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Articles 1 - 6 of 6
Full-Text Articles in Bioinformatics
The Identification Of Long Non-Coding Rna Zfas1 Through An Exploratory Rna-Sequencing Analysis And Its Association With Epithelial-To-Mesenchymal Transition In Colon Cancer Adenocarcinoma., Stephen J. O'Brien
Electronic Theses and Dissertations
Colorectal adenocarcinoma is the fourth most common cancer diagnosed worldwide and is a significant cause of morbidity and mortality. This dissertation performed an exploratory RNA-sequencing analysis comparing gene expression between colon adenocarcinoma tissue and paired normal colon epithelium. After identification of a number of lncRNAs that were increased in expression in colon adenocarcinoma compared to normal colon epithelium, we aimed to validate the expression and investigate their function in vitro. Specifically, we focused on the lncRNA ZFAS1 and its association with epithelial-to-mesenchymal transition. These studies found the following: 1. Seven candidate lncRNAs were identified from the exploratory RNA-sequencing analysis to …
Response Of Early Life Stage Homarus Americanus To Ocean Warming And Acidification: An Interpopulation Comparison, Maura K. Niemisto
Response Of Early Life Stage Homarus Americanus To Ocean Warming And Acidification: An Interpopulation Comparison, Maura K. Niemisto
Electronic Theses and Dissertations
Anthropogenic carbon released into the atmosphere is driving rapid, concurrent increases in temperature and acidity across the world’s oceans, most prominently in northern latitudes. The geographic range of the iconic American lobster (Homarus americanus) spans a steep thermal gradient and one of the most rapidly warming oceanic environments. Understanding the interactive effects of ocean warming and acidification on this species’ most vulnerable early life stages is important to predict its response to climate change on a stage-specific and population level. This study compares the responses of lobster larvae from two sub-populations spanning New England’s north-south temperature gradient (southern …
Designing And Sample Size Calculation In Presence Of Heterogeneity In Biological Studies Involving High-Throughput Data., Sudhir Srivastava
Designing And Sample Size Calculation In Presence Of Heterogeneity In Biological Studies Involving High-Throughput Data., Sudhir Srivastava
Electronic Theses and Dissertations
The designing and determination of sample size are important for conducting high-throughput biological experiments such as proteomics experiments and RNA-Seq expression studies, thus leading to better understanding of complex mechanisms underlying various biological processes. The variations in the biological data or technical approaches to data collection lead to heterogeneity for the samples under study. We critically worked on the issues of technical and biological heterogeneity. The quantitative measurements based on liquid chromatography (LC) coupled with mass spectrometry (MS) often suffer from the problem of missing values (MVs) and data heterogeneity. We considered a proteomics data set generated from human kidney …
Development Of Computational Techniques For Identification Of Regulatory Dna Motif, Cankun Wang
Development Of Computational Techniques For Identification Of Regulatory Dna Motif, Cankun Wang
Electronic Theses and Dissertations
Identifying precise transcription factor binding sites (TFBS) or regulatory DNA motif (motif) plays a fundamental role in researching transcriptional regulatory mechanism in cells and helping construct regulatory networks for biological investigation. Chromatin immunoprecipitation combined with sequencing (ChIP-seq) and lambda exonuclease digestion followed by high-throughput sequencing (ChIP-exo) enables researchers to identify TFBS on a genome-scale with improved resolution. Several algorithms have been developed to perform motif identification, employing widely different methods and often giving divergent results. In addition, these existing methods still suffer from prediction accuracy. Thesis focuses on the development of improved regulatory DNA motif identification techniques. We designed an …
Applying Machine Learning Algorithms For The Analysis Of Biological Sequences And Medical Records, Shaopeng Gu
Applying Machine Learning Algorithms For The Analysis Of Biological Sequences And Medical Records, Shaopeng Gu
Electronic Theses and Dissertations
The modern sequencing technology revolutionizes the genomic research and triggers explosive growth of DNA, RNA, and protein sequences. How to infer the structure and function from biological sequences is a fundamentally important task in genomics and proteomics fields. With the development of statistical and machine learning methods, an integrated and user-friendly tool containing the state-of-the-art data mining methods are needed. Here, we propose SeqFea-Learn, a comprehensive Python pipeline that integrating multiple steps: feature extraction, dimensionality reduction, feature selection, predicting model constructions based on machine learning and deep learning approaches to analyze sequences. We used enhancers, RNA N6- methyladenosine sites and …
Impact Of Seasonal And Host-Related Factors On The Intestinal Microbiome And Cestode Community Of Sorex Cinereus And Sorex Monticola, Katelyn D. Cranmer
Impact Of Seasonal And Host-Related Factors On The Intestinal Microbiome And Cestode Community Of Sorex Cinereus And Sorex Monticola, Katelyn D. Cranmer
Electronic Theses and Dissertations
The intestinal microbiome of mammals plays a significant role in host health and response to environmental stimuli and can include both beneficial native bacteria as well as parasitic worms. In this study, I examined the intestinal cestode and bacterial communities of two closely related species of shrew, Sorex monticola and Sorex cinereus, over a six month period in 2016. Specimens were collected approximately every three weeks from May to October from the Sangre de Cristo Mountains in Cowles, New Mexico. A total of 79 shrews were prepared with the gastrointestinal tracts removed and flash-frozen in liquid nitrogen. An additional …