Kelly Ruggles (email@example.com)
Daniel Depledge (firstname.lastname@example.org)
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.
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 18-22 Spring Break **
Week 8: External Committee Assessment I
April 2: Group 1
April 5: Group 2
Week 9: Interpreted data
Week 11-12: Data Summary
Week 13: External Committee Assessment II
May 7: Group 1
May 10: Group 2
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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