Matthew Redlinger (MS candidate in biological sciences) will defend his thesis on Friday, Jan. 26 at 2 p.m. in CPSB 120 and on Zoom.

Thesis Details

Title

Enrichment and Assembly of Viral Genomes for Next-Generation Sequencing

Abstract

Emerging techniques and technologies in the field of DNA sequencing have brought with them new challenges and opportunities. Here we present responses to these challenges and utilize the opportunities provided to improve sequencing of viral genomes: Epstein-Barr virus (EBV, a DNA virus), and viruses with RNA genomes: SARS-CoV-2,  hepatitis C virus (HCV), HIV, and orthoreovirus. Latent EBV DNA genomes were enriched using pulse field gel electrophoresis, Hirt extraction and lytic reactivation of latent EBV in cell culture. We used de novo and reference-based bioinformatics assembly methods to identify characteristics of EBV and HCV genomic populations discernible by nanopore but not short read sequencing. Following this we developed an assembly pipeline for tiling primer libraries capable of assembling genomes with a high level of variability, a shortcoming of the current tiling primer assemblers.

Event Details

Event location - CPSB 120 and Zoom
Event date - Jan. 26, 2024
Event start time - 2 p.m.
Event end time - 3:30 p.m.

Zoom Details

Meeting ID: 873 4761 3259
Passcode: 217443

Zoom Link

 

January Archive