AIMC Topic: Bacterial Proteins

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Use of high-content analysis and machine learning to characterize complex microbial samples via morphological analysis.

PloS one Sep 23, 2019
High Content Analysis (HCA) has become a cornerstone of cellular analysis within the drug discovery industry. To expand the capabilities of HCA, we have applied the same analysis methods, validated in numerous mammalian cell models, to microbiology m...
Bacillus megaterium Escherichia coli Bradyrhizobium Machine Learning Pseudomonas fluorescens Bacterial Proteins Anti-Bacterial Agents Colony Count, Microbial Bacteria
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SecProMTB: Support Vector Machine-Based Classifier for Secretory Proteins Using Imbalanced Data Sets Applied to Mycobacterium tuberculosis.

Proteomics Aug 8, 2019
Secretory proteins of Mycobacterium tuberculosis have created more concern, given their dominant immunogenicity and role in pathogenesis. In view of expensive and time-consuming traditional biochemical experiments, an advanced support vector machine ...
Support Vector Machine Databases, Protein Bacterial Proteins Algorithms Mycobacterium tuberculosis Computational Biology
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Morphology-based classification of mycobacteria-infected macrophages with convolutional neural network: reveal EsxA-induced morphologic changes indistinguishable by naked eyes.

Translational research : the journal of laboratory and clinical medicine Jun 28, 2019
EsxA is an essential virulence factor for Mycobacterium tuberculosis (Mtb) pathogenesis as well as an important biomarker for Mtb detection. In this study, we use light microscopy and deep learning-based image analysis to classify the morphologic cha...
Humans Mice A549 Cells Bacterial Proteins Virulence Factors Neural Networks, Computer Macrophages Animals RAW 264.7 Cells Mycobacterium marinum
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A Deep Learning-Based Automatic Mosquito Sensing and Control System for Urban Mosquito Habitats.

Sensors (Basel, Switzerland) Jun 21, 2019
Mosquito control is important as mosquitoes are extremely harmful pests that spread various infectious diseases. In this research, we present the preliminary results of an automated system that detects the presence of mosquitoes via image processing ...
Image Processing, Computer-Assisted Biosensing Techniques Animals Bacterial Proteins Mosquito Control Neural Networks, Computer Ecosystem Bacillus thuringiensis Deep Learning
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Machine Learning Applied to Predicting Microorganism Growth Temperatures and Enzyme Catalytic Optima.

ACS synthetic biology Jun 7, 2019
Enzymes that catalyze chemical reactions at high temperatures are used for industrial biocatalysis, applications in molecular biology, and as highly evolvable starting points for protein engineering. The optimal growth temperature (OGT) of organisms ...
Models, Biological Enzyme Stability Bacterial Physiological Phenomena Bacteria Proteome Bacterial Proteins Machine Learning Temperature Protein Engineering
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Soft-sensing method based on FDLS-SVM in marine alkaline protease fermentation process.

Preparative biochemistry & biotechnology May 27, 2019
To overcome the problem that soft-sensing model cannot be updated with the bioprocess changes, this article proposed a soft-sensing modeling method which combined fuzzy c-means clustering (FCM) algorithm with least squares support vector machine theo...
Equipment Design Models, Biological Aquatic Organisms Least-Squares Analysis Endopeptidases Algorithms Bioreactors Fermentation Bacteria Bacterial Proteins Support Vector Machine
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DEEPred: Automated Protein Function Prediction with Multi-task Feed-forward Deep Neural Networks.

Scientific reports May 14, 2019
Automated protein function prediction is critical for the annotation of uncharacterized protein sequences, where accurate prediction methods are still required. Recently, deep learning based methods have outperformed conventional algorithms in comput...
Gene Ontology Pseudomonas Infections Models, Biological Pseudomonas aeruginosa Data Mining Neural Networks, Computer Software Deep Learning Biofilms Proteins Bacterial Proteins Humans
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Machine-Learning-Based Predictor of Human-Bacteria Protein-Protein Interactions by Incorporating Comprehensive Host-Network Properties.

Journal of proteome research Apr 22, 2019
The large-scale identification of protein-protein interactions (PPIs) between humans and bacteria remains a crucial step in systematically understanding the underlying molecular mechanisms of bacterial infection. Computational prediction approaches a...
Molecular Mimicry Models, Statistical Francisella tularensis Databases, Protein Area Under Curve Protein Interaction Mapping Host-Pathogen Interactions Machine Learning Humans Bacillus anthracis Gene Expression Yersinia pestis Protein Binding Eukaryotic Cells Bacterial Proteins Proteome
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Unsupervised Learning Approach for Comparing Multiple Transposon Insertion Sequencing Studies.

mSphere Feb 20, 2019
Transposon insertion sequencing (TIS) is a widely used technique for conducting genome-scale forward genetic screens in bacteria. However, few methods enable comparison of TIS data across multiple replicates of a screen or across independent screens,...
Mutagenesis, Insertional High-Throughput Nucleotide Sequencing DNA Transposable Elements Vibrio cholerae Cluster Analysis Unsupervised Machine Learning Genomics Principal Component Analysis Bacterial Proteins
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SignalP 5.0 improves signal peptide predictions using deep neural networks.

Nature biotechnology Feb 18, 2019
Signal peptides (SPs) are short amino acid sequences in the amino terminus of many newly synthesized proteins that target proteins into, or across, membranes. Bioinformatic tools can predict SPs from amino acid sequences, but most cannot distinguish ...
Algorithms Computational Biology Bacterial Proteins Eukaryota Sequence Analysis, Protein Amino Acid Sequence Biotechnology Neural Networks, Computer Protein Sorting Signals Software Archaeal Proteins
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