AIMC Topic: Long Interspersed Nucleotide Elements

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An appropriate DNA input for bisulfite conversion reveals LINE-1 and Alu hypermethylation in tissues and circulating cell-free DNA from cancers.

PloS one Dec 30, 2024
The autonomous and active Long-Interspersed Element-1 (LINE-1, L1) and the non-autonomous Alu retrotransposon elements, contributing to 30% of the human genome, are the most abundant repeated sequences. With more than 90% of their sequences being met...
Sulfites Cell-Free Nucleic Acids Alu Elements Female Humans Breast Neoplasms Male DNA Methylation Neoplasms Long Interspersed Nucleotide Elements
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SquiggleNet: real-time, direct classification of nanopore signals.

Genome biology Oct 27, 2021
We present SquiggleNet, the first deep-learning model that can classify nanopore reads directly from their electrical signals. SquiggleNet operates faster than DNA passes through the pore, allowing real-time classification and read ejection. Using 1 ...
Deep Learning DNA, Bacterial Humans Metagenome Nanopore Sequencing Long Interspersed Nucleotide Elements Respiratory System
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Machine learning reveals bilateral distribution of somatic L1 insertions in human neurons and glia.

Nature neuroscience Jan 11, 2021
Retrotransposons can cause somatic genome variation in the human nervous system, which is hypothesized to have relevance to brain development and neuropsychiatric disease. However, the detection of individual somatic mobile element insertions present...
Adult Long Interspersed Nucleotide Elements Female Schizophrenia High-Throughput Nucleotide Sequencing Adaptor Proteins, Signal Transducing Neurons Humans Machine Learning Mental Disorders Pregnancy Neuroglia Cation Transport Proteins Embryonic Development Retroelements Genome Mutagenesis, Insertional HeLa Cells
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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.

Scientific reports May 10, 2019
The role of 3'-end stem-loops in retrotransposition was experimentally demonstrated for transposons of various species, where LINE-SINE retrotransposons share the same 3'-end sequences, containing a stem-loop. We have discovered that 62-68% of proces...
Pseudogenes 3' Untranslated Regions Genome, Human RNA, Messenger Long Interspersed Nucleotide Elements Alu Elements Area Under Curve Machine Learning ROC Curve Humans
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Attribute selection and model evaluation for the maternal and paternal imprinted genes in bovine (Bos Taurus) using supervised machine learning algorithms.

Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie Jan 29, 2019
Imprinted genes display biased expression of paternal and maternal alleles in mammals. They are marked through epigenetic process during gametogenesis. Characterization of imprinted genes has expanded our understanding of the regulation and function ...
Genomic Imprinting Selection, Genetic Cattle Maternal Inheritance Humans Paternal Inheritance Supervised Machine Learning Polymorphism, Single Nucleotide Long Interspersed Nucleotide Elements Animals Alleles
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