AIMC Topic: Bacterial Proteins

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Machine learning for phytopathology: from the molecular scale towards the network scale.

Briefings in bioinformatics
With the increasing volume of high-throughput sequencing data from a variety of omics techniques in the field of plant-pathogen interactions, sorting, retrieving, processing and visualizing biological information have become a great challenge. Within...

DeepVF: a deep learning-based hybrid framework for identifying virulence factors using the stacking strategy.

Briefings in bioinformatics
Virulence factors (VFs) enable pathogens to infect their hosts. A wealth of individual, disease-focused studies has identified a wide variety of VFs, and the growing mass of bacterial genome sequence data provides an opportunity for computational met...

iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning.

Nucleic acids research
Independent component analysis (ICA) of bacterial transcriptomes has emerged as a powerful tool for obtaining co-regulated, independently-modulated gene sets (iModulons), inferring their activities across a range of conditions, and enabling their ass...

Predicting bacterial virulence factors - evaluation of machine learning and negative data strategies.

Briefings in bioinformatics
Bacterial proteins dubbed virulence factors (VFs) are a highly diverse group of sequences, whose only obvious commonality is the very property of being, more or less directly, involved in virulence. It is therefore tempting to speculate whether their...

Machine learning predicts new anti-CRISPR proteins.

Nucleic acids research
The increasing use of CRISPR-Cas9 in medicine, agriculture, and synthetic biology has accelerated the drive to discover new CRISPR-Cas inhibitors as potential mechanisms of control for gene editing applications. Many anti-CRISPRs have been found that...

Recent Advancement in Predicting Subcellular Localization of Mycobacterial Protein with Machine Learning Methods.

Medicinal chemistry (Shariqah (United Arab Emirates))
Mycobacterium tuberculosis (MTB) can cause the terrible tuberculosis (TB), which is reported as one of the most dreadful epidemics. Although many biochemical molecular drugs have been developed to cope with this disease, the drug resistance-especiall...

DeepT3: deep convolutional neural networks accurately identify Gram-negative bacterial type III secreted effectors using the N-terminal sequence.

Bioinformatics (Oxford, England)
MOTIVATION: Various bacterial pathogens can deliver their secreted substrates also called effectors through Type III secretion systems (T3SSs) into host cells and cause diseases. Since T3SS secreted effectors (T3SEs) play important roles in pathogen-...

Bastion3: a two-layer ensemble predictor of type III secreted effectors.

Bioinformatics (Oxford, England)
MOTIVATION: Type III secreted effectors (T3SEs) can be injected into host cell cytoplasm via type III secretion systems (T3SSs) to modulate interactions between Gram-negative bacterial pathogens and their hosts. Due to their relevance in pathogen-hos...

Systematic analysis and prediction of type IV secreted effector proteins by machine learning approaches.

Briefings in bioinformatics
In the course of infecting their hosts, pathogenic bacteria secrete numerous effectors, namely, bacterial proteins that pervert host cell biology. Many Gram-negative bacteria, including context-dependent human pathogens, use a type IV secretion syste...

An account of in silico identification tools of secreted effector proteins in bacteria and future challenges.

Briefings in bioinformatics
Bacterial pathogens secrete numerous effector proteins via six secretion systems, type I to type VI secretion systems, to adapt to new environments or to promote virulence by bacterium-host interactions. Many computational approaches have been used i...