Heejung Shim

Accurate identification of mRNA alternative splicing using Oxford Nanopore sequencing

The pre-mRNA alternative splicing events enable a single gene to produce different proteins in eukaryotes, and they have been shown to affect various gene functions, and eventually disease. The alternative splicing can not only add or skip entire exons, but can also vary exon boundaries by selecting different nucleotides as splice sites. Oxford Nanopore sequencing produces long reads that have natural advantages for characterising alternative splicing events. Nanopore sequencing records changes in electrical current when a DNA or RNA strand is traversing through a pore. This raw signal, known as a squiggle, is then basecalled by computational methods. However, due to the high error rate in the basecalling process, it is challenging to accurately identify exon boundaries using the basecalled sequences. In this talk, I will introduce new methods that use the squiggle to characterise the exon boundaries, in addition to the basecalled sequences.

Dr Heejung Shim

Group leader at Melbourne Integrative Genomics
Lecturer in Statistical genomics at School of Mathematics and Statistics, University of Melbourne

Dr. Heejung Shim is a Group Leader in the Melbourne Integrative Genomics (MIG) and Lecturer in the School of Mathematics and Statistics at the University of Melbourne. She completed her BS in Mathematics (with a double major in Computer Science and Engineering) from the POSTECH, and her PhD in Statistics from the University of Wisconsin at Madison, advised by Prof. Bret Larget. She did a postdoc at the University of Chicago working with Prof. Matthew Stephens. Previous to her position at the University of Melbourne, she was an Assistant Professor in the Department of Statistics at the Purdue University for two years.
Currently she retains an affiliation with Purdue as an Adjunct Assistant Professor.