Samuel Liu

PIPS Host Organization: TopMD Precision Medicine

Samuel’s PIPS was with his CASE partner, TopMD Precision Medicine. During his placement, Samuel curated publicly available datasets containing transcriptomic data from cohorts containing people with dementias such as Alzheimer’s Disease and control patients. These datasets were fed through a custom TopMD topological machine learning algorithm, tuned specifically by Samuel for his datasets. The resulting analysis gave Samuel insight on the shape of the data presented, allowing for further exploration into gene clusters and identification of potential pathways of interest for experimentation in his wet lab work for the remainder of his PhD.

The placement allowed him to become proficient at data wrangling, especially in developing and using tools to convert data into compatible, custom formats. He also gained experience in using containers for computational work, which is an especially skill when using consistently updated software, shared by multiple users. In addition to these technical skills, the placement has also developed his professional skills including communication of problems, time management and especially problem solving.

Samuel’s PIPS also gave him insight on the importance of in silico work in modern science, with many wet lab pipelines now first starting in exploring data from publicly available datasets, where hypothesis are both formed and discarded before a pipette has even been lifted. With computation and omics being a growing focus in science, he is now more equipped to take on tomorrow’s scientific adventures.