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。The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data
Sarah B. Reiff et al.
NATURE COMMUNICATIONS (2022)
Balancing cohesin eviction and retention prevents aberrant chromosomal interactions, Polycomb-mediated repression, and X-inactivation
Andrea J. Kriz et al.
MOLECULAR CELL (2021)
Systematic evaluation of chromosome conformation capture assays
Betul Akgol Oksuz et al.
NATURE METHODS (2021)
4C-seq from beginning to end: A detailed protocol for sample preparation and data analysis
Peter H. L. Krijger et al.
METHODS (2020)
DeepHiC: A Generative Adversarial Network for Enhancing Hi-C Data Resolution
Hao Hong et al.
PLOS COMPUTATIONAL BIOLOGY (2020)
Resolving the 3D Landscape of Transcription-Linked Mammalian Chromatin Folding
Tsung-Han S. Hsieh et al.
MOLECULAR CELL (2020)
Ultrastructural Details of Mammalian Chromosome Architecture
Nils Krietenstein et al.
MOLECULAR CELL (2020)
SRHiC: A Deep Learning Model to Enhance the Resolution of Hi-C Data
Zhilan Li et al.
FRONTIERS IN GENETICS (2020)
Robust Hi-C Maps of Enhancer-Promoter Interactions Reveal the Function of Non-coding Genome in Neural Development and Diseases
Leina Lu et al.
MOLECULAR CELL (2020)
Trans- and cis-acting effects of Firre on epigenetic features of the inactive X chromosome
He Fang et al.
NATURE COMMUNICATIONS (2020)
Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection
Zhilian Jia et al.
GENOME BIOLOGY (2020)
HiCNN: a very deep convolutional neural network to better enhance the resolution of Hi-C data
Tong Liu et al.
BIOINFORMATICS (2019)
Multi-platform discovery of haplotype-resolved structural variation in human genomes
Mark J. P. Chaisson et al.
NATURE COMMUNICATIONS (2019)
Human evolved regulatory elements modulate genes involved in cortical expansion and neurodevelopmental disease susceptibility
Hyejung Won et al.
NATURE COMMUNICATIONS (2019)
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype
Daehwan Kim et al.
NATURE BIOTECHNOLOGY (2019)
KLF4 is involved in the organization and regulation of pluripotency-associated three-dimensional enhancer networks
Dafne Campigli Di Giammartino et al.
NATURE CELL BIOLOGY (2019)
A compendium of promoter-centered long-range chromatin interactions in the human genome
Inkyung Jung et al.
NATURE GENETICS (2019)
Simultaneous profiling of 3D genome structure and DNA methylation in single human cells
Dong-Sung Lee et al.
NATURE METHODS (2019)
Evolutionary and functional impact of common polymorphic inversions in the human genome
Carla Giner-Delgado et al.
NATURE COMMUNICATIONS (2019)
Epigenome editing strategies for the functional annotation of CTCF insulators
Daniel R. Tarjan et al.
NATURE COMMUNICATIONS (2019)
Revealing Hi-C subcompartments by imputing inter-chromosomal chromatin interactions
Kyle Xiong et al.
NATURE COMMUNICATIONS (2019)
HiCNN2: Enhancing the Resolution of Hi-C Data Using an Ensemble of Convolutional Neural Networks
Tong Liu et al.
GENES (2019)
Structural variant calling: the long and the short of it
Medhat Mahmoud et al.
GENOME BIOLOGY (2019)
CTCF modulates allele-specific sub-TAD organization and imprinted gene activity at the mouse Dlk1-Dio3 and Igf2-H19 domains
David Lleres et al.
GENOME BIOLOGY (2019)
Refined sgRNA efficacy prediction improves large- and small-scale CRISPR-Cas9 applications
Maurice Labuhn et al.
NUCLEIC ACIDS RESEARCH (2018)
The Dynamic Landscape of Open Chromatin during Human Cortical Neurogenesis
Luis de la Torre-Ubieta et al.
CELL (2018)
Endogenous Reprogramming of Alpha Cells into Beta Cells, Induced by Viral Gene Therapy, Reverses Autoimmune Diabetes
Xiangwei Xiao et al.
CELL STEM CELL (2018)
Nanopore sequencing and assembly of a human genome with ultra-long reads
Miten Jain et al.
NATURE BIOTECHNOLOGY (2018)
Transcription-coupled changes in nuclear mobility of mammalian cis-regulatory elements
Bo Gu et al.
SCIENCE (2018)
Enhancing Hi-C data resolution with deep convolutional neural network HiCPlus
Yan Zhang et al.
NATURE COMMUNICATIONS (2018)
Integrative detection and analysis of structural variation in cancer genomes
Jesse R. Dixon et al.
NATURE GENETICS (2018)
ChIA-PET2: a versatile and flexible pipeline for ChIA-PET data analysis
Guipeng Li et al.
NUCLEIC ACIDS RESEARCH (2017)
Cell-cycle dynamics of chromosomal organization at single-cell resolution
Takashi Nagano et al.
NATURE (2017)
Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements
Maxwell R. Mumbach et al.
NATURE GENETICS (2017)
Comparison of computational methods for Hi-C data analysis
Mattia Forcato et al.
NATURE METHODS (2017)
Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters
Biola M. Javierre et al.
CELL (2016)
Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq
Rongxin Fang et al.
CELL RESEARCH (2016)
The second decade of 3C technologies: detailed insights into nuclear organization
Annette Denker et al.
GENES & DEVELOPMENT (2016)
Chromosome conformation elucidates regulatory relationships in developing human brain
Hyejung Won et al.
NATURE (2016)
Structural organization of the inactive X chromosome in the mouse
Luca Giorgetti et al.
NATURE (2016)
HiChIP: efficient and sensitive analysis of protein-directed genome architecture
Maxwell R. Mumbach et al.
NATURE METHODS (2016)
A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome
Anthony D. Schmitt 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)
Human inversions and their functional consequences
Marta Puig et al.
BRIEFINGS IN FUNCTIONAL GENOMICS (2015)
CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription
Zhonghui Tang et al.
CELL (2015)
Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions
Dario G. Lupianez et al.
CELL (2015)
The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements
Stefan Schoenfelder et al.
GENOME RESEARCH (2015)
Chromatin architecture reorganization during stem cell differentiation
Jesse R. Dixon et al.
NATURE (2015)
Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C
Borbala Mifsud et al.
NATURE GENETICS (2015)
APPLICATIONS OF NEXT-GENERATION SEQUENCING Genetic variation and the de novo assembly of human genomes
Mark J. P. Chaisson et al.
NATURE REVIEWS GENETICS (2015)
Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes
Adrian L. Sanborn et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)
A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation
Anand Minajigi et al.
SCIENCE (2015)
The lncRNA Firre anchors the inactive X chromosome to the nucleolus by binding CTCF and maintains H3K27me3 methylation
Fan Yang et al.
GENOME BIOLOGY (2015)
CCTop: An Intuitive, Flexible and Reliable CRISPR/Cas9 Target Prediction Tool
Manuel Stemmer et al.
PLOS ONE (2015)
Bipartite structure of the inactive mouse X chromosome
Xinxian Deng et al.
GENOME BIOLOGY (2015)
A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
Suhas S. P. Rao et al.
CELL (2014)
Genome-wide map of regulatory interactions in the human genome
Nastaran Heidari et al.
GENOME RESEARCH (2014)
Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts
Ferhat Ay et al.
GENOME RESEARCH (2014)
Obesity-associated variants within FTO form long-range functional connections with IRX3
Scott Smemo et al.
NATURE (2014)
Whole-genome haplotyping using long reads and statistical methods
Volodymyr Kuleshov et al.
NATURE BIOTECHNOLOGY (2014)
CRISPR Reveals a Distal Super-Enhancer Required for Sox2 Expression in Mouse Embryonic Stem Cells
Yan Li et al.
PLOS ONE (2014)
Genomic Imprinting in Mammals
Denise P. Barlow et al.
COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY (2014)
Klf4 Organizes Long-Range Chromosomal Interactions with the Oct4 Locus inReprogramming andPluripotency
Zong Wei et al.
CELL STEM CELL (2013)
Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations
Yubo Zhang et al.
NATURE (2013)
A high-resolution map of the three-dimensional chromatin interactome in human cells
Fulai Jin et al.
NATURE (2013)
Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing
Siddarth Selvaraj et al.
NATURE BIOTECHNOLOGY (2013)
HiCNorm: removing biases in Hi-C data via Poisson regression
Ming Hu et al.
BIOINFORMATICS (2012)
The macrosatellite DXZ4 mediates CTCF-dependent long-range intrachromosomal interactions on the human inactive X chromosome
Andrea H. Horakova et al.
HUMAN MOLECULAR GENETICS (2012)
A map of the cis-regulatory sequences in the mouse genome
Yin Shen et al.
NATURE (2012)
An integrated encyclopedia of DNA elements in the human genome
Ian Dunham 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)
Iterative correction of Hi-C data reveals hallmarks of chromosome organization
Maxim Imakaev et al.
NATURE METHODS (2012)
Fast gapped-read alignment with Bowtie 2
Ben Langmead et al.
NATURE METHODS (2012)
Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture
Eitan Yaffe et al.
NATURE GENETICS (2011)
Distinct Epigenomic Landscapes of Pluripotent and Lineage-Committed Human Cells
R. David Hawkins et al.
CELL STEM CELL (2010)
The NIH Roadmap Epigenomics Mapping Consortium
Bradley E. Bernstein et al.
NATURE BIOTECHNOLOGY (2010)
Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells
Stefan Schoenfelder et al.
NATURE GENETICS (2010)
Mapping and sequencing of structural variation from eight human genomes (Reprinted from Nature, vol 453, pg 56-64, 2008)
Jeffrey M. Kidd et al.
NATURE GENETICS (2009)
Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
Erez Lieberman-Aiden et al.
SCIENCE (2009)
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
Ben Langmead et al.
GENOME BIOLOGY (2009)
Model-based Analysis of ChIP-Seq (MACS)
Yong Zhang et al.
GENOME BIOLOGY (2008)
Mapping and sequencing of structural variation from eight human genomes
Jeffrey M. Kidd et al.
NATURE (2008)
CTCF mediates long-range chromatin looping and local histone modification in the β-globin locus
Erik Splinter et al.
GENES & DEVELOPMENT (2006)
CTCF binding at the H19 imprinting control region mediates maternally inherited higher-order chromatin conformation to restrict enhancer access to Igf2
Sreenivasulu Kurukuti et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
Interaction between differentially methylated regions partitions the imprinted genes Igf2 and H19 into parent-specific chromatin loops
A Murrell et al.
NATURE GENETICS (2004)
A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly
LA Lettice et al.
HUMAN MOLECULAR GENETICS (2003)
The human genome browser at UCSC
WJ Kent et al.
GENOME RESEARCH (2002)
分享论文
