相关参考文献
注意：仅列出部分参考文献，下载原文获取全部文献信息。Cooler: scalable storage for Hi-C data and other genomically labeled arrays
Nezar Abdennur et al.
BIOINFORMATICS (2020)
Coolpup.py: versatile pile-up analysis of Hi-C data
Ilya M. Flyamer et al.
BIOINFORMATICS (2020)
HiNT: a computational method for detecting copy number variations and translocations from Hi-C data
Su Wang et al.
GENOME BIOLOGY (2020)
Epigenetic modulation of a hardwired 3D chromatin landscape in two naive states of pluripotency
Yaser Atlasi et al.
NATURE CELL BIOLOGY (2019)
Long-range enhancer-promoter contacts in gene expression control
Stefan Schoenfelder et al.
NATURE REVIEWS GENETICS (2019)
Enhancer Chromatin and 3D Genome Architecture Changes from Naive to Primed Human Embryonic Stem Cell States
Stephanie L. Battle et al.
STEM CELL REPORTS (2019)
Chromatin establishes an immature version of neuronal protocadherin selection during the naive-to-primed conversion of pluripotent stem cells
Angels Almenar-Queralt et al.
NATURE GENETICS (2019)
Untargeted histone profiling during naive conversion uncovers conserved modification markers between mouse and human
Laura De Clerck et al.
SCIENTIFIC REPORTS (2019)
DNA Methylation Directs Polycomb-Dependent 3D Genome Re-organization in Naive Pluripotency
Katy McLaughlin et al.
CELL REPORTS (2019)
Integrative Proteomic Profiling Reveals PRC2-Dependent Epigenetic Crosstalk Maintains Ground-State Pluripotency
Guido van Mierlo et al.
CELL STEM CELL (2019)
Histone H3 lysine 4 monomethylation modulates long-range chromatin interactions at enhancers
Jian Yan et al.
CELL RESEARCH (2018)
A Non-canonical BCOR-PRC1.1 Complex Represses Differentiation Programs in Human ESCs
Zheng Wang et al.
CELL STEM CELL (2018)
GRHL2-Dependent Enhancer Switching Maintains a Pluripotent Stem Cell Transcriptional Subnetwork after Exit from Naive Pluripotency
Amy F. Chen et al.
CELL STEM CELL (2018)
Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells
Tahsin Stefan Barakat et al.
CELL STEM CELL (2018)
Integrated analysis of single-cell embryo data yields a unified transcriptome signature for the human pre-implantation epiblast
Giuliano G. Stirparo et al.
DEVELOPMENT (2018)
TFAP2C regulates transcription in human naive pluripotency by opening enhancers
William A. Pastor et al.
NATURE CELL BIOLOGY (2018)
Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming
Ralph Stadhouders et al.
NATURE GENETICS (2018)
Detecting hierarchical genome folding with network modularity
Heidi K. Norton et al.
NATURE METHODS (2018)
Targeted in situ genome-wide profiling with high efficiency for low cell numbers
Peter J. Skene et al.
NATURE PROTOCOLS (2018)
Long-Range Enhancer Interactions Are Prevalent in Mouse Embryonic Stem Cells and Are Reorganized upon Pluripotent State Transition
Clara Lopes Novo et al.
CELL REPORTS (2018)
Promoter bivalency favors an open chromatin architecture in embryonic stem cells
Gloria Mas et al.
NATURE GENETICS (2018)
Organizational principles of 3D genome architecture
M. Jordan Rowley et al.
NATURE REVIEWS GENETICS (2018)
Gain of CTCF-Anchored Chromatin Loops Marks the Exit from Naive Pluripotency
Aleksandra Pekowska et al.
CELL SYSTEMS (2018)
Developmental enhancers and chromosome topology
Eileen E. M. Furlong et al.
SCIENCE (2018)
YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment
Jonathan A. Beagan et al.
GENOME RESEARCH (2017)
Complex multi-enhancer contacts captured by genome architecture mapping
Robert A. Beagrie et al.
NATURE (2017)
First critical repressive H3K27me3 marks in embryonic stem cells identified using designed protein inhibitor
James D. Moody et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)
PRC2 specifies ectoderm lineages and maintains pluripotency in primed but not naive ESCs
Yongli Shan et al.
NATURE COMMUNICATIONS (2017)
MrTADFinder: A network modularity based approach to identify topologically associating domains in multiple resolutions
Koon-Kiu Yan et al.
PLOS COMPUTATIONAL BIOLOGY (2017)
Global reorganisation of cis-regulatory units upon lineage commitment of human embryonic stem cells
Paula Freire-Pritchett et al.
ELIFE (2017)
Multiscale 3D Genome Rewiring during Mouse Neural Development
Boyan Bonev et al.
CELL (2017)
regioneR: an R/Bioconductor package for the association analysis of genomic regions based on permutation tests
Bernat Gel et al.
BIOINFORMATICS (2016)
Role of H1 linker histones in mammalian development and stem cell differentiation
Chenyi Pan et al.
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS (2016)
Spectral identification of topological domains
Jie Chen et al.
BIOINFORMATICS (2016)
Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos (vol 165, pg 1012, 2016)
Sophie Petropoulos et al.
CELL (2016)
3D Chromosome Regulatory Landscape of Human Pluripotent Cells
Xiong Ji et al.
CELL STEM CELL (2016)
Naive Human Pluripotent Cells Feature a Methylation Landscape Devoid of Blastocyst or Germline Memory
William A. Pastor et al.
CELL STEM CELL (2016)
Distinct features of H3K4me3 and H3K27me3 chromatin domains in pre-implantation embryos
Xiaoyu Liu et al.
NATURE (2016)
Enrichr: a comprehensive gene set enrichment analysis web server 2016 update
Maxim V. Kuleshov et al.
NUCLEIC ACIDS RESEARCH (2016)
Deletion of the Polycomb-Group Protein EZH2 Leads to Compromised Self-Renewal and Differentiation Defects in Human Embryonic Stem Cells
Adam Collinson et al.
CELL REPORTS (2016)
Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments
Neva C. Durand et al.
CELL SYSTEMS (2016)
CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data
Jonathan Cairns et al.
GENOME BIOLOGY (2016)
Integrating epigenomic data and 3D genomic structure with a new measure of chromatin assortativity
Vera Pancaldi et al.
GENOME BIOLOGY (2016)
Ground State Conditions Induce Rapid Reorganization of Core Pluripotency Factor Binding before Global Epigenetic Reprogramming
Christina Galonska et al.
CELL STEM CELL (2015)
Dynamic Reorganization of Extremely Long-Range Promoter-Promoter Interactions between Two States of Pluripotency
Onkar Joshi et al.
CELL STEM CELL (2015)
Defining the three cell lineages of the human blastocyst by single-cell RNA-seq
Paul Blakeley et al.
DEVELOPMENT (2015)
Histone variants as emerging regulators of embryonic stem cell identity
Valentina Turinetto et al.
EPIGENETICS (2015)
The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements
Stefan Schoenfelder et al.
GENOME RESEARCH (2015)
Epigenomic annotation of genetic variants using the Roadmap Epigenome Browser
Xin Zhou et al.
NATURE BIOTECHNOLOGY (2015)
Polycomb repressive complex PRC1 spatially constrains the mouse embryonic stem cell genome
Stefan Schoenfelder et al.
NATURE GENETICS (2015)
Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C
Borbala Mifsud et al.
NATURE GENETICS (2015)
HISAT: a fast spliced aligner with low memory requirements
Daehwan Kim et al.
NATURE METHODS (2015)
Orchestrating high-throughput genomic analysis with Bioconductor
Wolfgang Huber et al.
NATURE METHODS (2015)
Getting the genome in shape: the formation of loops, domains and compartments
Britta A. M. Bouwman et al.
GENOME BIOLOGY (2015)
Resetting Transcription Factor Control Circuitry toward Ground-State Pluripotency in Human
Yasuhiro Takashima et al.
CELL (2014)
A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
Suhas S. P. Rao et al.
CELL (2014)
Control of Cell Identity Genes Occurs in Insulated Neighborhoods in Mammalian Chromosomes
Jill M. Dowen et al.
CELL (2014)
Reorganization of Enhancer Patterns in Transition from Naive to Primed Pluripotency
Christa Buecker et al.
CELL STEM CELL (2014)
Epigenomic Comparison Reveals Activation of Seed Enhancers during Transition from Naive to Primed Pluripotency
Daniel C. Factor et al.
CELL STEM CELL (2014)
Systematic Identification of Culture Conditions for Induction and Maintenance of Naive Human Pluripotency (vol 15, pg 471, 2014)
Thorold W. Theunissen et al.
CELL STEM CELL (2014)
The 3D Genome in Transcriptional Regulation and Pluripotency
David U. Gorkin et al.
CELL STEM CELL (2014)
Unraveling architecture of the pluripotent genome
Jennifer E. Phillips-Cremins
CURRENT OPINION IN CELL BIOLOGY (2014)
A mechanistic link between gene regulation and genome architecture in mammalian development
Giancarlo Bonora et al.
CURRENT OPINION IN GENETICS & DEVELOPMENT (2014)
Gene Silencing Triggers Polycomb Repressive Complex 2 Recruitment to CpG Islands Genome Wide
Eva Madi Riising et al.
MOLECULAR CELL (2014)
deepTools: a flexible platform for exploring deep-sequencing data
Fidel Ramirez et al.
NUCLEIC ACIDS RESEARCH (2014)
ForceAtlas2, a Continuous Graph Layout Algorithm for Handy Network Visualization Designed for the Gephi Software
Mathieu Jacomy et al.
PLOS ONE (2014)
Otx2 and Oct4 Drive Early Enhancer Activation during Embryonic Stem Cell Transition from Naive Pluripotency
Shen-Hsi Yang et al.
CELL REPORTS (2014)
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Michael I. Love et al.
GENOME BIOLOGY (2014)
Ontogeny of CpG island methylation and specificity of DNMT3 methyltransferases during embryonic development in the mouse
Ghislain Auclair et al.
GENOME BIOLOGY (2014)
Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool
Edward Y. Chen et al.
BMC BIOINFORMATICS (2013)
Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers
Jakob Loven et al.
CELL (2013)
Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes
Warren A. Whyte et al.
CELL (2013)
Super-Enhancers in the Control of Cell Identity and Disease
Denes Hnisz et al.
CELL (2013)
Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment
Jennifer E. Phillips-Cremins et al.
CELL (2013)
Long-Range Chromatin Contacts in Embryonic Stem Cells Reveal a Role for Pluripotency Factors and Polycomb Proteins in Genome Organization
Matthew Denholtz et al.
CELL STEM CELL (2013)
FGF Signaling Inhibition in ESCs Drives Rapid Genome-wide Demethylation to the Epigenetic Ground State of Pluripotency
Gabriella Ficz et al.
CELL STEM CELL (2013)
Whole-Genome Bisulfite Sequencing of Two Distinct Interconvertible DNA Methylomes of Mouse Embryonic Stem Cells
Ehsan Habibi et al.
CELL STEM CELL (2013)
The Hierarchy of the 3D Genome
Johan H. Gibcus et al.
MOLECULAR CELL (2013)
Exploring long-range genome interactions using the WashU Epigenome Browser
Xin Zhou et al.
NATURE METHODS (2013)
Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data
Job Dekker et al.
NATURE REVIEWS GENETICS (2013)
Naive pluripotency is associated with global DNA hypomethylation
Harry G. Leitch et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2013)
Coordinate Regulation of DNA Methylation and H3K27me3 in Mouse Embryonic Stem Cells
James A. Hagarman et al.
PLOS ONE (2013)
Software for Computing and Annotating Genomic Ranges
Michael Lawrence et al.
PLOS COMPUTATIONAL BIOLOGY (2013)
Robust 3D DNA FISH Using Directly Labeled Probes
Daniel J. Bolland et al.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS (2013)
Synergistic Mechanisms of DNA Demethylation during Transition to Ground-State Pluripotency
Jamie A. Hackett et al.
STEM CELL REPORTS (2013)
The Transcriptional and Epigenomic Foundations of Ground State Pluripotency
Hendrik Marks et al.
CELL (2012)
Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome
Tom Sexton et al.
CELL (2012)
The long-range interaction landscape of gene promoters
Amartya Sanyal et al.
NATURE (2012)
A unique regulatory phase of DNA methylation in the early mammalian embryo
Zachary D. Smith et al.
NATURE (2012)
Topological domains in mammalian genomes identified by analysis of chromatin interactions
Jesse R. Dixon et al.
NATURE (2012)
Spatial partitioning of the regulatory landscape of the X-inactivation centre
Elphege P. Nora et al.
NATURE (2012)
ChromHMM: automating chromatin-state discovery and characterization
Jason Ernst et al.
NATURE METHODS (2012)
Fast gapped-read alignment with Bowtie 2
Ben Langmead et al.
NATURE METHODS (2012)
CTCF/cohesin-mediated DNA looping is required for protocadherin α promoter choice
Ya Guo et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)
Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications
Felix Krueger et al.
BIOINFORMATICS (2011)
FIMO: scanning for occurrences of a given motif
Charles E. Grant et al.
BIOINFORMATICS (2011)
The Human Epigenome Browser at Washington University
Xin Zhou et al.
NATURE METHODS (2011)
Chemically defined conditions for human iPSC derivation and culture
Guokai Chen et al.
NATURE METHODS (2011)
Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data
Robert C. McLeay et al.
BMC BIOINFORMATICS (2010)
Targets and dynamics of promoter DNA methylation during early mouse development
Julie Borgel et al.
NATURE GENETICS (2010)
The Sequence Alignment/Map format and SAMtools
Heng Li et al.
BIOINFORMATICS (2009)
Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
Erez Lieberman-Aiden et al.
SCIENCE (2009)
Fast unfolding of communities in large networks
Vincent D. Blondel et al.
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT (2008)
Model-based Analysis of ChIP-Seq (MACS)
Yong Zhang et al.
GENOME BIOLOGY (2008)
分享论文
