Abstract
Modification of DNA and RNA is highly conserved across species and plays a key role in the ability for organisms to adapt to the environment through epigenetic mechanisms. During this project the candidate will analyse exciting new data from Oxford Nanopore Technologies (ONT) MinION, a 3rd generation sequencing technology. Through this technology it is possible to directly determine both DNA and RNA modifications and the student will develop Machine Learning tools to robustly detect these modifications. Through the application of these tools to interesting model organisms, the student will investigate the role in which these modifications contribute to environmental adaptation.
References
Nanopore detection of bacterial DNA base modifications. Alexa B.R. McIntyre, Noah Alexander, Aaron S. Burton, Sarah Castro-Wallace, Charles Y. Chiu, Kristen K. John, Sarah E. Stahl, Sheng Li, Christopher E. Mason bioRxiv 127100; doi: https://doi.org/10.1101/127100
De novo Identification of DNA Modifications Enabled by Genome-Guided Nanopore Signal Processing. Marcus H Stoiber, Joshua Quick, Rob Egan, Ji Eun Lee, Susan E Celniker, Robert Neely, Nicholas Loman, Len Pennacchio, James B Brown bioRxiv 094672; doi: https://doi.org/10.1101/094672