Computational Genomics Summer 2026

2-5pm, July 13 - Aug 13, 2026 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

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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:

• (Pop Gen) Achieve an algorithmic understanding of major evolutionary processes (drift, mutation, recombination, and natural selection)
• (Computation) Implement the evolutionary algorithms in a programming language of choice (R, Python, or others)
• (Phylogenomics) Compare and analyze genomes in a phylogenetic framework
• (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): http://www.rstudio.com/download
• 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

Session 1 (7/13)

• Introduction. Lecture slides: File:QiuLab-CUNY-Hunter.pdf
• Gitee accounts & usage Course link on gitee; Demo: homework submission using Gitee
• Survey 1: Genomics & Data Science PDF file: File:KIZ-survey-1.pdf
• Survey 2: Tree-thinking Skills PDF file: File:Pretest-1.pdf
• Lecture: Tree-thinking Skills. Lecture slides: File:Phylogeny-lecture-slides-2024.pdf

Session 2 (7/14)

• Git usages (by Mr Liu)
  • Download the course repository: git clone https://gitee.com/huntercollege/comp-genomics-kiz.git
• Linux Tutorial I. File:Intro-unix-KIZ.pdf
  • Tree manipulations: reroot & tree distances
  • Gene tree vs Species tree; orthologous and paralogous genes; tree pruning & collapsing

Session 3 (7/16)

• Quiz #1
• Linux Tutorial II: BpWrapper Toolkit (https://github.com/bioperl/p5-bpwrapper) Updated sldies: File:Intro-unix-KIZ.pdf

Week 2

Session 6 (7/23)

• Quiz #2

Week 3

Session 9 (7/30)

• Quiz #3

Week 4

Session 12 (8/6)

• Quiz #4

Week 5

Session 14 (8/11)

• Presentations

Session 15 (8/13)

• Presentations
• Course evaluation