AIMC Topic: Phylogeny

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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...
Animals Phylogeny Mice Machine Learning Algorithms Reproducibility of Results Base Sequence Gene Ontology Nucleotide Motifs Humans Cluster Analysis MicroRNAs Exosomes
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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...
Phylogeny Principal Component Analysis Models, Theoretical Ecotype Neural Networks, Computer Cluster Analysis Poaceae Inflorescence Geography
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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...
Machine Learning Algorithms Databases, Genetic Plants DNA, Single-Stranded Phylogeny Computational Biology DNA, Viral Open Reading Frames Geminiviridae
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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...
Photosynthesis Phylogeny Plant Leaves Crops, Agricultural Machine Learning Phenotype
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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...
Microbiota Metagenomics Gene Ontology Archaea Bacteria RNA, Ribosomal, 16S Databases, Genetic Algorithms Phylogeny
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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...
Software Autophagy Models, Genetic Animals Humans Apoptosis Evolution, Molecular Phylogeny Molecular Sequence Annotation Gene Ontology
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The development of loop-mediated isothermal amplification combined with lateral flow dipstick for detection of Karlodinium veneficum.

Harmful algae Dec 21, 2016
The aim of this study was to develop a loop-mediated isothermal amplification (LAMP) combined with a chromatographic lateral flow dipstick (LFD) assay to rapidly and specifically detect the Karlodinium veneficum ITS gene. Four groups of LAMP primers ...
RNA, Algal Phylogeny RNA, Protozoan China Sensitivity and Specificity Chromatography Nucleic Acid Amplification Techniques Dinoflagellida DNA, Ribosomal Spacer
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Identification of DEP domain-containing proteins by a machine learning method and experimental analysis of their expression in human HCC tissues.

Scientific reports Dec 21, 2016
The Dishevelled/EGL-10/Pleckstrin (DEP) domain-containing (DEPDC) proteins have seven members. However, whether this superfamily can be distinguished from other proteins based only on the amino acid sequences, remains unknown. Here, we describe a com...
Humans Machine Learning Algorithms Phylogeny Gene Expression Profiling Signal Transduction Cluster Analysis Computational Biology Protein Domains Amino Acid Motifs RNA, Messenger Real-Time Polymerase Chain Reaction GTPase-Activating Proteins Gene Expression Regulation, Neoplastic Liver Neoplasms Dishevelled Proteins Carcinoma, Hepatocellular
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Expansion of the Gene Ontology knowledgebase and resources.

Nucleic acids research Nov 29, 2016
The Gene Ontology (GO) is a comprehensive resource of computable knowledge regarding the functions of genes and gene products. As such, it is extensively used by the biomedical research community for the analysis of -omics and related data. Our conti...
Web Browser Databases, Genetic Phylogeny Molecular Sequence Annotation Gene Ontology Genomics Computational Biology
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Integrated Automatic Workflow for Phylogenetic Tree Analysis Using Public Access and Local Web Services.

Journal of integrative bioinformatics Nov 28, 2016
At the present, coding sequence (CDS) has been discovered and larger CDS is being revealed frequently. Approaches and related tools have also been developed and upgraded concurrently, especially for phylogenetic tree analysis. This paper proposes an ...
Models, Genetic Software Internet Phylogeny
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