Large Scale Kmer-Based Proteomic Analysis: An Application Towards Evolutionary Constraint Discovery, Matthew Chak

Master's Theses

Large protein databases now make it possible to study short peptides across natural protein sequence space at unprecedented scale, but exhaustively counting k-mers across billions of protein sequences remains computationally difficult. This thesis develops an exact amino-acid k-mer counting method based on direct addressing, in which fixed-length amino-acid strings are encoded as base-20 integers and updated with a sliding-window recurrence. By avoiding key storage and collision resolution, this approach removes overhead inherent to hash-map-based methods when the k-mer space is sufficiently dense. A memory analysis shows when direct addressing is preferable to open-addressing hash tables, and expected-saturation calculations motivate its …

Topodino: Self-Supervised Topological Representation Learning For Neuronal Morphologies, Yasser Binbisher

Master's Theses

Neuronal cell types are categorized by transcriptomic identity, yet their morphological heterogeneity defies this classification. In response, researchers have adopted unsupervised graph representation learning as a tool to reveal morphological variation within single-class transcriptomic types. However, the complex geometry of neuronal morphology—especially long axons and dense dendrites—challenges graph neural networks, which struggle with message propagation across extended structures. To mitigate this, current approaches enforce sub-sampling on neuronal graphs and omit axons entirely, sacrificing critical biological features for computational efficiency. To overcome this trade-off, this thesis introduces TopoDINO, a self-supervised, topology-aware representation learning model designed to preserve the full hierarchical organization …

Annotation Of Non-Model Species’ Genomes, Taiya Jarva

Master's Theses

The innovations in high throughput sequencing technologies in recent decades has allowed unprecedented examination and characterization of the genetic make-up of both model and non-model species, which has led to a surge in the use of genomics in fields which were previously considered unfeasible. These advances have greatly expanded the realm of possibilities in the fields of ecology and conservation. It is now possible to the identification of large cohorts of genetic markers, including single nucleotide polymorphisms (SNPs) and larger structural variants, as well as signatures of selection and local adaptation. Markers can be used to identify species, define population …

Lotus: A Web-Based Computational Tool For The Preliminary Investigation Of A Novel Mst Method Utilizing A Library Of 16s Rrna Bacteroides Otus, Ginger Dewitte

Master's Theses

Microbial Source Tracking (MST) is a field of study that attempts to identify the source of fecal contamination in waterways in order to assist with development of remediation strategies. Biologists at Cal Poly Center for Applications in Biotechnology (CAB) are developing a new MST method using microbes from the genus Bacteroides. Bacteroides species are host-specific microorganisms that can theoretically be used to trace back to a single host species. After fecal samples are collected, biologists use Next-Generation Sequencing (NGS) techniques to obtain only the genetic sequences of microorganisms belonging to the phylum Bacteroidetes. Investigators hypothesize that similar sequences belong …

Characterizing Populations Of Non-Coding Rnas In Karenia Brevis At Different Times Of The Diel Cycle, Scott Boyd Anglin

Master's Theses

Karenia brevis is a mixotrophic, marine dinoflagellate found in the Gulf of Mexico that generates periodic, if not annual, harmful algal blooms (also known as “red tides”) in certain coastal areas. In an effort to better understand the biology of this organism, a functional genomics project has been initiated. As part of that project, it has been determined that a significant number of natural antisense transcripts (NATs) as well as double-stranded RNA (dsRNA) molecules exist within the transcriptome of K. brevis. I hypothesize that the non-coding NATs, similar to microRNAs (miRNAs) in other organisms play a role in regulating …

Detection Of Genomic Inversion From Single End Read, Pankaj Ghimire

Master's Theses

Structural Variations (SVs) are genomic rearrangements that include both copy-number variants,such as insertion,deletions, duplications and balanced variants like inversion and translocations. These SVs are getting more attentions for research and investigation because of their role on human phenotype, genetic diseases and genomic rearrangements. Evolution of Next-generation Sequencing has provided golden opportunities to investigate these variants and make their wider and clear spectrum in human genome. This investigation includes identification of type of SVs and their breakpoints at base pair level. For their effective identification and breakpoint resolution, many techniques are devised mainly based on paired end read. With relatively low …

Desert Hedgehog Is A Mammal-Specific Gene Expressed During Testicular And Ovarian Development In A Marsupial, William A. O'Hara

Master's Theses

Desert hedgehog (DHH) belongs to the hedgehog gene family that act as secreted intercellular signal transducers. DHH is an essential morphogen for normal testicular development and function in both mice and humans but is not present in the avian lineage. Like other hedgehog proteins, DHH signals through the patched (PTCH) receptors 1 and 2. Here we examine the expression and protein distribution of DHH, PTCH1 and PTCH2 in the developing testes of a marsupial mammal (the tammar wallaby) to determine whether DHH signalling is a conserved factor in gonadal development in all therian mammals.