Genome-wide detection of cytosine methylations in plants from nanopore data using deep learning
About Feng Luo
Dr. Feng Luo is a professor at the School of Computing, Clemson University. He holds a Ph.D. in computer science from the University of Texas at Dallas. He was a postdoctoral senior research associate in the Department of Pathology at the University of Texas, Southwestern Medical Center at Dallas. His research interests are machine learning/deep learning, bioinformatics, and big data analytics. He has published 62 journal and 31 conference papers in these areas.
In plants, 5mCs can happen in three sequence contexts as CpG, CHG, and CHH. Although long nanopore sequencing reads are advantageous in the detection of 5mCs, existing methods can only detect 5mCs in the CpG context. Here, we develop a deep learning tool to detect genome-wide 5mCs of all three contexts in plants from nanopore reads. We develop a denoising process to enable DeepSignal-plant to achieve high correlations with bisulfite sequencing for 5mC detection in all three contexts. Furthermore, DeepSignal-plant can profile more 5mC sites, which will help to provide a more complete understanding of epigenetic mechanisms of different biological processes.