Computational Genomics (KIZ, Fall 2024)

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Banner-comp-genomics.png
Thursdays 8:30-11:30am, Oct 10 - Dec 10, 2024
Guest Instructor: Weigang Qiu, Ph.D.
Professor, Department of Biological Sciences, City University of New York, Hunter College & Graduate Center
Adjunct Faculty, Department of Physiology and Biophysics, Institute for 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


Assistants: Mr Bei Liu & Dr Charles Adeola
Host: Dr Yun Gao, Ph.D.
Kunming Institute of Zoology (KIZ)

Course Overview

Welcome to Computational Genomics, a 9-week 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:

  • Use Linux commands & compose simple shell scripts to automate a bioinformatics pipeline
  • Program in Python for parsing texts and simulating evolution
  • Visualize data and perform statistical analysis using R/RStudio
  • Compose a bioinformatics research report

Web Links

Assignments, Quizzes, and Final Report

Student performance will be evaluated by attendance, three (3) quizzes, six (6) assignments, and a final report:

  • Attendance & participation: 30 pts
  • Assignments: 6 x 10 = 60 pts
  • Open-Book Quizzes: 3 x 20 pts = 60 pts
  • Final presentation: 50 pts

Total: 200 pts

Course Schedule

Week 1, Thursday, Oct 10, 2024

Week 2, Thursday, Oct 17, 2024

  • Git usages (by Mr Liu)
  • Linux Tutorial I.
  • Lecture: Tree manipulations: reroot & tree distances
  • Gene tree vs Species tree; orthologous and paralogous genes; tree pruning & collapsing

Week 3, Thursday, Oct 24, 2024

Week 4, Thursday, Oct 31, 2024

  • Python Tutorial II: Regular expression & scientific computing with Python
  • Assignment 3

Week 5, Thursday, Nov 7, 2024

  • Quiz #2
  • Computer setup: R & RStudio
  • R Tutorial 1: Basic R
  • Assignment 4

Week 6, Thursday, Nov 14, 2024

  • R Tutorial 2: Data visualization & basic statistics
  • Assignment 5

Week 7, Thursday, Nov 21, 2024

  • Quiz #3
  • Genomics Tutorial 1: Cluster analysis & scRNA analysis
  • Final report (draft 1: Background, Hypothesis, Significance, Material & Methods)

Week 8, Thursday, Nov 28, 2024

  • Genomics Tutorial 2. NGS data analysis
  • Final report (draft 2: Results & Discussion)

Week 9, Thursday, Dec 5, 2024

  • Genomics Tutorial 3. Monte Carlo simulations of genome evolution
  • Final report (draft 3: Conclusions, future directions, reference)
  • Final report due Nov 26

Week 10, Thursday, Dec 10, 2024

  • Final presentation