Genomics

BDSI.2024.GEN@umich.edu

Instructor:   Matt Zawistowski (mattz@umich.edu)

                     Xiang Zhou (xzhousph@umich.edu)

Co-mentor: Elysia Chou (elysian@umich.edu)

                     Zheng Li (zlisph@umich.edu)

The Genomics group will have multiple available projects connecting a health-related question to a large-scale genomic dataset, for example whole-genome Single Nucleotide Polymorphism data, single-cell RNA sequencing data or epigenetic methylation data. Students will form teams for a deep dive analysis on their specific project of interest with opportunity for open-ended exploration. Students will gain hands-on computing experience and valuable data manipulation skills working with the large genomic data files. We will apply many classical statistical techniques, learn about integration of complementary genomic data sources and explore machine learning and specialized genomic analysis methods. 

Pre-Readings

These resources are intended to provide you with some background information on the two datasets we will be working on: a single-cell multiome dataset collected from different cortex developmental stages and an imaging mass cytometry (IMC) dataset from cancer tissue.
For the Multiome Dataset:
  1. Review paper Download Review paper (attached) on the 3D organization of chromatin in a cell. You can skip the sections from "3D genome dynamics in gametogenesis" to "3D genome dynamics in early development" (i.e. skip p.538-542).
  2. Watch the first 5 minutes of the video on an Introduction to single-cell profiling technology. Links to an external site.
  3. Watch the video on 10X Genomics Multiome profiling (single-nucleus ATAC-Seq and RNA-Seq) Links to an external site..

For the IMC Dataset:

  1. Watch from 7:37 to 11:24 in the video Introduction to Imaging Mass Cytometry Links to an external site..
  2. Read pages 1-4 of the review paper Download review paper (attached): "Application of High-Throughput Imaging Mass Cytometry Hyperion in Cancer Research".

Introduction to Basic Genetics and Datasets

Slides Download Slides

Worksheets

1. Single-cell Pathology Data Download Single-cell Pathology Data (code Download code)

2. Single-cell Multi-ome Data Download Single-cell Multi-ome Data (code Download code)

 

Potential projects

Additional Readings

 

Posters

UM Template Links to an external site. (you can look for the UM Biostatistics logo too, plus your home institution's logo)

Elysia's sample poster Download Elysia's sample poster