“New sequencing technology, new data analytic methods and new insights in transcriptomics and epigenetics”
Hosted by the Department of Genetics
Abstract: Third Generation Sequencing/TGS (i.e., Oxford Nanopore Technologies/ONT and Pacific Biosciences/PacBio) can generate single-molecule long reads, ranging from a few kb to million bp. These data have been demonstrated very powerful to address many complex biomedical problems that remained unsolved by short reads. For example, the extensive applications of TGS data for genome research have been published in various biomedical contexts. Here, I will present the development of the bioinformatics methods and experimental assays for transcriptome and epigenetics research. In particular, we developed a series of software for identifying transcriptome events at the gene isoform level by integrating short reads and long reads, which resulted in the discovery of new pluripotency genes for nuclear reprogramming; we also established the first mathematical foundation to model the benefit of long reads in the quantitative analyses of transcriptome, such as gene isoform quantification; we also developed a new assay, MeSMLR-seq, to simultaneously characterize methylation, nucleosome occupancy and chromatin accessibility on single long DNA molecules, with which we were able to discover new epigenetic patterns at different transposable elements.
Full schedule, Genetics seminars
For inquiries contact Debbie Pfeiffer.
