I am Michael L. Rosenberg Assistant Professor in the Lyda Hill Department of Bioinformatics, and a Scholar of the Cancer Prevention Research Institute of Texas (CPRIT). See also my Google Scholar Page, CV, GitHub, and Faculty Profile at the University of Texas Southwestern Medical Center.
For my post-doctoral research (2013-2017) I joined the Center for Computational Biology at the Johns Hopkins University School of Medicine. I developed several software systems, most notably a new spliced aligner, HISAT. HISAT performs dramatically faster than competing methods, with equal or better alignment accuracy and low memory requirements. I am also a graduate of New England BioLabs’ annual two-week Molecular Biology Summer Workshop (2016), principally covering cloning, gene expression, Quantitative RT-PCR, RNA interference, CRISPR/Cas9, and DNA fingerprinting, and had since worked in the wet-lab of Prof. Taekjip Ha.
I completed my Ph.D. (May 2013) in the Department of Computer Science at the University of Maryland, College Park, where I joined the research group led by Dr. Steven Salzberg in the Center for Computational Biology and Bioinformatics. During this period I deepened my knowledge of various genomic computational tools, molecular biology, and biochemistry. While at the Center, I became the lead developer of the TopHat2 project. TopHat2 is an alignment system for RNA-sequencing reads and has been the most popular spliced aligner since its first release in 2008. I also devised a novel algorithm, TopHat-Fusion, to discover fusion genes, which result from the breakage and re-joining of two different chromosomes, a common occurrence in some types of cancer. TopHat-Fusion significantly reduced false positive discovery of fusions, the biggest problem suffered by other fusion finding programs, while allowing for more sensitive detection of fusions.
I have a B.S. in Computer Science and Engineering from Chung-Ang University, South Korea (February 2004). I worked for five years at a software development company in Korea (2003-2008) where I managed several project teams and worked as a lead developer for creating a variety of computer games, gaining professional-level programming skills for handling large-scale projects. This experience has proven essential to carrying out my work as an academic researcher.
I enjoy staying active through marathon and swimming training (see my Sports page). 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. I have come to appreciate that the genomics research I have been doing is best pursued with multi-disciplinary knowledge beyond computer science, such as in biology, medicine, chemistry, mathematics (statistics), and some other fields (see a list of related books I’ve read). There is so much out there to learn than can be studied in a human lifetime.