Computational Genomics Summer 2026
Professor, Department of Biological Sciences, City University of New York, Hunter College & Graduate Center
Adjunct Faculty, Department of Systems and Computational Biomedicine, Weil Cornell Medical College
Course Overview
Welcome to Computational Genomics, a computer workshop for graduate students. A genome is the total genetic content of an organism. Driven by breakthroughs such as the decoding of the first human genome and next-generation DNA -sequencing technologies, biomedical sciences are undergoing a rapid and irreversible transformation into a highly data-intensive field.
Genome information is revolutionizing virtually all aspects of life sciences including basic research, medicine, and agriculture. Meanwhile, use of genomic data requires life scientists to be familiar with concepts and skills in biology, computer science, as well as data analysis.
This workshop is designed to introduce computational analysis of genomic data through hands-on computational exercises, using published studies.
The pre-requisites of the course are college-level courses in molecular biology, cell biology, and genetics. Introductory courses in computer programming and statistics are preferred but not strictly required.
Learning goals
By the end of this course successful students will be able to:
- (Tree-thinking skills) Compare and analyze genomes in a phylogenetic framework
- (Algorithm-thinking skills) Implement the evolutionary algorithms in a programming language of choice (R, Python, or others)
- (Probability-thinking skills) Obtain probabilities by Monte Carlo simulations
- (Population-thinking skills) Achieve an algorithmic understanding of major evolutionary processes (drift, mutation, recombination, and natural selection)
- (Microbial evolution) Understand the distinctions between microbial and eukaryotic evolution
Web Links
- Install R base: https://cloud.r-project.org
- Install R Studio (Desktop version): https://docs.posit.co/ide/user/#rstudio-ide-oss-downloads
- R/Tidyverse reference book: R for Data Science (Wickharm et al)
- A textbook on microbial genomics & evolution by the instructor: Digital Genomes (Qiu 2026)
Assignments, Quizzes, and a Final Presentatio8n
Student performance will be evaluated by attendance, in-class quizzes and a final presentation
- Attendance & participation: 14 * 5 pts = 70 pts
- Daily assignments: 8 x 10 pts = 80 pts
- Open-Book Quizzes: 4 x 30 pts = 120 pts
- Final presentation: 30 pts
Total: 300 pts
Course Schedule
Week 1. Intro & Phylogenetics
Session 1 (7/13)
- Introduction. Lecture slides: File:QiuLab-CUNY-Hunter.pdf
- Gitee accounts & usage; Demo: homework submission using Gitee
- Survey 1: Genomics & Data Science
- Survey 2: Tree-thinking Skills; Handout: Pre-test 1
- Lecture: Tree-thinking Skills.
- Assignment 1. Pretest-1. Phylogenetic tree
Session 2 (7/14)
- Install Linux operating systems (Mac OSX or Windows WSL)
- Install miniconda & create a new conda environment
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict
conda create -n qiulab perl-bio-bpwrapper
- Git usages: Download the course repository:
git clone https://gitee.com/huntercollege/comp-genomics-kiz.git - Install R, Tidyverse, & Positron
- Tree manipulations: reroot & tree distances
- Gene tree vs Species tree; orthologous and paralogous genes; tree pruning & collapsing
- Assignment 2. Tree reroot & gene paralogy
Session 3 (7/16)
- Character reconstruction
- Phylogenetic analysis: Parsimony analysis
- Pre-test 2
- Assignment 3. Parsimony analysis
- To prepare for Quiz 1, review
- Lecture slides: File:Phylogeny-lecture-slides-2026.pdf
- Three assignments
Week 2. Linux & Command Line Interface
Session 4 (7/20)
- Linux Tutorial I. Basics. File:Part-1-intro-unix-2026.pdf
- Quiz #1. Phyogenetics
Session 5 (7/21)
- Linux Tutorial II. Advanced
Session 6 (7/23)
- Linux Tutorial III: BpWrapper Toolkit (https://github.com/bioperl/p5-bpwrapper)
- Probability by Monte Carlo simulations
Week 3. Simulations: Central Dogma
Session 7 (7/27)
- Quiz #2
Session 8 (7/28)
Session 9 (7/30)
- Quiz #3
Week 4. Simulations: Population genetics
Session 10 (8/3)
Session 11 (8/4)
Session 12 (8/6)
- Quiz #4
Week 5. Microbial genomics
Session 13 (8/10)
Session 14 (8/11)
- Presentations
Session 15 (8/13)
- Presentations
- Course evaluation