AIMC Topic: Sequence Analysis, DNA
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Large-scale machine learning for metagenomics sequence classification.
Bioinformatics (Oxford, England)
Nov 20, 2015
MOTIVATION: Metagenomics characterizes the taxonomic diversity of microbial communities by sequencing DNA directly from an environmental sample. One of the main challenges in metagenomics data analysis is the binning step, where each sequenced read i...
Genome-Wide Locations of Potential Epimutations Associated with Environmentally Induced Epigenetic Transgenerational Inheritance of Disease Using a Sequential Machine Learning Prediction Approach.
PloS one
Nov 16, 2015
Environmentally induced epigenetic transgenerational inheritance of disease and phenotypic variation involves germline transmitted epimutations. The primary epimutations identified involve altered differential DNA methylation regions (DMRs). Differen...
Spermatozoa
Environmental Exposure
Granulosa Cells
CpG Islands
Chromosomes
Humans
DDT
Machine Learning
Methoxychlor
DNA Methylation
Male
Cluster Analysis
Genome-Wide Association Study
Bayes Theorem
Phenotype
Genetic Predisposition to Disease
Mutation
Female
Computational Biology
Sertoli Cells
Epigenesis, Genetic
Reproducibility of Results
Databases, Genetic
Sequence Analysis, DNA
Codon bias and gene ontology in holometabolous and hemimetabolous insects.
Journal of experimental zoology. Part B, Molecular and developmental evolution
Oct 26, 2015
The relationship between preferred codon use (PCU), developmental mode, and gene ontology (GO) was investigated in a sample of nine insect species with sequenced genomes. These species were selected to represent two distinct modes of insect developme...
The identification of cis-regulatory elements: A review from a machine learning perspective.
Bio Systems
Oct 21, 2015
The majority of the human genome consists of non-coding regions that have been called junk DNA. However, recent studies have unveiled that these regions contain cis-regulatory elements, such as promoters, enhancers, silencers, insulators, etc. These ...
iTIS-PseKNC: Identification of Translation Initiation Site in human genes using pseudo k-tuple nucleotides composition.
Computers in biology and medicine
Sep 25, 2015
Translation is an essential genetic process for understanding the mechanism of gene expression. Due to the large number of protein sequences generated in the post-genomic era, conventional methods are unable to identify Translation Initiation Site (T...
Improving tRNAscan-SE Annotation Results via Ensemble Classifiers.
Molecular informatics
Sep 14, 2015
tRNAScan-SE is a tRNA detection program that is widely used for tRNA annotation; however, the false positive rate of tRNAScan-SE is unacceptable for large sequences. Here, we used a machine learning method to try to improve the tRNAScan-SE results. A...
Effects of bovine subclinical mastitis caused by Corynebacterium spp. on somatic cell count, milk yield and composition by comparing contralateral quarters.
Veterinary journal (London, England : 1997)
Aug 11, 2015
Subclinical mastitis caused by Corynebacterium spp. (as a group and at the species level) was investigated by evaluating contralateral (healthy and infected) mammary quarters for somatic cell count (SCC), milk yield and composition. Selection of cows...
Rediscovery of Good-Turing estimators via Bayesian nonparametrics.
Biometrics
Jul 29, 2015
The problem of estimating discovery probabilities originated in the context of statistical ecology, and in recent years it has become popular due to its frequent appearance in challenging applications arising in genetics, bioinformatics, linguistics,...
Genome Modeling System: A Knowledge Management Platform for Genomics.
PLoS computational biology
Jul 9, 2015
In this work, we present the Genome Modeling System (GMS), an analysis information management system capable of executing automated genome analysis pipelines at a massive scale. The GMS framework provides detailed tracking of samples and data coupled...
Application of comparative biology in GO functional annotation: the mouse model.
Mammalian genome : official journal of the International Mammalian Genome Society
Jul 4, 2015
The Gene Ontology (GO) is an important component of modern biological knowledge representation with great utility for computational analysis of genomic and genetic data. The Gene Ontology Consortium (GOC) consists of a large team of contributors incl...
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