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Whole-genome analysis ofAlurepeat elements reveals complex evolutionary history

https://doi.org/10.1101/gr.2693004
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1006/mgme.1999.2864openalex-snapshot
Alu Repeats and Human Disease
inferredcites →https://doi.org/10.1007/bf00160256openalex-snapshot
Phylogenetic evidence for multiple Alu source genes
inferredcites →https://doi.org/10.1007/bf00163204openalex-snapshot
Standardized nomenclature for Alu repeats
inferredcites →https://doi.org/10.1007/bf00182741openalex-snapshot
Phylogenetic isolation of a human alu flounder gene: Drift to new subfamily identity
inferredcites →https://doi.org/10.1007/bf00356889openalex-snapshot
The intranuclear states of snRNP complexes
inferredcites →https://doi.org/10.1007/bf02099850openalex-snapshot
Existence of at least three distinct Alu subfamilies
inferredcites →https://doi.org/10.1007/bf02100074openalex-snapshot
The Alu family developed through successive waves of fixation closely connected with primate lineage history
inferredcites →https://doi.org/10.1007/bf02102862openalex-snapshot
Evolution of the master Alu gene(s)
inferredcites →https://doi.org/10.1007/bf02515383openalex-snapshot
Reconstruction and analysis of human alu genes
inferredcites →https://doi.org/10.1007/s002390010240openalex-snapshot
Retroposition of the AFC Family of SINEs (Short Interspersed Repetitive Elements) Before and During the Adaptive Radiation of Cichlid Fishes in Lake Malawi and Related Inferences About Phylogeny
inferredcites →https://doi.org/10.1016/0168-9525(92)90139-uopenalex-snapshot
Master genes in mammalian repetitive DNA amplification
inferredcites →https://doi.org/10.1016/0168-9525(92)90262-3openalex-snapshot
Master genes in mammalian repetitive DNA amplification
inferredcites →https://doi.org/10.1016/0888-7543(91)90414-aopenalex-snapshot
A human-specific subfamily of Alu sequences
inferredcites →https://doi.org/10.1016/b978-0-08-094829-4.50010-6openalex-snapshot
Informed parsimonious inference of prototypical genetic sequences
inferredcites →https://doi.org/10.1016/s0168-9525(00)02093-xopenalex-snapshot
Repbase Update: a database and an electronic journal of repetitive elements
inferredcites →https://doi.org/10.1016/s0959-440x(98)80067-5openalex-snapshot
Repeats in genomic DNA: mining and meaning
inferredcites →https://doi.org/10.1038/301460c0openalex-snapshot
Ball lightning — all in the mind?
inferredcites →https://doi.org/10.1038/301460e0openalex-snapshot
Retroposons defined
inferredcites →https://doi.org/10.1038/318371a0openalex-snapshot
Upstream sequences modulate the internal promoter of the human 7SL RNA gene
inferredcites →https://doi.org/10.1038/35057062openalex-snapshot
Initial sequencing and analysis of the human genome
inferredcites →https://doi.org/10.1038/ng0903-15openalex-snapshot
Alu: a parasite's parasite?
inferredcites →https://doi.org/10.1038/ng1223openalex-snapshot
LINE-mediated retrotransposition of marked Alu sequences
inferredcites →https://doi.org/10.1038/nrg798openalex-snapshot
Alu repeats and human genomic diversity
inferredcites →https://doi.org/10.1073/pnas.2133766100openalex-snapshot
Alu elements and hominid phylogenetics
inferredcites →https://doi.org/10.1073/pnas.85.13.4770openalex-snapshot
Sources and evolution of human Alu repeated sequences.
inferredcites →https://doi.org/10.1073/pnas.85.13.4775openalex-snapshot
A fundamental division in the Alu family of repeated sequences.
inferredcites →https://doi.org/10.1073/pnas.96.18.10261openalex-snapshot
Phylogenetic relationships among cetartiodactyls based on insertions of short and long interpersed elements: Hippopotamuses are the closest extant relatives of whales
inferredcites →https://doi.org/10.1086/378594openalex-snapshot
An Alu Transposition Model for the Origin and Expansion of Human Segmental Duplications
inferredcites →https://doi.org/10.1090/s0002-9939-1956-0078686-7openalex-snapshot
On the shortest spanning subtree of a graph and the traveling salesman problem
inferredcites →https://doi.org/10.1093/bioinformatics/18.10.1374openalex-snapshot
Finding motifs in the twilight zone
inferredcites →https://doi.org/10.1093/molbev/msg204openalex-snapshot
Distinct Changes of Genomic Biases in Nucleotide Substitution at the Time of Mammalian Radiation
inferredcites →https://doi.org/10.1093/nar/17.7.2477openalex-snapshot
Sequence conservation in Alu evolution
inferredcites →https://doi.org/10.1093/nar/18.20.6019openalex-snapshot
Recently transposed Alu repeats result from multiple source genes
inferredcites →https://doi.org/10.1101/gr.2395204openalex-snapshot
De Novo Repeat Classification and Fragment Assembly
inferredcites →https://doi.org/10.1101/gr.88502openalex-snapshot
Automated De Novo Identification of Repeat Sequence Families in Sequenced Genomes
inferredcites →https://doi.org/10.1101/gr.894603openalex-snapshot
Genetic Variation Among World Populations: Inferences From 100 Alu Insertion Polymorphisms
inferredcites →https://doi.org/10.1109/tit.1982.1056489openalex-snapshot
Least squares quantization in PCM
inferredcites →https://doi.org/10.1111/j.1574-6968.1999.tb13575.xopenalex-snapshot
BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences
inferredcites →https://doi.org/10.1111/j.2517-6161.1977.tb01600.xopenalex-snapshot
Maximum Likelihood from Incomplete Data Via the EM Algorithm
inferredcites →https://doi.org/10.1126/science.1722352openalex-snapshot
Reverse Transcriptase Encoded by a Human Transposable Element
inferredcites →https://doi.org/10.1128/mcb.10.10.5424openalex-snapshot
A Transpositionally and Transcriptionally Competent Alu Subfamily
inferredcites →https://doi.org/10.1128/mcb.8.10.4566openalex-snapshot
Recently amplified Alu family members share a common parental Alu sequence.
inferredcites →https://doi.org/10.1128/mcb.8.10.4566-4569.1988openalex-snapshot
Recently Amplified Alu Family Members Share a Common Parental Alu Sequence
inferredcites →https://doi.org/10.1145/974614.974643openalex-snapshot
De novo repeat classification and fragment assembly
inferredcites →https://doi.org/10.1186/gb-2001-2-8-research0027openalex-snapshot
A clustering method for repeat analysis in DNA sequences
inferredcites →https://doi.org/10.1201/9781420050646.ptb6openalex-snapshot
Neural Networks
inferredcites →https://doi.org/10.2307/2033241openalex-snapshot
On the Shortest Spanning Subtree of a Graph and the Traveling Salesman Problem
inferredcites →https://doi.org/10.5555/93335.93346openalex-snapshot
Informed parsimonious inference of prototypical genetic sequences
inferredcites →https://doi.org/10.5860/choice.31-5500openalex-snapshot
Neural networks for pattern recognition

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.5281/zenodo.3970563openalex-extracted
Are the Available DNA Sequence Alignments and Search Tools Reliable for Alu Research?
inferred← citeshttps://doi.org/10.1002/ana.21380openalex-snapshot
Genomic investigation of α‐synuclein multiplication and parkinsonism
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Current awareness on comparative and functional genomics
inferred← citeshttps://doi.org/10.1002/evan.20283openalex-snapshot
LINEs and SINEs of primate evolution
inferred← citeshttps://doi.org/10.1002/humu.21156openalex-snapshot
Alu-repeat-induced deletions within theNCF2gene causing p67-phox-deficient chronic granulomatous disease (CGD)
inferred← citeshttps://doi.org/10.1002/jcb.21278openalex-snapshot
Most human Alu and Murine B1 repeats are unique
inferred← citeshttps://doi.org/10.1002/mgg3.1830openalex-snapshot
Easy and fast PCR‐based protocol allows characterization of breakpoints resulting from Alu/Alu‐mediated genomic rearrangements
inferred← citeshttps://doi.org/10.1007/978-1-4471-5304-7_8openalex-snapshot
Eukaryote Genomes
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Pharmacogenomics in Alzheimer's Disease
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Computational Methods for the Analysis of Primate Mobile Elements
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Human Genome
inferred← citeshttps://doi.org/10.1007/978-3-540-71681-5_14openalex-snapshot
Reconstructing the Phylogeny of Mobile Elements
inferred← citeshttps://doi.org/10.1007/978-3-642-16502-3_6openalex-snapshot
Multiple Roles of Alu-Related Noncoding RNAs
inferred← citeshttps://doi.org/10.1007/978-4-431-56603-8_5openalex-snapshot
Duplicated Genes
inferred← citeshttps://doi.org/10.1007/s00239-017-9811-yopenalex-snapshot
A Role for the Mutagenic DNA Self-Catalyzed Depurination Mechanism in the Evolution of 7SL-Derived RNAs
inferred← citeshttps://doi.org/10.1007/s00251-006-0175-5openalex-snapshot
HIGM syndrome caused by insertion of an AluYb8 element in exon 1 of the CD40LG gene
inferred← citeshttps://doi.org/10.1007/s00281-010-0224-xopenalex-snapshot
Human IRGM gene “to be or not to be”
inferred← citeshttps://doi.org/10.1007/s10142-010-0168-1openalex-snapshot
The transcript repeat element: the human Alu sequence as a component of gene networks influencing cancer
inferred← citeshttps://doi.org/10.1007/s10549-014-2946-2openalex-snapshot
Plasma DNA integrity as a biomarker for primary and metastatic breast cancer and potential marker for early diagnosis
inferred← citeshttps://doi.org/10.1007/s10709-010-9537-xopenalex-snapshot
Inactivation dates of the human and guinea pig vitamin C genes
inferred← citeshttps://doi.org/10.1007/s12016-011-8290-yopenalex-snapshot
Autoimmune Diseases and Polyamines
inferred← citeshttps://doi.org/10.1007/s12031-013-0014-8openalex-snapshot
Detection of Serum Alu Element Hypomethylation for the Diagnosis and Prognosis of Glioma
inferred← citeshttps://doi.org/10.1007/s13127-016-0279-1openalex-snapshot
The phylogenetic system of primates—character evolution in the light of a consolidated tree
inferred← citeshttps://doi.org/10.1007/s13238-015-0202-0openalex-snapshot
An intriguing RNA species—perspectives of circularized RNA
inferred← citeshttps://doi.org/10.1007/s13258-015-0370-6openalex-snapshot
Identification of transposable element-mediated deletions in 27 Korean individuals based on whole genome sequencing data
inferred← citeshttps://doi.org/10.1016/j.bbagrm.2019.194434openalex-snapshot
TDP-43 regulates transcription at protein-coding genes and Alu retrotransposons
inferred← citeshttps://doi.org/10.1016/j.braindev.2006.05.012openalex-snapshot
The first reported case of Menkes disease caused by an Alu insertion mutation
inferred← citeshttps://doi.org/10.1016/j.cancergen.2025.11.014openalex-snapshot
Multiple endocrine neoplasia type 1 syndrome due to novel Alu insertion
inferred← citeshttps://doi.org/10.1016/j.compbiolchem.2014.08.011openalex-snapshot
DNA clustering and genome complexity
inferred← citeshttps://doi.org/10.1016/j.febslet.2015.04.018openalex-snapshot
Opposite expression of CYP51A1 and its natural antisense transcript AluCYP51A1 in adenovirus type 37 infected retinal pigmented epithelial cells
inferred← citeshttps://doi.org/10.1016/j.fmre.2023.04.019openalex-snapshot
Dysregulation of circular RNAs in inflammation and cancers
inferred← citeshttps://doi.org/10.1016/j.freeradbiomed.2023.06.014openalex-snapshot
Quantitation of oxidized nuclear and mitochondrial DNA in plasma samples of patients with abdominal aortic aneurysm
inferred← citeshttps://doi.org/10.1016/j.gene.2006.09.011openalex-snapshot
Improved repeat identification and masking in Dipterans
inferred← citeshttps://doi.org/10.1016/j.gene.2007.02.028openalex-snapshot
SINEs, evolution and genome structure in the opossum
inferred← citeshttps://doi.org/10.1016/j.gene.2010.11.008openalex-snapshot
Visualization of sequence and structural features of genomes and chromosome fragments. Application to CpG islands, Alu sequences and whole genomes
inferred← citeshttps://doi.org/10.1016/j.gpb.2020.11.005openalex-snapshot
Gigantic Genomes Provide Empirical Tests of Transposable Element Dynamics Models
inferred← citeshttps://doi.org/10.1016/j.isci.2020.101345openalex-snapshot
Biosynthesis of Circular RNA ciRS-7/CDR1as Is Mediated by Mammalian-wide Interspersed Repeats
inferred← citeshttps://doi.org/10.1016/j.pop.2009.01.006openalex-snapshot
Obesity and Metabolic Disease
inferred← citeshttps://doi.org/10.1016/j.yfrne.2019.100773openalex-snapshot
Epigenetic regulation of POMC; implications for nutritional programming, obesity and metabolic disease
inferred← citeshttps://doi.org/10.1021/cr0683008openalex-snapshot
Genome Assembly, Rearrangement, and Repeats
inferred← citeshttps://doi.org/10.1021/pr050133popenalex-snapshot
Detection of Hypothetical Proteins in Human Fetal Perireticular Nucleus
inferred← citeshttps://doi.org/10.1038/emboj.2008.94openalex-snapshot
Alu element‐mediated gene silencing
inferred← citeshttps://doi.org/10.1038/hgv.2018.3openalex-snapshot
Identification of mutations in HEXA and HEXB in Sandhoff and Tay-Sachs diseases: a new large deletion caused by Alu elements in HEXA
inferred← citeshttps://doi.org/10.1038/ncomms5943openalex-snapshot
Caste-specific RNA editomes in the leaf-cutting ant Acromyrmex echinatior
inferred← citeshttps://doi.org/10.1038/nrg2640openalex-snapshot
The impact of retrotransposons on human genome evolution
inferred← citeshttps://doi.org/10.1038/s10038-019-0569-5openalex-snapshot
A 12-kb structural variation in progressive myoclonic epilepsy was newly identified by long-read whole-genome sequencing
inferred← citeshttps://doi.org/10.1038/s41467-024-53620-8openalex-snapshot
A Catalogue of Structural Variation across Ancestrally Diverse Asian Genomes
inferred← citeshttps://doi.org/10.1038/s41576-018-0050-xopenalex-snapshot
Computational tools to unmask transposable elements
inferred← citeshttps://doi.org/10.1038/s41586-025-08922-2openalex-snapshot
Human de novo mutation rates from a four-generation pedigree reference
inferred← citeshttps://doi.org/10.1038/s41587-020-0582-4openalex-snapshot
Automated assembly of centromeres from ultra-long error-prone reads
inferred← citeshttps://doi.org/10.1038/s41598-017-13402-3openalex-snapshot
Highly sensitive and specific Alu-based quantification of human cells among rodent cells
inferred← citeshttps://doi.org/10.1038/s41598-017-18528-yopenalex-snapshot
Mycobacterium tuberculosis Exploits a Molecular Off Switch of the Immune System for Intracellular Survival
inferred← citeshttps://doi.org/10.1038/s41598-019-43403-3openalex-snapshot
Recognition of 3′-end L1, Alu, processed pseudogenes, and mRNA stem-loops in the human genome using sequence-based and structure-based machine-learning models
inferred← citeshttps://doi.org/10.1038/s42003-018-0237-xopenalex-snapshot
Z-DNA and Z-RNA in human disease
inferred← citeshttps://doi.org/10.1038/s42003-023-05234-xopenalex-snapshot
Young SINEs in pig genomes impact gene regulation, genetic diversity, and complex traits
inferred← citeshttps://doi.org/10.1038/srep15644openalex-snapshot
Characterizing novel endogenous retroviruses from genetic variation inferred from short sequence reads
inferred← citeshttps://doi.org/10.1038/srep30851openalex-snapshot
Evolutionary dynamics of selfish DNA explains the abundance distribution of genomic subsequences
inferred← citeshttps://doi.org/10.1073/pnas.1921719117openalex-snapshot
DNA methylation enables transposable element-driven genome expansion
inferred← citeshttps://doi.org/10.1073/pnas.2210150119openalex-snapshot
ADAR regulates APOL1 via A-to-I RNA editing by inhibition of MDA5 activation in a paradoxical biological circuit
inferred← citeshttps://doi.org/10.1074/jbc.m116.719971openalex-snapshot
Preferential Protection of Genetic Fidelity within Open Chromatin by the Mismatch Repair Machinery
inferred← citeshttps://doi.org/10.1080/01485010701426422openalex-snapshot
Evidence of Alu and B1 Expression in dbEST
inferred← citeshttps://doi.org/10.1080/10020070612331343258openalex-snapshot
Identification of novel SINEs from Cyprinidae and their evolutionary significance
inferred← citeshttps://doi.org/10.1080/15476286.2017.1397261openalex-snapshot
DDX5/p68 associated lncRNA LOC284454 is differentially expressed in human cancers and modulates gene expression
inferred← citeshttps://doi.org/10.1080/15476286.2018.1429880openalex-snapshot
Alu exaptation enriches the human transcriptome by introducing new gene ends
inferred← citeshttps://doi.org/10.1080/15476286.2021.1989201openalex-snapshot
Alu RNA and their roles in human disease states
inferred← citeshttps://doi.org/10.1080/15476286.2024.2430817openalex-snapshot
The role of SRP9/SRP14 in regulating Alu RNA
inferred← citeshttps://doi.org/10.1080/15592294.2016.1183856openalex-snapshot
Detection of differential DNA methylation in repetitive DNA of mice and humans perinatally exposed to bisphenol A
inferred← citeshttps://doi.org/10.1080/17501911.2025.2501520openalex-snapshot
Regulatory roles of transposable elements on autism molecular neuropathology
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780195306750.001.0001openalex-snapshot
Darwinian Detectives
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780195306750.002.0003openalex-snapshot
Copyright Page
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780195306750.002.0004openalex-snapshot
Dedication
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780195306750.002.0005openalex-snapshot
Foreword
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780195306750.002.0006openalex-snapshot
Preface
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780195306750.003.0001openalex-snapshot
The Baby with the Baboon Heart
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780195306750.003.0002openalex-snapshot
Why Intelligent Design Is Not Science
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780195306750.003.0003openalex-snapshot
Negative Selection and the Neutral Theory of Molecular Evolution
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780195306750.003.0004openalex-snapshot
Detecting Positive Selection
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780195306750.003.0005openalex-snapshot
Balancing Selection and Disease
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780195306750.003.0006openalex-snapshot
Finding Our Roots
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780195306750.003.0007openalex-snapshot
Who Were the Neanderthals?
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780195306750.003.0008openalex-snapshot
Are We the Third Chimpanzee?
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780195306750.003.0009openalex-snapshot
What Are the Genetic Differences That Made Us Human?
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780195306750.003.0010openalex-snapshot
Clicks, Genes, and Languages
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780195306750.003.0011openalex-snapshot
Who Let the Dogs in?
inferred← citeshttps://doi.org/10.1093/acprof:oso/9780195306750.003.0012openalex-snapshot
Size Matters
inferred← citeshttps://doi.org/10.1093/bioinformatics/bti1018openalex-snapshot
De novo identification of repeat families in large genomes
inferred← citeshttps://doi.org/10.1093/bioinformatics/btq368openalex-snapshot
Parsimony and likelihood reconstruction of human segmental duplications
inferred← citeshttps://doi.org/10.1093/bioinformatics/btv238openalex-snapshot
IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis
inferred← citeshttps://doi.org/10.1093/g3journal/jkac054openalex-snapshot
RNA transcription and degradation of Alu retrotransposons depends on sequence features and evolutionary history
inferred← citeshttps://doi.org/10.1093/gbe/evp014openalex-snapshot
Calibration of Mutation Rates Reveals Diverse Subfamily Structure of Galliform CR1 Repeats
inferred← citeshttps://doi.org/10.1093/gbe/evs103openalex-snapshot
Slow DNA Loss in the Gigantic Genomes of Salamanders
inferred← citeshttps://doi.org/10.1093/gbe/evu143openalex-snapshot
Hellbender Genome Sequences Shed Light on Genomic Expansion at the Base of Crown Salamanders
inferred← citeshttps://doi.org/10.1093/gbe/evv167openalex-snapshot
Sequence Analysis and Characterization of Active HumanAlusubfamilies Based on the 1000 Genomes Pilot Project
inferred← citeshttps://doi.org/10.1093/gpbjnl/qzaf061openalex-snapshot
Deciphering Complex Interactions Between LTR Retrotransposons and Three Papaver Species Using LTR_Stream
inferred← citeshttps://doi.org/10.1093/jhered/esm017openalex-snapshot
Elevated Basal Slippage Mutation Rates among the Canidae
inferred← citeshttps://doi.org/10.1093/molbev/msn094openalex-snapshot
Molecular Evolution of a Primate-Specific microRNA Family
inferred← citeshttps://doi.org/10.1093/molbev/msr141openalex-snapshot
Human piRNAs Are Under Selection in Africans and Repress Transposable Elements
inferred← citeshttps://doi.org/10.1093/molbev/msz001openalex-snapshot
Evolution of an X-Linked miRNA Family Predominantly Expressed in Mammalian Male Germ Cells
inferred← citeshttps://doi.org/10.1093/mutage/gel022openalex-snapshot
Detection of Alu sequences and mtDNA in comets using padlock probes
inferred← citeshttps://doi.org/10.1093/nar/gkm1105openalex-snapshot
Genome-wide tracking of unmethylated DNA Alu repeats in normal and cancer cells
inferred← citeshttps://doi.org/10.1093/nar/gkp1094openalex-snapshot
The most frequent short sequences in non-coding DNA
inferred← citeshttps://doi.org/10.1093/nar/gks354openalex-snapshot
Shape-based alignment of genomic landscapes in multi-scale resolution
inferred← citeshttps://doi.org/10.1093/sysbio/syx088openalex-snapshot
A Two-State Model of Tree Evolution and Its Applications to Alu Retrotransposition
inferred← citeshttps://doi.org/10.1100/2012/931386openalex-snapshot
Evolution of the C-Type Lectin-Like Receptor Genes of the DECTIN-1 Cluster in the NK Gene Complex
inferred← citeshttps://doi.org/10.1101/094326openalex-snapshot
Strong and Fluctuating Sequence Constraints Drive Alu_ Evolution
inferred← citeshttps://doi.org/10.1101/123208openalex-snapshot
Transcription activation of early human development suggests DUX4 as an embryonic regulator
inferred← citeshttps://doi.org/10.1101/gr.083972.108openalex-snapshot
Comparative analysis of Alu repeats in primate genomes
inferred← citeshttps://doi.org/10.1101/gr.091546.109openalex-snapshot
Comparative genomics of protoploid Saccharomycetaceae
inferred← citeshttps://doi.org/10.1101/gr.115956.110openalex-snapshot
Alu repeat discovery and characterization within human genomes
inferred← citeshttps://doi.org/10.1101/gr.203992.116openalex-snapshot
Identification of the long, edited dsRNAome of LPS-stimulated immune cells
inferred← citeshttps://doi.org/10.1101/gr.277694.123openalex-snapshot
Unraveling the palindromic and nonpalindromic motifs of retroviral integration site sequences by statistical mixture models
inferred← citeshttps://doi.org/10.1101/gr.3492605openalex-snapshot
Under the genomic radar: The Stealth model of Alu amplification
inferred← citeshttps://doi.org/10.1101/gr.3493405openalex-snapshot
Orthologous repeats and mammalian phylogenetic inference
inferred← citeshttps://doi.org/10.1101/gr.5826307openalex-snapshot
The evolutionary history of human DNA transposons: Evidence for intense activity in the primate lineage
inferred← citeshttps://doi.org/10.1103/physreve.74.021913openalex-snapshot
Informational structure of two closely related eukaryotic genomes
inferred← citeshttps://doi.org/10.1103/physreve.78.061912openalex-snapshot
Duplication count distributions in DNA sequences
inferred← citeshttps://doi.org/10.1103/physreve.89.052105openalex-snapshot
DNA viewed as an out-of-equilibrium structure
inferred← citeshttps://doi.org/10.1109/bibe.2006.253337openalex-snapshot
Parsimony approach to test the Evolving Master Gene hypothesis for human Alu repeats
inferred← citeshttps://doi.org/10.1109/iccabs.2015.7344724openalex-snapshot
Identification of cancer-specific motifs in mimotope profiles of serum antibody repertoire
inferred← citeshttps://doi.org/10.1111/1755-0998.13030openalex-snapshot
DeviaTE: Assembly‐free analysis and visualization of mobile genetic element composition
inferred← citeshttps://doi.org/10.1111/age.13277openalex-snapshot
Whole‐genome identification of transposable elements reveals the equine repetitive element insertion polymorphism in Chinese horses
inferred← citeshttps://doi.org/10.1111/j.1365-3083.2010.02433.xopenalex-snapshot
Evolutionary Development and Expression Pattern of the Myeloid Lectin‐Like Receptor Gene Family Encoded Within the NK Gene Complex
inferred← citeshttps://doi.org/10.1111/j.1399-0004.2011.01782.xopenalex-snapshot
Aarskog‐Scott syndrome: first report of a duplication in the FGD1 gene
inferred← citeshttps://doi.org/10.1111/j.1538-7836.2010.04040.xopenalex-snapshot
Characterization of duplication breakpoints in the factor VIII gene
inferred← citeshttps://doi.org/10.1111/tpj.13676openalex-snapshot
Evolutionary modes of emergence of short interspersed nuclear element ( SINE ) families in grasses
inferred← citeshttps://doi.org/10.1111/tpj.14721openalex-snapshot
Divergence of 3′ ends as a driver of short interspersed nuclear element (SINE) evolution in the Salicaceae
inferred← citeshttps://doi.org/10.1124/dmd.113.056630openalex-snapshot
Polymorphisms and Haplotypes of the UDP-Glucuronosyltransferase 2B7 Gene Promoter
inferred← citeshttps://doi.org/10.1124/jpet.112.192658openalex-snapshot
Quantification of Hepatic UDP Glucuronosyltransferase 1A Splice Variant Expression and Correlation of UDP Glucuronosyltransferase 1A1 Variant Expression with Glucuronidation Activity
inferred← citeshttps://doi.org/10.1126/sciadv.1701256openalex-snapshot
Integrating networks and comparative genomics reveals retroelement proliferation dynamics in hominid genomes
inferred← citeshttps://doi.org/10.1134/s0026893308040213openalex-snapshot
A new polymorphic retroelement database (PRED) for the human genome
inferred← citeshttps://doi.org/10.1139/g10-043openalex-snapshot
Comparative genomic analysis of the false killer whale (Pseudorca crassidens) LMBR1 locus
inferred← citeshttps://doi.org/10.1142/s0219720008003527openalex-snapshot
MANGO: MULTIPLE ALIGNMENT WITH N GAPPED OLIGOS
inferred← citeshttps://doi.org/10.1161/jaha.117.007686openalex-snapshot
Liver X Receptor–Binding DNA Motif Associated With Atherosclerosis‐Specific DNA Methylation Profiles of Alu Elements and Neighboring CpG Islands
inferred← citeshttps://doi.org/10.1167/tvst.9.8.1openalex-snapshot
Lamivudine InhibitsAluRNA-induced Retinal Pigment Epithelium Degeneration via Anti-inflammatory and Anti-senescence Activities
inferred← citeshttps://doi.org/10.1186/1471-2105-7-427openalex-snapshot
MICA: desktop software for comprehensive searching of DNA databases
inferred← citeshttps://doi.org/10.1186/1471-2148-7-102openalex-snapshot
Analysis of the features and source gene composition of the AluYg6 subfamily of human retrotransposons
inferred← citeshttps://doi.org/10.1186/1471-2148-9-102openalex-snapshot
Source gene composition and gene conversion of the AluYh and AluYi lineages of retrotransposons
inferred← citeshttps://doi.org/10.1186/1471-2164-12-564openalex-snapshot
AluScan: a method for genome-wide scanning of sequence and structure variations in the human genome
inferred← citeshttps://doi.org/10.1186/1471-2164-13-172openalex-snapshot
Expansion of CORE-SINEs in the genome of the Tasmanian devil
inferred← citeshttps://doi.org/10.1186/1471-2164-14-325openalex-snapshot
A gene expression restriction network mediated by sense and antisense Alu sequences located on protein-coding messenger RNAs
inferred← citeshttps://doi.org/10.1186/1471-2164-8-23openalex-snapshot
Widespread Alu repeat-driven expansion of consensus DR2 retinoic acid response elements during primate evolution
inferred← citeshttps://doi.org/10.1186/1471-2407-10-44openalex-snapshot
Methylation status of individual CpG sites within Alu elements in the human genome and Alu hypomethylation in gastric carcinomas
inferred← citeshttps://doi.org/10.1186/1745-6150-6-2openalex-snapshot
Impact of Alu repeats on the evolution of human p53 binding sites
inferred← citeshttps://doi.org/10.1186/1759-8753-3-8openalex-snapshot
Orangutan Alu quiescence reveals possible source element: support for ancient backseat drivers
inferred← citeshttps://doi.org/10.1186/1759-8753-4-21openalex-snapshot
Transposable element evolution in Heliconius suggests genome diversity within Lepidoptera
inferred← citeshttps://doi.org/10.1186/1759-8753-4-25openalex-snapshot
Identification of three new Alu Yb subfamilies by source tracking of recently integrated Alu Yb elements
inferred← citeshttps://doi.org/10.1186/1759-8753-4-26openalex-snapshot
Analysis of western lowland gorilla (Gorilla gorilla gorilla) specific Alu repeats
inferred← citeshttps://doi.org/10.1186/gb-2006-7-1-r7openalex-snapshot
Identifying repeat domains in large genomes
inferred← citeshttps://doi.org/10.1186/s12864-016-3344-4openalex-snapshot
Conserved 3′ UTR stem-loop structure in L1 and Alu transposons in human genome: possible role in retrotransposition
inferred← citeshttps://doi.org/10.1186/s13059-016-0876-5openalex-snapshot
The contribution of Alu exons to the human proteome
inferred← citeshttps://doi.org/10.1186/s13071-023-05884-0openalex-snapshot
Efficiency of mitochondrial genes and nuclear Alu elements in detecting human DNA in blood meals of Anopheles stephensi mosquitoes: a time-course study
inferred← citeshttps://doi.org/10.1186/s13100-015-0038-4openalex-snapshot
Differential SINE evolution in vesper and non-vesper bats
inferred← citeshttps://doi.org/10.1186/s13100-017-0107-yopenalex-snapshot
Human transposable elements in Repbase: genomic footprints from fish to humans
inferred← citeshttps://doi.org/10.1186/s13100-018-0135-2openalex-snapshot
Phylogenomic analysis reveals splicing as a mechanism of parallel evolution of non-canonical SVAs in hominine primates
inferred← citeshttps://doi.org/10.1186/s13100-020-00230-yopenalex-snapshot
The Dfam community resource of transposable element families, sequence models, and genome annotations
inferred← citeshttps://doi.org/10.1186/s13100-021-00232-4openalex-snapshot
Transposable element subfamily annotation has a reproducibility problem
inferred← citeshttps://doi.org/10.1186/s13100-025-00389-2openalex-snapshot
ColabCuraTE: an easy-to-use, web-based pipeline for the manual curation of transposable elements
inferred← citeshttps://doi.org/10.1210/me.2009-0048openalex-snapshot
ALU Repeats in Promoters Are Position-Dependent Co-Response Elements (coRE) that Enhance or Repress Transcription by Dimeric and Monomeric Progesterone Receptors
inferred← citeshttps://doi.org/10.1261/rna.040444.113openalex-snapshot
RNAs nonspecifically inhibit RNA polymerase II by preventing binding to the DNA template
inferred← citeshttps://doi.org/10.1261/rna.079649.123openalex-snapshot
Nuclear SRP9/SRP14 heterodimer transcriptionally regulates 7SL and BC200 RNA expression
inferred← citeshttps://doi.org/10.1261/rna.080359.124openalex-snapshot
Alu RNA pseudoknot alterations influence SRP9/SRP14 association
inferred← citeshttps://doi.org/10.1371/journal.pgen.0030184openalex-snapshot
Alu Recombination-Mediated Structural Deletions in the Chimpanzee Genome
inferred← citeshttps://doi.org/10.1371/journal.pgen.1000225openalex-snapshot
Diverse Splicing Patterns of Exonized Alu Elements in Human Tissues
inferred← citeshttps://doi.org/10.1371/journal.pgen.1000469openalex-snapshot
Repair-Mediated Duplication by Capture of Proximal Chromosomal DNA Has Shaped Vertebrate Genome Evolution
inferred← citeshttps://doi.org/10.1371/journal.pgen.1004482openalex-snapshot
Inference of Transposable Element Ancestry
inferred← citeshttps://doi.org/10.1371/journal.pone.0004941openalex-snapshot
Genome-Wide Hypomethylation in Head and Neck Cancer Is More Pronounced in HPV-Negative Tumors and Is Associated with Genomic Instability
inferred← citeshttps://doi.org/10.1371/journal.pone.0142614openalex-snapshot
Efficient In Silico Identification of a Common Insertion in the MAK Gene which Causes Retinitis Pigmentosa
inferred← citeshttps://doi.org/10.1371/journal.pone.0316394openalex-snapshot
An appropriate DNA input for bisulfite conversion reveals LINE-1 and Alu hypermethylation in tissues and circulating cell-free DNA from cancers
inferred← citeshttps://doi.org/10.1517/14656566.6.12.1967openalex-snapshot
Pharmacogenomics and therapeutic prospects in Alzheimer’s disease
inferred← citeshttps://doi.org/10.1534/genetics.107.070805openalex-snapshot
The Genomic Landscape of Short Insertion and Deletion Polymorphisms in the Chicken (Gallus gallus) Genome: A High Frequency of Deletions in Tandem Duplicates
inferred← citeshttps://doi.org/10.18632/oncotarget.4671openalex-snapshot
Targeted or whole genome sequencing of formalin fixed tissue samples: potential applications in cancer genomics
inferred← citeshttps://doi.org/10.2144/000113494openalex-snapshot
Sensitive Measurement of Unmethylated Repeat DNA Sequences by End-Specific PCR
inferred← citeshttps://doi.org/10.31390/gradschool_dissertations.1572openalex-snapshot
Retrotransposon mediated genomic variation in the human and chimpanzee lineages
inferred← citeshttps://doi.org/10.31390/gradschool_dissertations.2016openalex-snapshot
SVA elements: hominid specific retrotransposons
inferred← citeshttps://doi.org/10.31390/gradschool_dissertations.3287openalex-snapshot
Alu elements and primate genomics
inferred← citeshttps://doi.org/10.31390/gradschool_dissertations.4023openalex-snapshot
Mobile elements and primate genomic variation
inferred← citeshttps://doi.org/10.31390/gradschool_dissertations.807openalex-snapshot
Retrotransposon mediated genomic fluidity in the human and chimpanzee lineages
inferred← citeshttps://doi.org/10.3233/978-1-60750-073-5-311openalex-snapshot
Parallel Data Mining from Multicore to Cloudy Grids
inferred← citeshttps://doi.org/10.3324/haematol.2019.228478openalex-snapshot
Analysis of retrotransposon subfamily DNA methylation reveals novel early epigenetic changes in chronic lymphocytic leukemia
inferred← citeshttps://doi.org/10.3390/d9040048openalex-snapshot
Duplex Alu Screening for Degraded DNA of Skeletal Human Remains
inferred← citeshttps://doi.org/10.3390/genes13040709openalex-snapshot
Methodologies for the De novo Discovery of Transposable Element Families
inferred← citeshttps://doi.org/10.3390/genes14071351openalex-snapshot
Occurrence of L1M Elements in Chromosomal Rearrangements Associated to Chronic Myeloid Leukemia (CML): Insights from Patient-Specific Breakpoints Characterization
inferred← citeshttps://doi.org/10.3390/ijms26104751openalex-snapshot
Modeling the Copy Number of HSATII Repeats in Human Pericentromere
inferred← citeshttps://doi.org/10.34626/15md-sp14openalex-snapshot
Consequences of Alu-mediated recombination events
inferred← citeshttps://doi.org/10.4018/978-1-4666-3604-0.ch016openalex-snapshot
Data Intensive Computing for Bioinformatics
inferred← citeshttps://doi.org/10.4018/978-1-61520-971-2.ch010openalex-snapshot
Data Intensive Computing for Bioinformatics
inferred← citeshttps://doi.org/10.4161/epi.20221openalex-snapshot
Different measures of “genome-wide” DNA methylation exhibit unique properties in placental and somatic tissues
inferred← citeshttps://doi.org/10.4161/mge.21470openalex-snapshot
Alu elements and human common diseases like obesity
inferred← citeshttps://doi.org/10.4161/mge.25675openalex-snapshot
Identification and characterization of MGEs and their insertion sites in thegorillagenome
inferred← citeshttps://doi.org/10.5812/ircmj.21633openalex-snapshot
First Case Report of EX3del4765 Mutation in PAH Gene in Asian Population
inferred← citeshttps://doi.org/10.6084/m9.figshare.13565922openalex-snapshot
Additional file 1 of The Dfam community resource of transposable element families, sequence models, and genome annotations
inferred← citeshttps://doi.org/10.6084/m9.figshare.13565925openalex-snapshot
Additional file 2 of The Dfam community resource of transposable element families, sequence models, and genome annotations
inferred← citeshttps://doi.org/10.6084/m9.figshare.13565931openalex-snapshot
Additional file 4 of The Dfam community resource of transposable element families, sequence models, and genome annotations
inferred← citeshttps://doi.org/10.70675/90dfd1eczcfebz4ccfz9115z46efa92c2877openalex-snapshot
Étude des éléments cis-régulateurs à différentes échelles : approches fondamentales à appliquer
inferred← citeshttps://doi.org/10.70675/dd1ee9e6z52fez46d7za781ze5573e9c1277openalex-snapshot
Structure de la chromatine et éléments transposables : une approche évolutive
inferred← citeshttps://doi.org/10.7301/z04j0cbvopenalex-snapshot
Algorithms for Analyzing Human Genome Rearrangements
inferred← citeshttps://doi.org/10.7554/elife.53868openalex-snapshot
RNA-guided retargeting of Sleeping Beauty transposition in human cells
inferred← citeshttps://doi.org/10.9735/0975-3087.3.1.142-147openalex-snapshot
INVESTIGATING THE MALE-DRIVEN EVOLUTION HYPOTHESIS USING GENOME WIDE POINT MUTATIONS IN HUMAN ALU REPEATS
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