Combined analysis of dissimilar promoter accessibility and gene expression profiles identifies tissue-specific genes and actively repressed networks

The Dynamic Landscape of Open Chromatin during Human Cortical Neurogenesis

(2018) Luis de la Torre-Ubieta et al.   CELL

IL-10 Signaling Remodels Adipose Chromatin Architecture to Limit Thermogenesis and Energy Expenditure

(2018) Prashant Rajbhandari et al.   CELL

Comparative analysis of mouse and human placentae across gestation reveals species-specific regulators of placental development

(2018) Francesca Soncin et al.   DEVELOPMENT

Molecular transitions in early progenitors during human cord blood hematopoiesis

(2018) Shiwei Zheng et al.   Molecular Systems Biology

TissueEnrich: Tissue-specific gene enrichment analysis

(2018) Ashish Jain et al.   BIOINFORMATICS

Chromatin accessibility dynamics reveal novel functional enhancers inC. elegans

(2017) Aaron C. Daugherty et al.   GENOME RESEARCH

Neuronal activity modifies the chromatin accessibility landscape in the adult brain

(2017) Yijing Su et al.   NATURE NEUROSCIENCE

Dynamic reorganization of open chromatin underlies diverse transcriptomes during spermatogenesis

(2017) So Maezawa et al.   NUCLEIC ACIDS RESEARCH

Inactivation of Lsd1 triggers senescence in trophoblast stem cells by induction of Sirt4

(2017) Josefina Castex et al.   Cell Death & Disease

Mapping the chromatin landscape and Blimp1 transcriptional targets that regulate trophoblast differentiation

(2017) Andrew C. Nelson et al.   Scientific Reports

Alpha TC1 and Beta-TC-6 genomic profiling uncovers both shared and distinct transcriptional regulatory features with their primary islet counterparts

(2017) Nathan Lawlor et al.   Scientific Reports

Layer-specific chromatin accessibility landscapes reveal regulatory networks in adult mouse visual cortex

(2017) Lucas T Gray et al.   eLife

Cell Type-Specific Epigenomic Analysis Reveals a Uniquely Closed Chromatin Architecture in Mouse Rod Photoreceptors

(2017) Andrew E. O. Hughes et al.   Scientific Reports

A Comprehensive Mouse Transcriptomic BodyMap across 17 Tissues by RNA-seq

(2017) Bin Li et al.   Scientific Reports

Epigenetic Memory Underlies Cell-Autonomous Heterogeneous Behavior of Hematopoietic Stem Cells

(2016) Vionnie W.C. Yu et al.   CELL

Lipoprotein lipase and lipid profiles in plasma and placenta from normal pregnancies compared with patients with intrahepatic cholestasis of pregnancy

(2016) Z.M. Hao et al.   European Journal of Obstetrics & Gynecology and Reproductive Biology

Dynamic Changes in Chromatin Accessibility Occur in CD8 + T Cells Responding to Viral Infection

(2016) James P. Scott-Browne et al.   IMMUNITY

Brain REST/NRSF Is Not Only a Silent Repressor but Also an Active Protector

(2016) Yangang Zhao et al.   MOLECULAR NEUROBIOLOGY

The landscape of accessible chromatin in mammalian preimplantation embryos

(2016) Jingyi Wu et al.   NATURE

Changes in the enhancer landscape during early placental development uncover a trophoblast invasion gene-enhancer network

(2016) Geetu Tuteja et al.   PLACENTA

Integration of ATAC-seq and RNA-seq identifies human alpha cell and beta cell signature genes

(2016) Amanda M. Ackermann et al.   Molecular Metabolism

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

MPE-seq, a new method for the genome-wide analysis of chromatin structure

(2015) Haruhiko Ishii et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2014) S. Anders et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Enhancer Interaction Networks as a Means for Singular Olfactory Receptor Expression

(2014) Eirene Markenscoff-Papadimitriou et al.   CELL

A novel Wnt5a-Frizzled4 signaling pathway mediates activity-independent dendrite morphogenesis via the distal PDZ motif of Frizzled 4

(2014) Wen-Jie Bian et al.   Developmental Neurobiology

Transcriptional enhancers: from properties to genome-wide predictions

(2014) Daria Shlyueva et al.   NATURE REVIEWS GENETICS

STRING v10: protein–protein interaction networks, integrated over the tree of life

(2014) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

The Human Placenta Project: Placental structure, development, and function in real time

(2014) A.E. Guttmacher et al.   PLACENTA

Preeclampsia Is Associated with Alterations in the p53-Pathway in Villous Trophoblast

(2014) Andrew N. Sharp et al.   PLoS One

IGFBP-4 and −5 are expressed in first-trimester villi and differentially regulate the migration of HTR-8/SVneo cells

(2014) Erin J Crosley et al.   Reproductive Biology and Endocrinology

MORC1 represses transposable elements in the mouse male germline

(2014) William A. Pastor et al.   Nature Communications

Automated Discovery of Tissue-Targeting Enhancers and Transcription Factors from Binding Motif and Gene Function Data

(2014) Geetu Tuteja et al.   PLoS Computational Biology

PRISM offers a comprehensive genomic approach to transcription factor function prediction

(2013) A. M. Wenger et al.   GENOME RESEARCH

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Structure-aided prediction of mammalian transcription factor complexes in conserved non-coding elements

(2013) H. Guturu et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Transcription Factor Positive Regulatory Domain 4 (PRDM4) Recruits Protein Arginine Methyltransferase 5 (PRMT5) to Mediate Histone Arginine Methylation and Control Neural Stem Cell Proliferation and Differentiation

(2012) Alexandra Chittka et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Genome-wide localization and expression profiling establish Sp2 as a sequence-specific transcription factor regulating vitally important genes

(2012) Gloria Terrados et al.   NUCLEIC ACIDS RESEARCH

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Review: Transport of maternal cholesterol to the fetal circulation

(2011) L.A. Woollett   PLACENTA

GLay: community structure analysis of biological networks

(2010) G. Su et al.   BIOINFORMATICS

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Histone H3 lysine 36 methyltransferase Hypb/Setd2 is required for embryonic vascular remodeling

(2010) M. Hu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition

(2010) Andrew Adey et al.   GENOME BIOLOGY

Epidermal Growth Factor (EGF) Promotes the In Vitro Differentiation of Neural Crest Cells to Neurons and Melanocytes

(2009) Ricardo Castilho Garcez et al.   CELLULAR AND MOLECULAR NEUROBIOLOGY

REST selectively represses a subset of RE1-containing neuronal genes in mouse embryonic stem cells

(2009) H. F. Jorgensen et al.   DEVELOPMENT

NRSF downregulation induces neuronal differentiation in mouse embryonic stem cells

(2009) Shailesh Kumar Gupta et al.   DIFFERENTIATION

SetDB1 contributes to repression of genes encoding developmental regulators and maintenance of ES cell state

(2009) S. Bilodeau et al.   GENES & DEVELOPMENT

Abnormal Placental Development and Early Embryonic Lethality in EpCAM-Null Mice

(2009) Keisuke Nagao et al.   PLoS One

ERG-associated protein with SET domain (ESET)-Oct4 interaction regulates pluripotency and represses the trophectoderm lineage

(2009) Leng-Siew Yeap et al.   Epigenetics & Chromatin

nuScore: a web-interface for nucleosome positioning predictions

(2008) M. Y. Tolstorukov et al.   BIOINFORMATICS

High-Resolution Mapping and Characterization of Open Chromatin across the Genome

(2008) Alan P. Boyle et al.   CELL

Genomic evolution of the placenta using co-option and duplication and divergence

(2008) K. Knox et al.   GENOME RESEARCH

REST maintains self-renewal and pluripotency of embryonic stem cells

(2008) Sanjay K. Singh et al.   NATURE

Cis-regulatory modules in the mammalian liver: composition depends on strength of Foxa2 consensus site

(2008) Geetu Tuteja et al.   NUCLEIC ACIDS RESEARCH