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BME 311: Computational Genomics

Quarter Offered

Winter : TTh 9:30-10:50am ; Ji

Prerequisites

Bio 215, BME 220 or equivalent, and coding experience

Description

The course introduces state-of-the-art genomic sequencing technologies and computational modeling of high-throughput sequencing datasets. Through the course, students will learn how to apply these experimental and computational genomics technologies to study gene expression regulation underlying various biological processes, such as oncogenesis. Students will also apply computational and statistical skills, using linux and R/Matlab/Python.

Who Takes It?

Junior and senior undergraduate student, and graduate students. The students who are taking the course need to have good knowledge of molecular biology and statistics with coding experience.

Mini-Syllabus

  1. RNA sequencing and differential gene expression
  2. Clustering and visualization
  3. Gene ontology and pathway analyses
  4. Single-cell RNA sequencing
  5. Epigenetics and ChIP sequencing for histone modifications
  6. Chromatin accessibility and transcription factor recruitment
  7. ChIP sequencing for transcription factors and gene transcriptional network
  8. 3D structure of chromatin and Hi-C

Textbook

None