STA 290 Seminar Series
DATE: Friday, January 13th 2017, 4:10pm
LOCATION: MSB 1147, Colloquium Room
SPEAKER: Tzu-Yu (Joyce) Liu, University of Pennsylvania
TITLE: “Translation Dynamics Revealed by Statistical Learning for Ribosome Profiling Data”
ABSTRACT: Ribosome profiling is a useful technique for studying translational dynamics and quantifying protein synthesis. Applications of this technique have shown that ribosomes are not uniformly distributed along mRNA transcripts. Understanding how each transcript-specific distribution arises is important for unraveling the translation mechanism. In this talk, we will first discuss using kernel smoothing and wavelet analysis to construct predictive features and to build a sparse model predicting the shape of ribosome footprint profiles from transcript sequences alone. Results on Saccharomyces cerevisiae data show that the steady state marginal ribosome densities can be predicted with high accuracy.
We will then discuss extending the use of ribosome profiling to study multiple myeloma cells during cancer therapy. Longitudinal mRNA-seq, ribosome profiling, and pulse-chase isotopic labeling mass spectrometry-based proteomics are integrated to directly monitor the synthesis of new proteins and degradation of existing proteins across a time course. We model the dynamic changes with a system of differential equations and solve the equation using functional data analysis. The developed model, in combination with the experimental data, predicts changes in proteome remodeling under a variety of cellular perturbations.