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Week 1 and 2: Project Overview 

Week 3: Data Analysis Proposal

Weeks 4 & 5: Raw Data

Weeks 6 & 7: Processed Data

Week 8: External Committee Assessment I 

Weeks 9 & 10: Interpreted Data

Weeks 11 & 12: Summary Data

Week 13: External Committee Assessment II

Week 14: Final Analysis Summary 

Integrative omics

SB 920
Tuesdays/Fridays 2-3:30PM

3 credits

Course Director
Kelly Ruggles (

Course Description

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, to be decided upon by the External Faculty Committee the year prior to the course offering. Appropriate archived frozen biological samples will be obtained from the NYU Langone Health Center for Biospecimen Research and Development (CBRD) and will undergo appropriate ‘omics analysis (including genomics, transcriptomics, epigenomics, proteomics, and/or metabolomics) by our NYU Langone Health Core Facilities prior to the start of the course. Raw data will be available for processing 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 manuscript 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. 

​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. 

Class size is limited and requires prerequisites.

Apply for the course here by December 31, 2018