucleosome positioning in the human genome. Cell (2008) 15.60
PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol (2009) 11.28
Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat Methods (2009) 10.17
Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature (2010) 6.87
Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Genome Res (2010) 5.40
The uniqueome: a mappability resource for short-tag sequencing. Bioinformatics (2010) 1.79
Inherent signals in sequencing-based Chromatin-ImmunoPrecipitation control libraries. PLoS One (2009) 1.49
RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res (2008) 62.07
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
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
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
Completing the map of human genetic variation. Nature (2007) 4.38
Sex-specific genetic architecture of human disease. Nat Rev Genet (2008) 4.01
Sex-specific and lineage-specific alternative splicing in primates. Genome Res (2009) 3.61
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
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
Different noses for different people. Nat Genet (2003) 2.10
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
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
Efficient counting of k-mers in DNA sequences using a bloom filter. BMC Bioinformatics (2011) 1.76
Gene expression and isoform variation analysis using Affymetrix Exon Arrays. BMC Genomics (2008) 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
Social environment is associated with gene regulatory variation in the rhesus macaque immune system. Proc Natl Acad Sci U S A (2012) 1.63
Gene expression levels are a target of recent natural selection in the human genome. Mol Biol Evol (2008) 1.63
Expression quantitative trait loci detected in cell lines are often present in primary tissues. Hum Mol Genet (2009) 1.57
Characterizing the expression of the human olfactory receptor gene family using a novel DNA microarray. Genome Biol (2007) 1.56
Evolutionary constraints in conserved nongenic sequences of mammals. Genome Res (2005) 1.50
Using DNA microarrays to study gene expression in closely related species. Bioinformatics (2007) 1.50
Prediction of the odorant binding site of olfactory receptor proteins by human-mouse comparisons. Protein Sci (2004) 1.48
Taxonomic classification of bacterial 16S rRNA genes using short sequencing reads: evaluation of effective study designs. PLoS One (2013) 1.46
Adaptive evolution of conserved noncoding elements in mammals. PLoS Genet (2007) 1.45
Evolution of bitter taste receptors in humans and apes. Mol Biol Evol (2004) 1.45
Copy number variation of CCL3-like genes affects rate of progression to simian-AIDS in Rhesus Macaques (Macaca mulatta). PLoS Genet (2009) 1.43
Characterizing natural variation using next-generation sequencing technologies. Trends Genet (2009) 1.39
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
The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels. PLoS Genet (2012) 1.25
An evolutionarily conserved sexual signature in the primate brain. PLoS Genet (2008) 1.21
Gene expression differences among primates are associated with changes in a histone epigenetic modification. Genetics (2011) 1.20
The combination of a genome-wide association study of lymphocyte count and analysis of gene expression data reveals novel asthma candidate genes. Hum Mol Genet (2012) 1.18
Using reporter gene assays to identify cis regulatory differences between humans and chimpanzees. Genetics (2007) 1.18