DNA Methylation Restricts Lineage-specific Functions of Transcription Factor Gata4 during Embryonic Stem Cell Differentiation

Functions of DNA methylation: islands, start sites, gene bodies and beyond

(2012) Peter A. Jones   NATURE REVIEWS GENETICS

Inferring direct DNA binding from ChIP-seq

(2012) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

DREME: motif discovery in transcription factor ChIP-seq data

(2011) Timothy L. Bailey   BIOINFORMATICS

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

Reference Maps of Human ES and iPS Cell Variation Enable High-Throughput Characterization of Pluripotent Cell Lines

(2011) Christoph Bock et al.   CELL

Epigenetic reprogramming in mouse pre-implantation development and primordial germ cells

(2011) M. Saitou et al.   DEVELOPMENT

Pancreatic β Cell Identity Is Maintained by DNA Methylation-Mediated Repression of Arx

(2011) Sangeeta Dhawan et al.   DEVELOPMENTAL CELL

DNA methylation status predicts cell type-specific enhancer activity

(2011) Malgorzata Wiench et al.   EMBO JOURNAL

GATA4 Regulates Estrogen Receptor-α-Mediated Osteoblast Transcription

(2011) Gustavo A. Miranda-Carboni et al.   MOLECULAR ENDOCRINOLOGY

Induction of functional hepatocyte-like cells from mouse fibroblasts by defined factors

(2011) Pengyu Huang et al.   NATURE

Direct conversion of mouse fibroblasts to hepatocyte-like cells by defined factors

(2011) Sayaka Sekiya et al.   NATURE

Incomplete DNA methylation underlies a transcriptional memory of somatic cells in human iPS cells

(2011) Yuki Ohi et al.   NATURE CELL BIOLOGY

Dnmt3a is essential for hematopoietic stem cell differentiation

(2011) Grant A Challen et al.   NATURE GENETICS

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns

(2011) Sam John et al.   NATURE GENETICS

Mammalian Gcm genes induce Hes5 expression by active DNA demethylation and induce neural stem cells

(2011) Seiji Hitoshi et al.   NATURE NEUROSCIENCE

Direct Reprogramming of Fibroblasts into Functional Cardiomyocytes by Defined Factors

(2010) Masaki Ieda et al.   CELL

Epigenetic memory in induced pluripotent stem cells

(2010) K. Kim et al.   NATURE

Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET

(2010) Toshiyuki Matsui et al.   NATURE

Direct conversion of fibroblasts to functional neurons by defined factors

(2010) Thomas Vierbuchen et al.   NATURE

Cell type of origin influences the molecular and functional properties of mouse induced pluripotent stem cells

(2010) Jose M Polo et al.   NATURE BIOTECHNOLOGY

Targets and dynamics of promoter DNA methylation during early mouse development

(2010) Julie Borgel et al.   NATURE GENETICS

Active DNA demethylation: many roads lead to Rome

(2010) Susan C. Wu et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Epigenetic control of neural precursor cell fate during development

(2010) Yusuke Hirabayashi et al.   NATURE REVIEWS NEUROSCIENCE

Dnmt3a-Dependent Nonpromoter DNA Methylation Facilitates Transcription of Neurogenic Genes

(2010) H. Wu et al.   SCIENCE

Direct Conversion of C. elegans Germ Cells into Specific Neuron Types

(2010) B. Tursun et al.   SCIENCE

DNA Methyltransferase 1 Is Essential for and Uniquely Regulates Hematopoietic Stem and Progenitor Cells

(2009) Jennifer J. Trowbridge et al.   Cell Stem Cell

High-throughput bisulfite sequencing in mammalian genomes

(2009) Zachary D. Smith et al.   METHODS

Directed transdifferentiation of mouse mesoderm to heart tissue by defined factors

(2009) Jun K. Takeuchi et al.   NATURE

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Forcing cells to change lineages

(2009) Thomas Graf et al.   NATURE

DNA methylation protects hematopoietic stem cell multipotency from myeloerythroid restriction

(2009) Ann-Marie Bröske et al.   NATURE GENETICS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

(2009) Elodie Portales-Casamar et al.   NUCLEIC ACIDS RESEARCH

BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources

(2009) Chunlei Wu et al.   GENOME BIOLOGY

BioVenn – a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams

(2008) Tim Hulsen et al.   BMC GENOMICS

Stem Cells, the Molecular Circuitry of Pluripotency and Nuclear Reprogramming

(2008) Rudolf Jaenisch et al.   CELL

Lives of a Heart Cell: Tracing the Origins of Cardiac Progenitors

(2008) Silvia Martin-Puig et al.   Cell Stem Cell

Lineage-Specific Polycomb Targets and De Novo DNA Methylation Define Restriction and Potential of Neuronal Progenitors

(2008) Fabio Mohn et al.   MOLECULAR CELL

Dissecting direct reprogramming through integrative genomic analysis

(2008) Tarjei S. Mikkelsen et al.   NATURE

Induction of pluripotent stem cells by defined factors is greatly improved by small-molecule compounds

(2008) Danwei Huangfu et al.   NATURE BIOTECHNOLOGY

Epigenetic restriction of embryonic cell lineage fate by methylation of Elf5

(2008) Ray Kit Ng et al.   NATURE CELL BIOLOGY

Epigenetic events in mammalian germ-cell development: reprogramming and beyond

(2008) Hiroyuki Sasaki et al.   NATURE REVIEWS GENETICS

QUMA: quantification tool for methylation analysis

(2008) Y. Kumaki et al.   NUCLEIC ACIDS RESEARCH

UniPROBE: an online database of protein binding microarray data on protein-DNA interactions

(2008) D. E. Newburger et al.   NUCLEIC ACIDS RESEARCH