AIMC Topic: Genome, Bacterial
Clear Filters Showing 61 to 70 of 92 articles
Pre_GI: a global map of ontological links between horizontally transferred genomic islands in bacterial and archaeal genomes.
Database : the journal of biological databases and curation
Jun 17, 2015
The Predicted Genomic Islands database (Pre_GI) is a comprehensive repository of prokaryotic genomic islands (islands, GIs) freely accessible at http://pregi.bi.up.ac.za/index.php. Pre_GI, Version 2015, catalogues 26 744 islands identified in 2407 ba...
Analysis of strand-specific RNA-seq data using machine learning reveals the structures of transcription units in Clostridium thermocellum.
Nucleic acids research
Mar 12, 2015
Identification of transcription units (TUs) encoded in a bacterial genome is essential to elucidation of transcriptional regulation of the organism. To gain a detailed understanding of the dynamically composed TU structures, we have used four strand-...
EcoliNet: a database of cofunctional gene network for Escherichia coli.
Database : the journal of biological databases and curation
Feb 2, 2015
During the past several decades, Escherichia coli has been a treasure chest for molecular biology. The molecular mechanisms of many fundamental cellular processes have been discovered through research on this bacterium. Although much basic research n...
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...
Genome Mining and Chemistry-Driven Discovery of a Cell Wall Lipopeptide Signature for subsp. Ancestral Lineage.
ACS infectious diseases
Jun 13, 2025
subsp. () causes Johne's disease (JD), a chronic infection responsible for considerable economic losses to dairy industries worldwide. Genetically clonal, has evolved into three distinct genetic lineages designated CII, for bovine strains, and SI ...
Deciphering the biosynthetic potential of microbial genomes using a BGC language processing neural network model.
Nucleic acids research
Apr 10, 2025
Biosynthetic gene clusters (BGCs), key in synthesizing microbial secondary metabolites, are mostly hidden in microbial genomes and metagenomes. To unearth this vast potential, we present BGC-Prophet, a transformer-based language model for BGC predict...
Negative dataset selection impacts machine learning-based predictors for multiple bacterial species promoters.
Bioinformatics (Oxford, England)
Mar 29, 2025
MOTIVATION: Advances in bacterial promoter predictors based on machine learning have greatly improved identification metrics. However, existing models overlooked the impact of negative datasets, previously identified in GC-content discrepancies betwe...
Predicting the bacterial host range of plasmid genomes using the language model-based one-class support vector machine algorithm.
Microbial genomics
Feb 1, 2025
The prediction of the plasmid host range is crucial for investigating the dissemination of plasmids and the transfer of resistance and virulence genes mediated by plasmids. Several machine learning-based tools have been developed to predict plasmid h...
Using core genome and machine learning for serovar prediction in Salmonella enterica subspecies I strains.
FEMS microbiology letters
Jan 10, 2025
This study presents a dual investigation of Salmonella enterica subspecies I, focusing on serovar prediction and core genome characteristics. We utilized two large genomic datasets (panX and NCBI Pathogen Detection) to test machine learning methods f...
PanKB: An interactive microbial pangenome knowledgebase for research, biotechnological innovation, and knowledge mining.
Nucleic acids research
Jan 6, 2025
The exponential growth of microbial genome data presents unprecedented opportunities for unlocking the potential of microorganisms. The burgeoning field of pangenomics offers a framework for extracting insights from this big biological data. Recent a...
Don't Miss the Future of Medicine
Join thousands of healthcare professionals staying informed about the latest AI breakthroughs in medicine. Get curated insights delivered to your inbox.
Subscribe NowPopular Topics
- Machine Learning 30978
- Neural Networks, Computer 29696
- Algorithms 26813
- Deep Learning 26324
- Artificial Intelligence 24267
- Robotics 13307
- Image Processing, Computer-Assisted 9512
- Retrospective Studies 9097
- Magnetic Resonance Imaging 6173
- Reproducibility of Results 5589
- Tomography, X-Ray Computed 4765
- Support Vector Machine 4678
- Computational Biology 4229
- Brain 4045
- Computer Simulation 3877
Recent Journals
- Scientific reports 5865
- Sensors (Basel, Switzerland) 4794
- PloS one 4011
- Neural networks : the official journal of the International Neural Network Society 2928
- Computational intelligence and neuroscience 1931
- Computers in biology and medicine 1839
- Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference 1686
- Studies in health technology and informatics 1278
- IEEE journal of biomedical and health informatics 1129
- Journal of chemical information and modeling 994
- Nature communications 938
- Computer methods and programs in biomedicine 883
- Bioinformatics (Oxford, England) 861
- Briefings in bioinformatics 850
- IEEE transactions on neural networks and learning systems 823