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(2012) Shane Neph et al.   BIOINFORMATICS

Cfp1 integrates both CpG content and gene activity for accurate H3K4me3 deposition in embryonic stem cells

(2012) T. Clouaire et al.   GENES & DEVELOPMENT

Protection against De Novo Methylation Is Instrumental in Maintaining Parent-of-Origin Methylation Inherited from the Gametes

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(2012) Stefanie Seisenberger et al.   MOLECULAR CELL

R-Loop Formation Is a Distinctive Characteristic of Unmethylated Human CpG Island Promoters

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(2012) Yuchun Guo et al.   PLoS Computational Biology

Contribution of Intragenic DNA Methylation in Mouse Gametic DNA Methylomes to Establish Oocyte-Specific Heritable Marks

(2012) Hisato Kobayashi et al.   PLoS Genetics

DREME: motif discovery in transcription factor ChIP-seq data

(2011) Timothy L. Bailey   BIOINFORMATICS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

CpG islands and the regulation of transcription

(2011) A. M. Deaton et al.   GENES & DEVELOPMENT

Genome-wide Analysis of Transcription Factor E2F1 Mutant Proteins Reveals That N- and C-terminal Protein Interaction Domains Do Not Participate in Targeting E2F1 to the Human Genome

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In Embryonic Stem Cells, ZFP57/KAP1 Recognize a Methylated Hexanucleotide to Affect Chromatin and DNA Methylation of Imprinting Control Regions

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Identification of genetic elements that autonomously determine DNA methylation states

(2011) Florian Lienert et al.   NATURE GENETICS

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The Dnmt3a PWWP Domain Reads Histone 3 Lysine 36 Trimethylation and Guides DNA Methylation

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CpG islands influence chromatin structure via the CpG-binding protein Cfp1

(2010) John P. Thomson et al.   NATURE

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Molecular basis of histone H3K36me3 recognition by the PWWP domain of Brpf1

(2010) Alessandro Vezzoli et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Chromatin methylation activity of Dnmt3a and Dnmt3a/3L is guided by interaction of the ADD domain with the histone H3 tail

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Orphan CpG Islands Identify Numerous Conserved Promoters in the Mammalian Genome

(2010) Robert S. Illingworth et al.   PLoS Genetics

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Transcription is required for establishment of germline methylation marks at imprinted genes

(2009) M. Chotalia et al.   GENES & DEVELOPMENT

CG dinucleotide periodicities recognized by the Dnmt3a–Dnmt3L complex are distinctive at retroelements and imprinted domains

(2009) Jacob L. Glass et al.   MAMMALIAN GENOME

The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores

(2009) Rafael A Irizarry et al.   NATURE GENETICS

MEME SUITE: tools for motif discovery and searching

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Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

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Mouse development with a single E2F activator

(2008) Shih-Yin Tsai et al.   NATURE

Formation of nucleoprotein filaments by mammalian DNA methyltransferase Dnmt3a in complex with regulator Dnmt3L

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(2008) Yong Zhang et al.   GENOME BIOLOGY

Sexual dimorphism in parental imprint ontogeny and contribution to embryonic development

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