AbbVie Pharmaceuticals

Bioinformatics Intern, May - August 2020


About Ribosome Profiling:

Global cellular translation rate is often measured through RNA-seq, but there is a disconnect between levels of mRNA present in a cell and the actual amount of associated protein produced due to varying translation and protein degradation rates. Ribosome Profiling (ribo-seq) is a variation of RNA-seq that sequences only RNA segments currently being translated. This provides a much more accurate measurement of cellular translation. The experimental technique involves inhibiting translating ribosomes and degrading all unprotected mRNA, which isolates ~30 nt protected fragments from within the ribosomes. Then, mapping these sequenced reads to the genome or transcriptome indicates translation locations. Variations in this protocol with different ribosome-stalling molecules can detect specific start and stop sites, revealing new open reading frames.

My Role:

My goal was to improve the existing analysis platform by adding analysis tools and modifying the framework to easily adapt the code to new data sets. I first did a literature review on 23 different analysis packages and then tested or used 12 of these. After analyzing the current system, I re-designed steps with outdated packages and demonstrated use of visualization for quality control. Next, I designed and implemented a small open reading frame (sORF) detection pipeline and integrated it into the main system. Using a published data set, I validated results from sORF detection pipeline and demonstrated the use of visualization to detect sORFs.

As part of the protein engineering and expression group, this analysis will help engineer stable cell lines by ensuring transgenic cells produce the correct protein output. Ribo-seq also assists in target discovery and validation by playing a similar, but more accurate, role as RNA-seq.

Skills Developed:​

  • Learned bash shell scripting and improved knowledge of R
  • Integration of individual code into pipeline
  • Literature review
  • Scientific communication through an hour-long seminar presentation and poster session