AIMC Topic: Phylogeny

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Evaluation of fingerprinting techniques to assess genotype variation among Zygosaccharomyces strains.

Food microbiology Dec 1, 2017
Molecular typing techniques are key tools in surveillance of food spoilage yeasts, in investigations on intra-species population diversity, and in tracing selected starters during fermentation. Unlike previous works on strain typing of Zygosaccharomy...
Amplified Fragment Length Polymorphism Analysis Food Microbiology Polymorphism, Restriction Fragment Length DNA, Ribosomal Spacer DNA, Fungal Phylogeny Mycological Typing Techniques Zygosaccharomyces Genotype
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Phylogeny analysis from gene-order data with massive duplications.

BMC genomics Oct 16, 2017
BACKGROUND: Gene order changes, under rearrangements, insertions, deletions and duplications, have been used as a new type of data source for phylogenetic reconstruction. Because these changes are rare compared to sequence mutations, they allow the i...
Likelihood Functions Gene Duplication Gene Order Phylogeny
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Reconstructing One-Articulated Networks with Distance Matrices.

Journal of computational biology : a journal of computational molecular cell biology Oct 13, 2017
Given a distance matrix M that represents evolutionary distances between any two species, an edge-weighted phylogenetic network N is said to satisfy M if between any pair of species, there exists a path in N with a length equal to the corresponding e...
Neural Networks, Computer Algorithms Phylogeny
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Patchy promiscuity: machine learning applied to predict the host specificity of and .

Microbial genomics Oct 3, 2017
and are bacterial species that colonize different animal hosts with sub-types that can cause life-threatening infections in humans. Source attribution of zoonoses is an important goal for infection control as is identification of isolates in reserv...
Phylogeny Escherichia coli Salmonella enterica Machine Learning Humans Genomic Library Animals Zoonoses Host Specificity
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Clustering and Candidate Motif Detection in Exosomal miRNAs by Application of Machine Learning Algorithms.

Interdisciplinary sciences, computational life sciences Jul 22, 2017
BACKGROUND: The clustering pattern and motifs give immense information about any biological data. An application of machine learning algorithms for clustering and candidate motif detection in miRNAs derived from exosomes is depicted in this paper. Re...
Machine Learning Algorithms Reproducibility of Results Humans Exosomes Base Sequence Nucleotide Motifs Mice Animals Gene Ontology Cluster Analysis Phylogeny MicroRNAs
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Differentiating Thamnocalamus Munro from Fargesia Franchet emend. Yi (Bambusoideae, Poaceae): novel evidence from morphological and neural-network analyses.

Scientific reports Jun 23, 2017
Fargesia Franchet emend. Yi is closely allied with Thamnocalamus Munro but differs in many major morphological characteristics. Based on traditional morphological characters, it is difficult to differentiate these two genera. The current study measur...
Poaceae Geography Ecotype Cluster Analysis Principal Component Analysis Inflorescence Phylogeny Models, Theoretical Neural Networks, Computer
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Geminivirus data warehouse: a database enriched with machine learning approaches.

BMC bioinformatics May 5, 2017
BACKGROUND: The Geminiviridae family encompasses a group of single-stranded DNA viruses with twinned and quasi-isometric virions, which infect a wide range of dicotyledonous and monocotyledonous plants and are responsible for significant economic los...
Open Reading Frames Geminiviridae Databases, Genetic Plants DNA, Single-Stranded Computational Biology DNA, Viral Algorithms Machine Learning Phylogeny
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Machine Learning Techniques for Predicting Crop Photosynthetic Capacity from Leaf Reflectance Spectra.

Molecular plant Apr 28, 2017
Harnessing natural variation in photosynthetic capacity is a promising route toward yield increases, but physiological phenotyping is still too laborious for large-scale genetic screens. Here, we evaluate the potential of leaf reflectance spectroscop...
Crops, Agricultural Photosynthesis Machine Learning Plant Leaves Phenotype Phylogeny
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SILVA, RDP, Greengenes, NCBI and OTT - how do these taxonomies compare?

BMC genomics Mar 14, 2017
BACKGROUND: A key step in microbiome sequencing analysis is read assignment to taxonomic units. This is often performed using one of four taxonomic classifications, namely SILVA, RDP, Greengenes or NCBI. It is unclear how similar these are and how to...
Bacteria RNA, Ribosomal, 16S Microbiota Metagenomics Databases, Genetic Algorithms Phylogeny Gene Ontology Archaea
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Large-scale inference of gene function through phylogenetic annotation of Gene Ontology terms: case study of the apoptosis and autophagy cellular processes.

Database : the journal of biological databases and curation Dec 26, 2016
We previously reported a paradigm for large-scale phylogenomic analysis of gene families that takes advantage of the large corpus of experimentally supported Gene Ontology (GO) annotations. This 'GO Phylogenetic Annotation' approach integrates GO ann...
Gene Ontology Humans Autophagy Software Molecular Sequence Annotation Models, Genetic Animals Apoptosis Phylogeny Evolution, Molecular
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