AIMC Topic: Genes, Bacterial

Clear Filters Showing 21 to 30 of 32 articles

Biomedical event extraction based on GRU integrating attention mechanism.

BMC bioinformatics Aug 13, 2018
BACKGROUND: Biomedical event extraction is a crucial task in biomedical text mining. As the primary forum for international evaluation of different biomedical event extraction technologies, BioNLP Shared Task represents a trend in biomedical text min...
Environmental Microbiology Natural Language Processing Humans Publications Attention Bacteria Genes, Bacterial Data Mining
View on PubMed DOI

Gene Prediction in Metagenomic Fragments with Deep Learning.

BioMed research international Nov 8, 2017
Next generation sequencing technologies used in metagenomics yield numerous sequencing fragments which come from thousands of different species. Accurately identifying genes from metagenomics fragments is one of the most fundamental issues in metagen...
Bacteria Databases, Genetic Metagenomics Machine Learning Sequence Analysis, DNA Genes, Bacterial Models, Statistical
View on PubMed DOI

ProClaT, a new bioinformatics tool for in silico protein reclassification: case study of DraB, a protein coded from the draTGB operon in Azospirillum brasilense.

BMC bioinformatics Dec 15, 2016
BACKGROUND: Azopirillum brasilense is a plant-growth promoting nitrogen-fixing bacteria that is used as bio-fertilizer in agriculture. Since nitrogen fixation has a high-energy demand, the reduction of N to NH by nitrogenase occurs only under limitin...
Nitrogen Fixation Genes, Bacterial Nitrogenase Azospirillum brasilense Operon Computational Biology Bacterial Proteins
View on PubMed DOI

InteGO2: a web tool for measuring and visualizing gene semantic similarities using Gene Ontology.

BMC genomics Aug 31, 2016
BACKGROUND: The Gene Ontology (GO) has been used in high-throughput omics research as a major bioinformatics resource. The hierarchical structure of GO provides users a convenient platform for biological information abstraction and hypothesis testing...
Gene Ontology Computational Biology Genes, Bacterial Software Algorithms Gene Regulatory Networks
View on PubMed DOI

Semi-Supervised Multi-View Learning for Gene Network Reconstruction.

PloS one Dec 7, 2015
The task of gene regulatory network reconstruction from high-throughput data is receiving increasing attention in recent years. As a consequence, many inference methods for solving this task have been proposed in the literature. It has been recently ...
Escherichia coli Genes, Bacterial Software Gene Regulatory Networks Machine Learning Saccharomyces cerevisiae Genes, Fungal
View on PubMed DOI

Genomic language models (gLMs) decode bacterial genomes for improved gene prediction and translation initiation site identification.

Briefings in bioinformatics Jul 2, 2025
Accurate bacterial gene prediction is essential for understanding microbial functions and advancing biotechnology. Traditional methods based on sequence homology and statistical models often struggle with complex genetic variations and novel sequence...
Bacteria Computational Biology Genes, Bacterial Genomics Models, Genetic Genome, Bacterial Natural Language Processing Peptide Chain Initiation, Translational
View on PubMed DOI

PLM-ARG: antibiotic resistance gene identification using a pretrained protein language model.

Bioinformatics (Oxford, England) Nov 1, 2023
MOTIVATION: Antibiotic resistance presents a formidable global challenge to public health and the environment. While considerable endeavors have been dedicated to identify antibiotic resistance genes (ARGs) for assessing the threat of antibiotic resi...
Metagenome Artificial Intelligence Drug Resistance, Microbial Anti-Bacterial Agents Genes, Bacterial
View on PubMed DOI

CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database.

Nucleic acids research Jan 6, 2023
The Comprehensive Antibiotic Resistance Database (CARD; card.mcmaster.ca) combines the Antibiotic Resistance Ontology (ARO) with curated AMR gene (ARG) sequences and resistance-conferring mutations to provide an informatics framework for annotation a...
Software Anti-Bacterial Agents Databases, Factual Machine Learning Data Curation Likelihood Functions Molecular Sequence Annotation Drug Resistance, Microbial Genes, Bacterial
View on PubMed DOI

Computational prediction and interpretation of both general and specific types of promoters in Escherichia coli by exploiting a stacked ensemble-learning framework.

Briefings in bioinformatics Mar 22, 2021
Promoters are short consensus sequences of DNA, which are responsible for transcription activation or the repression of all genes. There are many types of promoters in bacteria with important roles in initiating gene transcription. Therefore, solving...
Genes, Bacterial Datasets as Topic Reproducibility of Results Escherichia coli Promoter Regions, Genetic Machine Learning
View on PubMed DOI

Machine-Learning Classification Suggests That Many Alphaproteobacterial Prophages May Instead Be Gene Transfer Agents.

Genome biology and evolution Oct 1, 2019
Many of the sequenced bacterial and archaeal genomes encode regions of viral provenance. Yet, not all of these regions encode bona fide viruses. Gene transfer agents (GTAs) are thought to be former viruses that are now maintained in genomes of some b...
Genes, Viral Alphaproteobacteria Prophages Genes, Bacterial Genome, Bacterial Support Vector Machine
View on PubMed DOI
Popular Topics
Recent Journals