AIMC Topic: Molecular Sequence Annotation

Clear Filters Showing 1 to 10 of 260 articles

Bering: joint cell segmentation and annotation for spatial transcriptomics with transferred graph embeddings.

Nature communications Jul 18, 2025
Single-cell spatial transcriptomics can provide subcellular resolution for a deep understanding of molecular mechanisms. However, accurate segmentation and annotation remain a major challenge that limits downstream analysis. Current machine learning ...
Humans Algorithms Animals Single-Cell Analysis Computational Biology Molecular Sequence Annotation Gene Expression Profiling Transcriptome Deep Learning
View on PubMed DOI

A comprehensive machine learning for high throughput Tuberculosis sequence analysis, functional annotation, and visualization.

Scientific reports Jul 16, 2025
With human guidance, computers now use machine learning (ML) in artificial intelligence (AI) to learn from data, detect trends, and make predictions. Software can adapt and improve with new information. Imaging scans leverage pattern recognition to p...
Mycobacterium tuberculosis Molecular Sequence Annotation Computational Biology Humans Support Vector Machine Tuberculosis Machine Learning Algorithms
View on PubMed DOI

Ensemble machine learning-based pre-trained annotation approach for scRNA-seq data using gradient boosting with genetic optimizer.

BMC bioinformatics Jul 1, 2025
Single-cell RNA sequencing (scRNA-seq) has revolutionized the study of gene expression by allowing researchers to analyze the transcriptomes of individual cells. This technology provides unprecedented insights into cellular heterogeneity, cellular st...
Humans Machine Learning Algorithms Single-Cell Analysis Single-Cell Gene Expression Analysis Sequence Analysis, RNA RNA-Seq Molecular Sequence Annotation
View on PubMed DOI

Genome-wide annotation and comparative analysis of miniature inverted-repeat transposable elements (MITEs) in six pear species.

Planta Jun 16, 2025
Through multi-faceted comparative analysis of MITEs across six pear genomes, we revealed their distribution patterns, functional impacts and their significant role as genomic origins for miRNAs, with copy number being the most critical factor for MIT...
Evolution, Molecular Molecular Sequence Annotation Inverted Repeat Sequences Phylogeny MicroRNAs Genome, Plant DNA Transposable Elements Pyrus
View on PubMed DOI

ProFun-SOM: Protein Function Prediction for Specific Ontology Based on Multiple Sequence Alignment Reconstruction.

IEEE transactions on neural networks and learning systems May 2, 2025
Protein function prediction is crucial for understanding species evolution, including viral mutations. Gene ontology (GO) is a standardized representation framework for describing protein functions with annotated terms. Each ontology is a specific fu...
Computational Biology Proteins Databases, Protein Molecular Sequence Annotation Gene Ontology Sequence Alignment Neural Networks, Computer Algorithms Deep Learning Humans
View on PubMed DOI

A hybrid machine learning framework for functional annotation of mitochondrial glutathione transport and metabolism proteins in cancers.

BMC bioinformatics Feb 11, 2025
BACKGROUND: Alterations of metabolism, including changes in mitochondrial metabolism as well as glutathione (GSH) metabolism are a well appreciated hallmark of many cancers. Mitochondrial GSH (mGSH) transport is a poorly characterized aspect of GSH m...
Molecular Sequence Annotation Machine Learning Humans Neoplasms Biological Transport Cell Line, Tumor Mitochondria Glutathione
View on PubMed DOI

SProtFP: a machine learning-based method for functional classification of small ORFs in prokaryotes.

NAR genomics and bioinformatics Jan 7, 2025
Small proteins (≤100 amino acids) play important roles across all life forms, ranging from unicellular bacteria to higher organisms. In this study, we have developed SProtFP which is a machine learning-based method for functional annotation of prokar...
Humans Neural Networks, Computer Machine Learning Bacteria Computational Biology Antimicrobial Peptides Bacterial Proteins Gastrointestinal Microbiome Open Reading Frames Molecular Sequence Annotation
View on PubMed DOI

Improved enzyme functional annotation prediction using contrastive learning with structural inference.

Communications biology Dec 23, 2024
Recent years have witnessed the remarkable progress of deep learning within the realm of scientific disciplines, yielding a wealth of promising outcomes. A prominent challenge within this domain has been the task of predicting enzyme function, a comp...
Molecular Sequence Annotation Enzymes Prochlorococcus Databases, Protein Amino Acid Sequence Deep Learning Computational Biology Proteome
View on PubMed DOI

Representation of non-coding RNA-mediated regulation of gene expression using the Gene Ontology.

RNA biology Oct 7, 2024
Regulatory non-coding RNAs (ncRNAs) are increasingly recognized as integral to the control of biological processes. This is often through the targeted regulation of mRNA expression, but this is by no means the only mechanism through which regulatory ...
Computational Biology RNA, Small Interfering Humans Molecular Sequence Annotation MicroRNAs Animals Gene Expression Regulation Gene Ontology RNA, Long Noncoding RNA, Untranslated
View on PubMed DOI

HELP: A computational framework for labelling and predicting human common and context-specific essential genes.

PLoS computational biology Sep 27, 2024
Machine learning-based approaches are particularly suitable for identifying essential genes as they allow the generation of predictive models trained on features from multi-source data. Gene essentiality is neither binary nor static but determined by...
Software Algorithms Databases, Genetic Computational Biology Humans Genes, Essential Machine Learning Molecular Sequence Annotation
View on PubMed DOI
Popular Topics
Recent Journals