Locus-specific chromatin profiling of evolutionarily young transposable elements
Published 2021 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Locus-specific chromatin profiling of evolutionarily young transposable elements
Authors
Keywords
-
Journal
NUCLEIC ACIDS RESEARCH
Volume -, Issue -, Pages -
Publisher
Oxford University Press (OUP)
Online
2021-12-02
DOI
10.1093/nar/gkab1232
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Twelve years of SAMtools and BCFtools
- (2021) Petr Danecek et al. GigaScience
- Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition
- (2020) Bernardo Rodriguez-Martin et al. NATURE GENETICS
- On transposons and totipotency
- (2020) Maria-Elena Torres-Padilla PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
- Mobile genomics: tools and techniques for tackling transposons
- (2020) Kathryn O'Neill et al. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
- Measuring and interpreting transposable element expression
- (2020) Sophie Lanciano et al. NATURE REVIEWS GENETICS
- Endogenous retroviruses are a source of enhancers with oncogenic potential in acute myeloid leukaemia
- (2020) Özgen Deniz et al. Nature Communications
- A Field Guide to Eukaryotic Transposable Elements
- (2020) Jonathan N. Wells et al. Annual Review of Genetics
- Nanopore Sequencing Enables Comprehensive Transposable Element Epigenomic Profiling
- (2020) Adam D. Ewing et al. MOLECULAR CELL
- SQuIRE reveals locus-specific regulation of interspersed repeat expression
- (2019) Wan R Yang et al. NUCLEIC ACIDS RESEARCH
- Author Correction: Regulation of transposable elements by DNA modifications
- (2019) Özgen Deniz et al. NATURE REVIEWS GENETICS
- Transposable elements drive widespread expression of oncogenes in human cancers
- (2019) Hyo Sik Jang et al. NATURE GENETICS
- Hominoid-Specific Transposable Elements and KZFPs Facilitate Human Embryonic Genome Activation and Control Transcription in Naive Human ESCs
- (2019) Julien Pontis et al. Cell Stem Cell
- Functional evaluation of transposable elements as enhancers in mouse embryonic and trophoblast stem cells
- (2019) Christopher D Todd et al. eLife
- WashU Epigenome Browser update 2019
- (2019) Daofeng Li et al. NUCLEIC ACIDS RESEARCH
- Host–transposon interactions: conflict, cooperation, and cooption
- (2019) Rachel L Cosby et al. GENES & DEVELOPMENT
- Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype
- (2019) Daehwan Kim et al. NATURE BIOTECHNOLOGY
- L1EM: a tool for accurate locus specific LINE-1 RNA quantification
- (2019) Wilson McKerrow et al. BIOINFORMATICS
- The Nuclear Matrix Protein SAFB Cooperates with Major Satellite RNAs to Stabilize Heterochromatin Architecture Partially through Phase Separation
- (2019) Xiangru Huo et al. MOLECULAR CELL
- Tools and best practices for retrotransposon analysis using high-throughput sequencing data
- (2019) Aurélie Teissandier et al. Mobile DNA
- A LINE1-Nucleolin Partnership Regulates Early Development and ESC Identity
- (2018) Michelle Percharde et al. CELL
- Exaptation of transposable element coding sequences
- (2018) Zoé Joly-Lopez et al. CURRENT OPINION IN GENETICS & DEVELOPMENT
- Transcription factor profiling reveals molecular choreography and key regulators of human retrotransposon expression
- (2018) Xiaoji Sun et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Computational tools to unmask transposable elements
- (2018) Patricia Goerner-Potvin et al. NATURE REVIEWS GENETICS
- Nimble and Ready to Mingle: Transposon Outbursts of Early Development
- (2018) Diego Rodriguez-Terrones et al. TRENDS IN GENETICS
- Organizational principles of 3D genome architecture
- (2018) M. Jordan Rowley et al. NATURE REVIEWS GENETICS
- Selective silencing of euchromatic L1s revealed by genome-wide screens for L1 regulators
- (2017) Nian Liu et al. NATURE
- Allelic reprogramming of 3D chromatin architecture during early mammalian development
- (2017) Zhenhai Du et al. NATURE
- Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements
- (2017) Maxwell R Mumbach et al. NATURE GENETICS
- An integrated model for detecting significant chromatin interactions from high-resolution Hi-C data
- (2017) Mark Carty et al. Nature Communications
- Sim3C: simulation of Hi-C and Meta3C proximity ligation sequencing technologies
- (2017) Matthew Z DeMaere et al. GigaScience
- Establishing Chromatin Regulatory Landscape during Mouse Preimplantation Development
- (2016) Falong Lu et al. CELL
- Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq
- (2016) Rongxin Fang et al. CELL RESEARCH
- Hide and seek: how chromatin-based pathways silence retroelements in the mammalian germline
- (2016) Antoine Molaro et al. CURRENT OPINION IN GENETICS & DEVELOPMENT
- Distinct features of H3K4me3 and H3K27me3 chromatin domains in pre-implantation embryos
- (2016) Xiaoyu Liu et al. NATURE
- The landscape of accessible chromatin in mammalian preimplantation embryos
- (2016) Jingyi Wu et al. NATURE
- HiChIP: efficient and sensitive analysis of protein-directed genome architecture
- (2016) Maxwell R Mumbach et al. NATURE METHODS
- Mapping 3D genome architecture through in situ DNase Hi-C
- (2016) Vijay Ramani et al. Nature Protocols
- Regulatory activities of transposable elements: from conflicts to benefits
- (2016) Edward B. Chuong et al. NATURE REVIEWS GENETICS
- A comprehensive approach to expression of L1 loci
- (2016) Prescott Deininger et al. NUCLEIC ACIDS RESEARCH
- deepTools2: a next generation web server for deep-sequencing data analysis
- (2016) Fidel Ramírez et al. NUCLEIC ACIDS RESEARCH
- Activation of individual L1 retrotransposon instances is restricted to cell-type dependent permissive loci
- (2016) Claude Philippe et al. eLife
- Roles for retrotransposon insertions in human disease
- (2016) Dustin C. Hancks et al. Mobile DNA
- Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments
- (2016) Neva C. Durand et al. Cell Systems
- The Developmental Control of Transposable Elements and the Evolution of Higher Species
- (2015) Marc Friedli et al. Annual Review of Cell and Developmental Biology
- TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets
- (2015) Ying Jin et al. BIOINFORMATICS
- DNA-Demethylating Agents Target Colorectal Cancer Cells by Inducing Viral Mimicry by Endogenous Transcripts
- (2015) David Roulois et al. CELL
- Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C
- (2015) Tsung-Han S. Hsieh et al. CELL
- Transcriptional landscape of repetitive elements in normal and cancer human cells
- (2014) Steven W Criscione et al. BMC GENOMICS
- A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
- (2014) Suhas S.P. Rao et al. CELL
- Widespread contribution of transposable elements to the innovation of gene regulatory networks
- (2014) Vasavi Sundaram et al. GENOME RESEARCH
- Suv39h-Dependent H3K9me3 Marks Intact Retrotransposons and Silences LINE Elements in Mouse Embryonic Stem Cells
- (2014) Aydan Bulut-Karslioglu et al. MOLECULAR CELL
- The enemy within: endogenous retroelements and autoimmune disease
- (2014) Hannah E Volkman et al. NATURE IMMUNOLOGY
- The retrovirus HERVH is a long noncoding RNA required for human embryonic stem cell identity
- (2014) Xinyi Lu et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Characterisation of the potential function of SVA retrotransposons to modulate gene expression patterns
- (2013) Abigail L Savage et al. BMC EVOLUTIONARY BIOLOGY
- Genome assembly and haplotyping with Hi-C
- (2013) Jan O Korbel et al. NATURE BIOTECHNOLOGY
- LOcating Non-Unique matched Tags (LONUT) to Improve the Detection of the Enriched Regions for ChIP-seq Data
- (2013) Rui Wang et al. PLoS One
- Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages
- (2012) Dominic Schmidt et al. CELL
- Chromatin measurements reveal contributions of synthesis and decay to steady-state mRNA levels
- (2012) Sylvia C Tippmann et al. Molecular Systems Biology
- Embryonic stem cell potency fluctuates with endogenous retrovirus activity
- (2012) Todd S. Macfarlan et al. NATURE
- Fast gapped-read alignment with Bowtie 2
- (2012) Ben Langmead et al. NATURE METHODS
- The genomic landscape shaped by selection on transposable elements across 18 mouse strains
- (2012) Christoffer Nellåker et al. GENOME BIOLOGY
- Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications
- (2011) Felix Krueger et al. BIOINFORMATICS
- Discovering Transcription Factor Binding Sites in Highly Repetitive Regions of Genomes with Multi-Read Analysis of ChIP-Seq Data
- (2011) Dongjun Chung et al. PLoS Computational Biology
- BEDTools: a flexible suite of utilities for comparing genomic features
- (2010) Aaron R. Quinlan et al. BIOINFORMATICS
- Transposable elements have rewired the core regulatory network of human embryonic stem cells
- (2010) Galih Kunarso et al. NATURE GENETICS
- Model-based Analysis of ChIP-Seq (MACS)
- (2008) Yong Zhang et al. GENOME BIOLOGY
Create your own webinar
Interested in hosting your own webinar? Check the schedule and propose your idea to the Peeref Content Team.
Create NowAsk a Question. Answer a Question.
Quickly pose questions to the entire community. Debate answers and get clarity on the most important issues facing researchers.
Get Started