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Articles 1 - 7 of 7
Full-Text Articles in Life Sciences
Classification Of Breast Cancer Patients Using Somatic Mutation Profiles And Machine Learning Approaches, Suleyman Vural
Classification Of Breast Cancer Patients Using Somatic Mutation Profiles And Machine Learning Approaches, Suleyman Vural
Theses & Dissertations
The high degree of heterogeneity observed in breast cancers makes it very difficult to classify cancer patients into distinct clinical subgroups and consequently limits the ability to devise effective therapeutic strategies. In this study, we explore the use of gene mutation profiles to classify, characterize and predict the subgroups of breast cancers. We analyzed the whole exome sequencing data from 358 ethnically similar breast cancer patients in The Cancer Genome Atlas (TCGA) project. Identified somatic and non-synonymous single nucleotide variants were assigned a quantitative score (C-score) that represents the extent of negative impact on the function of the gene. Using …
Multipartite Graph Algorithms For The Analysis Of Heterogeneous Data, Charles Alexander Phillips
Multipartite Graph Algorithms For The Analysis Of Heterogeneous Data, Charles Alexander Phillips
Doctoral Dissertations
The explosive growth in the rate of data generation in recent years threatens to outpace the growth in computer power, motivating the need for new, scalable algorithms and big data analytic techniques. No field may be more emblematic of this data deluge than the life sciences, where technologies such as high-throughput mRNA arrays and next generation genome sequencing are routinely used to generate datasets of extreme scale. Data from experiments in genomics, transcriptomics, metabolomics and proteomics are continuously being added to existing repositories. A goal of exploratory analysis of such omics data is to illuminate the functions and relationships of …
Apply Data Clustering To Gene Expression Data, Abdullah Jameel Abualhamayl Mr.
Apply Data Clustering To Gene Expression Data, Abdullah Jameel Abualhamayl Mr.
Electronic Theses, Projects, and Dissertations
Data clustering plays an important role in effective analysis of gene expression. Although DNA microarray technology facilitates expression monitoring, several challenges arise when dealing with gene expression datasets. Some of these challenges are the enormous number of genes, the dimensionality of the data, and the change of data over time. The genetic groups which are biologically interlinked can be identified through clustering. This project aims to clarify the steps to apply clustering analysis of genes involved in a published dataset. The methodology for this project includes the selection of the dataset representation, the selection of gene datasets, Similarity Matrix Selection, …
Demographics And Transfer Of Escherichia Coli Within Bos Taurus Populations, Joshua Ryan Dillard
Demographics And Transfer Of Escherichia Coli Within Bos Taurus Populations, Joshua Ryan Dillard
Master's Theses
In the United States, symptoms caused by pathogenic strains of Escherichia coli are on the rise. A major source of these pathogenic strains is the E. coli in the digestive tract of cattle. The purpose of this project was to determine if E. coli are transferred between individuals of the same species and if interspecies transmission is possible. Proximity of cattle was also studied as a contributing factor to the transfer of E. coli. To accomplish this goal, E. coli isolates from cattle and cohabitating ground squirrels were compared through a new method of bacterial strain typing called pyroprinting. …
Plsi: A Computational Software Pipeline For Pathway Level Disease Subtype Identification, Michele Donato
Plsi: A Computational Software Pipeline For Pathway Level Disease Subtype Identification, Michele Donato
Wayne State University Theses
It is accepted that many complex diseases, like cancer, consist in collections of distinct genetic diseases. Clinical advances in treatments are attributed to molecular treatments aimed at specific genes resulting in greater ecacy and fewer debilitating side effects. This proves that it is important to identify and appropriately treat each individual disease subtype. Our current understanding of subtypes is limited: despite targeted treatment advances, targeted therapies often fail for some patients. The main limitation of current methods for subtype identification is that they focus on gene expression, and they are subject to its intrinsic noise. Signaling pathways describe biological processes …
Global Analysis Of Gene Expression And Projection Target Correlations In The Mouse Brain, Ahmed Fakhry, Tao Zeng, Hanchuan Peng, Shuiwang Ji
Global Analysis Of Gene Expression And Projection Target Correlations In The Mouse Brain, Ahmed Fakhry, Tao Zeng, Hanchuan Peng, Shuiwang Ji
Computer Science Faculty Publications
Recent studies have shown that projection targets in the mouse neocortex are correlated with their gene expression patterns. However, a brain-wide quantitative analysis of the relationship between voxel genetic composition and their projection targets is lacking to date. Here we extended those studies to perform a global, integrative analysis of gene expression and projection target correlations in the mouse brain. By using the Allen Brain Atlas data, we analyzed the relationship between gene expression and projection targets. We first visualized and clustered the two data sets separately and showed that they both exhibit strong spatial autocorrelation. Building upon this initial …
The Structural Heterogeneity And Dynamics Of Base Stacking And Unstacking In Nucleic Acids, Ada Anna Sedova
The Structural Heterogeneity And Dynamics Of Base Stacking And Unstacking In Nucleic Acids, Ada Anna Sedova
Legacy Theses & Dissertations (2009 - 2024)
Base stacking provides stability to nucleic acid duplexes, and base unstacking is involved in numerous biological functions related to nucleic acids, including replication, repair, transcription, and translation. The patterns of base stacking and unstacking in available nucleic acid crystal structures were classified after separation into their individual single strand dinucleotide components and clustering using a k-means-based ensemble clustering method. The A- and B-form proximity of these dinucleotide structures were assessed to discover that RNA dinucleotides can approach B-form-like structures. Umbrella sampling molecular dynamics simulations were used to obtain the potential of mean force profiles for base unstacking at 5'-termini for …