Protein Function Prediction: From Traditional Classifier to Deep Learning
Sign Up to like & getrecommendations! Published in 2019 at "PROTEOMICS"
DOI: 10.1002/pmic.201900119
Abstract: Deep learning demonstrates greater competence over traditional machine learning techniques for many tasks. In last several years, deep learning has been applied to protein function prediction and a series of good achievements has been obtained.… read more here.
Keywords: protein function; deep learning; function prediction;
From Gene Annotation to Function Prediction for Metagenomics.
Sign Up to like & getrecommendations! Published in 2017 at "Methods in molecular biology"
DOI: 10.1007/978-1-4939-7015-5_3
Abstract: Microbes play important roles in almost every aspect of life, including human health and diseases. Facilitated by the rapid development of sequencing technologies, metagenomics research has accelerated the accumulation of genomic sequences of microbial species… read more here.
Keywords: prediction metagenomics; annotation; gene annotation; annotation function ... See more keywords
RNA Function Prediction.
Sign Up to like & getrecommendations! Published in 2017 at "Methods in molecular biology"
DOI: 10.1007/978-1-4939-7231-9_2
Abstract: Recent studies have shown that a considerable proportion of eukaryotic genomes are transcribed as noncoding RNA (ncRNA), and regulatory ncRNAs have attracted much attention from researchers in many fields, especially of microRNA (miRNA) and long… read more here.
Keywords: function; rna function; biology; function prediction ... See more keywords
Gene function prediction based on Gene Ontology Hierarchy Preserving Hashing.
Sign Up to like & getrecommendations! Published in 2019 at "Genomics"
DOI: 10.1016/j.ygeno.2018.02.008
Abstract: Gene Ontology (GO) uses structured vocabularies (or terms) to describe the molecular functions, biological roles, and cellular locations of gene products in a hierarchical ontology. GO annotations associate genes with GO terms and indicate the… read more here.
Keywords: gene; gene function; ontology; function prediction ... See more keywords
DeepText2GO: Improving large-scale protein function prediction with deep semantic text representation.
Sign Up to like & getrecommendations! Published in 2018 at "Methods"
DOI: 10.1016/j.ymeth.2018.05.026
Abstract: As of April 2018, UniProtKB has collected more than 115 million protein sequences. Less than 0.15% of these proteins, however, have been associated with experimental GO annotations. As such, the use of automatic protein function… read more here.
Keywords: protein; deep semantic; protein function; function prediction ... See more keywords
Enhancing Protein Function Prediction Performance by Utilizing AlphaFold-Predicted Protein Structures
Sign Up to like & getrecommendations! Published in 2022 at "Journal of chemical information and modeling"
DOI: 10.1021/acs.jcim.2c00885
Abstract: The structure of a protein is of great importance in determining its functionality, and this characteristic can be leveraged to train data-driven prediction models. However, the limited number of available protein structures severely limits the… read more here.
Keywords: protein structures; predicted structures; function prediction; alphafold predicted ... See more keywords
Multi-Instance Metric Transfer Learning for Genome-Wide Protein Function Prediction
Sign Up to like & getrecommendations! Published in 2017 at "Scientific Reports"
DOI: 10.1038/srep41831
Abstract: Multi-Instance (MI) learning has been proven to be effective for the genome-wide protein function prediction problems where each training example is associated with multiple instances. Many studies in this literature attempted to find an appropriate… read more here.
Keywords: genome wide; wide protein; protein function; multi instance ... See more keywords
Identification, biogenesis, and function prediction of a novel circRNA_3238 of chicken.
Sign Up to like & getrecommendations! Published in 2022 at "Animal biotechnology"
DOI: 10.1080/10495398.2022.2102504
Abstract: With the development of high-throughput sequencing, circular RNA has come into people's vision and attracted more and more attention. Many studies have found that circular RNA plays an important role in a variety of biological… read more here.
Keywords: novel circrna; circrna 3238; prediction novel; function prediction ... See more keywords
MGEGFP: a multi-view graph embedding method for gene function prediction based on adaptive estimation with GCN
Sign Up to like & getrecommendations! Published in 2022 at "Briefings in bioinformatics"
DOI: 10.1093/bib/bbac333
Abstract: In recent years, a number of computational approaches have been proposed to effectively integrate multiple heterogeneous biological networks, and have shown impressive performance for inferring gene function. However, the previous methods do not fully represent… read more here.
Keywords: function; function prediction; multi view; gene function ... See more keywords
Accurate and efficient gene function prediction using a Multi-Bacterial network.
Sign Up to like & getrecommendations! Published in 2020 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btaa885
Abstract: MOTIVATION Nearly 40% of the genes in sequenced genomes have no experimentally- or computationally-derived functional annotations. To fill this gap, we seek to develop methods for network-based gene function prediction that can integrate heterogeneous data… read more here.
Keywords: network; gene function; function prediction; prediction ... See more keywords
NetQuilt: deep multispecies network-based protein function prediction using homology-informed network similarity
Sign Up to like & getrecommendations! Published in 2021 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btab098
Abstract: Abstract Motivation Transferring knowledge between species is challenging: different species contain distinct proteomes and cellular architectures, which cause their proteins to carry out different functions via different interaction networks. Many approaches to protein functional annotation… read more here.
Keywords: network based; network; similarity; function prediction ... See more keywords