Open Access. Powered by Scholars. Published by Universities.®
- Keyword
-
- Bioinformatics (1)
- COVID-19 (1)
- Chaos Game Representation (1)
- Chiroptera (1)
- Cimicidae (1)
-
- Comparative genomics (1)
- DNA (1)
- Digital Signal Processing (1)
- Genetic differentiation (1)
- Genetic diversity (1)
- Landscape genetics (1)
- Machine Learning (1)
- Mitochondrial genome (1)
- Nucleomorph genome (1)
- Organelle gene expression (1)
- Pervasive transcription (1)
- Phylogenetics. (1)
- Plastid genome (1)
- RNA-seq (1)
- Species' relatedness (1)
- Taxonomic classification (1)
- Whole genome analysis (1)
Articles 1 - 4 of 4
Full-Text Articles in Life Sciences
Machine Learning With Digital Signal Processing For Rapid And Accurate Alignment-Free Genome Analysis: From Methodological Design To A Covid-19 Case Study, Gurjit Singh Randhawa
Machine Learning With Digital Signal Processing For Rapid And Accurate Alignment-Free Genome Analysis: From Methodological Design To A Covid-19 Case Study, Gurjit Singh Randhawa
Electronic Thesis and Dissertation Repository
In the field of bioinformatics, taxonomic classification is the scientific practice of identifying, naming, and grouping of organisms based on their similarities and differences. The problem of taxonomic classification is of immense importance considering that nearly 86% of existing species on Earth and 91% of marine species remain unclassified. Due to the magnitude of the datasets, the need exists for an approach and software tool that is scalable enough to handle large datasets and can be used for rapid sequence comparison and analysis. We propose ML-DSP, a stand-alone alignment-free software tool that uses Machine Learning and Digital Signal Processing to …
Unravelling Organelle Genome Transcription Using Publicly Available Rna-Sequencing Data, Matheus Sanita Lima
Unravelling Organelle Genome Transcription Using Publicly Available Rna-Sequencing Data, Matheus Sanita Lima
Electronic Thesis and Dissertation Repository
The study of organelles helped forge theories of genome evolution because of their unconventional genomes and gene expression regimes. The organelle genomics field (~35 years old) has seen the development of next generation sequencing (NGS) techniques and the consequent skyrocketing of genomic and transcriptomic data. However, these data are being underused in the studies of organelle genome transcription. My thesis investigates how NGS has affected the field of organelle genomics at both the DNA and RNA levels. First, I demonstrate that although organelle genomes are being sequenced as never before, they are un-characterized as they are published mostly as “organelle …
Evolutionary Genetic Aspects Of Host Association In Generalist Ectoparasites, Benoit Talbot
Evolutionary Genetic Aspects Of Host Association In Generalist Ectoparasites, Benoit Talbot
Electronic Thesis and Dissertation Repository
Despite the use of the host for dispersal by most parasite species, the extremely loose relationship typical between highly mobile hosts and generalist ectoparasites may lead to very different gene flow patterns between the two, leading in turn to different spatial genetic structure, and potentially different demographic history. I examined how similar gene flow patterns are between Cimex adjunctus, a generalist ectoparasite of bats present throughout North America, and two of its key bat hosts. I first analyzed the continent-scale genetic structure and demographic history of C. adjunctus and compared it to that of two of its hosts, the …
A Quantitative Method For Measuring And Visualizing Species' Relatedness In A Two-Dimensional Euclidean Space., Abu Sadat Md. Sayem
A Quantitative Method For Measuring And Visualizing Species' Relatedness In A Two-Dimensional Euclidean Space., Abu Sadat Md. Sayem
Electronic Thesis and Dissertation Repository
Representing DNA sequences graphically and evaluating, as well as displaying, species’ relationships have been considered to be an important aspect of molecular biology research. A novel approach is proposed in this thesis that combines three methods: a) Chaos Game Representation (CGR), to portray quantitative characteristics of a DNA sequence as a black-and -white image, b) Structural Similarity (SSIM) index, an image comparison method, to compute pair-wise distances between these images, and c) Multidimensional Scaling (MDS), to visually display each sequence as a point in a two-dimensional Euclidean space. The proposed method produces a visual representation called Genome Distance Map (GDM) …