标题
Functional signatures of evolutionarily young CTCF binding sites
作者
关键词
-
出版物
BMC BIOLOGY
Volume 18, Issue 1, Pages -
出版商
Springer Science and Business Media LLC
发表日期
2020-09-28
DOI
10.1186/s12915-020-00863-8
参考文献
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注意:仅列出部分参考文献,下载原文获取全部文献信息。- Redundant and specific roles of cohesin STAG subunits in chromatin looping and transcriptional control
- (2020) Valentina Casa et al. GENOME RESEARCH
- PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix
- (2018) Giovanna Ambrosini et al. BIOINFORMATICS
- Transposable elements generate regulatory novelty in a tissue-specific fashion
- (2018) Marco Trizzino et al. BMC GENOMICS
- Contribution of transposable elements and distal enhancers to evolution of human-specific features of interphase chromatin architecture in embryonic stem cells
- (2018) Gennadi V. Glinsky CHROMOSOME RESEARCH
- Repeat associated mechanisms of genome evolution and function revealed by theMus caroliandMus paharigenomes
- (2018) David Thybert et al. GENOME RESEARCH
- Distinct roles of cohesin-SA1 and cohesin-SA2 in 3D chromosome organization
- (2018) Aleksandar Kojic et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Distinct roles of cohesin-SA1 and cohesin-SA2 in 3D chromosome organization
- (2018) Aleksandar Kojic et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci
- (2018) Jingtao Lilue et al. NATURE GENETICS
- PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools
- (2018) Huaiyu Mi et al. NUCLEIC ACIDS RESEARCH
- GENCODE reference annotation for the human and mouse genomes
- (2018) Adam Frankish et al. NUCLEIC ACIDS RESEARCH
- The Gene Ontology Resource: 20 years and still GOing strong
- (2018) NUCLEIC ACIDS RESEARCH
- Ensembl 2019
- (2018) Fiona Cunningham et al. NUCLEIC ACIDS RESEARCH
- Interplay of cis and trans mechanisms driving transcription factor binding and gene expression evolution
- (2017) Emily S. Wong et al. Nature Communications
- Topologically associating domains are ancient features that coincide with Metazoan clusters of extreme noncoding conservation
- (2017) Nathan Harmston et al. Nature Communications
- CTCF-Mediated Chromatin Loops between Promoter and Gene Body Regulate Alternative Splicing across Individuals
- (2017) Mariana Ruiz-Velasco et al. Cell Systems
- Complex heatmaps reveal patterns and correlations in multidimensional genomic data
- (2016) Zuguang Gu et al. BIOINFORMATICS
- 3D Chromosome Regulatory Landscape of Human Pluripotent Cells
- (2016) Xiong Ji et al. Cell Stem Cell
- The Role of Retrotransposons in Gene Family Expansions in the Human and Mouse Genomes
- (2016) Václav Janoušek et al. Genome Biology and Evolution
- Activation of proto-oncogenes by disruption of chromosome neighborhoods
- (2016) D. Hnisz et al. SCIENCE
- The MEME Suite
- (2015) Timothy L. Bailey et al. NUCLEIC ACIDS RESEARCH
- Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes
- (2015) Adrian L. Sanborn et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Comparative Hi-C Reveals that CTCF Underlies Evolution of Chromosomal Domain Architecture
- (2015) Matteo Vietri Rudan et al. Cell Reports
- Evidence for a common evolutionary rate in metazoan transcriptional networks
- (2015) Anne-Ruxandra Carvunis et al. eLife
- HTSeq--a Python framework to work with high-throughput sequencing data
- (2014) S. Anders et al. BIOINFORMATICS
- Widespread contribution of transposable elements to the innovation of gene regulatory networks
- (2014) Vasavi Sundaram et al. GENOME RESEARCH
- A comparative encyclopedia of DNA elements in the mouse genome
- (2014) Feng Yue et al. NATURE
- CTCF: an architectural protein bridging genome topology and function
- (2014) Chin-Tong Ong et al. NATURE REVIEWS GENETICS
- Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution
- (2014) J. Vierstra et al. SCIENCE
- Tracing the Evolution of Lineage-Specific Transcription Factor Binding Sites in a Birth-Death Framework
- (2014) Ken Daigoro Yokoyama et al. PLoS Computational Biology
- HAL: a hierarchical format for storing and analyzing multiple genome alignments
- (2013) Glenn Hickey et al. BIOINFORMATICS
- The role of retrotransposons in gene family expansions: insights from the mouse Abp gene family
- (2013) Václav Janoušek et al. BMC EVOLUTIONARY BIOLOGY
- CTCF and Cohesin: Linking Gene Regulatory Elements with Their Targets
- (2013) Matthias Merkenschlager et al. CELL
- Cooperativity and Rapid Evolution of Cobound Transcription Factors in Closely Related Mammals
- (2013) Klara Stefflova et al. CELL
- Cohesin-mediated interactions organize chromosomal domain architecture
- (2013) Sevil Sofueva et al. EMBO JOURNAL
- CTCF: the protein, the binding partners, the binding sites and their chromatin loops
- (2013) S. J. B. Holwerda et al. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
- Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells
- (2013) J. Zuin et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Distinct evolution process among type I interferon in mammals
- (2013) Lei Xu et al. Protein & Cell
- BEDOPS: high-performance genomic feature operations
- (2012) Shane Neph et al. BIOINFORMATICS
- STAR: ultrafast universal RNA-seq aligner
- (2012) Alexander Dobin et al. BIOINFORMATICS
- Comparative Epigenomic Annotation of Regulatory DNA
- (2012) Shu Xiao et al. CELL
- Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages
- (2012) Dominic Schmidt et al. CELL
- Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules
- (2012) A. J. Faure et al. GENOME RESEARCH
- Extensive compensatory cis-trans regulation in the evolution of mouse gene expression
- (2012) A. Goncalves et al. GENOME RESEARCH
- Latent Regulatory Potential of Human-Specific Repetitive Elements
- (2012) Michelle C. Ward et al. MOLECULAR CELL
- Analyses of pig genomes provide insight into porcine demography and evolution
- (2012) Martien A. M. Groenen et al. NATURE
- Topological domains in mammalian genomes identified by analysis of chromatin interactions
- (2012) Jesse R. Dixon et al. NATURE
- CTCFBSDB 2.0: a database for CTCF-binding sites and genome organization
- (2012) Jesse D. Ziebarth et al. NUCLEIC ACIDS RESEARCH
- Comprehensive Identification and Annotation of Cell Type-Specific and Ubiquitous CTCF-Binding Sites in the Human Genome
- (2012) Hebing Chen et al. PLoS One
- Dynamic long-range chromatin interactions controlMybproto-oncogene transcription during erythroid development
- (2011) Ralph Stadhouders et al. EMBO JOURNAL
- Dioxin receptor and SLUG transcription factors regulate the insulator activity of B1 SINE retrotransposons via an RNA polymerase switch
- (2011) A. C. Roman et al. GENOME RESEARCH
- Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega
- (2011) F. Sievers et al. Molecular Systems Biology
- Mouse genomic variation and its effect on phenotypes and gene regulation
- (2011) Thomas M. Keane et al. NATURE
- Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals
- (2011) Vincent J Lynch et al. NATURE GENETICS
- BEDTools: a flexible suite of utilities for comparing genomic features
- (2010) Aaron R. Quinlan et al. BIOINFORMATICS
- Functional Analysis of CTCF During Mammalian Limb Development
- (2010) Natalia Soshnikova et al. DEVELOPMENTAL CELL
- 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
- Transposable elements have rewired the core regulatory network of human embryonic stem cells
- (2010) Galih Kunarso et al. NATURE GENETICS
- Analysing biological pathways in genome-wide association studies
- (2010) Kai Wang et al. NATURE REVIEWS GENETICS
- 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
- Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding
- (2010) D. Schmidt et al. SCIENCE
- The Sequence Alignment/Map format and SAMtools
- (2009) H. Li et al. BIOINFORMATICS
- Fast and accurate short read alignment with Burrows-Wheeler transform
- (2009) H. Li et al. BIOINFORMATICS
- CTCF: Master Weaver of the Genome
- (2009) Jennifer E. Phillips et al. CELL
- Cohesins form chromosomal cis-interactions at the developmentally regulated IFNG locus
- (2009) Suzana Hadjur et al. NATURE
- MEME SUITE: tools for motif discovery and searching
- (2009) T. L. Bailey et al. NUCLEIC ACIDS RESEARCH
- CTCF regulates cell cycle progression of αβ T cells in the thymus
- (2008) Helen Heath et al. EMBO JOURNAL
- Evolution of the mammalian transcription factor binding repertoire via transposable elements
- (2008) G. Bourque et al. GENOME RESEARCH
- Transposable elements and the evolution of regulatory networks
- (2008) Cédric Feschotte NATURE REVIEWS GENETICS
- Model-based Analysis of ChIP-Seq (MACS)
- (2008) Yong Zhang et al. GENOME BIOLOGY
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