Computational Genomics Summer 2026

2-5pm, July 13 - Aug 13, 2026 Course link on gitee Guest Instructor: Weigang Qiu, Ph.D.
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 Office: B402 Belfer Research Building, 413 East 69th Street, New York, NY 10021, USA Email: wqiu@hunter.cuny.edu Lab Website: https://wiki.genometracker.org

Host & Assistants

---

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 Presentation

Student performance will be evaluated by attendance, in-class quizzes and a final presentation

• Attendance & participation: 12 * 5 pts = 60 pts
• Daily assignments: 8 x 10 pts = 80 pts
• Open-Book Quizzes: 3 x 30 pts = 90 pts
• Final presentation: 30 pts

Total: 260 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
• Assignment 4. Linux Intermezzos 1-4

Session 6 (7/23)

• Linux Tutorial III: BpWrapper Toolkit (https://github.com/bioperl/p5-bpwrapper)
• Probability by Monte Carlo simulations
• Assignment 5. BbWrapper utilities

Week 3. Simulations: Central Dogma

Session 7 (7/27)

• Quiz #2. Linux commands & BpWraper genomics utilities
• The Birthday Problem
  • Probability by Monte Carlo simulation
  • Simulation algorithms
  • Implementation in R or Python
  • Visualization

Session 8 (7/28)

• Random DNA sequences
• DNA replication
• DNA transcription
• Assignment 6. Implement algorithms & make visualization: B-Day problem; DNA replication & transcription

Session 9 (7/30)

• 6-frame translation
  • Algorithm
  • Visualization
• Assignment 7. Implement & Visualize 6-frame translation

Week 4. Simulations: Population genetics

Session 10 (8/3)

• Intro: Genetic drift
• Quiz #3: Central Dogma

Session 11 (8/4)

• Simulations: Genetic drift
• Simulations: Drift with mutation
• Assignment 8

Session 12 (8/6)

• No class (work from home)
• Upload a presentation draft (a tentative title, your name, name of the PI, a 150-words abstract)

Week 5. Final Presentations

Session 13 (8/10)

• No class (work from home)
• Upload your 5-slide presentation (in PDF)

Session 14 (8/11)

File:KIZ2026-presentation-flyer-4.pdf

• Presentations: Group 1

Session 15 (8/13)

• Presentations: Group 2
• Course evaluation