AIMC Topic: Genome, Bacterial

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ML-DSP: Machine Learning with Digital Signal Processing for ultrafast, accurate, and scalable genome classification at all taxonomic levels.

BMC genomics Apr 3, 2019
BACKGROUND: Although software tools abound for the comparison, analysis, identification, and classification of genomic sequences, taxonomic classification remains challenging due to the magnitude of the datasets and the intrinsic problems associated ...
Computer Simulation Animals Genomics Machine Learning Software Algorithms Genome, Mitochondrial Genome, Bacterial Vertebrates Humans Signal Processing, Computer-Assisted Dengue Virus Genome, Viral
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Incorporating microbial community data with machine learning techniques to predict feed substrates in microbial fuel cells.

Biosensors & bioelectronics Mar 13, 2019
The complicated interactions that occur in mixed-species biotechnologies, including biosensors, hinder chemical detection specificity. This lack of specificity limits applications in which biosensors may be deployed, such as those where an unknown fe...
Bacteria Acetates Microbiota Carbohydrates Genome, Bacterial Algorithms Biosensing Techniques Genomics Machine Learning Wastewater
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Using Machine Learning To Predict Antimicrobial MICs and Associated Genomic Features for Nontyphoidal .

Journal of clinical microbiology Jan 30, 2019
Nontyphoidal species are the leading bacterial cause of foodborne disease in the United States. Whole-genome sequences and paired antimicrobial susceptibility data are available for strains because of surveillance efforts from public health agencie...
Humans Machine Learning Drug Resistance, Bacterial Foodborne Diseases Genotyping Techniques Salmonella Infections Microbial Sensitivity Tests Salmonella United States Genome, Bacterial
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Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance.

Nature communications Oct 17, 2018
Mycobacterium tuberculosis is a serious human pathogen threat exhibiting complex evolution of antimicrobial resistance (AMR). Accordingly, the many publicly available datasets describing its AMR characteristics demand disparate data-type analyses. He...
Gene Frequency Selection, Genetic Genome, Bacterial Machine Learning Drug Resistance, Bacterial Mycobacterium tuberculosis
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Functional Annotation of Proteins Encoded by the Minimal Bacterial Genome Based on Secondary Structure Element Alignment.

Journal of proteome research May 24, 2018
In synthetic biology, one of the key focuses is building a minimal artificial cell which can provide basic chassis for functional study. Recently, the J. Craig Venter Institute published the latest version of the minimal bacterial genome JCVI-syn3.0,...
Genome, Bacterial Protein Structure, Secondary Sequence Homology, Amino Acid Bacterial Proteins Supervised Machine Learning Molecular Sequence Annotation Artificial Intelligence Algorithms
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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 Software Reproducibility of Results Promoter Regions, Genetic Transcription, Genetic Genome, Bacterial Amino Acid Motifs DNA-Directed RNA Polymerases RNA Polymerase Sigma 54 Escherichia coli Proteins Base Sequence False Positive Reactions Computational Biology Escherichia coli Models, Statistical
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1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life.

Nature biotechnology Jun 12, 2017
We present 1,003 reference genomes that were sequenced as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) initiative, selected to maximize sequence coverage of phylogenetic space. These genomes double the number of existing type strai...
Chromosome Mapping Encyclopedias as Topic Genome, Archaeal Datasets as Topic Genome, Bacterial Database Management Systems Knowledge Bases Reference Values High-Throughput Nucleotide Sequencing Databases, Genetic
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An improved method for identification of small non-coding RNAs in bacteria using support vector machine.

Scientific reports Apr 6, 2017
Bacterial small non-coding RNAs (sRNAs) are not translated into proteins, but act as functional RNAs. They are involved in diverse biological processes like virulence, stress response and quorum sensing. Several high-throughput techniques have enable...
Machine Learning Reproducibility of Results Computational Biology RNA, Bacterial Support Vector Machine RNA, Small Untranslated Databases, Genetic Genome, Bacterial
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Genomic Islands: an overview of current software and future improvements.

Journal of integrative bioinformatics Dec 22, 2016
Microbes are highly diverse and widely distributed organisms. They account for ~60% of Earth’s biomass and new predictions point for the existence of 1011 to 1012 species, which are constantly sharing genes through several different mechanisms....
Sequence Analysis, DNA Software Genomic Islands Bacteria Genome, Bacterial
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Genome-wide prediction of prokaryotic two-component system networks using a sequence-based meta-predictor.

BMC bioinformatics Sep 18, 2015
BACKGROUND: Two component systems (TCS) are signalling complexes manifested by a histidine kinase (receptor) and a response regulator (effector). They are the most abundant signalling pathways in prokaryotes and control a wide range of biological pro...
Protein Kinases Genome, Bacterial Histidine Kinase Support Vector Machine Area Under Curve ROC Curve Bacterial Proteins Protein Interaction Maps Bacteria
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