Yale University Gerstein Lab

Name: Chan Long Landon
Institute: Gerstein Lab
University: Yale University
Period: Summer, 2015

Thanks to the GPS program, I had the opportunity to attach to the Gerstein Lab, Yale University for 10 weeks in the summer 2015.

The Gerstein Lab is one of the biggest bioinformatics labs in the United States. It is involved in many international consortiums related to genomic annotations and comparative genomics such as the Encyclopedia of DNA Elements (ENCODE) and 1000 Genomes Project.

This summer, I worked on a project on targeted enhancer predictions under the supervision of Dr. Anurag Sethi. Enhancers are one of the key genomic regulatory elements that increase gene expressions. Understanding enhancers are particularly important in developmental biology and certain diseases’ mechanisms such as cancer and autoimmune diseases. However, we do not know the genomic locations for most enhancers. One reason is that we are only able to detect active enhancers but only a fraction of enhancers are active in any one tissue. Another reason being enhancers are often located far away from the genes that they control, making it a difficult task to estimate their locations using distance.

Because of these difficulties, Dr. Sethi developed a computational model to predict regulatory elements on the genome for all tissue types. My work is to validate these predictions and to develop further methods to distinguish promoters and enhancers given any regions on the genome for any tissues. I found the task tremendously interesting and challenging. I got to utilize all the knowledge and skills I acquired through my previous research experiences, including biology, genomics, statistics and computer science, to tackle this research question. In particular, I found the adoption of Bayesian statistics in this project very elegant.

Outside of working on my project, I also enjoyed the many heated discussions with other colleagues in the subgroup meetings and journal clubs, as well as our daily conversations that were never short of supplies of laughter and hidden jokes during lunch hour. Furthermore, the weather was the most superb while I was there and the scenery was simply gorgeous, which made the whole experience very memorable.

All in all, I must thank the Faculty of Medicine of CUHK, and Prof. Mark Gerstein for enabling this wonderful learning opportunity for me. With this experience, I have strengthened my research interest in computational genomics and my belief in its potential clinical utilities. Upon returning to Hong Kong, I hope to translate these research findings to patient care and to develop personalized genomics in both diagnostics and therapeutics directions in the future.