AIMC Topic: Escherichia coli Proteins

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Understanding and predicting ciprofloxacin minimum inhibitory concentration in Escherichia coli with machine learning.

Scientific reports Sep 14, 2020
It is important that antibiotics prescriptions are based on antimicrobial susceptibility data to ensure effective treatment outcomes. The increasing availability of next-generation sequencing, bacterial whole genome sequencing (WGS) can facilitate a ...
Anti-Bacterial Agents Drug Resistance, Bacterial Escherichia coli Mutation Machine Learning Escherichia coli Proteins Toxicity Tests DNA Gyrase Intracellular Signaling Peptides and Proteins Ciprofloxacin Inhibitory Concentration 50 Genes, Bacterial
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Emergence of mcr-1 mediated colistin resistant Escherichia coli from a hospitalized patient in Bangladesh.

Journal of infection in developing countries Aug 31, 2019
INTRODUCTION: The emergence of plasmid mediated mcr in bacteria has become global public health threat. Herein, we report a mcr-1 positive E. coli in normal human flora from a patient admitted in Dhaka Medical College Hospital (DMCH).
Hospitals Escherichia coli Infections Humans Bangladesh Microbial Sensitivity Tests Anti-Bacterial Agents Plasmids Escherichia coli Colistin Drug Resistance, Bacterial Escherichia coli Proteins
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Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models.

Nature communications Dec 7, 2018
Knowing the catalytic turnover numbers of enzymes is essential for understanding the growth rate, proteome composition, and physiology of organisms, but experimental data on enzyme turnover numbers is sparse and noisy. Here, we demonstrate that machi...
Biocatalysis Escherichia coli Proteins Machine Learning Algorithms Proteome Escherichia coli Metabolic Networks and Pathways Kinetics Models, Biological
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In vitro activity of flomoxef against extended-spectrum β-lactamase-producing Escherichia coli and Klebsiella pneumoniae in Korea.

Diagnostic microbiology and infectious disease Nov 26, 2018
To find an alternative regimen for the treatment of extended-spectrum β-lactamase (EBSL)-producing Enterobacteriaceae infections, we examined the in vitro activity of flomoxef against Escherichia coli and Klebsiella pneumoniae having CTX-M-1 group an...
Escherichia coli Escherichia coli Infections beta-Lactamases Hospitals, University Cephalosporins Humans Microbial Sensitivity Tests Escherichia coli Proteins Anti-Bacterial Agents Klebsiella pneumoniae Korea Klebsiella Infections
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Computational Prediction of Sigma-54 Promoters in Bacterial Genomes by Integrating Motif Finding and Machine Learning Strategies.

IEEE/ACM transactions on computational biology and bioinformatics Mar 15, 2018
Sigma factor, as a unit of RNA polymerase holoenzyme, is a critical factor in the process of gene transcriptional regulation. It recognizes the specific DNA sites and brings the core enzyme of RNA polymerase to the upstream regions of target genes. T...
Machine Learning Escherichia coli Models, Statistical Escherichia coli Proteins Base Sequence Software Reproducibility of Results Computational Biology Genome, Bacterial False Positive Reactions Amino Acid Motifs DNA-Directed RNA Polymerases Promoter Regions, Genetic Transcription, Genetic RNA Polymerase Sigma 54
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Boosted neural networks scoring functions for accurate ligand docking and ranking.

Journal of bioinformatics and computational biology Feb 4, 2018
Predicting the native poses of ligands correctly is one of the most important steps towards successful structure-based drug design. Binding affinities (BAs) estimated by traditional scoring functions (SFs) are typically used to score and rank-order p...
Ligands Escherichia coli Proteins tRNA Methyltransferases Proteins Databases, Protein Structure-Activity Relationship Neural Networks, Computer Machine Learning Drug Design Protein Binding Algorithms Molecular Docking Simulation
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Sequence-Based Prediction of Cysteine Reactivity Using Machine Learning.

Biochemistry Oct 26, 2017
As one of the most intrinsically reactive amino acids, cysteine carries a variety of important biochemical functions, including catalysis and redox regulation. Discovery and characterization of cysteines with heightened reactivity will help annotate ...
Amino Acid Motifs Tandem Mass Spectrometry Escherichia coli Proteins Cysteine Recombinant Proteins Sequence Alignment Proteomics Chromatography, Liquid Machine Learning Decision Support Techniques Humans
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Recurrent neural network-based modeling of gene regulatory network using elephant swarm water search algorithm.

Journal of bioinformatics and computational biology Jun 13, 2017
Correct inference of genetic regulations inside a cell from the biological database like time series microarray data is one of the greatest challenges in post genomic era for biologists and researchers. Recurrent Neural Network (RNN) is one of the mo...
Models, Genetic Escherichia coli Escherichia coli Proteins Gene Expression Regulation, Bacterial Neural Networks, Computer Gene Regulatory Networks Algorithms Computational Biology
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Multitask Protein Function Prediction through Task Dissimilarity.

IEEE/ACM transactions on computational biology and bioinformatics Mar 17, 2017
Automated protein function prediction is a challenging problem with distinctive features, such as the hierarchical organization of protein functions and the scarcity of annotated proteins for most biological functions. We propose a multitask learning...
Humans Machine Learning Models, Statistical Proteins Algorithms Computational Biology Escherichia coli Proteins Drosophila Proteins Gene Ontology
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A New Feature Vector Based on Gene Ontology Terms for Protein-Protein Interaction Prediction.

IEEE/ACM transactions on computational biology and bioinformatics Apr 20, 2016
Protein-protein interaction (PPI) plays a key role in understanding cellular mechanisms in different organisms. Many supervised classifiers like Random Forest (RF) and Support Vector Machine (SVM) have been used for intra or inter-species interaction...
Saccharomyces cerevisiae Proteins Escherichia coli Proteins Drosophila Proteins Gene Ontology Protein Interaction Mapping Support Vector Machine Proteins Humans Databases, Protein Animals ROC Curve Computational Biology
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