Cargando…

Machine learning reveals bilateral distribution of somatic L1 insertions in human neurons and glia

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 insertion (MEIs) presents a difficult signal-to-noise problem. Using...

Descripción completa

Detalles Bibliográficos
Autores principales:	Zhu, Xiaowei, Zhou, Bo, Pattni, Reenal, Gleason, Kelly, Tan, Chunfeng, Kalinowski, Agnieszka, Sloan, Steven, Fiston-Lavier, Anna-Sophie, Mariani, Jessica, Petrov, Dmitri, Barres, Ben A., Duncan, Laramie, Abyzov, Alexej, Vogel, Hannes, Moran, John V., Vaccarino, Flora M., Tamminga, Carol A., Levinson, Douglas F., Urban, Alexander E.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	2021
Materias:	Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8806165/ https://www.ncbi.nlm.nih.gov/pubmed/33432196 http://dx.doi.org/10.1038/s41593-020-00767-4

Ejemplares similares

One thousand somatic SNVs per skin fibroblast cell set baseline of mosaic mutational load with patterns that suggest proliferative origin
por: Abyzov, Alexej, et al.
Publicado: (2017)

Somatic genomic mosaicism in the brain during aging: Scratching the surface
por: Bae, Taejeong, et al.
Publicado: (2022)

SCELLECTOR: ranking amplification bias in single cells using shallow sequencing
por: Sarangi, Vivekananda, et al.
Publicado: (2020)

T-lex: a program for fast and accurate assessment of transposable element presence using next-generation sequencing data
por: Fiston-Lavier, Anna-Sophie, et al.
Publicado: (2011)

T-lex2: genotyping, frequency estimation and re-annotation of transposable elements using single or pooled next-generation sequencing data
por: Fiston-Lavier, Anna-Sophie, et al.
Publicado: (2015)

All(2): A tool for selecting mosaic mutations from comprehensive multi-cell comparisons
por: Sarangi, Vivekananda, et al.
Publicado: (2022)

Correction: All(2): A tool for selecting mosaic mutations from comprehensive multi-cell comparisons
por: Sarangi, Vivekananda, et al.
Publicado: (2022)

Characterization of enhancer activity in early human neurodevelopment using Massively parallel reporter assay (MPRA) and forebrain organoids
por: Capauto, Davide, et al.
Publicado: (2023)

Haplotype-resolved and integrated genome analysis of the cancer cell line HepG2
por: Zhou, Bo, et al.
Publicado: (2019)

Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562
por: Zhou, Bo, et al.
Publicado: (2019)

Complex mosaic structural variations in human fetal brains
por: Sekar, Shobana, et al.
Publicado: (2020)

Somatic copy-number mosaicism in human skin revealed by induced pluripotent stem cells
por: Abyzov, Alexej, et al.
Publicado: (2012)

Extensive and deep sequencing of the Venter/HuRef genome for developing and benchmarking genome analysis tools
por: Zhou, Bo, et al.
Publicado: (2018)

Comprehensive performance comparison of high-resolution array platforms for genome-wide Copy Number Variation (CNV) analysis in humans
por: Haraksingh, Rajini R., et al.
Publicado: (2017)

1q21.1 microduplication: large verbal–nonverbal performance discrepancy and ddPCR assays of HYDIN/HYDIN2 copy number
por: Xavier, Jean, et al.
Publicado: (2018)

BREC: an R package/Shiny app for automatically identifying heterochromatin boundaries and estimating local recombination rates along chromosomes
por: Mansour, Yasmine, et al.
Publicado: (2021)

Efficient reconstruction of cell lineage trees for cell ancestry and cancer
por: Jang, Yeongjun, et al.
Publicado: (2023)

Neonatal loss of FGFR2 in astroglial cells affects locomotion, sociability, working memory, and glia-neuron interactions in mice
por: Stevens, Hanna E., et al.
Publicado: (2023)

Increased activation product of complement 4 protein in plasma of individuals with schizophrenia
por: Kalinowski, Agnieszka, et al.
Publicado: (2021)

PlasForest: a homology-based random forest classifier for plasmid detection in genomic datasets
por: Pradier, Léa, et al.
Publicado: (2021)

Illumina TruSeq Synthetic Long-Reads Empower De Novo Assembly and Resolve Complex, Highly-Repetitive Transposable Elements
por: McCoy, Rajiv C., et al.
Publicado: (2014)

AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision
por: Abyzov, Alexej, et al.
Publicado: (2011)

Elevated variant density around SV breakpoints in germline lineage lends support to error-prone replication hypothesis
por: Dhokarh, Dhananjay, et al.
Publicado: (2016)

Chromatin organization modulates the origin of heritable structural variations in human genome
por: Roychowdhury, Tanmoy, et al.
Publicado: (2019)

LongAGE: defining breakpoints of genomic structural variants through optimal and memory efficient alignments of long reads
por: Tran, Quang, et al.
Publicado: (2020)

Genome-Wide Mapping of Copy Number Variation in Humans: Comparative Analysis of High Resolution Array Platforms
por: Haraksingh, Rajini R., et al.
Publicado: (2011)

A comprehensive analysis of non-sequential alignments between all protein structures
por: Abyzov, Alexej, et al.
Publicado: (2007)

The somatic piRNA pathway controls germline transposition over generations
por: Barckmann, Bridlin, et al.
Publicado: (2018)

Understanding genome structural variations
por: Abyzov, Alexej, et al.
Publicado: (2015)

TOPOFIT-DB, a database of protein structural alignments based on the TOPOFIT method
por: Leslin, Chesley M., et al.
Publicado: (2007)

Stress response, behavior, and development are shaped by transposable element-induced mutations in Drosophila
por: Rech, Gabriel E., et al.
Publicado: (2019)

Ten simple rules for switching from face-to-face to remote conference: An opportunity to estimate the reduction in GHG emissions
por: Guignon, Valentin, et al.
Publicado: (2021)

Structure SNP (StSNP): a web server for mapping and modeling nsSNPs on protein structures with linkage to metabolic pathways
por: Uzun, Alper, et al.
Publicado: (2007)

Landscape and variation of novel retroduplications in 26 human populations
por: Zhang, Yan, et al.
Publicado: (2017)

Growing Glia: Cultivating Human Stem Cell Models of Gliogenesis in Health and Disease
por: Lanjewar, Samantha N., et al.
Publicado: (2021)

Comprehensive identification of somatic nucleotide variants in human brain tissue
por: Wang, Yifan, et al.
Publicado: (2021)

Integrated functional genomic analyses of Klinefelter and Turner syndromes reveal global network effects of altered X chromosome dosage
por: Zhang, Xianglong, et al.
Publicado: (2020)

An AP Endonuclease 1–DNA Polymerase β Complex: Theoretical Prediction of Interacting Surfaces
por: Abyzov, Alexej, et al.
Publicado: (2008)

CNVpytor: a tool for copy number variation detection and analysis from read depth and allele imbalance in whole-genome sequencing
por: Suvakov, Milovan, et al.
Publicado: (2021)

TrEMOLO: accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches
por: Mohamed, Mourdas, et al.
Publicado: (2023)

Cannot write session to /tmp/vufind_sessions/sess_c7cq16nlm5rredm8tut93rh21t