STEP Reflection – Investigating Irregular CHH Methylation Patterns

William Powers

Undergraduate Research


For my STEP Signature Project, I conducted undergraduate research in the fields of biophysics and bioinformatics. I worked with Reduced Representation Bisulphite Sequencing (RRBS) to investigate methylation in DNA. Methylation is an epigenetic factor with important links to cancer and other diseases. For my project I investigated the significance of methylation in the infrequent CHH context.

Conducting research for my STEP Signature Project helped me learn about the process of scientific research and what a career in a research oriented field could look like. Before my STEP project, I had minimal experience with scientific research.  Now that I have some experience with research, I have more confidence in myself and I feel ready to pursue graduate school. Additionally, I learned much about doing data analysis on large data sets using high performance computing. These skills are adaptable to many fields besides bioinformatics. I am considering studying either biophysics or astronomy in graduate school. Computational skills are highly relevant in both fields

For my research, I primarily worked on data analysis. I would analysis data sets consisting of nearly 40 million reads. To process this by hand would be impossible, so I used the resources of the Ohio Supercomputer Center. To do this I had to learn how to write scripts to run data analysis software on the supercomputer. I also had to write code to interpret the processed data. And in a few cases, I had to write the some of the analysis code myself. These skills are valuable, and not limited to bioinformatics. Much research in physics and other sciences now involves large data, and relies on computers to process data.

Throughout my research, I had to report on my progress at biweekly group meetings. By attending group meetings, I improved my presentation skills. Due to conflicts with my courses, these meetings could not last long, so I learned how to succinctly and effectively communicate a message. I learned how to effectively present data and figures in a way that is easily and quickly understood. I also used this time receive advice and constructive criticism from other group members, and to collaborate on our various projects.

While the general topic of my research remained the same throughout the project, the details of it changed significantly. In a project that another undergraduate researcher was working on, there was an unexplained phenomenon in the data related to DNA methylation. Certain samples exhibited bizarre patterns in CHH context methylation. As we looked into this project, it turned out that it was related to the topic of my research. This then became the major focus of my project, and could yield publishable results. This experience demonstrated the importance of collaboration, and furthermore the importance of flexibility in research. The research process generally does not follow a straight path, and can lead to unexpected discoveries.

After I graduate, I plan to go to graduate school in either biophysics, or astronomy. The data analysis and computer skills I learned from my STEP project will be valuable in either field. More importantly, having experience in research has shown me some nuances I did not expect in research. Now that I have experience in research, I know what to expect and what to look for in these research-heavy graduate programs. Thanks to my STEP project I now feel more confident in my career plans.

One thought on “STEP Reflection – Investigating Irregular CHH Methylation Patterns

  1. Great to see that you learned more about yourself as a scientist and how you would like to continue in this role.

    Wow, now being able to say that you are trained and able to use a Supercomputer will be beneficial for future interviews. This is a skill set that will help you stand out.

    Learning how much time and effort goes into publication is a great life lesson to learn. This will help you know what your goals can be in the future and estimate the time it takes to meet these goals.

    Best of luck with your graduate school!

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