Regulation of DNA demethylation by the XPC DNA repair complex in somatic and pluripotent stem cells

Bright photoactivatable fluorophores for single-molecule imaging

(2016) Jonathan B Grimm et al.   NATURE METHODS

Neil DNA glycosylases promote substrate turnover by Tdg during DNA demethylation

(2016) Lars Schomacher et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

(2016) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

Neil DNA glycosylases promote substrate turnover by Tdg during DNA demethylation

(2016) Lars Schomacher et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Base-resolution maps of 5-formylcytosine and 5-carboxylcytosine reveal genome-wide DNA demethylation dynamics

(2015) Xingyu Lu et al.   CELL RESEARCH

XPC: Going where no DNA damage sensor has gone before

(2015) Leah Nemzow et al.   DNA REPAIR

A general method to improve fluorophores for live-cell and single-molecule microscopy

(2015) Jonathan B Grimm et al.   NATURE METHODS

Functional and mechanistic studies of XPC DNA-repair complex as transcriptional coactivator in embryonic stem cells

(2015) Claudia Cattoglio et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Probing the target search of DNA-binding proteins in mammalian cells using TetR as model searcher

(2015) Davide Normanno et al.   Nature Communications

Single-Base Resolution Analysis of 5-Formyl and 5-Carboxyl Cytosine Reveals Promoter DNA Methylation Dynamics

(2015) Francesco Neri et al.   Cell Reports

Single-Molecule Dynamics of Enhanceosome Assembly in Embryonic Stem Cells

(2014) Jiji Chen et al.   CELL

Hypoxia-Inducible Factors Have Distinct and Stage-Specific Roles during Reprogramming of Human Cells to Pluripotency

(2014) Julie Mathieu et al.   Cell Stem Cell

Tet and TDG Mediate DNA Demethylation Essential for Mesenchymal-to-Epithelial Transition in Somatic Cell Reprogramming

(2014) Xiao Hu et al.   Cell Stem Cell

DNA methylation dynamics of the human preimplantation embryo

(2014) Zachary D. Smith et al.   NATURE

Tet oxidizes thymine to 5-hydroxymethyluracil in mouse embryonic stem cell DNA

(2014) Toni Pfaffeneder et al.   Nature Chemical Biology

HIF-2α Regulates NANOG Expression in Human Embryonic Stem Cells following Hypoxia and Reoxygenation through the Interaction with an Oct-Sox Cis Regulatory Element

(2014) Raffaella Petruzzelli et al.   PLoS One

Genome-wide Analysis Reveals TET- and TDG-Dependent 5-Methylcytosine Oxidation Dynamics

(2013) Li Shen et al.   CELL

Genome-wide Profiling of 5-Formylcytosine Reveals Its Roles in Epigenetic Priming

(2013) Chun-Xiao Song et al.   CELL

TET enzymes, TDG and the dynamics of DNA demethylation

(2013) Rahul M. Kohli et al.   NATURE

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Facilitators and Impediments of the Pluripotency Reprogramming Factors' Initial Engagement with the Genome

(2012) Abdenour Soufi et al.   CELL

HIF1α induced switch from bivalent to exclusively glycolytic metabolism during ESC-to-EpiSC/hESC transition

(2012) Wenyu Zhou et al.   EMBO JOURNAL

Identifying ChIP-seq enrichment using MACS

(2012) Jianxing Feng et al.   Nature Protocols

Recognition and potential mechanisms for replication and erasure of cytosine hydroxymethylation

(2012) Hideharu Hashimoto et al.   NUCLEIC ACIDS RESEARCH

A benchmark for chromatin binding measurements in live cells

(2012) Davide Mazza et al.   NUCLEIC ACIDS RESEARCH

HIF-2α Suppresses p53 to Enhance the Stemness and Regenerative Potential of Human Embryonic Stem Cells

(2012) Bikul Das et al.   STEM CELLS

SUMO-1 regulates the conformational dynamics of Thymine-DNA Glycosylase regulatory domain and competes with its DNA binding activity

(2011) Caroline Smet-Nocca et al.   BMC BIOCHEMISTRY

Thymine DNA Glycosylase Is Essential for Active DNA Demethylation by Linked Deamination-Base Excision Repair

(2011) Salvatore Cortellino et al.   CELL

A DNA Repair Complex Functions as an Oct4/Sox2 Coactivator in Embryonic Stem Cells

(2011) Yick W. Fong et al.   CELL

Thymine DNA Glycosylase Can Rapidly Excise 5-Formylcytosine and 5-Carboxylcytosine

(2011) Atanu Maiti et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Embryonic lethal phenotype reveals a function of TDG in maintaining epigenetic stability

(2011) Daniel Cortázar et al.   NATURE

The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes

(2011) Tian-Peng Gu et al.   NATURE

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

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

(2011) Yuki Ohi et al.   NATURE CELL BIOLOGY

A more efficient method to generate integration-free human iPS cells

(2011) Keisuke Okita et al.   NATURE METHODS

Energy Metabolism in Human Pluripotent Stem Cells and Their Differentiated Counterparts

(2011) Sandra Varum et al.   PLoS One

Tet-Mediated Formation of 5-Carboxylcytosine and Its Excision by TDG in Mammalian DNA

(2011) Y.-F. He et al.   SCIENCE

Tet Proteins Can Convert 5-Methylcytosine to 5-Formylcytosine and 5-Carboxylcytosine

(2011) S. Ito et al.   SCIENCE

Lonely death dance of human pluripotent stem cells: ROCKing between metastable cell states

(2011) Masatoshi Ohgushi et al.   TRENDS IN CELL BIOLOGY

NER Factors Are Recruited to Active Promoters and Facilitate Chromatin Modification for Transcription in the Absence of Exogenous Genotoxic Attack

(2010) Nicolas Le May et al.   MOLECULAR CELL

Epigenetic memory in induced pluripotent stem cells

(2010) K. Kim et al.   NATURE

Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification

(2010) Shinsuke Ito et al.   NATURE

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications

(2010) R Alan Harris et al.   NATURE BIOTECHNOLOGY

Quantitative comparison of genome-wide DNA methylation mapping technologies

(2010) Christoph Bock et al.   NATURE BIOTECHNOLOGY

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

(2010) Jose M Polo et al.   NATURE BIOTECHNOLOGY

DNA methylation and cellular reprogramming

(2010) Daniel D. De Carvalho et al.   TRENDS IN CELL BIOLOGY

Hypoxia Enhances the Generation of Induced Pluripotent Stem Cells

(2009) Yoshinori Yoshida et al.   Cell Stem Cell

A p53-mediated DNA damage response limits reprogramming to ensure iPS cell genomic integrity

(2009) Rosa M. Marión et al.   NATURE

The Ink4/Arf locus is a barrier for iPS cell reprogramming

(2009) Han Li et al.   NATURE

Reprogramming towards pluripotency requires AID-dependent DNA demethylation

(2009) Nidhi Bhutani et al.   NATURE

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by MLL Partner TET1

(2009) M. Tahiliani et al.   SCIENCE

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

The Thymine−DNA Glycosylase Regulatory Domain: Residual Structure and DNA Binding†

(2008) Caroline Smet-Nocca et al.   BIOCHEMISTRY

Defining Molecular Cornerstones during Fibroblast to iPS Cell Reprogramming in Mouse

(2008) Matthias Stadtfeld et al.   Cell Stem Cell

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis

(2008) Thomas A Down et al.   NATURE BIOTECHNOLOGY

Dynamic multiple-target tracing to probe spatiotemporal cartography of cell membranes

(2008) Arnauld Sergé et al.   NATURE METHODS

Highly inclined thin illumination enables clear single-molecule imaging in cells

(2008) Makio Tokunaga et al.   NATURE METHODS

Induced Pluripotent Stem Cell Generation Using a Single Lentiviral Stem Cell Cassette

(2008) Cesar A. Sommer et al.   STEM CELLS