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<center>'''Biomedical Genomics'''</center> | |||
<center>July 8-19, 2019</center> | |||
<center>'''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 Physiology and Biophysics | |||
Institute for 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:''' weigang@genectr.hunter.cuny.edu</center> | |||
<center>'''Lab Website:''' http://diverge.hunter.cuny.edu/labwiki/</center> | |||
---- | |||
[[File:Lp54-gain-loss.png|400px|thumbnail|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 and R Studio | |||
* Unix Tutorial | |||
* Textbook | |||
==Quizzes and Exams== | |||
Student performance will be evaluated by attendance, three (4) quizzes and a final report: | |||
* Attendance: 50 pts | |||
* Quizzes: 2 x 25 pts = 50 pts | |||
* Mid-term: 50 pts | |||
* Final presentation: 50 pts | |||
Total: 200 pts | |||
==Course Schedule== | |||
{| class="wikitable" | |||
|- | |||
! Date & Hour !! Tutorial & Lecture !! Paper !! Quiz & Exam | |||
|- | |||
| July 8 (Mon), 8:40-12:10 || Introduction; R Tutorial I; NGS || NGS || | |||
|- | |||
| July 9 (Tu), 8:40-12:10 || NGS; R Tutorial II || NGS || | |||
|- | |||
| July 10 (Wed), 8:40-12:10 || Microbial ecology I; R Tutorial III || Fish diet || Quiz I | |||
|- | |||
| July 11 (Thur), 8:40-12:10 || Microbial ecology II; R Tutorial IV || Lyme OspC (cont'd) || | |||
|- | |||
| July 12 (Fri), 8:40-12:10 || Functional genomics I || Essential genes (RNA-SEQ/CHIP-SEQ) || Mid-term Exam | |||
|- | |||
| July 15 (Mon), 8:00-12:10 || Functional genomics II || Cancer proteomics || | |||
|- | |||
| July 16 (Tu), 8:00-12:10 || Genome variation I || TB || Quiz II | |||
|- | |||
| July 17 (Wed), 8:00-12:10 || Genome variation II || Human || | |||
|- | |||
| July 18 (Thur), 8:00-12:10 || Human genomic variations || Paper 5 (cont'd) || | |||
|- | |||
| July 19 (Fri), 8:00-12:10|| Example || Example || Presentations | |||
|} | |||
==Papers & Datasets== | |||
{| class="wikitable sortable" | |||
|- | |||
! Omics Application !! Paper link !! Data set !! NGS Technology | |||
|- | |||
| Microbiome || [https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0193652 Rimoldi_etal_2018_PlosOne] || [https://doi.org/10.1371/journal.pone.0193652.s004 S1 Dataset] || 16S rDNA amplicon sequencing | |||
|- | |||
| Transcriptome || [https://science.sciencemag.org/content/350/6264/1096 Wang_etal_2015_Science] || Tables S2 & S4 || RNA-Seq | |||
|- | |||
| Transcriptome & Regulome || [https://bmcmedgenomics.biomedcentral.com/articles/10.1186/s12920-019-0477-8 Nava_etal_2019_BMCGenomics] || Tables S2 & S3 || RNA-Seq & CHIP-Seq | |||
|- | |||
| Proteome || [https://www.ncbi.nlm.nih.gov/pubmed/28232952 Qiu_etal_2017_NPJ] || (to be posted) || SILAC | |||
|- | |||
| Population genomics (Lyme) || [https://jcm.asm.org/content/56/11/e00940-18.long Di_etal_2018_JCM] || [https://github.com/weigangq/ocseq Data & R codes] || Amplicon sequencing (antigen locus) | |||
|- | |||
| Population genomics/GWAS (Human) || [https://science.sciencemag.org/content/351/6274/737.long Simonti_etal_2016_Science] || [https://science.sciencemag.org/highwire/filestream/673591/field_highwire_adjunct_files/1/aad2149-Simonti-SM.Table.S2.xlsx Table S2] || whole-genome sequencing (WGS); [http://www.internationalgenome.org/ 1000 Genome Project (IGSR)] | |||
|- | |||
| TB surveillance || [https://jcm.asm.org/content/53/7/2230 Brow_etal_2015] || [https://www.ebi.ac.uk/ena/data/view/PRJEB9206 Sequence Archives]|| Whole-genome sequencing (WGS) | |||
|- | |||
| Example || Example || Example || Example | |||
|- | |||
| Example || Example || Example || Example | |||
|- | |||
| Example || Example || Example || Example | |||
|} | |} | ||
Revision as of 01:59, 23 June 2019
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
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 and R Studio
- Unix Tutorial
- Textbook
Quizzes and Exams
Student performance will be evaluated by attendance, three (4) quizzes and a final report:
- Attendance: 50 pts
- Quizzes: 2 x 25 pts = 50 pts
- Mid-term: 50 pts
- Final presentation: 50 pts
Total: 200 pts
Course Schedule
Date & Hour | Tutorial & Lecture | Paper | Quiz & Exam |
---|---|---|---|
July 8 (Mon), 8:40-12:10 | Introduction; R Tutorial I; NGS | NGS | |
July 9 (Tu), 8:40-12:10 | NGS; R Tutorial II | NGS | |
July 10 (Wed), 8:40-12:10 | Microbial ecology I; R Tutorial III | Fish diet | Quiz I |
July 11 (Thur), 8:40-12:10 | Microbial ecology II; R Tutorial IV | Lyme OspC (cont'd) | |
July 12 (Fri), 8:40-12:10 | Functional genomics I | Essential genes (RNA-SEQ/CHIP-SEQ) | Mid-term Exam |
July 15 (Mon), 8:00-12:10 | Functional genomics II | Cancer proteomics | |
July 16 (Tu), 8:00-12:10 | Genome variation I | TB | Quiz II |
July 17 (Wed), 8:00-12:10 | Genome variation II | Human | |
July 18 (Thur), 8:00-12:10 | Human genomic variations | Paper 5 (cont'd) | |
July 19 (Fri), 8:00-12:10 | Example | Example | 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 |