AIMC Topic: High-Throughput Nucleotide Sequencing

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Neoantigen-driven cancer vaccines in personalized oncology: progress, obstacles, and translational prospects.

Molecular biology reports
The development of neoantigen-based cancer vaccines has emerged as a groundbreaking approach in the field of personalized oncology. Neoantigens, originating from tumor-specific somatic mutations, possess considerable immunogenic potential and are abs...

Multiplex mapping of protein-protein interaction interfaces.

Proceedings of the National Academy of Sciences of the United States of America
We describe peptide mapping through Split Antibiotic Resistance Complementation (SpARC-map), a method to identify the probable interface between two interacting proteins. Our method is based on in vivo affinity selection inside a bacterial host and u...

Blastulation and ploidy prediction using morphology assessment in 33,999 day-3 embryos.

Scientific reports
Although contemporary practice in in vitro fertilization (IVF) favors embryo transfer at blastocyst stage, several centres worldwide employ cleavage-stage Day-3 embryo transfers. The advantage of cultures extended to Day-5 and beyond, is to ensure th...

ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling.

Nature communications
Accurate detection of somatic variants in tumors is of critical importance and remains challenging. Current methods typically require matched normal samples for reliable detection, which are often unavailable in real-world research and clinical scena...

Metagenomic next-generation sequencing unraveled the characteristic of lung microbiota in patients with checkpoint inhibitor pneumonitis: results from a prospective cohort study.

Journal for immunotherapy of cancer
BACKGROUND: Checkpoint inhibitor pneumonitis (CIP) is among the most lethal immune-related adverse events in patients with cancer receiving immunotherapy. This study aims to characterize the lung microbiome in patients with CIP and evaluate its diagn...

Machine learning reveals distinct T-cell receptor clusters in plasma cell dyscrasias compared to healthy controls.

PloS one
T-cell receptor (TCR) repertoire diversity has been implicated in the progression and prognosis of multiple myeloma (MM). This study aimed to evaluate the association between T-cell clonality, immune response, and clinical outcomes in patients with p...

Advancing DNA and RNA Modification Detection via Nanopore Sequencing.

ACS nano
DNA/RNA modifications are crucial for biological processes. To understand their regulatory mechanisms, precise mapping and quantification of these modifications are essential. Although next-generation sequencing can detect the location and stoichiome...

Image-based DNA sequencing encoding for detecting low-mosaicism somatic mobile element insertions.

Nature communications
Active mobile elements in the human genome can create novel mobile element insertions (MEIs) in somatic tissues. Detection of somatic MEIs, particularly those with low mosaicism, remains a significant challenge due to sequencing artifacts and alignme...

DeepRNA-Reg: a deep-learning based approach for comparative analysis of CLIP experiments.

RNA biology
DeepRNA-Reg employs advances in deep learning to enable high-fidelity comparative analysis of paired datasets of high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP). In a HITS-CLIP experimental paradigm where Ag...

Genomic Identification and Validation of Candidate Genes Associated with Alkalinity Tolerance in Exopalaemon carinicauda.

Marine biotechnology (New York, N.Y.)
China harbors extensive saline-alkaline water resources with considerable potential for aquaculture development. However, their utilization is constrained by high pH, elevated carbonate alkalinity, and complex ionic composition. Exopalaemon carinicau...