I’m so glad to learn about Jo’s research since it changed my view of computational biology completely. Somehow my idea of computational biology is always biased. For many years I just thought of it as some kind of boring work that one does in front of a computer. (I’m sorry comp bio people, I don’t really mean that 😉 ) However, getting to know Jo’s research opened my mind. I was amazed by the fact that my work is so related to, and dependent on her research, and by how important computational biology is.
Jo’s work involves building a model of transcription factor binding sites based on DNase digestion data, CHIP-seq data, and consensus sequence matrix of different transcription factors. I got excited when I first learnt about her project. Needless to say, identifying transcription factor binding sites is important for my research since it provides great insights for the interaction between natural transcription factor and my synthetic transcription factors. It would be very interesting to see the difference between targeting natural transcription factor binding sites and avoiding transcription binding sites. My synthetic transcription factor might block the binding of natural transcription factors and weaken the regulating effect; or it might help recruit the natural transcription factor and enhance the regulating effect. Therefore, the knowledge of natural transcription binding sites provides important guideline for designing synthetic transcription factors.
Moreover, Jo told me that her next step is to utilize this model and analyze tissue specific transcription factor binding patterns. This is so cool since it provides great insights into the interaction and regulation of different transcription factors in different cell types. I’ve always been intrigued by the fact that different cell types are so different even though the genotypes of them are very similar. One of the explanations to the dramatic differences is different regulation pattern– and this is exactly what Jo is trying to unravel. From a more pragmatic standpoint, Jo’s research could potentially give me an idea of the specific transcription factor binding pattern of smooth muscle cell, so that my reprogramming strategy is more specific and effective.
Most importantly, my idea of computational biology has changed drastically. I realized that even though it’s mostly computer work, it is really related to real life. It deals with fundamental questions that are important in many fields, and it is a powerful method of finding patterns.
