Accurate annotation of accessible chromatin in mouse and human primordial germ cells

Ground rules of the pluripotency gene regulatory network

(2017) Mo Li et al.   NATURE REVIEWS GENETICS

Causes and evolutionary consequences of primordial germ-cell specification mode in metazoans

(2017) Carrie A. Whittle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Establishing Chromatin Regulatory Landscape during Mouse Preimplantation Development

(2016) Falong Lu et al.   CELL

Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution

(2016) Hannah K. Long et al.   CELL

Re-engineering the zinc fingers of PRDM9 reverses hybrid sterility in mice

(2016) Benjamin Davies et al.   NATURE

Distinct features of H3K4me3 and H3K27me3 chromatin domains in pre-implantation embryos

(2016) Xiaoyu Liu et al.   NATURE

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

Specification and epigenetic programming of the human germ line

(2016) Walfred W. C. Tang et al.   NATURE REVIEWS GENETICS

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

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Lineage-specific enhancers activate self-renewal genes in macrophages and embryonic stem cells

(2016) E. L. Soucie et al.   SCIENCE

The Transcriptome and DNA Methylome Landscapes of Human Primordial Germ Cells

(2015) Fan Guo et al.   CELL

Enhancer Evolution across 20 Mammalian Species

(2015) Diego Villar et al.   CELL

Quantitative Dynamics of Chromatin Remodeling during Germ Cell Specification from Mouse Embryonic Stem Cells

(2015) Kazuki Kurimoto et al.   Cell Stem Cell

Transcription and imprinting dynamics in developing postnatal male germline stem cells

(2015) Saher Sue Hammoud et al.   GENES & DEVELOPMENT

Affinity-seq detects genome-wide PRDM9 binding sites and reveals the impact of prior chromatin modifications on mammalian recombination hotspot usage

(2015) Michael Walker et al.   Epigenetics & Chromatin

Reorganization of Enhancer Patterns in Transition from Naive to Primed Pluripotency

(2014) Christa Buecker et al.   Cell Stem Cell

Histone-Fold Domain Protein NF-Y Promotes Chromatin Accessibility for Cell Type-Specific Master Transcription Factors

(2014) Andrew J. Oldfield et al.   MOLECULAR CELL

Chromatin state dynamics during blood formation

(2014) D. Lara-Astiaso et al.   SCIENCE

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

(2014) J. Vierstra et al.   SCIENCE

Recombination initiation maps of individual human genomes

(2014) F. Pratto et al.   SCIENCE

Spermatogonial Stem Cell Self-Renewal and Development

(2013) Mito Kanatsu-Shinohara et al.   Annual Review of Cell and Developmental Biology

Sequence-Specific Transcription Factor NF-Y Displays Histone-like DNA Binding and H2B-like Ubiquitination

(2013) Marco Nardini et al.   CELL

Rapid and Pervasive Changes in Genome-wide Enhancer Usage during Mammalian Development

(2013) Alex S. Nord et al.   CELL

The Evolution of Lineage-Specific Regulatory Activities in the Human Embryonic Limb

(2013) Justin Cotney et al.   CELL

The Transcriptional and Functional Properties of Mouse Epiblast Stem Cells Resemble the Anterior Primitive Streak

(2013) Yoji Kojima et al.   Cell Stem Cell

The mammalian germline as a pluripotency cycle

(2013) H. G. Leitch et al.   DEVELOPMENT

High-resolution DNA methylome analysis of primordial germ cells identifies gender-specific reprogramming in mice

(2013) H. Kobayashi et al.   GENOME RESEARCH

Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification

(2013) Housheng Hansen He et al.   NATURE METHODS

Meiotic recombination in mammals: localization and regulation

(2013) Frédéric Baudat et al.   NATURE REVIEWS GENETICS

A set of genes critical to development is epigenetically poised in mouse germ cells from fetal stages through completion of meiosis

(2013) B. J. Lesch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sensitive mapping of recombination hotspots using sequencing-based detection of ssDNA

(2012) P. P. Khil et al.   GENOME RESEARCH

The Dynamics of Genome-wide DNA Methylation Reprogramming in Mouse Primordial Germ Cells

(2012) Stefanie Seisenberger et al.   MOLECULAR CELL

An expansive human regulatory lexicon encoded in transcription factor footprints

(2012) Shane Neph et al.   NATURE

Genetic recombination is directed away from functional genomic elements in mice

(2012) Kevin Brick et al.   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Primordial Germ Cells in Mice

(2012) M. Saitou et al.   Cold Spring Harbor Perspectives in Biology

NF-Y is necessary for hematopoietic stem cell proliferation and survival

(2011) G. Bungartz et al.   BLOOD

Genome-wide analysis reveals novel molecular features of mouse recombination hotspots

(2011) Fatima Smagulova et al.   NATURE

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns

(2011) Sam John et al.   NATURE GENETICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

ChIP-Seq identification of weakly conserved heart enhancers

(2010) Matthew J Blow et al.   NATURE GENETICS

Conservation of recombination hotspots in yeast

(2010) Isheng J. Tsai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PRDM9 Is a Major Determinant of Meiotic Recombination Hotspots in Humans and Mice

(2010) F. Baudat et al.   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Cell cycle analysis of fetal germ cells during sex differentiation in mice

(2009) Cassy Spiller et al.   BIOLOGY OF THE CELL

Global mapping of protein-DNA interactions in vivo by digital genomic footprinting

(2009) Jay R Hesselberth et al.   NATURE METHODS

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

(2009) Da Wei Huang et al.   Nature Protocols

Chromatin dynamics during epigenetic reprogramming in the mouse germ line

(2008) Petra Hajkova et al.   NATURE

Critical function of Prdm14 for the establishment of the germ cell lineage in mice

(2008) Masashi Yamaji et al.   NATURE GENETICS

Gdnf Upregulates c-Fos Transcription via the Ras/Erk1/2 Pathway to Promote Mouse Spermatogonial Stem Cell Proliferation

(2007) Zuping He et al.   STEM CELLS

Dynamic Regulation of Mitotic Arrest in Fetal Male Germ Cells

(2007) Patrick S. Western et al.   STEM CELLS