I am a post-doctoral research fellow in the Center for Computational Biology at the Johns Hopkins University School of Medicine, where I have the privilege of working closely with its director, Dr. Steven Salzberg. My research interests include RNA-seq analysis, with a focus on alignment and transcript reconstruction. I developed a new spliced aligner, HISAT (Hierarchical Indexing for Spliced Alignment of Transcript). HISAT achieves dramatically faster performance than any other method, with equal or better alignment accuracy and low memory requirements. HISAT uses a new indexing scheme, hierarchical indexing, which is based on the Burrows-Wheeler transform and the Ferragina-Manzini (FM) index. Hierarchical indexing employs two types of indexes for alignment: (1) a whole-genome FM index to anchor each alignment, and (2) numerous local FM indexes for very rapid extensions of these alignments. For example, HISAT’s hierarchical index for the human genome contains 48,000 local FM indexes, each representing a genomic region of ~64,000 bp. See more details at the HISAT website. I have recently developed HISAT2 by extending HISAT to enable alignment against a population of genomes.

I received my Ph.D. degree in Computer Science from the University of Maryland, College Park (May 2013). During my Ph.D. studies, I led the development of TopHat2, a spliced aligner for RNA-sequencing reads. I have also been working on Cufflinks, which assembles and quantifies transcripts (mRNA). In particular, based on TopHat2 and Cufflinks, I have designed and implemented a new software pipeline to identify fusion genes, which result from the breakage and re-joining of two different chromosomes, or from rearrangements within a chromosome.

Before beginning my Ph.D. program in the fall of 2008, I spent five years working at a software development company for computer games in South Korea where I managed several project teams and worked as a main developer. While working at the company, I had the chance to learn a variety of programming skills including 3D graphics rendering engines such as Ogre, Gamebryo, Torque and networking programing based on ACE for both server and client sides. In addition, I spent considerable time with my colleagues developing a general framework for computer games, all of which turned out to be very helpful for doing my own research. Some screen shots of the games I worked on can be found at pic1, pic2, and pic3.

I enjoy staying active through marathon and swimming trainning. I have so far participated in thirteen marathons including the Boston marathon, the New York City marathon, the Chicago marathon, and the Marine Corps marathon. I have also enjoyed studying different martial arts, including taekwondo, hapkido, and judo. I have done some rollerblading too but I have since then been focusing on the marathon training. Besides doing research and working out, I like to explore a variety of subjects. It turns out that the cell research I've been doing requires many disciplines in addition to computer science, such as biology, medicine, chemistry, mathematics (statistics), and some others, which means I have enough materials to study in my life (see the list of books I've read and the list of courses I've taken). There is so much out there to learn than can be studied in a human lifetime.