Computational Genomics Summer 2026: Difference between revisions

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[[File:Banner-comp-genomics.png|800px|center]]
[[File:Banner-comp-genomics.png|800px|center]]
<center>2-5pm, July 13 - Aug 13, 2026</center>
<center>2-5pm, July 13 - Aug 13, 2026</center>
<center>[https://edu.gitee.com/huntercollege/courses/5124/noticeboard Course link on gitee]</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>'''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>'''Office:''' B402 Belfer Research Building, 413 East 69th Street, New York, NY 10021, USA</center>
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==Learning goals==
==Learning goals==
By the end of this course successful students will be able to:  
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)
* ('''Tree-thinking''' skills) Compare and analyze genomes in a phylogenetic framework
* ('''Computation''') Implement the evolutionary algorithms in a programming language of choice (R, Python, or others)
* ('''Algorithm-thinking''' skills) Implement the evolutionary algorithms in a programming language of choice (R, Python, or others)
* ('''Phylogenomics''') Compare and analyze genomes in a phylogenetic framework
* ('''Probability-thinking''' skills) Obtain probabilities by Monte Carlo simulations
* ('''Microbial evolution''') Understand the distinctions between microbial and eukaryotic evolution  
* ('''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==
==Web Links==
* Install R base: https://cloud.r-project.org
* Install R base: https://cloud.r-project.org
* Install R Studio (Desktop version): http://www.rstudio.com/download
* Install R Studio (Desktop version): https://docs.posit.co/ide/user/#rstudio-ide-oss-downloads
* R/Tidyverse reference book: [https://r4ds.hadley.nz/ R for Data Science (Wickharm et al)]
* R/Tidyverse reference book: [https://r4ds.hadley.nz/ R for Data Science (Wickharm et al)]
* A textbook on microbial genomics & evolution by the instructor: [https://www.wiley.com/en-us/shop/general-introductory-life-sciences/digital-genomes-monte-carlo-simulations-of-microbes-and-evolution-p-9781394314621 ''Digital Genomes (Qiu 2026)'']
* A textbook on microbial genomics & evolution by the instructor: [https://www.wiley.com/en-us/shop/general-introductory-life-sciences/digital-genomes-monte-carlo-simulations-of-microbes-and-evolution-p-9781394314621 ''Digital Genomes (Qiu 2026)'']
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==Course Schedule==
==Course Schedule==
===Week 1===
===Week 1. Intro & Phylogenetics===
====Session 1 (7/13)====
====Session 1 (7/13)====
* Introduction. Lecture slides: [[File:QiuLab-CUNY-Hunter.pdf|thumb]]
* Introduction. Lecture slides: [[File:QiuLab-CUNY-Hunter.pdf|thumb]]
* Gitee accounts & usage [https://edu.gitee.com/huntercollege/courses/3030/noticeboard Course link on gitee]; Demo: homework submission using Gitee
* Gitee accounts & usage; Demo: homework submission using Gitee
* <span style="color: blue">Survey 1: Genomics & Data Science</span>
* Survey 1: Genomics & Data Science  
* <span style="color: blue">Survey 2: Tree-thinking Skills</span>; Handout: Pre-test 1
* Survey 2: Tree-thinking Skills; Handout: Pre-test 1
* Lecture: Tree-thinking Skills. Lecture slides: [[File:Phylogeny-lecture-slides-2026.pdf]]
* Lecture: Tree-thinking Skills.  
* Assignment 1. Pretest-1. Phylogenetic tree
* <span style="color: green">Assignment 1. Pretest-1. Phylogenetic tree


====Session 2 (7/14)====
====Session 2 (7/14)====
* Git usages (by Mr Liu)
* Install Linux operating systems (Mac OSX or Windows WSL)
** Download the course repository: <code>git clone https://gitee.com/huntercollege/comp-genomics-kiz.git</code>  
* Install miniconda & create a new conda environment
* Linux Tutorial I. [[File:Intro-unix-KIZ.pdf|thumb]]
<syntaxhighlight lang=bash>
** Tree manipulations: reroot & tree distances
conda config --add channels defaults
** Gene tree vs Species tree; orthologous and paralogous genes; tree pruning & collapsing
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict
conda create -n qiulab perl-bio-bpwrapper
</syntaxhighlight>
* Git usages: Download the course repository: <code>git clone https://gitee.com/huntercollege/comp-genomics-kiz.git</code>
* Install R, Tidyverse, & Positron
* Tree manipulations: reroot & tree distances
* Gene tree vs Species tree; orthologous and paralogous genes; tree pruning & collapsing
* <span style="color: green">Assignment 2. Tree reroot & gene paralogy


====Session 3 (7/16)====
====Session 3 (7/16)====
* <span style="color: red">Quiz #1
* Character reconstruction
* <span style="color: green">Linux Tutorial II: BpWrapper Toolkit (https://github.com/bioperl/p5-bpwrapper)</span> Updated sldies: [[File:Intro-unix-KIZ.pdf|thumb]]
* Phylogenetic analysis: Parsimony analysis
* Pre-test 2
* <span style="color: green">Assignment 3. Parsimony analysis
* To prepare for Quiz 1, review
** Lecture slides: [[File:Phylogeny-lecture-slides-2026.pdf]]
** Three assignments


===Week 2===
===Week 2. Linux & Command Line Interface===
====Session 4 (7/20)====
====Session 4 (7/20)====
* Linux Tutorial I. Basics. [[File:Part-1-intro-unix-2026.pdf|thumb]]
* <span style="color: red">Quiz #1. Phyogenetics
====Session 5 (7/21)====
====Session 5 (7/21)====
* Linux Tutorial II. Advanced
====Session 6 (7/23)====
====Session 6 (7/23)====
* <span style="color: red">Quiz #2
* Linux Tutorial III: BpWrapper Toolkit (https://github.com/bioperl/p5-bpwrapper)
* Probability by Monte Carlo simulations


===Week 3===
===Week 3. Simulations: Central Dogma===
====Session 7 (7/27)====
====Session 7 (7/27)====
* <span style="color: red">Quiz #2
====Session 8 (7/28)====
====Session 8 (7/28)====
====Session 9 (7/30)====
====Session 9 (7/30)====
* <span style="color: red">Quiz #3
* <span style="color: red">Quiz #3


===Week 4===
===Week 4. Simulations: Population genetics===
====Session 10 (8/3)====
====Session 10 (8/3)====
====Session 11 (8/4)====
====Session 11 (8/4)====
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* <span style="color: red">Quiz #4
* <span style="color: red">Quiz #4


===Week 5===
===Week 5. Microbial genomics===
====Session 13 (8/10)====
====Session 13 (8/10)====
====Session 14 (8/11)====
====Session 14 (8/11)====

Latest revision as of 05:59, 20 July 2026

Banner-comp-genomics.png
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

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

Week 2. Linux & Command Line Interface

Session 4 (7/20)

Session 5 (7/21)

  • Linux Tutorial II. Advanced

Session 6 (7/23)

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
Retrieved from "https://wiki.genometracker.org/index.php?title=Computational_Genomics_Summer_2026&oldid=6738"