SB 920
Tuesdays/Fridays 2-3:30PM

3-5 credits

Course Director
Kelly Ruggles (

Daniel Depledge (

Teaching Assistant: 

Menghan Liu

Course overview
The primary goal of this course is to train biomedical graduate students to work collaboratively towards a common interdisciplinary research goal through the analysis of a complex multimodal ‘omics data set to answer novel scientific questions. To address this goal, we require both a diverse student team and an interesting and high-quality data set. To address the latter, an original data set of interest will be chosen for each academic year. 

Raw data will be available prior to the start of the semester and students will be responsible for all downstream analysis and biological interpretation (with guidance from appropriate faculty).   A major objective of the course is to complete the data analysis and finalize a collaborative draft summarizing the results, with figures and writing done collectively by the students.  Students will be graded on their analytic and writing contributions and collaborative efforts and judged by both the course director and an external faculty committee. 

Course Assessment
100% of grade will be determined by projects and participation​

Class size is limited and requires prerequisites.

Apply for the course here by December 31, 2018

Week 1: Overview


February 5: Project Introduction
February 8: Project Introduction

Week 2: Data Types
February 12: Data Types I
February 15: Data Types II

Week 3: Data Analysis Proposal
February 19: Data Analysis Proposal Group 1
February 22: Data Analysis Proposal Group 2

Week 4: Raw Data
February 26: Raw Data Normalization Overview
March 1: Raw Data Normalization presentations

Week 5: QC
March 5: Data QC Overview
March 8: Data QC presentations

Week 6: Data Processing
March 12
March 15

** March 18-22 Spring Break **
March 26
March 29

Week 8: External Committee Assessment I 
April 2: Group 1
April 5: Group 2

Week 9: Interpreted data
April 9
April 12
April 16
April 19

Week 11-12: Data Summary
April 23
April 26

April 30
May 3

Week 13: External Committee Assessment II
May 7: Group 1
May 10: Group 2

Integrative omics

Spring 2019 Dataset: Herpes simplex virus (HSV) is an important human pathogen which established lifelong latency in peripheral neurons, periodically reactivating to cause fresh disease. While initially thought to encode just 80 genes and a handful of microRNAs, recent studies have suggested far greater transcriptional complexity that results from alternative transcription initiation, alternative splicing, alternative polyadenylation, and read-through transcription. The major aim of this work is to integrate diverse RNA sequencing and proteomic datasets and produce a new updated annotation of the HSV-1 genome that will inform new biological explorations and interpretations.

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