AIMC Topic: DNA, Bacterial

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Effects of bovine subclinical mastitis caused by Corynebacterium spp. on somatic cell count, milk yield and composition by comparing contralateral quarters.

Veterinary journal (London, England : 1997) Aug 11, 2015
Subclinical mastitis caused by Corynebacterium spp. (as a group and at the species level) was investigated by evaluating contralateral (healthy and infected) mammary quarters for somatic cell count (SCC), milk yield and composition. Selection of cows...
Asymptomatic Infections RNA, Ribosomal, 16S Mammary Glands, Animal Corynebacterium Sequence Analysis, DNA Milk Cell Count Corynebacterium Infections Mastitis, Bovine Lactation Female Animals Cattle DNA, Bacterial
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Genomics and Machine Learning for Taxonomy Consensus: The Mycobacterium tuberculosis Complex Paradigm.

PloS one Jul 8, 2015
Infra-species taxonomy is a prerequisite to compare features such as virulence in different pathogen lineages. Mycobacterium tuberculosis complex taxonomy has rapidly evolved in the last 20 years through intensive clinical isolation, advances in sequ...
Polymorphism, Restriction Fragment Length Machine Learning Bacterial Typing Techniques DNA, Bacterial Polymerase Chain Reaction Algorithms Genotype Databases, Genetic Prevalence Molecular Epidemiology Tuberculosis Computational Biology Cluster Analysis Genomics Mycobacterium tuberculosis Internet Polymorphism, Single Nucleotide
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Predicting bacterial transcription factor binding sites through machine learning and structural characterization based on DNA duplex stability.

Briefings in bioinformatics Sep 23, 2024
Transcriptional factors (TFs) in bacteria play a crucial role in gene regulation by binding to specific DNA sequences, thereby assisting in the activation or repression of genes. Despite their central role, deciphering shape recognition of bacterial ...
Bacterial Proteins Nucleic Acid Conformation Machine Learning Binding Sites Computational Biology Protein Binding Algorithms Transcription Factors DNA, Bacterial Bacteria DNA
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Achieving pan-microbiome biological insights via the dbBact knowledge base.

Nucleic acids research Jul 21, 2023
16S rRNA amplicon sequencing provides a relatively inexpensive culture-independent method for studying microbial communities. Although thousands of such studies have examined diverse habitats, it is difficult for researchers to use this vast trove of...
Microbiota Knowledge Bases RNA, Ribosomal, 16S Bacteria Sequence Analysis, DNA DNA, Bacterial
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Explainability in transformer models for functional genomics.

Briefings in bioinformatics Sep 2, 2021
The effectiveness of deep learning methods can be largely attributed to the automated extraction of relevant features from raw data. In the field of functional genomics, this generally concerns the automatic selection of relevant nucleotide motifs fr...
Transcription Factors Escherichia coli Genomics DNA, Bacterial Binding Sites Genome, Bacterial Transcription Initiation Site Base Sequence Promoter Regions, Genetic Deep Learning
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Prediction of prokaryotic transposases from protein features with machine learning approaches.

Microbial genomics Jul 1, 2021
Identification of prokaryotic transposases (Tnps) not only gives insight into the spread of antibiotic resistance and virulence but the process of DNA movement. This study aimed to develop a classifier for predicting Tnps in bacteria and archaea usin...
Metagenome DNA Transposable Elements Transposases Virulence Factors Amino Acid Sequence Computational Biology DNA, Bacterial Drug Resistance, Bacterial Bacteria Machine Learning
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