Dynamic epigenomic landscapes during early lineage specification in mouse embryos

Epigenetic restriction of extraembryonic lineages mirrors the somatic transition to cancer

(2017) Zachary D. Smith et al.   NATURE

Allelic reprogramming of 3D chromatin architecture during early mammalian development

(2017) Zhenhai Du et al.   NATURE

Naive Human Pluripotent Cells Feature a Methylation Landscape Devoid of Blastocyst or Germline Memory

(2016) William A. Pastor et al.   Cell Stem Cell

Maternal DNA Methylation Regulates Early Trophoblast Development

(2016) Miguel R. Branco et al.   DEVELOPMENTAL CELL

Enhancer methylation dynamics contribute to cancer plasticity and patient mortality

(2016) Rachel E. Bell et al.   GENOME RESEARCH

De novo DNA methylation drives 5hmC accumulation in mouse zygotes

(2016) Rachel Amouroux et al.   NATURE CELL BIOLOGY

Non-CG Methylation in the Human Genome

(2015) Yupeng He et al.   Annual Review of Genomics and Human Genetics

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation

(2015) Tuncay Baubec et al.   NATURE

Early Developmental and Evolutionary Origins of Gene Body DNA Methylation Patterns in Mammalian Placentas

(2015) Diane I. Schroeder et al.   PLoS Genetics

Chromatin dynamics and the role of G9a in gene regulation and enhancer silencing during early mouse development

(2015) Jan J Zylicz et al.   eLife

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Programming and Inheritance of Parental DNA Methylomes in Mammals

(2014) Lu Wang et al.   CELL

DNA methylation dynamics of the human preimplantation embryo

(2014) Zachary D. Smith et al.   NATURE

The DNA methylation landscape of human early embryos

(2014) Hongshan Guo et al.   NATURE

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

Mapping the route from naive pluripotency to lineage specification

(2014) T. Kalkan et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution

(2014) J. Vierstra et al.   SCIENCE

Genome-wide Bisulfite Sequencing in Zygotes Identifies Demethylation Targets and Maps the Contribution of TET3 Oxidation

(2014) Julian R. Peat et al.   Cell Reports

Epigenomic Analysis of Multilineage Differentiation of Human Embryonic Stem Cells

(2013) Wei Xie et al.   CELL

Whole-Genome Bisulfite Sequencing of Two Distinct Interconvertible DNA Methylomes of Mouse Embryonic Stem Cells

(2013) Ehsan Habibi et al.   Cell Stem Cell

Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages

(2013) Yusuke Ohnishi et al.   NATURE CELL BIOLOGY

Large conserved domains of low DNA methylation maintained by Dnmt3a

(2013) Mira Jeong et al.   NATURE GENETICS

Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues

(2013) Gary C Hon et al.   NATURE GENETICS

DNA methylation: roles in mammalian development

(2013) Zachary D. Smith et al.   NATURE REVIEWS GENETICS

Identification of active regulatory regions from DNA methylation data

(2013) Lukas Burger et al.   NUCLEIC ACIDS RESEARCH

Organization of the Mitotic Chromosome

(2013) N. Naumova et al.   SCIENCE

Loss of DNMT1o Disrupts Imprinted X Chromosome Inactivation and Accentuates Placental Defects in Females

(2013) Serge McGraw et al.   PLoS Genetics

Oct4 Is Required ∼E7.5 for Proliferation in the Primitive Streak

(2013) Brian DeVeale et al.   PLoS Genetics

Transcriptional regulatory networks in epiblast cells and during anterior neural plate development as modeled in epiblast stem cells

(2012) M. Iwafuchi-Doi et al.   DEVELOPMENT

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen et al.   NATURE

A unique regulatory phase of DNA methylation in the early mammalian embryo

(2012) Zachary D. Smith et al.   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Iterative correction of Hi-C data reveals hallmarks of chromosome organization

(2012) Maxim Imakaev et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Dynamics of anterior–posterior axis formation in the developing mouse embryo

(2012) Samantha A. Morris et al.   Nature Communications

The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes

(2011) Tian-Peng Gu et al.   NATURE

Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina–associated domains

(2011) Benjamin P Berman et al.   NATURE GENETICS

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Blastocyst lineage formation, early embryonic asymmetries and axis patterning in the mouse

(2009) J. Rossant et al.   DEVELOPMENT

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Making a firm decision: multifaceted regulation of cell fate in the early mouse embryo

(2009) Magdalena Zernicka-Goetz et al.   NATURE REVIEWS GENETICS

Making a commitment: cell lineage allocation and axis patterning in the early mouse embryo

(2009) Sebastian J. Arnold et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

The Endoderm of the Mouse Embryo Arises by Dynamic Widespread Intercalation of Embryonic and Extraembryonic Lineages

(2008) Gloria S. Kwon et al.   DEVELOPMENTAL CELL

Regulation of DNA methylation activity through Dnmt3L promoter methylation by Dnmt3 enzymes in embryonic development

(2008) Ye-Guang Hu et al.   HUMAN MOLECULAR GENETICS

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH