AIMC Topic: Bacterial Proteins
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Contrastive-learning of language embedding and biological features for cross modality encoding and effector prediction.
Nature communications
Feb 3, 2025
Identifying and characterizing virulence proteins secreted by Gram-negative bacteria are fundamental for deciphering microbial pathogenicity as well as aiding the development of therapeutic strategies. Effector predictors utilizing pre-trained protei...
SProtFP: a machine learning-based method for functional classification of small ORFs in prokaryotes.
NAR genomics and bioinformatics
Jan 7, 2025
Small proteins (≤100 amino acids) play important roles across all life forms, ranging from unicellular bacteria to higher organisms. In this study, we have developed SProtFP which is a machine learning-based method for functional annotation of prokar...
ProPr54 web server: predicting σ promoters and regulon with a hybrid convolutional and recurrent deep neural network.
NAR genomics and bioinformatics
Jan 7, 2025
σ serves as an unconventional sigma factor with a distinct mechanism of transcription initiation, which depends on the involvement of a transcription activator. This unique sigma factor σ is indispensable for orchestrating the transcription of genes ...
DeepGOMeta for functional insights into microbial communities using deep learning-based protein function prediction.
Scientific reports
Dec 30, 2024
Analyzing microbial samples remains computationally challenging due to their diversity and complexity. The lack of robust de novo protein function prediction methods exacerbates the difficulty in deriving functional insights from these samples. Tradi...
Analysis of high-molecular-weight proteins using MALDI-TOF MS and machine learning for the differentiation of clinically relevant Clostridioides difficile ribotypes.
European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology
Dec 17, 2024
PURPOSE: Clostridioides difficile is the main cause of antibiotic related diarrhea and some ribotypes (RT), such as RT027, RT181 or RT078, are considered high risk clones. A fast and reliable approach for C. difficile ribotyping is needed for a corre...
Lipid discovery enabled by sequence statistics and machine learning.
eLife
Dec 10, 2024
Bacterial membranes are complex and dynamic, arising from an array of evolutionary pressures. One enzyme that alters membrane compositions through covalent lipid modification is MprF. We recently identified that MprF synthesizes lysyl-phosphatidylgl...
Machine Learning-Assisted, Dual-Channel CRISPR/Cas12a Biosensor-In-Microdroplet for Amplification-Free Nucleic Acid Detection for Food Authenticity Testing.
ACS nano
Dec 2, 2024
The development of novel detection technology for meat species authenticity is imperative. Here, we developed a machine learning-supported, dual-channel biosensor-in-microdroplet platform for meat species authenticity detection named CC-drop (RISPR/C...
Extending visual range of bacteria with upconversion nanoparticles and constructing NIR-responsive bio-microrobots.
Journal of colloid and interface science
Dec 1, 2024
The motility of bacteria is crucial for navigating competitive environments and is closely linked to physiological activities essential for their survival, such as biofilm development. Precise regulation of bacterial motility enhances our understandi...
Deciphering Cas9 specificity: Role of domain dynamics and RNA:DNA hybrid interactions revealed through machine learning and accelerated molecular simulations.
International journal of biological macromolecules
Nov 19, 2024
CRISPR/Cas9 technology is widely used for gene editing, but off-targeting still remains a major concern in therapeutic applications. Although Cas9 variants with better mismatch discrimination have been developed, they have significantly lower rates o...
A novel machine-learning aided platform for rapid detection of urine ESBLs and carbapenemases: URECA-LAMP.
Journal of clinical microbiology
Oct 24, 2024
Pathogenic gram-negative bacteria frequently carry genes encoding extended-spectrum beta-lactamases (ESBL) and/or carbapenemases. Of great concern are carbapenem resistant , , and . Despite the need for rapid AMR diagnostics globally, current molecu...
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