DeepRNA-Twist: Language-Model-Guided RNA Torsion Angle Prediction with Attention-Inception Network

Information Science, Computer Science, Artificial Intelligence, Life Sciences, Biochemistry, Bioengineering, Biophysics,
RNA language model   torsion and pseudo-torsion angles   inception network   deep learning   RNA structure prediction   bioinformatics   long-range dependencies  

1. Academic Background and Research Motivation With the rapid development of life sciences and bioinformatics, research into RNA molecular structure and function has become a hot topic. RNA is not merely a carrier of genetic information, but also plays critical roles in regulation, catalysis, and various physiological processes. The three-dimension...

Ensemble Learning Based on Matrix Completion Improves Microbe-Disease Association Prediction

Information Science, Computer Science, Artificial Intelligence, Medicine, Life Sciences, Microbiology,
microbe-disease association   ensemble learning   matrix completion   prediction algorithm   bioinformatics  

Academic Background and Research Problem Microorganisms, as one of the most widely distributed forms of life on Earth, are closely related to oceans, soil, and the human body. The human body contains approximately 350 trillion microbial cells, which are intricately linked to human health and the onset and progression of diseases. In recent years, w...

Multi-Modal Interpretable Representation for Non-Coding RNA Classification and Class Annotation

Life Sciences, Bioengineering, Genetics,
non-coding RNA   multi-modal learning   deep learning   classification   annotation   bioinformatics   interpretability  

Non-coding RNAs (ncRNAs) play critical roles in cellular processes and disease development. Although genome sequencing projects have revealed a vast number of non-coding genes, the functional classification of ncRNAs remains a complex and challenging issue. The diversity, complexity, and functionality of ncRNAs make them important subjects in biome...

CryoTEN: Efficiently Enhancing Cryo-EM Density Maps Using Transformers

Information Science, Computer Science, Artificial Intelligence, Life Sciences, Biochemistry, Bioengineering, Biophysics,
Cryo-EM   density map enhancement   Transformer   deep learning   protein structure   image processing   bioinformatics  

Academic Background Cryogenic Electron Microscopy (Cryo-EM) is a crucial experimental technique for determining the structures of macromolecules such as proteins. However, the effectiveness of Cryo-EM is often hindered by noise and missing density values caused by experimental conditions such as low contrast and conformational heterogeneity. Althou...

Relative Quantification of Proteins and Post-Translational Modifications in Proteomic Experiments with Shared Peptides: A Weight-Based Approach

Life Sciences, Biochemistry, Bioengineering,
protein quantification   post-translational modifications   shared peptides   mass spectrometry   bioinformatics  

In proteomics research, mass spectrometry (MS) is widely used to analyze changes in protein abundance and structure. However, protein quantification faces a critical challenge: many proteins share the same peptides (shared peptides), meaning these peptides appear in the sequences of multiple proteins. Traditional methods typically rely solely on un...