Open Access. Powered by Scholars. Published by Universities.®
Articles 1 - 2 of 2
Full-Text Articles in Life Sciences
The Evolution Of Transposable Elements As Cis-Regulatory Elements In Mammals, Alan Y. Du
The Evolution Of Transposable Elements As Cis-Regulatory Elements In Mammals, Alan Y. Du
Arts & Sciences Electronic Theses and Dissertations
Transposable elements (TEs) are mobile genetic elements that make up a large proportion of mammalian genomes. Although TEs are highly prevalent genomic sequences, they have been understudied as they were once labeled as “junk DNA.” Despite their initial status as simple genomic parasites, recent studies have implicated TEs as cis-regulatory elements, supplying promoters, enhancers, and boundary elements. Functional testing of regulatory activity, however, remains a significant bottleneck. Nonetheless, due to their repetitive nature, TEs provide a unique model to examine the evolution of cis-regulatory elements, which has traditionally been difficult to study due to lack of homology at the sequence …
Robust Algorithms For Detecting Hidden Structure In Biological Data, Roman Sloutsky
Robust Algorithms For Detecting Hidden Structure In Biological Data, Roman Sloutsky
Arts & Sciences Electronic Theses and Dissertations
Biological data, such as molecular abundance measurements and protein
sequences, harbor complex hidden structure that reflects its underlying
biological mechanisms. For example, high-throughput abundance measurements
provide a snapshot the global state of a living cell, while homologous
protein sequences encode the residue-level logic of the proteins' function
and provide a snapshot of the evolutionary trajectory of the protein family.
In this work I describe algorithmic approaches and analysis software I
developed for uncovering hidden structure in both kinds of data.
Clustering is an unsurpervised machine learning technique commonly used
to map the structure of data collected in high-throughput experiments,
such …