Post-Dog (courtesy of C. Vogel)
Annie joined the lab in September 2015 at the age of 5 months. She has been a role model for every post-dog ever since, producing lots of papers and securing several research grants. Her appetite is paralleled by no other beagles and she prefers hanging out with strangers and other dogs of all shapes and sizes in dog parks.
I grew up in Seoul, learning philosophy, history, and Spanish language and literature in college, none of which was meant to be part of what I do for living today. After rounds of trial and error, I found passion in something I barely understood: statistics. My professional career turned into something I had never conjured when Dr. Jun Li, one of the smartest people I've known, generously gave me a chance to work in the genome sequencing center at Stanford and opened the door to bioinformatics for me. After six years in a small midwestern town of Ann Arbor and two years in Austin, my usual digression into high-dimensional data analysis, computational proteomics, small molecules, and many other unfamiliar topics has become a day job, and they continue to perplex me as I learn more about them. Eight years in Singapore and counting, I am trying to be a bridge between basic biologists and clinicians.
Project: Interactive visualization of high-throughput molecular data sets
In the second year of my undergraduate degree, one of our lecturers was able to inspire our entire cohort so much that almost everyone started developing some quirky app. In this flurry of enthusiasm I found one of my passions, building web-based applications. In the following years I developed several such applications and participated in many tech fests. A big turn in my life came when I got my first job, where in less than three years I got exposed to various aspects of enterprise software development. I had the opportunity to work on business intelligence, data warehousing and even software quality assurance projects. Eight years ago, I decided to leave the familiar and venture further, and soon found myself embroiled in my master’s course in Singapore. During this time I delved into image processing and machine learning. This led me to my next job, where I developed several image and statistical data analysis tools for protein quantification. While on this job I was introduced to genomic and proteomic data analysis. As my eagerness to get a deeper understanding in these areas grew, I eventually took the plunge and started my PhD under Dr. Choi’s supervision. I am fortunate enough to be working on a PhD project that combines several of my passions. The project involves developing web-based interactive data visualization tools for studying time-series measurements of molecular markers with applications in immunology. In the future I will be extending this tool for high-throughput, multi-omics and multi-experiment data analysis as well. Currently, I am also involved in bioinformatics and statistical analysis of high throughput NGS data at IMCB. With my mixed bag of experience I hope to bring a different perspective to bioinformatics.
Hiromi Wai Ling Koh
Project: Integration of multi-omics data for patient subtype discovery in The Cancer Genome Atlas
I always had interest in science, in particular biology and mathematics. I wanted to understand how living things function and why we are structured the way we are. In junior college, mathematics and biology were not offered together and I was forced to choose between the two. I chose something which I was good at, math. I was exposed to statistics for the first time - I learned about probability and many different types of distributions which I never knew existed. I was very intrigued by the subject and how it can be applied to our daily activities and I knew it is exactly what I wanted to do. I went to college here in National University of Singapore and graduated with a degree in Statistics and a specialization in biostatistics.
Following graduation, I took a research position in NUS doing mostly epidemiological work, reporting prevalence, incidence rates for diseases and creating prediction models, which eventually became mundane exercises over time. I went to further my studies in statistics, and just when I thought I was done with studying and epidemiology, I met Hyungwon (yikes!). He pulled me into the realm of bioinformatics where I first heard about "proteins." He made me realize how important it is to know both statistics and programming, rather than depending on statistical tools that are available. I came to appreciate statistics more since I learned scientific programming. At the same time, my passion for biology was reignited and I was convinced that this is what I want to do, what I love (numbers, biology, programming all fused together). I am currently a PhD student under Hyungwon learning bioinformatics and data integration, and I never looked back ever since.
Project: PTM site and protein structure prediction, Proteogenomic analysis of genomic variations in cancer
I joined the lab in August 2014 after graduation from Shandong University. I majored math in undergraduate, but I was busy learning it and seldom thought about the future. When I was senior in college, I started to think about what I can do. I realized continuing graduate level mathematics was not my calling, and I wanted to do something more applied, a topic related to science. In the last semester, I got to know a PhD student majoring in bioinformatics, and he guided me through my undergraduate thesis. It was a simple project on classification of exons and introns of DNA sequence, and I was exposed to scientific programming for the first time. I felt this is the “something” I would like to pursue. When I joined the lab, I barely knew anything concrete about bioinformatics. Hyungwon and other group members helped me a lot in all aspects. My first project is developing a software called PTMtopographer for predicting PTM sites. I have to say research is much harder than I imagined three years ago, but I am still confident it will eventually pay off. Continuing on the PTMtopographer tool development, I will be investigating genetic variants associated with high priority PTM sites and structural domains, and studying how these functional coding variants are related to cancer phenotypes. I hope I can build useful tools for biologists and other researchers so that people work together towards better understanding of cancer.
Project: Computational tools for mass spectrometry data processing
I enrolled in the PhD program in Statistics at NUS after graduation from Nanyang Technological University as a math major in 2010. I was undecided on my research focus for my PhD until Hyungwon gave a seminar on his research work. I developed computational proteomics softwares for my PhD project in his laboratory and worked on an integrative -omics modeling approach called Protein Expression Control Analysis (PECA) for dynamic gene expression regulation analysis for my postdoc in Christine Vogel lab, Center for Genomics and Systems Biology, New York University. After two years, I returned to the CSSB lab to work on mass spec data processing for metabolomics applications, with focus on spectral library building and targeted data extraction in data independent acquisition mode of mass spectrometry.