R/BioConductor Programming in Bioinformatics

(Monday, July 30, 2007 - Thursday, August 16, 2007)

Syllabus

The open source software R (http://www.r-project.org) has revolutionized statistical data analysis, and has rapidly become the platform of choice for both statisticians and bioinformaticians. Furthermore, BioConductor (http://www.bioconductor.org/), an open source and open development software project, has been increasingly used for the analysis of genomic and gene expression microarray data. In this summer course, the participants will learn how to use R packages in statistical modeling and for mining high-dimensional data. We show users how to use BioConductor packages to normalize microarray data, to identify differentially expressed genes, to cluster gene expression profiles and to identify affected biological pathways.

The course is free of charge. Scroll down for scripts, files and lecture slides.

The schedule of the summer course is as follows.

Lecture 1. Basic Introduction to R (I)
Date: Monday, July 30, 2007
Time: 12:30PM-2:30PM
Location: HSPH Kresge LL-6
Instructor: Dr. Jaroslaw Harezlak
This lecture will provide an introduction to command syntax, basic functions, and basic libraries of R.

Lecture 2. Basic Introduction to R (II)
Date: Thursday, August 2, 2007
Time: 12:30PM-2:30PM
Location: HSPH Kresge LL-6
Instructor: Drs. Jaroslaw Harezlak
This lecture will provide an introduction to graphics and basic statistical models of R.

Lecture 3. Microarray Analysis with R & BioConductor (I)
Date: Tuesday, August 7, 2007
Time: 12:30PM-2:30PM
Location: HSPH Kresge LL-6
Instructor: Dr. Deanne Taylor
Description: This lecture will introduce R/BioConductor functions for: (1) data import/export, (2) background correction and normalization procedures for Affymetrix and cDNA arrays, (3) array quality inspection,

Lecture 4. Microarray Analysis with R & BioConductor (II)
Date: Friday, August 10, 2007
Time: 12:30PM-2:30PM
Location: HSPH Kresge LL-6
Instructor: Dr. Deanne Taylor
Description: This lecture will introduce R/BioConductor functions for: (1) visualization of genomic information, (2) overview on clustering methods, and (3) Gene Ontology (GO) analysis.

Lecture 5. Clustering Techniques in R
Date: Tuesday, August 14, 2007
Time: 12:30PM-2:30PM
Location: HSPH Kresge LL-6
Instructor: Dr. Aedín Culhane
This lecture will provide an overview on the usage of the most common clustering techniques in R, such as hierarchical clustering and K-means.

Lecture 6. Machine Learning Techniques in R
Date: Thursday, August 16, 2007
Time: 12:30PM-2:30PM
Location: HSPH Kresge LL-6
Instructor: Dr. Tianhua Niu
This lecture will provide an overview on the usage of the most common machine learning techniques in R, such as neural networks, support vector machine, boosting and bagging.

Mini-Course on Genome-Wide and Pathway-based Association Studies of Complex Diseases

(Friday, April 27, 2007 - Friday, June 1, 2007)

Syllabus

With the advent of high-throughput genotyping platforms such as the Affymetrix Human SNP Array 5.0 (containing the conventional two-chip Mapping 500K SNP Array Set plus additional probes covering other genetic variations such as copy number variations), Illumina Sentrix HumanHap 650Y, 1M Genotyping BeadChips (tag SNP content providing genomic coverage) and Human CNV370-Duo DNA Analysis BeadChip (covering copy number variant regions), genome-wide association studies have been gaining increasing interests in genetic dissection of complex human diseases. Furthermore, pathway-centric studies have been recognized to provide significantly greater biological insights into the molecular mechanisms underlying disease pathogenesis than classic single-gene studies. With the rapid advances in ultra-low-cost whole genome sequencing technologies, profoundly novel study designs could be devised and implemented based on the entire human genome sequence for exploring genetic susceptibilities underlying complex diseases in large population cohorts. This mini-course gathers together pioneers in these emerging fields to address key biological and statistical issues involved in performing these studies and to present their up-to-date results for a variety of human disorders. This mini-course will offer participants a great opportunity to both gain novel knowledge and to learn new strategies in carrying out genome-wide and pathway-based association studies. 

(1) Date: Friday, April 27, 2007
Place: Kresge G3, HSPH

1:30PM-2:25PM
Lecture 1
David Hunter, MBBS, MPH, ScD
Vincent L. Gregory Professor of Cancer Prevention & Director
Program in Molecular and Genetic Epidemiology
Dept. of Epidemiology, HSPH
"Genome-Wide Association Studies of Breast Cancer"  (Presentation)

2:35PM-3:30PM
Lecture 2
Stephen J. Chanock, MD
Senior Investigator and Director
Core Genotyping Facility, the Advanced Technology Center
National Cancer Institute
"Genome-Wide Association Studies of Prostate Cancer" (Presentation)

(video for both lectures)

(2) Date: Friday, May 4, 2007
Place: Kresge G2, HSPH
1:30PM-2:25PM
Lecture 3
Shaun Purcell, PhD
Center for Human Genetic Research, Massachusetts General Hospital
Harvard Medical School
Program in Medical and Population Genetics, Broad Institute of Harvard and MIT
"PLINK: A Toolset for Genome-Wide Data Analysis" (Presentation)

2:35PM-3:30PM
Lecture 4
David Altshuler, MD, PhD
Associate Professor of Genetics and Medicine
Massachusetts General Hospital, Harvard Medical School
Director, Program in Medical and Population Genetics
Broad Institute of Harvard and MIT
“Application of HapMap in Genome-Wide Association Studies" (Presentation)

(video for both lectures)

(3) Date: Friday, May 11, 2007
Place: Kresge G2, HSPH
1:30PM-2:25PM
Lecture 5
Christoph Lange, PhD
Assistant Professor of Biostatistics
Dept. of Epidemiology, HSPH
"PBAT: A Powerful Biostatistical Tool for Genome-Wide Association Studies" (Presentation)

2:35PM-3:30PM
Lecture 6 
Robert Sladek, MD 
Assistant Professor
Departments of Human Genetics and Medicine
McGill University
"A Genome-Wide Association Study of Type II Diabetes Mellitus" (Presentation)

(video for both lectures)

(4) Date: Friday, May 18, 2007
Place: Kresge G2, HSPH
1:30PM-2:25PM
Lecture 7
Mark Daly, PhD
Assistant Professor of Medicine
Center for Human Genetic Research, Massachusetts General Hospital
Harvard Medical School
Program in Medical and Population Genetics, Broad Institute of Harvard and MIT
"A Genome-Wide Association Study of Inflammatory Bowel Disease" (Presentation)

2:35PM-3:30PM
Lecture 8 
Peter Kraft, PhD 
Assistant Professor of Epidemiology
Dept. of Epidemiology, HSPH
"Efficiency and Power of Multi-stage Design for Genome-Wide Association Studies" (Presentation)

(video for both lectures)

(5) Date: Friday, May 25, 2007
Place: Kresge G3, HSPH
1:30PM-2:25PM
Lecture 9
Joel N. Hirschhorn, MD, PhD
Assistant Professor of Genetics and Pediatrics, Harvard Medical School
Program in Medical and Population Genetics, Broad Institute of Harvard and MIT
"Performing and Interpreting Association Studies" (Presentation)

2:35PM-3:30PM
Lecture 10
Christopher J. O'Donnell, MD, MPH
National Heart, Lung and Blood Institute (NHLBI)
Senior Advisor to the Director for Genome Research
Associate Director, NHLBI's Framingham Heart Study
"Genome Wide Association Studies for Cardiovascular Disease in Observational Cohorts"

(video for both lectures)

(6) Date: Friday, June 1, 2007
Place: Kresge G3, HSPH
1:30PM-2:25PM
Lecture 11
Stacey Gabriel, PhD
Director, Genetic Analysis Platform
Broad Institute of Harvard and MIT
"High-Throughput Genotyping Platforms for Genome-Wide and Pathway-based Genetic Association Studies"

2:35PM-3:30PM
Lecture 12
George Church, PhD
Professor of Genetics, Harvard Medical School, MIT Health Sciences & Technology
Senior Associate of the Broad Inst. of Harvard & MIT
Director, The Lipper Center for Computational Genetics,
MIT-Harvard DOE Genomes to Life Center,
NIH Center for Excellence in Genomic Science
"Advanced Sequencing Technologies and the Personal Genome Project" (Presentation)

(video for both lectures)