AIMC Topic: High-Throughput Nucleotide Sequencing

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Next-generation sequencing based deep learning model for prediction of HER2 status and response to HER2-targeted neoadjuvant chemotherapy.

Journal of cancer research and clinical oncology
INTRODUCTION: For patients with breast cancer, the amplification of Human Epidermal Growth Factor 2 (HER2) is closely related to their prognosis and treatment decisions. This study aimed to further improve the accuracy and efficiency of HER2 amplific...

An Information Fusion System-Driven Deep Neural Networks With Application to Cancer Mortality Risk Estimate.

IEEE transactions on neural networks and learning systems
Next-generation sequencing (NGS) genomic data offer valuable high-throughput genomic information for computational applications in medicine. Using genomic data to identify disease-associated genes to estimate cancer mortality risk remains challenging...

Spatially resolved transcriptomics and graph-based deep learning improve accuracy of routine CNS tumor diagnostics.

Nature cancer
The diagnostic landscape of brain tumors integrates comprehensive molecular markers alongside traditional histopathological evaluation. DNA methylation and next-generation sequencing (NGS) have become a cornerstone in central nervous system (CNS) tum...

Artificial intelligence and machine learning in cell-free-DNA-based diagnostics.

Genome research
The discovery of circulating fetal and tumor cell-free DNA (cfDNA) molecules in plasma has opened up tremendous opportunities in noninvasive diagnostics such as the detection of fetal chromosomal aneuploidies and cancers and in posttransplantation mo...

A deep multiple instance learning framework improves microsatellite instability detection from tumor next generation sequencing.

Nature communications
Microsatellite instability (MSI) is a critical phenotype of cancer genomes and an FDA-recognized biomarker that can guide treatment with immune checkpoint inhibitors. Previous work has demonstrated that next-generation sequencing data can be used to ...

High-Risk Sequence Prediction Model in DNA Storage: The LQSF Method.

IEEE transactions on nanobioscience
Traditional DNA storage technologies rely on passive filtering methods for error correction during synthesis and sequencing, which result in redundancy and inadequate error correction. Addressing this, the Low Quality Sequence Filter (LQSF) was intro...

Trans-m5C: A transformer-based model for predicting 5-methylcytosine (m5C) sites.

Methods (San Diego, Calif.)
5-Methylcytosine (m5C) plays a pivotal role in various RNA metabolic processes, including RNA localization, stability, and translation. Current high-throughput sequencing technologies for m5C site identification are resource-intensive in terms of cos...

Optimizing sequence data analysis using convolution neural network for the prediction of CNV bait positions.

BMC bioinformatics
BACKGROUND: Accurate prediction of copy number variations (CNVs) from targeted capture next-generation sequencing (NGS) data relies on effective normalization of read coverage profiles. The normalization process is particularly challenging due to hid...

The Role of ctDNA in the Management of Non-Small-Cell Lung Cancer in the AI and NGS Era.

International journal of molecular sciences
Liquid biopsy (LB) involves the analysis of circulating tumour-derived DNA (ctDNA), providing a minimally invasive method for gathering both quantitative and qualitative information. Genomic analysis of ctDNA through next-generation sequencing (NGS) ...

Comparative Analysis of Generative Pre-Trained Transformer Models in Oncogene-Driven Non-Small Cell Lung Cancer: Introducing the Generative Artificial Intelligence Performance Score.

JCO clinical cancer informatics
PURPOSE: Precision oncology in non-small cell lung cancer (NSCLC) relies on biomarker testing for clinical decision making. Despite its importance, challenges like the lack of genomic oncology training, nonstandardized biomarker reporting, and a rapi...