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Co-option of the lineage-specific LAVA retrotransposon in the gibbon genome
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Outgoing claims: the papers this work cites, builds on, or argues with.
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Transposable elements in gene regulation and in the evolution of vertebrate genomes
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SVA Elements: A Hominid-specific Retroposon Family
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Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities
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SVA retrotransposons as potential modulators of neuropeptide gene expression
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A mobile threat to genome stability: The impact of non-LTR retrotransposons upon the human genome
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Phylogenetic relationships and divergence dates of the whole mitochondrial genome sequences among three gibbon genera
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The hitch-hiking effect of a favourable gene
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Tandem repeat sequences evolutionarily related to SVA-type retrotransposons are expanded in the centromere region of the western hoolock gibbon, a small ape
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An integrated encyclopedia of DNA elements in the human genome
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Gibbon genome and the fast karyotype evolution of small apes
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Integration site selection by retroviruses and transposable elements in eukaryotes
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MMSET/WHSC1 enhances DNA damage repair leading to an increase in resistance to chemotherapeutic agents
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Computational tools to unmask transposable elements
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Fast and accurate short read alignment with Burrows–Wheeler transform
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The Sequence Alignment/Map format and SAMtools
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edgeR : a Bioconductor package for differential expression analysis of digital gene expression data
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BEDTools: a flexible suite of utilities for comparing genomic features
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Matrix eQTL: ultra fast eQTL analysis via large matrix operations
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BEDOPS: high-performance genomic feature operations
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STAR: ultrafast universal RNA-seq aligner
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Trimmomatic: a flexible trimmer for Illumina sequence data
inferredcites →https://doi.org/10.1093/biostatistics/kxr054openalex-snapshot
Removing technical variability in RNA-seq data using conditional quantile normalization
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Centromere Remodeling in Hoolock leuconedys (Hylobatidae) by a New Transposable Element Unique to the Gibbons
inferredcites →https://doi.org/10.1093/gbe/evw224openalex-snapshot
The Flow of the Gibbon LAVA Element Is Facilitated by the LINE-1 Retrotransposition Machinery
inferredcites →https://doi.org/10.1093/molbev/mst256openalex-snapshot
Hominoid Composite Non-LTR Retrotransposons—Variety, Assembly, Evolution, and Structural Determinants of Mobilization
inferredcites →https://doi.org/10.1093/molbev/msx277openalex-snapshot
Coalescent-Based Analyses of Genomic Sequence Data Provide a Robust Resolution of Phylogenetic Relationships among Major Groups of Gibbons
inferredcites →https://doi.org/10.1093/molbev/msy109openalex-snapshot
Developmental Loci Harbor Clusters of Accelerated Regions That Evolved Independently in Ape Lineages
inferredcites →https://doi.org/10.1093/nar/27.2.573openalex-snapshot
Tandem repeats finder: a program to analyze DNA sequences
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MUSCLE: multiple sequence alignment with high accuracy and high throughput
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The Encyclopedia of DNA elements (ENCODE): data portal update
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The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology
inferredcites →https://doi.org/10.1101/gr.218149.116openalex-snapshot
Transposable elements are the primary source of novelty in primate gene regulation
inferredcites →https://doi.org/10.1101/gr.233874.117openalex-snapshot
Epigenetic maintenance of topological domains in the highly rearranged gibbon genome
inferredcites →https://doi.org/10.1111/j.2517-6161.1995.tb02031.xopenalex-snapshot
Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
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Wnt Antagonist SFRP1 Functions as a Secreted Mediator of Senescence
inferredcites →https://doi.org/10.1128/mcb.26.5.1850-1864.2006openalex-snapshot
Mammalian Rad9 Plays a Role in Telomere Stability, S- and G2-Phase-Specific Cell Survival, and Homologous Recombinational Repair
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Spi-1/PU.1 Oncogene Accelerates DNA Replication Fork Elongation and Promotes Genetic Instability in the Absence of DNA Breakage
inferredcites →https://doi.org/10.1186/1471-2164-10-321openalex-snapshot
Exaptation of an ancient Alu short interspersed element provides a highly conserved vitamin D-mediated innate immune response in humans and primates
inferredcites →https://doi.org/10.1186/1471-2164-15-583openalex-snapshot
Transcriptional landscape of repetitive elements in normal and cancer human cells
inferredcites →https://doi.org/10.1186/gb-2008-9-9-r137openalex-snapshot
Model-based Analysis of ChIP-Seq (MACS)
inferredcites →https://doi.org/10.1186/s12859-014-0356-4openalex-snapshot
ANGSD: Analysis of Next Generation Sequencing Data
inferredcites →https://doi.org/10.1186/s12864-015-1543-zopenalex-snapshot
Lineage specific evolution of the VNTR composite retrotransposon central domain and its role in retrotransposition of gibbon LAVA elements
inferredcites →https://doi.org/10.1186/s12864-018-4850-3openalex-snapshot
Transposable elements generate regulatory novelty in a tissue-specific fashion
inferredcites →https://doi.org/10.1186/s13059-014-0550-8openalex-snapshot
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
inferredcites →https://doi.org/10.1186/s13059-018-1577-zopenalex-snapshot
Ten things you should know about transposable elements
inferredcites →https://doi.org/10.1186/s13100-015-0055-3openalex-snapshot
Transposable element detection from whole genome sequence data
inferredcites →https://doi.org/10.1186/s13100-020-00208-wopenalex-snapshot
The UCSC repeat browser allows discovery and visualization of evolutionary conflict across repeat families
inferredcites →https://doi.org/10.1371/journal.pgen.0020223openalex-snapshot
A High-Resolution Map of Synteny Disruptions in Gibbon and Human Genomes
inferredcites →https://doi.org/10.1371/journal.pone.0014419openalex-snapshot
Mitochondrial Genome Sequences Effectively Reveal the Phylogeny of Hylobates Gibbons
inferredcites →https://doi.org/10.15252/embr.201643179openalex-snapshot
TET3‐mediated DNA oxidation promotes ATR‐dependent DNA damage response
inferredcites →https://doi.org/10.15252/embr.201846821openalex-snapshot
The lysine‐specific methyltransferase KMT2C/MLL3 regulates DNA repair components in cancer
inferredcites →https://doi.org/10.1534/genetics.105.043786openalex-snapshot
Recombination and the Properties of Tajima's D in the Context of Approximate-Likelihood Calculation
inferredcites →https://doi.org/10.1534/genetics.115.174425openalex-snapshot
Examining Phylogenetic Relationships Among Gibbon Genera Using Whole Genome Sequence Data Using an Approximate Bayesian Computation Approach
inferredcites →https://doi.org/10.3389/fgene.2017.00063openalex-snapshot
An Enhancer's Length and Composition Are Shaped by Its Regulatory Task
inferredcites →https://doi.org/10.4161/15384101.2014.958386openalex-snapshot
The checkpoint clamp protein Rad9 facilitates DNA-end resection and prevents alternative non-homologous end joining
inferredcites →https://doi.org/10.7554/elife.02482openalex-snapshot
SETD2 is required for DNA double-strand break repair and activation of the p53-mediated checkpoint
inferredcites →https://doi.org/10.7554/elife.22519openalex-snapshot
Co-option of an endogenous retrovirus envelope for host defense in hominid ancestors
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inferred← citeshttps://doi.org/10.1073/pnas.2006038117openalex-snapshot
Co-option of the lineage-specific LAVA retrotransposon in the gibbon genome
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