相关论文: ProtGO: A Transformer based Fusion Model for accur…
A large number of protein sequences are becoming available through the application of novel high-throughput sequencing technologies. Experimental functional characterization of these proteins is time-consuming and expensive, and is often…
Accurate prediction of protein function is essential for elucidating molecular mechanisms and advancing biological and therapeutic discovery. Yet experimental annotation lags far behind the rapid growth of protein sequence data.…
The present gap between the amount of available protein sequence due to the development of next generation sequencing technology (NGS) and slow and expensive experimental extraction of useful information like annotation of protein sequence…
Public repositories for genome and proteome annotations, such as the Gene Ontology (GO), rarely stores negative annotations, i.e. proteins not possessing a given function. This leaves undefined or ill defined the set of negative examples,…
The increasing availability of high throughput data arising from gene expression studies leads to the necessity of methods for summarizing the available information. As annotation quality improves it is becoming common to rely on the Gene…
Gene Ontology (GO) terms are frequently used to score alignments between protein-protein interaction (PPI) networks. Methods exist to measure the GO similarity between two proteins in isolation, but pairs of proteins in a network alignment…
In recent years, deep learning algorithms have outperformed the state-of-the art methods in several areas thanks to the efficient methods for training and for preventing overfitting, advancement in computer hardware, the availability of…
We applied machine learning to predict whether a gene is involved in axon regeneration. We extracted 31 features from different databases and trained five machine learning models. Our optimal model, a Random Forest Classifier with 50…
Automatic protein function prediction (AFP) is classified as a large-scale multi-label classification problem aimed at automating protein enrichment analysis to eliminate the current reliance on labor-intensive wet-lab methods. Currently,…
The Gene Ontology (GO) is a major bioinformatics ontology that provides structured controlled vocabularies to classify gene and proteins function and role. The GO and its annotations to gene products are now an integral part of functional…
Gene Ontology (GO) is the primary gene function knowledge base that enables computational tasks in biomedicine. The basic element of GO is a term, which includes a set of genes with the same function. Existing research efforts of GO mainly…
The Gene Ontology Consortium launched the GO-PAINT project (Phylogenetic Annotation and INference Tool) 9 years ago and is currently being used in the GO Reference Genome Annotation Project to support inference of GO function terms…
The Gene Ontology (GO) project is the largest resource for cataloguing gene function. The combination of solid conceptual underpinnings and a practical set of features have made the GO a widely adopted resource in the research community and…
Self-supervised protein language models have proved their effectiveness in learning the proteins representations. With the increasing computational power, current protein language models pre-trained with millions of diverse sequences can…
The last decade has seen the advent and consolidation of ontology based tools for the identification and biological interpretation of classes of genes, such as the Gene Ontology. The information accumulated time-by-time and included in the…
Gene studies are crucial for fields such as protein structure prediction, drug discovery, and cancer genomics, yet they face challenges in fully utilizing the vast and diverse information available. Gene studies require clean, factual…
Summary: TreeGrafter is a new software tool for annotating protein sequences using annotated phylogenetic trees. Cur-rently, the tool provides annotations to Gene Ontology terms, and PANTHER protein class, family and subfamily. The…
The Gene Ontology (GO) is a formidable resource but there are several considerations about it that are essential to understand the data and interpret it correctly. The GO is sufficiently simple that it can be used without deep understanding…
Proteomics is the large-scale analysis of the proteins. The common method for identifying proteins and characterising their amino acid sequences is to digest the proteins into peptides, analyse the peptides using mass spectrometry and…
The Gene Ontology (GO) provides biologists with a controlled terminology that describes how genes are associated with functions and how functional terms are related to each other. These term-term relationships encode how scientists conceive…