Published in Methods on April 27, 2010
Epigenome-wide association studies for common human diseases. Nat Rev Genet (2011) 7.96
Differential expression in RNA-seq: a matter of depth. Genome Res (2011) 7.13
Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol (2010) 7.00
Identifying ChIP-seq enrichment using MACS. Nat Protoc (2012) 3.60
DNA methylome analysis using short bisulfite sequencing data. Nat Methods (2012) 2.77
Genomic mapping of 5-hydroxymethylcytosine in the human brain. Nucleic Acids Res (2011) 2.53
Evaluation of affinity-based genome-wide DNA methylation data: effects of CpG density, amplification bias, and copy number variation. Genome Res (2010) 1.77
Protocol matters: which methylome are you actually studying? Epigenomics (2010) 1.37
An atlas of DNA methylomes in porcine adipose and muscle tissues. Nat Commun (2012) 1.28
Double restriction-enzyme digestion improves the coverage and accuracy of genome-wide CpG methylation profiling by reduced representation bisulfite sequencing. BMC Genomics (2013) 1.18
A comparison of the whole genome approach of MeDIP-seq to the targeted approach of the Infinium HumanMethylation450 BeadChip(®) for methylome profiling. PLoS One (2012) 1.16
Quality evaluation of methyl binding domain based kits for enrichment DNA-methylation sequencing. PLoS One (2013) 1.15
Genome-wide mapping of DNA methylation in chicken. PLoS One (2011) 1.11
Methylcap-seq reveals novel DNA methylation markers for the diagnosis and recurrence prediction of bladder cancer in a Chinese population. PLoS One (2012) 1.03
The DNA methylome and transcriptome of different brain regions in schizophrenia and bipolar disorder. PLoS One (2014) 1.01
Astrocytic abnormalities and global DNA methylation patterns in depression and suicide. Mol Psychiatry (2014) 0.99
Is There a Relationship between DNA Methylation and Phenotypic Plasticity in Invertebrates? Front Physiol (2012) 0.99
Testing two models describing how methylome-wide studies in blood are informative for psychiatric conditions. Epigenomics (2013) 0.94
High resolution profiling of human exon methylation by liquid hybridization capture-based bisulfite sequencing. BMC Genomics (2011) 0.94
Genome-wide DNA methylation profiles and their relationships with mRNA and the microRNA transcriptome in bovine muscle tissue (Bos taurine). Sci Rep (2014) 0.93
High quality methylome-wide investigations through next-generation sequencing of DNA from a single archived dry blood spot. Epigenetics (2013) 0.91
Identification of an interleukin 13-induced epigenetic signature in allergic airway inflammation. Am J Transl Res (2012) 0.89
Bringing epigenetics into the diagnostics of the andrology laboratory: challenges and perspectives. Asian J Androl (2014) 0.88
Estimation of CpG coverage in whole methylome next-generation sequencing studies. BMC Bioinformatics (2013) 0.87
Exploring genome wide bisulfite sequencing for DNA methylation analysis in livestock: a technical assessment. Front Genet (2014) 0.86
High density methylation QTL analysis in human blood via next-generation sequencing of the methylated genomic DNA fraction. Genome Biol (2015) 0.85
Using animal models to disentangle the role of genetic, epigenetic, and environmental influences on behavioral outcomes associated with maternal anxiety and depression. Front Psychiatry (2011) 0.84
Co-methylated genes in different adipose depots of pig are associated with metabolic, inflammatory and immune processes. Int J Biol Sci (2012) 0.84
A genome-wide scan reveals important roles of DNA methylation in human longevity by regulating age-related disease genes. PLoS One (2015) 0.82
∆ DNMT3B4-del Contributes to Aberrant DNA Methylation Patterns in Lung Tumorigenesis. EBioMedicine (2015) 0.82
Genome-wide DNA methylation changes between the superficial and deep backfat tissues of the pig. Int J Mol Sci (2012) 0.81
A comparison of digital gene expression profiling and methyl DNA immunoprecipitation as methods for gene discovery in honeybee (Apis mellifera) behavioural genomic analyses. PLoS One (2013) 0.80
Methods for cancer epigenome analysis. Adv Exp Med Biol (2013) 0.80
No Variation at 29 Microsatellites in the Genome of Jatropha curcas. J Genomics (2014) 0.79
Cancer control and prevention by nutrition and epigenetic approaches. Antioxid Redox Signal (2012) 0.79
Personal genomic information management and personalized medicine: challenges, current solutions, and roles of HIM professionals. Perspect Health Inf Manag (2014) 0.79
Genome-Wide Differences in DNA Methylation Changes in Two Contrasting Rice Genotypes in Response to Drought Conditions. Front Plant Sci (2016) 0.78
Epigenetic landscape correlates with genetic subtype but does not predict outcome in childhood acute lymphoblastic leukemia. Epigenetics (2015) 0.78
The Impact of DNA Methylation in Hematopoietic Malignancies. Trends Cancer (2016) 0.78
DNA methylome in spleen of avian pathogenic Escherichia coli-challenged broilers and integration with mRNA expression. Sci Rep (2014) 0.78
Genome-wide DNA methylation detection by MethylCap-seq and Infinium HumanMethylation450 BeadChips: an independent large-scale comparison. Sci Rep (2015) 0.77
Aberrant methylation of CDH13 can be a diagnostic biomarker for lung adenocarcinoma. J Cancer (2016) 0.77
A Whole Methylome CpG-SNP Association Study of Psychosis in Blood and Brain Tissue. Schizophr Bull (2015) 0.77
MBRidge: an accurate and cost-effective method for profiling DNA methylome at single-base resolution. J Mol Cell Biol (2015) 0.76
Genome-wide analysis of DNA methylation in obese, lean, and miniature pig breeds. Sci Rep (2016) 0.76
Epigenetic regulation of sex ratios may explain natural variation in self-fertilization rates. Proc Biol Sci (2015) 0.76
Human ESC/iPSC-based "Omics" and Bioinformatics for Translational Research. Drug Discov Today Dis Models (2012) 0.75
Unsupervised detection of regulatory gene expression information in different genomic regions enables gene expression ranking. BMC Bioinformatics (2017) 0.75
Genome-wide DNA methylation profile of developing deciduous tooth germ in miniature pigs. BMC Genomics (2016) 0.75
MBDDiff: an R package designed specifically for processing MBDcap-seq datasets. BMC Genomics (2016) 0.75
Hypergeometric analysis of tiling-array and sequence data: detection and interpretation of peaks. Adv Appl Bioinform Chem (2013) 0.75
Genome-wide epigenomic profiling for biomarker discovery. Clin Epigenetics (2016) 0.75
Obesity is associated with depot-specific alterations in adipocyte DNA methylation and gene expression. Adipocyte (2017) 0.75
Comparative analysis of MBD-seq and MeDIP-seq and estimation of gene expression changes in a rodent model of schizophrenia. Genomics (2017) 0.75
High Resolution Imaging of DNA Methylation Dynamics using a Zebrafish Reporter. Sci Rep (2017) 0.75
A Concise Review on Multi-Omics Data Integration for Terroir Analysis in Vitis vinifera. Front Plant Sci (2017) 0.75
SOAP: short oligonucleotide alignment program. Bioinformatics (2008) 68.13
The diploid genome sequence of an Asian individual. Nature (2008) 46.29
De novo assembly of human genomes with massively parallel short read sequencing. Genome Res (2009) 45.91
A human gut microbial gene catalogue established by metagenomic sequencing. Nature (2010) 43.63
A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science (2002) 42.78
SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics (2009) 39.47
Enterotypes of the human gut microbiome. Nature (2011) 24.36
SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience (2012) 20.89
Characterization of microRNAs in serum: a novel class of biomarkers for diagnosis of cancer and other diseases. Cell Res (2008) 20.59
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proc Natl Acad Sci U S A (2002) 20.48
International network of cancer genome projects. Nature (2010) 20.35
Guidelines for the use and interpretation of assays for monitoring autophagy. Autophagy (2012) 20.08
Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01
SNP detection for massively parallel whole-genome resequencing. Genome Res (2009) 15.96
The sequence and de novo assembly of the giant panda genome. Nature (2009) 15.76
WEGO: a web tool for plotting GO annotations. Nucleic Acids Res (2006) 13.06
Mapping copy number variation by population-scale genome sequencing. Nature (2011) 12.55
A systematic survey of loss-of-function variants in human protein-coding genes. Science (2012) 12.25
A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature (2012) 11.68
Sequencing of 50 human exomes reveals adaptation to high altitude. Science (2010) 11.27
A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome. Science (2002) 9.59
TreeFam: a curated database of phylogenetic trees of animal gene families. Nucleic Acids Res (2006) 8.83
Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res (2011) 8.38
The genome of the mesopolyploid crop species Brassica rapa. Nat Genet (2011) 8.23
The genome of the cucumber, Cucumis sativus L. Nat Genet (2009) 8.19
An abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people. Science (2012) 7.94
Genome sequence and analysis of the tuber crop potato. Nature (2011) 7.77
The Genomes of Oryza sativa: a history of duplications. PLoS Biol (2005) 7.67
Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature (2010) 7.51
A double-negative feedback loop between ZEB1-SIP1 and the microRNA-200 family regulates epithelial-mesenchymal transition. Cancer Res (2008) 7.45
Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4. N Engl J Med (2011) 7.11
Whole-genome mapping of histone H3 Lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cells. Cell Stem Cell (2007) 7.05
Richness of human gut microbiome correlates with metabolic markers. Nature (2013) 6.93
TreeFam: 2008 Update. Nucleic Acids Res (2007) 6.63
A draft sequence for the genome of the domesticated silkworm (Bombyx mori). Science (2004) 6.62
Aberrant excitatory neuronal activity and compensatory remodeling of inhibitory hippocampal circuits in mouse models of Alzheimer's disease. Neuron (2007) 6.60
Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition. Genome Biol (2010) 6.07
Comparative isoschizomer profiling of cytosine methylation: the HELP assay. Genome Res (2006) 5.99
Frequent mutations of chromatin remodeling genes in transitional cell carcinoma of the bladder. Nat Genet (2011) 5.73
Single-cell exome sequencing reveals single-nucleotide mutation characteristics of a kidney tumor. Cell (2012) 5.62
Analyses of pig genomes provide insight into porcine demography and evolution. Nature (2012) 5.58
Building the sequence map of the human pan-genome. Nat Biotechnol (2009) 5.53
Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants. Nat Genet (2010) 5.44
The oyster genome reveals stress adaptation and complexity of shell formation. Nature (2012) 5.30
A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature (2004) 5.24
Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat Genet (2010) 5.20
Single-cell exome sequencing and monoclonal evolution of a JAK2-negative myeloproliferative neoplasm. Cell (2012) 5.16
Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat Biotechnol (2011) 4.84
An Aboriginal Australian genome reveals separate human dispersals into Asia. Science (2011) 4.84
Hippo pathway inhibits Wnt signaling to restrain cardiomyocyte proliferation and heart size. Science (2011) 4.76
Non-invasive prenatal assessment of trisomy 21 by multiplexed maternal plasma DNA sequencing: large scale validity study. BMJ (2011) 4.50
Distinct DNA methylomes of newborns and centenarians. Proc Natl Acad Sci U S A (2012) 4.26
The DNA methylome of human peripheral blood mononuclear cells. PLoS Biol (2010) 4.25
Regression of castrate-recurrent prostate cancer by a small-molecule inhibitor of the amino-terminus domain of the androgen receptor. Cancer Cell (2010) 4.16
KaKs_Calculator: calculating Ka and Ks through model selection and model averaging. Genomics Proteomics Bioinformatics (2006) 4.15
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience (2013) 4.11
Dynamic T cell migration program provides resident memory within intestinal epithelium. J Exp Med (2010) 4.09