Computational Genomics Summer 2026 - Revision history

Wikiuser: Created page with "center 9-12 noon, July 13 - Aug 6, 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
2026-07-02T10:31:02Z

Created page with "800px|center <center>9-12 noon, July 13 - Aug 6, 2026</center> <center>'''Guest Instructor:''' Weigang Qiu, Ph.D.<br>Professor, Department of Biological Sciences, City University of New York, Hunter College & Graduate Center<br>Adjunct Faculty, Department of Systems and Computational Biomedicine, Weil Cornell Medical College</center> <center>'''Office:''' B402 Belfer Research Building, 413 East 69th Street, New York, NY 10021, USA</cente..."

New page
[[File:Banner-comp-genomics.png|800px|center]]
<center>9-12 noon, July 13 - Aug 6, 2026</center>
<center>'''Guest Instructor:''' Weigang Qiu, Ph.D.<br>Professor, Department of Biological Sciences, City University of New York, Hunter College & Graduate Center<br>Adjunct Faculty, Department of Systems and Computational Biomedicine, Weil Cornell Medical College</center>
<center>'''Office:''' B402 Belfer Research Building, 413 East 69th Street, New York, NY 10021, USA</center>
<center>'''Email:''' wqiu@hunter.cuny.edu</center>
<center>'''Lab Website:''' https://wiki.genometracker.org</center>
<br>
<center>'''Host & Assistants'''</center>
----
==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==
* Install R base: https://cloud.r-project.org
* Install R Studio (Desktop version): http://www.rstudio.com/download
* Download: [http://www.r4all.org/books/datasets R datasets]
* A reference book: [https://r4ds.hadley.nz/ R for Data Science (Wickharm et al)]
* Github repository: [https://github.com/weigangq/CSB-BIOL425/tree/master/lecture-materials Computational Skills for Biologists (Allesina & Wilmes)]

==Assignments, Quizzes, and Final Report==
Student performance will be evaluated by attendance, three (3) quizzes and a final presentation
* Attendance & participation: 60 pts
* Open-Book Quizzes: 3 x 30 pts = 60 pts
* Final presentation: 30 pts
Total: 150 pts

==Course Schedule==
===Week 1===
====Session 1, 7/13 (Monday)====
* Introudction. Lecture slides: [[File:QiuLab-CUNY-Hunter.pdf|thumb]]
* Computer setup: gitee accounts (for course management). [https://edu.gitee.com/huntercollege/courses/3030/noticeboard Course link on gitee]
* <span style="color: blue">Survey 1: Genomics & Data Science</span> PDF file: [[File:KIZ-survey-1.pdf|thumb]]
* <span style="color: blue">Survey 2: Tree-thinking Skills</span> PDF file: [[File:Pretest-1.pdf|thumb]]
* Computer setup: Linux accounts (on the "phylonet.net" server)
* Lecture: Tree-thinking Skills. Lecture slides: [[File:Phylogeny-lecture-slides-2024.pdf]]

====Session 2, 7/14 (Tuesday)====
* Git usages (by Mr Liu)
Demo: homework submission using Gitee
Download the course repository: <code>git clone https://gitee.com/huntercollege/comp-genomics-kiz.git</code>
* Linux Tutorial I. [[File:Intro-unix-KIZ.pdf|thumb]]
* Phylogenetics lecture: [[File:Part-1-tree-thinking.pdf|thumb]]
Tree manipulations: reroot & tree distances
Gene tree vs Species tree; orthologous and paralogous genes; tree pruning & collapsing

====Session 3, 7/16 (Thursday)====
* Review: Tree manipulations
* <span style="color: red">Quiz #1. tree terms & tree manipulations</span> (20 pts); open-book; 9-10am, in-class
* <span style="color: green">Linux Tutorial II: BpWrapper Toolkit (https://github.com/bioperl/p5-bpwrapper)</span> Updated sldies: [[File:Intro-unix-KIZ.pdf|thumb]]

===Week 4, Thursday, Oct 31, 2024 (Halloween)===
* <span style="color: red">Quiz #2. Linux commands & BpWrappper toolkits</span>: 20 pts, 9-10:30am
* <span style="color: orange">AFSV Genomics I </span>: Download and align genomes.
Fork a copy of [https://edu.gitee.com/huntercollege/projects/696311/repos/huntercollege/afsv-genomics/sources the ASFV project repository].
Instructions to fork a repository (prepared by Mr Liu): https://zwmqn249t3y.feishu.cn/wiki/OVdEwB00ciNx9Xkxvxsc7lJEncc?from=from_copylink
** Project overview: Lecture slides: [[File:Afsv-project-kiz.pdf|thumb]]

===Week 5, Thursday, Nov 7, 2024===
* ASFV project:
<code> git clone https://gitee.com/huntercollege/asfv-genomics.git </code>
Align genomes: protocol-1
SNP calls; quality check by Ts/Tv ratio (Protocol 1)
Annotate SNPs: Protocol 2
** IQ-tree to get genome tree: Protocol-3
* Trait evolution and comparative analysis [[File:Trait-evolution-KIZ.pdf|thumb]]
* Assignment: Pre-test 2

===Week 6, Thursday, Nov 14, 2024===
* Computer setup: R & RStudio; <span style="color: orange">R Tutorial Part 1: Basic R & Data manipulations</span>. Lecture slides [[File:R-tutorials-KIZ-part-1.pdf|thumb]]
* Assignment: Practice-1 & -2

===Week 7, Thursday, Nov 21, 2024===
* R Tutorial 2. Data visualization & statistics. Slides: [[File:R-tutorials-KIZ-part-2.pdf|thumb]]
** Assignment: Practice-3 & -4
* Final project:
Introduction to Ka/Ks analysis
File distribution: each student is assigned 10 random genes; Run <code>git pull</code>; or if you haven't cloned the repository, run <code>git clone https://gitee.com/huntercollege/asfv-genomics.git</code>
** Follow the protocol in "doc/protocol-4-paml.txt"

===Week 8, Thursday, Nov 28, 2024 (Thanksgiving)===
* R Tutorial 3. [https://borreliabase.org/~wgqiu/r-demo-2024.html Cluster analysis]:
Part 4. Heatmap (hierarchical clustering) & principal component analysis (PCA)
Part 5. Gene expression analysis.
** Assignment: reproduce the cluster analysis
* Final project: [https://borreliabase.org/~wgqiu/asfv-genomics-visual.html R Markdown Demo]
Visualize tree with <code>ggtree</code>
Plot Ka/Ks for genes
** Run IQ-TREE to obtain site-specific rates; Plot site-specific rates

===Week 9, Thursday, Dec 5, 2024===
* Final presentations: student demos & trouble shooting

===Week 10, Thursday, Dec 10, 2024===
* ASFV project overview slides: [[File:Asfv-project-kiz-Dec-5-2024.pdf|thumb]]
* Final presentations (30 pts):
(10 pts) 3 slides & 5 min
(15 pts) Show & interpret results for a single gene (no need to show all genes on PPT, although you will upload all MLC and tree files). Pick a genes that is the most interesting to you (e.g., significant position selection, apparent inconsistency with the genome tree, important gene function, etc).
** (5 pts) Conclusions & future directions. Find gene name and function from this paper: https://www.mdpi.com/2076-2615/14/15/2187 (you need to first find the gene name using the "BA71.gff3" file with <code>grep</code>)
* Course evaluation