Sheryse's First STEPs into the World of Bioinformatics


By Sheryse Taylor posted 12-15-2016 14:43


Through the generous support of the Society of Toxicology Supplemental Training for Education Program (SOT STEP Award), I was able to gain much needed exposure to the field of bioinformatics through the intensive two-week Advanced Sequencing Technologies Course offered by Cold Spring Harbor Laboratories. The course is run by multiple instructors (Drs. Obi Griffith, Malachi Griffith, Elaine Mardis, W. Richard McCombie, and Aaron Quinlan) and hosts multiple guest lecturers who are experts in their respective fields and also includes an appearance by Dr. James Watson.


Advanced Sequencing Technologies Course Participants

My thesis work is on understanding the response of pulmonary macrophages to epithelial disruption such as fibrosis, acute lung injury, and cystic growths in the disease lymphangioleiomyomatosis, with focus on nitric oxide metabolism. This course presented a unique opportunity to aid my long-term career goals, which include becoming an independent immuno-oncology research scientist by allowing me to learn about a very essential technique in this field. Next generation sequencing has fueled novel understanding and therapeutics in cancer.

As a student in this course, I was able to learn both essential laboratory and computer-based aspects of massively parallel sequencing. One of the key things that I was able to gain from participation in this course was the understanding of the different types of questions that can be answered by not only the different types of sequencing such as RNA vs. whole exome vs. transcriptome, but also the large number of programing platforms that may be used to analyze the generated data with advantages and pitfalls. In my opinion, this is the most beneficial thing that students are able to obtain from the course. Rather than merely running programs and experiments, students are able to tailor their understanding to their specific research needs and questions. As this was a completely new field for me, I was able to learn the essentials of the laboratory skills such as creating a library and using Pacific Biosciences or Illumina to sequence samples as well as understanding which systems are appropriate for which models.

I was very intrigued by the computing analysis portion of the class. I had often heard of coding in regards to computer science and software development but did not realize that this was a key component in the massively parallel sequencing. Though it was completely foreign to me, the course provided many tutorials on various coding systems. Attendance at this course has allowed me to realize that a postdoctoral project that would immerse me in this area would better equip me for my intended research field. I plan to continue to learn coding to become proficient in R and continue to learn Unix. Additionally, I will become proficient with the Galaxy platform with full understanding of the algorithms that are available on a graphic user interface for researchers that are less familiar with coding.

The course also provided an opportunity for networking and career development, as instructors, guest lecturers, and course participants were all very willing to provide help during the course and willingly exchanged contact information.

Participation in this course further confirmed that I should delve deeper into the field of bioinformatics to attain my career goals.