AIMC Topic: DNA Repair

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Extrachromosomal circular DNA drives dynamic genome plasticity: emerging roles in disease progression and clinical potential.

Theranostics May 25, 2025
Extrachromosomal circular DNA (eccDNA) has emerged as a dynamic and versatile genomic element with key roles in physiological regulation and disease pathology. This review synthesizes current knowledge on eccDNA, covering its classification, biogenes...
Neoplasms Disease Progression DNA Repair DNA, Circular Humans Animals
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Low-pass whole genome sequencing of circulating tumor cells to evaluate chromosomal instability in triple-negative breast cancer.

Scientific reports Sep 3, 2024
Chromosomal Instability (CIN) is a common and evolving feature in breast cancer. Large-scale Transitions (LSTs), defined as chromosomal breakages leading to gains or losses of at least 10 Mb, have recently emerged as a metric of CIN due to their stan...
Neoplastic Cells, Circulating Whole Genome Sequencing Feasibility Studies Humans DNA Repair Predictive Learning Models Machine Learning Triple Negative Breast Neoplasms Chromosomal Instability Female Cell Proliferation Reproducibility of Results DNA Copy Number Variations Cell Line, Tumor Area Under Curve
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High-confidence cancer patient stratification through multiomics investigation of DNA repair disorders.

Cell death & disease Nov 26, 2022
Multiple cancer types have limited targeted therapeutic options, in part due to incomplete understanding of the molecular processes underlying tumorigenesis and significant intra- and inter-tumor heterogeneity. Identification of novel molecular bioma...
Sarcoma DNA Repair Centrioles Humans Artificial Intelligence Carcinogenesis
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DrABC: deep learning accurately predicts germline pathogenic mutation status in breast cancer patients based on phenotype data.

Genome medicine Feb 25, 2022
BACKGROUND: Identifying breast cancer patients with DNA repair pathway-related germline pathogenic variants (GPVs) is important for effectively employing systemic treatment strategies and risk-reducing interventions. However, current criteria and ris...
Deep Learning Genetic Predisposition to Disease Mutation DNA Repair Humans Phenotype Female Breast Neoplasms Germ Cells Germ-Line Mutation BRCA1 Protein BRCA2 Protein
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Computed structures of core eukaryotic protein complexes.

Science (New York, N.Y.) Dec 10, 2021
Protein-protein interactions play critical roles in biology, but the structures of many eukaryotic protein complexes are unknown, and there are likely many interactions not yet identified. We take advantage of advances in proteome-wide amino acid coe...
Acyltransferases Homologous Recombination Chromosome Segregation Ligases Protein Biosynthesis Ribosomes Multiprotein Complexes Evolution, Molecular Models, Molecular Protein Conformation Saccharomyces cerevisiae Ubiquitin Protein Interaction Mapping Saccharomyces cerevisiae Proteins DNA Repair Protein Interaction Maps Computational Biology Proteome Computer Simulation Membrane Proteins Deep Learning
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Co-evolution based machine-learning for predicting functional interactions between human genes.

Nature communications Nov 9, 2021
Over the next decade, more than a million eukaryotic species are expected to be fully sequenced. This has the potential to improve our understanding of genotype and phenotype crosstalk, gene function and interactions, and answer evolutionary question...
DNA Repair Humans Machine Learning Phylogeny Sequence Analysis, DNA Evolution, Molecular
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Predicting CRISPR/Cas9-Induced Mutations for Precise Genome Editing.

Trends in biotechnology Sep 13, 2019
SpCas9 creates blunt end cuts in the genome and generates random and unpredictable mutations through error-prone repair systems. However, a growing body of recent evidence points instead to Cas9-induced staggered end generation, nonrandomness of muta...
Gene Editing Machine Learning DNA Repair Models, Genetic DNA End-Joining Repair CRISPR-Cas Systems Mutation
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Unlocking HDR-mediated nucleotide editing by identifying high-efficiency target sites using machine learning.

Scientific reports Feb 26, 2019
Editing individual nucleotides is a crucial component for validating genomic disease association. It is currently hampered by CRISPR-Cas-mediated "base editing" being limited to certain nucleotide changes, and only achievable within a small window ar...
Machine Learning Animals Mice Mice, Inbred C57BL CRISPR-Cas Systems Mutation Gene Editing DNA Breaks, Double-Stranded DNA Repair RNA, Guide, CRISPR-Cas Systems Oligodeoxyribonucleotides
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Predictable and precise template-free CRISPR editing of pathogenic variants.

Nature Nov 7, 2018
Following Cas9 cleavage, DNA repair without a donor template is generally considered stochastic, heterogeneous and impractical beyond gene disruption. Here, we show that template-free Cas9 editing is predictable and capable of precise repair to a pre...
CRISPR-Associated Protein 9 Hermanski-Pudlak Syndrome Humans Menkes Kinky Hair Syndrome Machine Learning Templates, Genetic K562 Cells Substrate Specificity Reproducibility of Results HCT116 Cells DNA Repair Fibroblasts HEK293 Cells CRISPR-Cas Systems Base Sequence Alleles Gene Editing
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The Effect of Leonurus sibiricus Plant Extracts on Stimulating Repair and Protective Activity against Oxidative DNA Damage in CHO Cells and Content of Phenolic Compounds.

Oxidative medicine and cellular longevity Dec 14, 2015
Leonurus sibiricus L. has been used as a traditional and medicinal herb for many years in Asia and Europe. This species is known to have antibacterial, anti-inflammatory, and antioxidant activity and has demonstrated a reduction of intracellular reac...
DNA Repair Leonurus Cytoprotection Cricetinae CHO Cells Wound Healing DNA Breaks, Double-Stranded Animals Chromatography, High Pressure Liquid Cricetulus Cell Survival Oxidation-Reduction Antioxidants Protective Agents Regeneration DNA Damage Plant Extracts Spectrometry, Mass, Electrospray Ionization Phenols Gene Expression Regulation
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