AIMC Topic: Sequence Analysis, RNA

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The role of lactylation in plasma cells and its impact on rheumatoid arthritis pathogenesis: insights from single-cell RNA sequencing and machine learning.

Frontiers in immunology
INTRODUCTION: Rheumatoid arthritis (RA) is a chronic autoimmune disorder characterized by persistent synovitis, systemic inflammation, and autoantibody production. This study aims to explore the role of lactylation in plasma cells and its impact on R...

Predicting RNA sequence-structure likelihood via structure-aware deep learning.

BMC bioinformatics
BACKGROUND: The active functionalities of RNA are recognized to be heavily dependent on the structure and sequence. Therefore, a model that can accurately evaluate a design by giving RNA sequence-structure pairs would be a valuable tool for many rese...

Integrating cellular experiments, single-cell sequencing, and machine learning to identify endoplasmic reticulum stress biomarkers in idiopathic pulmonary fibrosis.

Annals of medicine
BACKGROUND: Idiopathic Pulmonary Fibrosis (IPF) presents a severe respiratory challenge with a poor prognosis due to the lack of reliable biomarkers. Recent evidence suggests that Endoplasmic Reticulum Stress (ERS) may be associated with IPF pathogen...

Wfold: A new method for predicting RNA secondary structure with deep learning.

Computers in biology and medicine
Precise estimations of RNA secondary structures have the potential to reveal the various roles that non-coding RNAs play in regulating cellular activity. However, the mainstay of traditional RNA secondary structure prediction methods relies on thermo...

Advanced Prediction of Hepatic Oncogenic Transformation in HBV Patients via RNA-Seq Data Analysis and Deep Learning Techniques.

International journal of molecular sciences
Liver cancer, recognized as a significant global health issue, is increasingly correlated with Hepatitis B virus (HBV) infection, as evidenced by numerous scientific studies. This study aims to examine the correlation between HBV infection and the de...

A natural language processing system for the efficient extraction of cell markers.

Scientific reports
Single-cell RNA sequencing (scRNA-seq) has emerged as a pivotal tool for exploring cellular landscapes across diverse species and tissues. Precise annotation of cell types is essential for understanding these landscapes, relying heavily on empirical ...

Joint trajectory inference for single-cell genomics using deep learning with a mixture prior.

Proceedings of the National Academy of Sciences of the United States of America
Trajectory inference methods are essential for analyzing the developmental paths of cells in single-cell sequencing datasets. It provides insights into cellular differentiation, transitions, and lineage hierarchies, helping unravel the dynamic proces...

Identification of immune-related biomarkers for intracerebral hemorrhage diagnosis based on RNA sequencing and machine learning.

Frontiers in immunology
BACKGROUND: Intracerebral hemorrhage (ICH) is a severe stroke subtype with high morbidity, disability, and mortality rates. Currently, no biomarkers for ICH are available for use in clinical practice. We aimed to explore the roles of RNAs in ICH path...

COMPREHENSIVE CHARACTERIZATION OF CYTOKINES IN PATIENTS UNDER EXTRACORPOREAL MEMBRANE OXYGENATION: EVIDENCE FROM INTEGRATED BULK AND SINGLE-CELL RNA SEQUENCING DATA USING MULTIPLE MACHINE LEARNING APPROACHES.

Shock (Augusta, Ga.)
Background : Extracorporeal membrane oxygenation (ECMO) is an effective technique for providing short-term mechanical support to the heart, lungs, or both. During ECMO treatment, the inflammatory response, particularly involving cytokines, plays a cr...