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Wikiuser — Wed, 12 Aug 2026 01:12:07 GMT

Course/Lecture syllabi

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	==Course/Lecture syllabi==		==Course/Lecture syllabi==
	* [http://genometracker.org/~weigang/Day1_Intro_to_R.html ~~NYRaMP Informatics Workshop~~] (~~August 4,~~ 11~~, &~~ 18~~, 2026,~~ by ~~Dr.~~ Brandon Ely		===Informatics Workshop (NYRaMP & Belfer)===
	*[[NYRaMP-Informatics-~~2025~~\|~~NYRaMP Workshop~~ (~~August 2025~~, ~~by Brandon Ely~~)]]		* Summer 2026 (by Dr. Brandon Ely)
			** [http://genometracker.org/~weigang/Day1_Intro_to_R.html Day 1 (Aug 4)]
			** [http://genometracker.org/~weigang/day_2_central_dogma.html Day 2 (Aug 11)]
			** Day 3 (Aug 18)
			*[[NYRaMP-Informatics-2025\| Summer 2025 (by Brandon Ely)]]
			*[[NYRaMP-Informatics-2024\| Summer 2024 (Weigang & Brandon) ]]
			*[[BigData 2020\|Big Data (Summer, 2020)]]
			**[http://borreliabase.org/~wgqiu/tutorial-markdown.html Tutorial: R Markdown (Spring 2024)]
			**[http://borreliabase.org/~wgqiu/cluster-analysis.html Tutorial: Cluster analysis (Spring 2024)]
			**[http://borreliabase.org/~wgqiu/scRNA-analysis.html Tutorial: single-cel transcriptome analysis (Spring 2024)]
			===Computational Genomics (in China)===
	*[[Computational Genomics Summer 2026 \| KIZ Genomics Workshop, Summer 2026]]		*[[Computational Genomics Summer 2026 \| KIZ Genomics Workshop, Summer 2026]]
	*[[Computational Genomics (KIZ, Fall 2024)]]		*[[Computational Genomics (KIZ, Fall 2024)]]
	*[[~~NYRaMP~~-~~Informatics-2024~~\|~~NYRaMP Workshop~~ (~~August 2024~~)]]		*[[Southwest-University\|Southwest University R course (Summer, 2019)]]
			===Upper-level courses===
	*BIOL47120 BioMedical Genomics (Spring 2024). Tutorials: [https://borreliabase.org/~wgqiu/tutorial-markdown.html R Markdown] [https://borreliabase.org/~wgqiu/cluster-analysis.html Cluster analysis] [https://borreliabase.org/~wgqiu/scRNA-analysis.html single-cell RNA-seq]		*BIOL47120 BioMedical Genomics (Spring 2024). Tutorials: [https://borreliabase.org/~wgqiu/tutorial-markdown.html R Markdown] [https://borreliabase.org/~wgqiu/cluster-analysis.html Cluster analysis] [https://borreliabase.org/~wgqiu/scRNA-analysis.html single-cell RNA-seq]
			*[[BioMed-R-2020\|BIOL47120 Biomedical Genomics II (Spring, 2020)]]
	*BIOL425 Computational Molecular Biology (Spring, 2023). [https://github.com/weigangq/CSB-BIOL425/tree/master/lecture-materials Lecture material on github]		*BIOL425 Computational Molecular Biology (Spring, 2023). [https://github.com/weigangq/CSB-BIOL425/tree/master/lecture-materials Lecture material on github]
			*[[Biol425 2020\|BIOL425 Computational Molecular Biology (Spring, 2020)]]
	*BIOL714 Cell Biology: [http://borreliabase.org/~wgqiu/r-demo-2024.html R Demo (Spring 2024)] [http://borreliabase.org/~wgqiu/r-demo-2023.html R Demo (Spring 2023)]		*BIOL714 Cell Biology: [http://borreliabase.org/~wgqiu/r-demo-2024.html R Demo (Spring 2024)] [http://borreliabase.org/~wgqiu/r-demo-2023.html R Demo (Spring 2023)]
			*[[Biol375 2019\|BIOL37500, Molecular Evolution (Fall, 2019)]]
			*[[Biol20N02 2017\|Analysis of Biological Data (Spring, 2017)]]
			*[[Bioinformatics_Workshop_2014\|Bioinformatics Workshop (Summer, 2014)]]
			===Entry-level courses (lab modules)===
	*QuBi module: [[QuBi/module/bio203-lab12—2022\|BIOL20300 Molecular Genetics, Lab 12 (2023)]]		*QuBi module: [[QuBi/module/bio203-lab12—2022\|BIOL20300 Molecular Genetics, Lab 12 (2023)]]
	*QuBi module: [[QuBi/modules/biol203-geno-pheno-association-2022\|BIOL20300 Molecular Genetics, Lab 13 (2022)]]		*QuBi module: [[QuBi/modules/biol203-geno-pheno-association-2022\|BIOL20300 Molecular Genetics, Lab 13 (2022)]]
	*QuBi module: [[QuBi/modules/biol303\|BIOL30300 Cell Biology, Bioinformatics Lab (transcriptome analysis)]]		*QuBi module: [[QuBi/modules/biol303\|BIOL30300 Cell Biology, Bioinformatics Lab (transcriptome analysis)]]
	*[[BigData 2020\|Big Data (Summer, 2020)]]
	*[[BioMed-R-2020\|BIOL47120 Biomedical Genomics II (Spring, 2020)]]
	**[http://borreliabase.org/~wgqiu/tutorial-markdown.html Tutorial: R Markdown (Spring 2024)]
	**[http://borreliabase.org/~wgqiu/cluster-analysis.html Tutorial: Cluster analysis (Spring 2024)]
	**[http://borreliabase.org/~wgqiu/scRNA-analysis.html Tutorial: single-cel transcriptome analysis (Spring 2024)]
	*[[Biol425 2020\|BIOL425 Computational Molecular Biology (Spring, 2020)]]
	*[[Biol375 2019\|BIOL37500, Molecular Evolution (Fall, 2019)]]
	*[[Southwest-University\|Southwest University R course (Summer, 2019)]]
	*[[Biol20N02 2017\|Analysis of Biological Data (Spring, 2017)]]
	*[[Bioinformatics_Workshop_2014\|Bioinformatics Workshop (Summer, 2014)]]

	==SARS-CoV-2 genome evolution==		==SARS-CoV-2 genome evolution==

Computational Genomics Summer 2026

Wikiuser — Tue, 11 Aug 2026 01:43:15 GMT

Week 5. Microbial genomics

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	* Upload a presentation draft (a tentative title, your name, name of the PI, a 150-words abstract)		* Upload a presentation draft (a tentative title, your name, name of the PI, a 150-words abstract)

	===Week 5. ~~Microbial genomics~~===		===Week 5. Final Presentations===
	====Session 13 (8/10)====		====Session 13 (8/10)====
	* No class (work from home)		* No class (work from home)
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	====Session 14 (8/11)====		====Session 14 (8/11)====
			[[File:KIZ2026-presentation-flyer-4.pdf\|thumb\|Presentation program]]
	* Presentations: Group 1		* Presentations: Group 1

File:KIZ2026-presentation-flyer-4.pdf

Wikiuser — Tue, 11 Aug 2026 01:40:56 GMT

Wikiuser uploaded File:KIZ2026-presentation-flyer-4.pdf

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Computational Genomics Summer 2026

Wikiuser — Tue, 04 Aug 2026 07:55:19 GMT

Session 12 (8/6)

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	* 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)'']

	==Assignments, Quizzes, and a Final ~~Presentatio8n~~==		==Assignments, Quizzes, and a Final Presentation==
	Student performance will be evaluated by attendance, in-class quizzes and a final presentation		Student performance will be evaluated by attendance, in-class quizzes and a final presentation
	* Attendance & participation: 14 * 5 pts = 70 pts		* Attendance & participation: 12 * 5 pts = 60 pts
	* Daily assignments: 8 x 10 pts = 80 pts		* Daily assignments: 8 x 10 pts = 80 pts
	* Open-Book Quizzes: 4 x 30 pts = ~~120~~ pts		* Open-Book Quizzes: 3 x 30 pts = 90 pts
	* Final presentation: 30 pts		* Final presentation: 30 pts
	Total: ~~300~~ pts		Total: 260 pts

	==Course Schedule==		==Course Schedule==
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	===Week 4. Simulations: Population genetics===		===Week 4. Simulations: Population genetics===
	====Session 10 (8/3)====		====Session 10 (8/3)====
			* Intro: Genetic drift
	* <span style="color: red">Quiz #3: Central Dogma		* <span style="color: red">Quiz #3: Central Dogma

	====Session 11 (8/4)====		====Session 11 (8/4)====
			* Simulations: Genetic drift
			* Simulations: Drift with mutation
			* <span style="color: green">Assignment 8
	====Session 12 (8/6)====		====Session 12 (8/6)====
	* ~~<span style="color: red">Quiz #4~~		* No class (work from home)
			* Upload a presentation draft (a tentative title, your name, name of the PI, a 150-words abstract)

	===Week 5. Microbial genomics===		===Week 5. Microbial genomics===
	====Session 13 (8/10)====		====Session 13 (8/10)====
			* No class (work from home)
			* Upload your 5-slide presentation (in PDF)

	====Session 14 (8/11)====		====Session 14 (8/11)====
	* Presentations		* Presentations: Group 1

	====Session 15 (8/13)====		====Session 15 (8/13)====
	* Presentations		* Presentations: Group 2
	* Course evaluation		* Course evaluation

Main Page

Wikiuser — Mon, 03 Aug 2026 07:11:46 GMT

Course/Lecture syllabi

← Older revision		Revision as of 07:11, 3 August 2026
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	==Course/Lecture syllabi==		==Course/Lecture syllabi==
	*[[NYRaMP-Informatics~~-2026\|NYRaMP~~ Workshop (August 2026, by Brandon Ely~~)]]~~		* [http://genometracker.org/~weigang/Day1_Intro_to_R.html NYRaMP Informatics Workshop] (August 4, 11, & 18, 2026, by Dr. Brandon Ely
	*[[NYRaMP-Informatics-2025\|NYRaMP Workshop (August 2025, by Brandon Ely)]]		*[[NYRaMP-Informatics-2025\|NYRaMP Workshop (August 2025, by Brandon Ely)]]
	*[[Computational Genomics Summer 2026 \| KIZ Genomics Workshop, Summer 2026]]		*[[Computational Genomics Summer 2026 \| KIZ Genomics Workshop, Summer 2026]]

Computational Genomics Summer 2026

Wikiuser — Mon, 27 Jul 2026 07:23:05 GMT

Session 9 (7/30)

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	===Week 2. Linux & Command Line Interface===		===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		* <span style="color: red">Quiz #1. Phyogenetics
	* Linux Tutorial I. [[File:Part-1-intro-unix-2026.pdf\|thumb]]
	* Linux Tutorial II: BpWrapper Toolkit (https://github.com/bioperl/p5-bpwrapper)

	====Session 5 (7/21)====		====Session 5 (7/21)====
			* Linux Tutorial II. Advanced
			* <span style="color: green">Assignment 4. Linux Intermezzos 1-4

	====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
			* <span style="color: green">Assignment 5. BbWrapper utilities

	===Week 3. Simulations: Central Dogma===		===Week 3. Simulations: Central Dogma===
	====Session 7 (7/27)====		====Session 7 (7/27)====
			* <span style="color: red">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)====		====Session 8 (7/28)====
			* Random DNA sequences
			* DNA replication
			* DNA transcription
			* <span style="color: green">Assignment 6. Implement algorithms & make visualization: B-Day problem; DNA replication & transcription

	====Session 9 (7/30)====		====Session 9 (7/30)====
	* <span style="color: ~~red~~">~~Quiz #3~~		* 6-frame translation
			** Algorithm
			** Visualization
			* <span style="color: green">Assignment 7. Implement & Visualize 6-frame translation

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

	====Session 11 (8/4)====		====Session 11 (8/4)====
	====Session 12 (8/6)====		====Session 12 (8/6)====

File:Phylogeny-lecture-slides-2026.pdf

Wikiuser — Sun, 19 Jul 2026 01:53:38 GMT

Wikiuser uploaded a new version of File:Phylogeny-lecture-slides-2026.pdf

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