AIMC Topic: High-Throughput Nucleotide Sequencing

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Application and clinical utility assessment of natural language processing-based software for copy-number variants interpretation.

Journal of translational medicine
BACKGROUND: Manual interpretation of copy-number variant (CNV) according to the guideline published by the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resources (ClinGen) in 2020 is labor-intensive and time-consum...

Predicting chromatin conformation contact maps.

PloS one
Over the past 15 years, a variety of next-generation sequencing assays have been developed for measuring the 3D conformation of DNA in the nucleus. Each of these assays gives, for a particular cell or tissue type, a distinct picture of 3D chromatin a...

Applications of New Generation Sequencing (NGS) in Ocular Oncology.

International ophthalmology clinics
Next-generation sequencing (NGS) has revolutionized cancer genomics, offering unparalleled insights into the molecular landscape of various malignancies, including ocular cancers. This review explores the role of NGS in ocular oncology, highlighting ...

Development and Validation of an Automated DNA-Encoded Library Screening Data Analysis Platform: PB-DEL Autoscreening Analysis (PB-DELASA).

Journal of chemical information and modeling
Tools available for analyzing next-generation sequencing (NGS) data produced from DNA-encoded library (DEL) screening campaigns are often constrained to customized methods developed internally by individual institutes, which usually generate data spe...

Increasing pathogenic germline variant diagnosis rates in precision medicine: current best practices and future opportunities.

Human genomics
The accurate diagnosis of pathogenic variants is essential for effective clinical decision making within precision medicine programs. Despite significant advances in both the quality and quantity of molecular patient data, diagnostic rates remain sub...

A review on multi-omics integration for aiding study design of large scale TCGA cancer datasets.

BMC genomics
BACKGROUND: Rapid advancements in high-throughput sequencing technologies allow for detailed and accurate measurement of omics features within their biological context. The integration of different omics types creates heterogeneous datasets, presenti...

Advancements in DNA methylation technologies and their application in cancer diagnosis.

Epigenetics
DNA methylation is a common epigenetic modification that maintains the integrity of the DNA sequence while profoundly influencing gene expression and phenotypic variation. Aberrant DNA methylation has been associated with the onset and progression of...

Nanopore full length 16S rRNA gene sequencing increases species resolution in bacterial biomarker discovery.

Scientific reports
Discovery of disease-related bacterial biomarkers could be a useful approach for early prevention or diagnosis of various afflictions, such as colorectal cancer. This typically involves analyzing small regions of the 16S rRNA gene (e.g. V3V4) through...

Distribution patterns of N6-methyladenine in the rye genome.

Scientific reports
N6-methyladenine (6 mA) has emerged as a potential epigenetic marker in eukaryotic genomes, yet its precise distribution patterns and biological functions in plant genomes are still not fully understood. In this study, we investigated the occurrence,...

Advancing fungal phylogenetics: integrating modern sequencing, dark taxa discovery, and machine learning.

Archives of microbiology
The study of fungal genetics has undergone transformative advancements in recent decades, profoundly reshaping our understanding of fungal diversity, evolution, and pathogenesis. This review synthesizes cutting-edge molecular techniques revolutionizi...