Reproducible evaluation of transposable element detectors with McClintock 2 guides accurate inference of Ty insertion patterns in yeast
出版年份 2023 全文链接
标题
Reproducible evaluation of transposable element detectors with McClintock 2 guides accurate inference of Ty insertion patterns in yeast
作者
关键词
-
出版物
Mobile DNA
Volume 14, Issue 1, Pages -
出版商
Springer Science and Business Media LLC
发表日期
2023-07-14
DOI
10.1186/s13100-023-00296-4
参考文献
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。- Structural basis of Ty1 integrase tethering to RNA polymerase III for targeted retrotransposon integration
- (2023) Phong Quoc Nguyen et al. Nature Communications
- Paths to adaptation under fluctuating nitrogen starvation: The spectrum of adaptive mutations in Saccharomyces cerevisiae is shaped by retrotransposons and microhomology-mediated recombination
- (2023) Michelle Hays et al. PLoS Genetics
- Epistatic selection on a selfish Segregation Distorter supergene – drive, recombination, and genetic load
- (2022) Beatriz Navarro-Dominguez et al. eLife
- Ongoing transposition in cell culture reveals the phylogeny of diverse Drosophila S2 sublines
- (2022) Shunhua Han et al. GENETICS
- Local assembly of long reads enables phylogenomics of transposable elements in a polyploid cell line
- (2022) Shunhua Han et al. NUCLEIC ACIDS RESEARCH
- Bergerac strains of Caenorhabditis elegans revisited: expansion of Tc1 elements imposes a significant genomic and fitness cost
- (2022) Austin T Daigle et al. G3-Genes Genomes Genetics
- yEvo: experimental evolution in high school classrooms selects for novel mutations that impact clotrimazole resistance in Saccharomyces cerevisiae
- (2022) Matthew Bryce Taylor et al. G3-Genes Genomes Genetics
- Multiple origins, one evolutionary trajectory: gradual evolution characterizes distinct lineages of allotetraploid Brachypodium
- (2022) Virginia T Scarlett et al. GENETICS
- Stage-specific transposon activity in the life cycle of the fairy-ring mushroom Marasmius oreades
- (2022) Markus Hiltunen et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Light and shadow on the mechanisms of integration site selection in yeast Ty retrotransposon families
- (2021) Amandine Bonnet et al. CURRENT GENETICS
- A benchmark and an algorithm for detecting germline transposon insertions and measuring de novo transposon insertion frequencies
- (2021) Tianxiong Yu et al. NUCLEIC ACIDS RESEARCH
- Asexual Experimental Evolution of Yeast Does Not Curtail Transposable Elements
- (2021) Piaopiao Chen et al. MOLECULAR BIOLOGY AND EVOLUTION
- Species-Wide Transposable Element Repertoires Retrace the Evolutionary History of the Saccharomyces cerevisiae Host
- (2021) Claudine Bleykasten-Grosshans et al. MOLECULAR BIOLOGY AND EVOLUTION
- Towards population-scale long-read sequencing
- (2021) Wouter De Coster et al. NATURE REVIEWS GENETICS
- A population-level invasion by transposable elements triggers genome expansion in a fungal pathogen
- (2021) Ursula Oggenfuss et al. eLife
- Transposable element profiles reveal cell line identity and loss of heterozygosity in Drosophila cell culture
- (2021) Shunhua Han et al. GENETICS
- TE Hub: A community-oriented space for sharing and connecting tools, data, resources, and methods for transposable element annotation
- (2021) et al. Mobile DNA
- Transposon activation is a major driver in the genome evolution of cultivated olive trees ( Olea europaea L.)
- (2020) Jaime Jiménez‐Ruiz et al. Plant Genome
- Various modes of HP1a interactions with the euchromatic chromosome arms in Drosophila ovarian somatic cells
- (2020) Artem A. Ilyin et al. CHROMOSOMA
- A small targeting domain in Ty1 integrase is sufficient to direct retrotransposon integration upstream of tRNA genes
- (2020) Amna Asif‐Laidin et al. EMBO JOURNAL
- Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird‐of‐paradise
- (2020) Valentina Peona et al. Molecular Ecology Resources
- Devia TE : Assembly‐free analysis and visualization of mobile genetic element composition
- (2019) Lukas Weilguny et al. Molecular Ecology Resources
- Local features determine Ty3 targeting frequency at RNA polymerase III transcription start sites
- (2019) Kurt Patterson et al. GENOME RESEARCH
- Asexual reproduction reduces transposable element load in experimental yeast populations
- (2019) Jens Bast et al. eLife
- Absolute nucleosome occupancy map for the Saccharomyces cerevisiae genome
- (2019) Elisa Oberbeckmann et al. GENOME RESEARCH
- Nuclear Ccr4-Not mediates the degradation of telomeric and transposon transcripts at chromatin in the Drosophila germline
- (2019) Maria Kordyukova et al. NUCLEIC ACIDS RESEARCH
- A benchmark of transposon insertion detection tools using real data
- (2019) Pol Vendrell-Mir et al. Mobile DNA
- panISa: Ab initio detection of insertion sequences in bacterial genomes from short read sequence data
- (2018) Panisa Treepong et al. BIOINFORMATICS
- Conserved Noncoding Elements Influence the Transposable Element Landscape in Drosophila
- (2018) Manee M Manee et al. Genome Biology and Evolution
- L1 retrotransposition is a common feature of mammalian hepatocarcinogenesis
- (2018) Stephanie N. Schauer et al. GENOME RESEARCH
- Bioconda: sustainable and comprehensive software distribution for the life sciences
- (2018) Björn Grüning et al. NATURE METHODS
- Genome evolution across 1,011 Saccharomyces cerevisiae isolates
- (2018) Jackson Peter et al. NATURE
- Genome-Wide Estimates of Transposable Element Insertion and Deletion Rates in Drosophila Melanogaster
- (2017) Jeffrey R. Adrion et al. Genome Biology and Evolution
- The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology
- (2017) Eugene J. Gardner et al. GENOME RESEARCH
- Piwi interacts with chromatin at nuclear pores and promiscuously binds nuclear transcripts in Drosophila ovarian somatic cells
- (2017) Artem A. Ilyin et al. NUCLEIC ACIDS RESEARCH
- Sex Chromosome Evolution, Heterochiasmy, and Physiological QTL in the Salmonid Brook Charr Salvelinus fontinalis
- (2017) Ben J.G. Sutherland et al. G3-Genes Genomes Genetics
- RelocaTE2: a high resolution transposable element insertion site mapping tool for population resequencing
- (2017) Jinfeng Chen et al. PeerJ
- Genomic analysis of P elements in natural populations of Drosophila melanogaster
- (2017) Casey M. Bergman et al. PeerJ
- MultiQC: summarize analysis results for multiple tools and samples in a single report
- (2016) Philip Ewels et al. BIOINFORMATICS
- Benchmarking computational tools for polymorphic transposable element detection
- (2016) Lavanya Rishishwar et al. BRIEFINGS IN BIOINFORMATICS
- PoPoolationTE2: Comparative Population Genomics of Transposable Elements Using Pool-Seq
- (2016) Robert Kofler et al. MOLECULAR BIOLOGY AND EVOLUTION
- The 100-genomes strains, anS. cerevisiaeresource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen
- (2015) Pooja K. Strope et al. GENOME RESEARCH
- An RNA polymerase III subunit determines sites of retrotransposon integration
- (2015) A. Bridier-Nahmias et al. SCIENCE
- Transposable element detection from whole genome sequence data
- (2015) Adam D. Ewing Mobile DNA
- bwtool: a tool for bigWig files
- (2014) Andy Pohl et al. BIOINFORMATICS
- Comparative analysis of methods for genome-wide nucleosome cartography
- (2014) Luis Quintales et al. BRIEFINGS IN BIOINFORMATICS
- UpSet: Visualization of Intersecting Sets
- (2014) Alexander Lex et al. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS
- TEMP: a computational method for analyzing transposable element polymorphism in populations
- (2014) Jiali Zhuang et al. NUCLEIC ACIDS RESEARCH
- Genome-wide analysis of intraspecific transposon diversity in yeast
- (2013) Claudine Bleykasten-Grosshans et al. BMC GENOMICS
- Mobile element biology: new possibilities with high-throughput sequencing
- (2013) Jinchuan Xing et al. TRENDS IN GENETICS
- The Use of RelocaTE and Unassembled Short Reads to Produce High-Resolution Snapshots of Transposable Element Generated Diversity in Rice
- (2013) Sofia M. C. Robb et al. G3-Genes Genomes Genetics
- RetroSeq: transposable element discovery from next-generation sequencing data
- (2012) Thomas M. Keane et al. BIOINFORMATICS
- Snakemake--a scalable bioinformatics workflow engine
- (2012) J. Koster et al. BIOINFORMATICS
- Retrotransposon Ty1 integration targets specifically positioned asymmetric nucleosomal DNA segments in tRNA hotspots
- (2012) L. Mularoni et al. GENOME RESEARCH
- Retrotransposon profiling of RNA polymerase III initiation sites
- (2012) X. Qi et al. GENOME RESEARCH
- A nucleosomal surface defines an integration hotspot for the Saccharomyces cerevisiae Ty1 retrotransposon
- (2012) J. A. Baller et al. GENOME RESEARCH
- Two large-scale analyses of Ty1 LTR-retrotransposon de novo insertion events indicate that Ty1 targets nucleosomal DNA near the H2A/H2B interface
- (2012) Antoine Bridier-Nahmias et al. Mobile DNA
- ART: a next-generation sequencing read simulator
- (2011) Weichun Huang et al. BIOINFORMATICS
- The variant call format and VCFtools
- (2011) P. Danecek et al. BIOINFORMATICS
- Reading TE leaves: New approaches to the identification of transposable element insertions
- (2011) D. A. Ray et al. GENOME RESEARCH
- The self-assessment trap: can we all be better than average?
- (2011) R. Norel et al. Molecular Systems Biology
- Repetitive DNA and next-generation sequencing: computational challenges and solutions
- (2011) Todd J. Treangen et al. NATURE REVIEWS GENETICS
- BigWig and BigBed: enabling browsing of large distributed datasets
- (2010) W. J. Kent et al. BIOINFORMATICS
- BEDTools: a flexible suite of utilities for comparing genomic features
- (2010) Aaron R. Quinlan et al. BIOINFORMATICS
- Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
- (2009) Ben Langmead et al. GENOME BIOLOGY
- Computational Approaches and Tools Used in Identification of Dispersed Repetitive DNA Sequences
- (2008) Surya Saha et al. Tropical Plant Biology
Add your recorded webinar
Do you already have a recorded webinar? Grow your audience and get more views by easily listing your recording on Peeref.
Upload 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