Teaching and Resources

Recently Taught Courses

Instat 2026 - Advanced Statistical Methods for Genetic Association Studies

This seminar presents advanced statistical methods for genetic association research, synthesizing theoretical foundations with applied workflows. It addresses the analytical challenges that arise in large-scale genome-wide association studies (GWAS), molecular QTL mapping, co-localization, Mendelian Randomization (MR), and transcriptome-wide association studies (TWAS), and it explains why rigorous statistical treatment for reliable inference is essential in genetics.

• Session 1: GWAS Fundamentals and Data Preparation
• Session 2: Advanced Association Models and Fine-Mapping
• Session 3: Polygenic Risk Scores
• Session 4: Molecular QTL Mapping and Covariate Control
• Session 5: Co-Localization Theory and Practice
• Session 6: Integrating Molecular QTL with GWAS Results by Mendelian Randomization
• Session 7: TWAS/PWAS and Integrative Reproducible Pipelines
• Session 8: TWAS/PWAS Using Summary-Level xQTL and GWAS Data
• Session 9: Fine-Mapping TWAS/PWAS Results

SISG 2025 - Gene Regulation Modules

1. Introduction to TWAS
2. TWAS with Summary xQTL Data and Finemapping
3. TWAS and Mendelian Randomization
4. ChIP-seq Analysis Pipeline
5. Analysis with Functions of Noncoding Variants

BIOS-770 - Advanced Statistical Genetics: GWAS

1. Genotype Imputation, Single Variant GWAS
2. QC, Population Stratification, LMM
3. Finemap, Bayesian Functional GWAS
4. Rare Variant Test, Pleiotropy, Mendelian Randomization

IBS-519 - Data Analysis using R

1. Linear Regression
2. ANOVA
3. Power Analysis
4. Permutation Test
5. Introductions to Machine Learning

IBS-538 - Data Science

1. Multivariate Analysis with Application to RNAseq Differential Gene Expression Analysis

High Performance and Cloud Computing Cluster

HGCC

• Introduction to New HGCC
• Run Computation Tools and Submit Jobs on HGCC
  • Slurm User Guide from University of Michigan
• Introduction to BASH.
  • Bash Scripting Tutorial

RHPC

• Introduction to RHPC
• RSPH High Performance Computing Github : Starting guides are provided.
• Helpful tips from Dr. Hao Wu

HyPER-C3

• Start Guide for using HyPER-C3 HPC

Emory Amazon Web Service (AWS)

• Introduction to Emory AWS
• AWS Documentation

Other Resources

Bioinformatics

1. Bioinformatics workshop documentations by UCDAVIS Bioinformatics Core with the following Covered Topics:
   • Bioinformatics Prerequisites (Command Line and R)
   • Single-Cell RNA-Seq Analysis
   • RNA-seq Analysis
   • Microbial Community Analysis (Amplicon)
   • Variant Analysis (Variant calling with GATK, Variant Annotation)

2. Analysis of single cell RNA-seq data by Hemberg lab, Welcome Sanger Institute, UK

3. ENAR 2021 short course on single cell RNA-seq analysis by Hao Wu, Emory University, and Ziyi Li, MD Anderson Cancer Center

4. Bioinformatics Training at the Harvard Chan Bioinformatics Core

Linux

• Beginner’s Guide for Linux (long version)

  • bash-scripting-tutorial-linux-shell-script-and-command-line-for-beginners (short version)

  • Essential Linux Commands

  • Tutorial of AWK: AWK is a powerful tool for handling large text files in Linux system.

  • Tmux Cheat Sheet: Tmux is a useful tool to split terminal screens.

  • Learn VIM : Vim is a useful text editor tool in Linux.

• Visual Studio Code is recommend for connecting to clusters and editing scripts on clusters.
  • YouTube Instructions about Connecting VS Code to HPC
  • VS Code Instructions by NYU

• Get started with GitHub : GitHub is a cloud-based platform where you can store, share, and work together with others to write code.

• Cheat Sheets of AWK, C++, Python, R, Vim, Git, etc.

R

• R/Rstudio Tutorial Essential Videos

Coursera Python Courses

• Programming for Everybody (Getting Started with Python)
• Applied Data Science with Python

Jupyter Notebook (Recommended for Programing with Python)

• Introduction to Jupyter Notebooks
• Jupyter Kernels

Scientific Writing and Presentations

Scientific Writing

• Write ASHG Abstract
• Ten simple rules for structuring papers. PLOS Computational Biology, 2017.
• Ten simple rules for writing a response to reviewers. PLOS Computational Biology, 2017.
  • Example peer review process for PLOS Genetics with reviewers’ comments and response letters.
• Me write pretty one day: how to write a good scientific paper. Journal of Cell Biology, 2004.

Scientific Presentations

Poster Presentations

• How to Make An Effective Poster

Oral Scientific Presentations

• Scientific Presentations 101
• Structure of a 10-minute Oral Scientific Presentation
• The Art of Great Talks