Published in Cell on May 27, 2011
Charting a dynamic DNA methylation landscape of the human genome. Nature (2013) 5.80
Identification of genetic elements that autonomously determine DNA methylation states. Nat Genet (2011) 4.04
Sperm methylation profiles reveal features of epigenetic inheritance and evolution in primates. Cell (2011) 3.39
Variation in the mutation rate across mammalian genomes. Nat Rev Genet (2011) 3.09
Interplay between the cancer genome and epigenome. Cell (2013) 3.05
Epigenetic polymorphism and the stochastic formation of differentially methylated regions in normal and cancerous tissues. Nat Genet (2012) 2.20
DNA methylation dynamics during epigenetic reprogramming in the germline and preimplantation embryos. Genes Dev (2014) 1.55
EpiExplorer: live exploration and global analysis of large epigenomic datasets. Genome Biol (2012) 1.40
The effects of chromatin organization on variation in mutation rates in the genome. Nat Rev Genet (2015) 1.37
Dynamic and static maintenance of epigenetic memory in pluripotent and somatic cells. Nature (2014) 1.34
Subtelomeric hotspots of aberrant 5-hydroxymethylcytosine-mediated epigenetic modifications during reprogramming to pluripotency. Nat Cell Biol (2013) 1.27
Human genes with CpG island promoters have a distinct transcription-associated chromatin organization. Genome Biol (2012) 1.13
Human-specific CpG "beacons" identify loci associated with human-specific traits and disease. Epigenetics (2012) 1.07
High-throughput engineering of a mammalian genome reveals building principles of methylation states at CG rich regions. Elife (2014) 1.03
Active DNA demethylation at enhancers during the vertebrate phylotypic period. Nat Genet (2016) 0.97
Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. Cell (2014) 0.96
The role of DNA methylation in directing the functional organization of the cancer epigenome. Genome Res (2015) 0.94
Short sequences can efficiently recruit histone H3 lysine 27 trimethylation in the absence of enhancer activity and DNA methylation. Proc Natl Acad Sci U S A (2014) 0.94
Genome-wide genetic variations are highly correlated with proximal DNA methylation patterns. Genome Res (2012) 0.93
Biochemical reconstitution of TET1-TDG-BER-dependent active DNA demethylation reveals a highly coordinated mechanism. Nat Commun (2016) 0.92
GC skew is a conserved property of unmethylated CpG island promoters across vertebrates. Nucleic Acids Res (2015) 0.90
Interaction-based evolution: how natural selection and nonrandom mutation work together. Biol Direct (2013) 0.87
Fundamental diversity of human CpG islands at multiple biological levels. Epigenetics (2014) 0.87
Drosophila functional elements are embedded in structurally constrained sequences. PLoS Genet (2013) 0.87
G9a/GLP-dependent H3K9me2 patterning alters chromatin structure at CpG islands in hematopoietic progenitors. Epigenetics Chromatin (2014) 0.85
The mouse DXZ4 homolog retains Ctcf binding and proximity to Pls3 despite substantial organizational differences compared to the primate macrosatellite. Genome Biol (2012) 0.85
Extensive and biased intergenomic nonreciprocal DNA exchanges shaped a nascent polyploid genome, Gossypium (cotton). Genetics (2014) 0.84
Human-specific epigenetic variation in the immunological Leukotriene B4 Receptor (LTB4R/BLT1) implicated in common inflammatory diseases. Genome Med (2014) 0.83
Whole-genome bisulfite sequencing maps from multiple human tissues reveal novel CpG islands associated with tissue-specific regulation. Hum Mol Genet (2015) 0.82
DNA Methylation: Insights into Human Evolution. PLoS Genet (2015) 0.82
Poised chromatin in the mammalian germ line. Development (2014) 0.82
The influence of cis-regulatory elements on DNA methylation fidelity. PLoS One (2012) 0.81
Comparative analysis using K-mer and K-flank patterns provides evidence for CpG island sequence evolution in mammalian genomes. Nucleic Acids Res (2013) 0.80
The origin of the RB1 imprint. PLoS One (2013) 0.80
Hydroxymethylated cytosines are associated with elevated C to G transversion rates. PLoS Genet (2014) 0.79
Profiling ascidian promoters as the primordial type of vertebrate promoter. BMC Genomics (2011) 0.79
Hypomethylation marks enhancers within transposable elements. Nat Genet (2013) 0.79
CpG islands under selective pressure are enriched with H3K4me3, H3K27ac and H3K36me3 histone modifications. BMC Evol Biol (2013) 0.78
Evidence for evolutionary and nonevolutionary forces shaping the distribution of human genetic variants near transcription start sites. PLoS One (2014) 0.78
The mutation spectrum in genomic late replication domains shapes mammalian GC content. Nucleic Acids Res (2016) 0.78
The heritability and patterns of DNA methylation in normal human colorectum. Hum Mol Genet (2016) 0.78
Relating gene expression evolution with CpG content changes. BMC Genomics (2014) 0.77
Aberrant repair initiated by mismatch-specific thymine-DNA glycosylases provides a mechanism for the mutational bias observed in CpG islands. Nucleic Acids Res (2014) 0.77
Explaining the correlations among properties of mammalian promoters. Nucleic Acids Res (2014) 0.77
Identification of sequences common to more than one therapeutic target to treat complex diseases: simulating the high variance in sequence interactivity evolved to modulate robust phenotypes. BMC Genomics (2015) 0.77
Do short, frequent DNA sequence motifs mould the epigenome? Nat Rev Mol Cell Biol (2016) 0.77
New repeat polymorphism in the AKT1 gene predicts striatal dopamine D2/D3 receptor availability and stimulant-induced dopamine release in the healthy human brain. J Neurosci (2017) 0.76
Epigenetic inheritance: a contributor to species differentiation? DNA Cell Biol (2012) 0.76
CpGislandEVO: a database and genome browser for comparative evolutionary genomics of CpG islands. Biomed Res Int (2013) 0.76
The Impact of Linked Selection in Chimpanzees: A Comparative Study. Genome Biol Evol (2016) 0.75
Factors to preserve CpG-rich sequences in methylated CpG islands. BMC Genomics (2015) 0.75
DNA Methylation Patterns in the Hypothalamus of Female Pubertal Goats. PLoS One (2016) 0.75
Preservation of methylated CpG dinucleotides in human CpG islands. Biol Direct (2016) 0.75
Steering tumor progression through the transcriptional response to growth factors and stroma. FEBS Lett (2014) 0.75
Bilaterian-like promoters in the highly compact Amphimedon queenslandica genome. Sci Rep (2016) 0.75
Genomic landscape of CpG rich elements in human. BMC Evol Biol (2017) 0.75
Simplification, Innateness, and the Absorption of Meaning from Context: How Novelty Arises from Gradual Network Evolution. Evol Biol (2017) 0.75
Three-dimensional folding and functional organization principles of the Drosophila genome. Cell (2012) 9.19
Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture. Nat Genet (2011) 5.97
Quantification of protein half-lives in the budding yeast proteome. Proc Natl Acad Sci U S A (2006) 5.62
Deterministic direct reprogramming of somatic cells to pluripotency. Nature (2013) 5.18
Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types. Science (2014) 4.91
Frequent switching of Polycomb repressive marks and DNA hypermethylation in the PC3 prostate cancer cell line. Proc Natl Acad Sci U S A (2008) 4.20
A global view of pleiotropy and phenotypically derived gene function in yeast. Mol Syst Biol (2005) 3.70
Functional enhancers at the gene-poor 8q24 cancer-linked locus. PLoS Genet (2009) 3.59
EXPANDER--an integrative program suite for microarray data analysis. BMC Bioinformatics (2005) 3.43
Functional anatomy of polycomb and trithorax chromatin landscapes in Drosophila embryos. PLoS Biol (2009) 3.24
BLUEPRINT to decode the epigenetic signature written in blood. Nat Biotechnol (2012) 3.24
Cohesin-mediated interactions organize chromosomal domain architecture. EMBO J (2013) 2.48
Robust 4C-seq data analysis to screen for regulatory DNA interactions. Nat Methods (2012) 2.42
Epigenetic polymorphism and the stochastic formation of differentially methylated regions in normal and cancerous tissues. Nat Genet (2012) 2.20
Expander: from expression microarrays to networks and functions. Nat Protoc (2010) 2.12
H2A.Z maintenance during mitosis reveals nucleosome shifting on mitotically silenced genes. Mol Cell (2010) 1.85
Comparative analysis of DNA replication timing reveals conserved large-scale chromosomal architecture. PLoS Genet (2010) 1.68
Constitutive nucleosome depletion and ordered factor assembly at the GRP78 promoter revealed by single molecule footprinting. PLoS Genet (2006) 1.48
A probabilistic methodology for integrating knowledge and experiments on biological networks. J Comput Biol (2006) 1.47
Minreg: inferring an active regulator set. Bioinformatics (2002) 1.33
Addiction of t(8;21) and inv(16) acute myeloid leukemia to native RUNX1. Cell Rep (2013) 1.22
Dynamic combinatorial interactions of RUNX1 and cooperating partners regulates megakaryocytic differentiation in cell line models. Blood (2010) 1.18
Widespread compensatory evolution conserves DNA-encoded nucleosome organization in yeast. PLoS Comput Biol (2010) 1.07
Modeling and analysis of heterogeneous regulation in biological networks. J Comput Biol (2004) 1.03
DNA methylation programming and reprogramming in primate embryonic stem cells. Genome Res (2009) 0.99
Evolution and selection in yeast promoters: analyzing the combined effect of diverse transcription factor binding sites. PLoS Comput Biol (2008) 0.96
A systematic approach to understand the functional consequences of non-protein coding risk regions. Cell Cycle (2010) 0.96
Drosophila functional elements are embedded in structurally constrained sequences. PLoS Genet (2013) 0.87
Corrigendum: Derivation of novel human ground state naive pluripotent stem cells. Nature (2015) 0.85
Cell-autonomous function of Runx1 transcriptionally regulates mouse megakaryocytic maturation. PLoS One (2013) 0.83
Hypomethylation marks enhancers within transposable elements. Nat Genet (2013) 0.79
Corrigendum: Deterministic direct reprogramming of somatic cells to pluripotency. Nature (2015) 0.77
Inferring divergence of context-dependent substitution rates in Drosophila genomes with applications to comparative genomics. Mol Biol Evol (2012) 0.76
Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors. Cell (2016) 0.75