Southwest-University

Biomedical Genomics July 8-19, 2019 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: weigang@genectr.hunter.cuny.edu Lab Website: http://diverge.hunter.cuny.edu/labwiki/

Host: Shunqin Zhu (祝顺琴), Ph.D.
Associate Professor, School of Life Science, South West University

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Figure 1. Gains & losses of host-defense genes among Lyme pathogen genomes (Qiu & Martin 2014)

Course Overview

Welcome to BioMedical Genomics, a computer workshop for advanced undergraduates and 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:

• Describe next-generation sequencing (NGS) technologies & contrast it with traditional Sanger sequencing
• Explain applications of NGS technology including pathogen genomics, cancer genomics, human genomic variation, transcriptomics, meta-genomics, epi-genomics, and microbiome.
• Visualize and explore genomics data using RStudio
• Replicate key results using a raw data set produced by a primary research paper

Web Links

• Install R base: https://cloud.r-project.org
• Install R Studio (Desktop version): http://www.rstudio.com/download
• Download: R datasets
• A reference book: R for Data Science (Wickharm & Grolemund)

Quizzes and Exams

Student performance will be evaluated by attendance, three (4) quizzes and a final report:

• Attendance: 50 pts
• Assignments: 5 x 10 = 50 pts
• Quizzes: 2 x 25 pts = 50 pts
• Mid-term: 50 pts
• Final presentation: 50 pts

Total: 250 pts

Course Schedule

Date & Hour	Tutorials	Assignment	Quiz & Exam
July 8 (Mon), 8:40-12:10	Introduction; R Tutorial I; NGS	Assignment #1 Install R/R studio and the "tidyverse" package on your own computer Recreate Script 1 & Mini-Practical Show help page for function "seq" Download dataset Create a new folder (e.g., Desktop/rtutor) Create a sub-folder (e.g., Desktop/rtutor/data/) Download from http://www.r4all.org/the-book/datasets Save to the sub-folder Unzip the file
July 9 (Tu), 8:40-12:10	NGS; R Tutorial II	Assignment #2 List pros & cons of Sanger vs NGS Compare accuracy, read length, and error rate between Illumina and PacBio Describe sequence information captured with each of the following file formats: FASTA, FASTQ, SAM, VCF Wide vs Tall data frames Variable names (informative, case sensitive) Read file
July 10 (Wed), 8:40-12:10	Microbiome I; R Tutorial III	Assignment #3	Quiz I
July 11 (Thur), 8:40-12:10	Microbiome II; R Tutorial IV	Assignment #4
July 12 (Fri), 8:40-12:10			Mid-term Exam
Weekend	Break
July 15 (Mon), 8:00-12:10	Transcriptome; R Tutorial V	Assignment #5
July 16 (Tu), 8:00-12:10	Proteome
July 17 (Wed), 8:00-12:10	Genomics I		Quiz II
July 18 (Thur), 8:00-12:10	Genomics II
July 19 (Fri), 8:00-12:10	Presentations

Papers & Datasets

Omics Application	Paper link	Data set	NGS Technology
Microbiome	Rimoldi_etal_2018_PlosOne	S1 Dataset	16S rDNA amplicon sequencing
Transcriptome	Wang_etal_2015_Science	Tables S2 & S4	RNA-Seq
Transcriptome & Regulome	Nava_etal_2019_BMCGenomics	Tables S2 & S3	RNA-Seq & CHIP-Seq
Proteome	Qiu_etal_2017_NPJ	(to be posted)	SILAC
Population genomics (Lyme)	Di_etal_2018_JCM	Data & R codes	Amplicon sequencing (antigen locus)
Population genomics/GWAS (Human)	Simonti_etal_2016_Science	Table S2	whole-genome sequencing (WGS); 1000 Genome Project (IGSR)
TB surveillance	Brow_etal_2015	Sequence Archives	Whole-genome sequencing (WGS)
Example	Example	Example	Example
Example	Example	Example	Example
Example	Example	Example	Example