Genome 372
Genomics
and Proteomics
Course Instructors:
Michael J. MacCoss, Ph.D. - maccoss@u.washington.edu, 206-616-7451
John Stamatoyannopoulos, M.D. - jstam@u.washington.edu, 206-267-1098
Teaching Assistant:
Max Boeck - maxboeck@u.washington.edu, 206-221-4584
Course Objectives
This class provides an introduction to the modern scientific disciplines of Genomics and Proteomics. Emphasis will be placed on understanding molecular and computational technologies used to sequence, map, and analyze the genomes and proteomes of living organisms from humans to bacteria. Lectures combine the description of technologies with their application to major biological questions. Lab activities provide the opportunity for students to perform analyses of 'real world' data using bioinformatics tools.
Proposed Assignments / Text:
The text book Discovering Genomics Proteomics and Bioinformatics, M Campbell and L Meyer, 2nd edition, 2007 is recommended but not required. Suggested readings from this text and additional tutorials will be provided (as PDFs) prior to each class for download from the course website. The course will include one mid-term exam and a final exam. Other graded assignments will be problem sets distributed throughout the quarter. Some problem sets will involve use of web resources for data analysis and mining.
Course Website:
http://proteome.gs.washington.edu/classes/Genome372/
Genome 372 Course outline
| Class | Instructor | Topic | Notes | Readings | ||
| Sep 24 | (JS) | What is genomics? | Introduction to genome/gene organization and function | |||
| Sep 26 | (MM) | What is proteomics? | Why study many proteins simultaneously? | |||
| Sep 29 | (JS) | Genome databases and browsers | Display of genome sequence and annotations using public genome browsers | |||
| Searching sequence databases (BLAST, etc) | ||||||
| Oct 1 | (MM) | Identifying and measuring proteins | One gene -> multiple transcripts -> many proteins. Complexity of the proteome | O'Farrell et al. | ||
| Tools of protein biochemistry | Classical technologies for separating and detecting proteins | |||||
| Oct 3 | (MM) | Introduction to mass spectrometry | Basics of mass spectrometry. Why use mass spectrometry for the analysis of proteins? | Steen and Mann Chapter 8.4 Measuring Proteins |
||
| Oct 6 | (JS) | Genome sequencing and assembly I | How DNA sequencing works on a small and a large scale | |||
| Oct 8 | (JS) | Genome sequencing and assembly II | Shotgun sequencing and assembly of genomes | |||
| Oct 10 | (JS) | Annotating genomes I: Finding genes | How genes are identified and annotated | |||
| Oct 13 | (MM) | Identifying and measuring proteins (Sequencing Peptides) | ||||
| Oct 15 | (MM) | Identifying and measuring proteins (Shotgun Proteomics) | Washburn et al. Yates |
|||
| Oct 17 | (JS) | Annotating genomes II: Comparative genomics | Basic concepts of comparative genomics | Human Genome What Is a HMM |
DNA sequencing | |
| Oct 20 | (MM) | Applications of Shotgun Proteomics | ||||
| Oct 22 | (JS) | Measuring gene activity I | Basics of microarray design, synthesis, and use | |||
| Oct 24 | (JS) | Measuring gene activity II | Finding differentially regulated genes | |||
| Applied technology: | Breast Cancer | |||||
| Oct 27 | (MM/JS) | Midterm Exam | ||||
| Oct 29 | (MM) | Methods for identifying protein complexes | ||||
| Oct 31 | (MM) | Identifying and measuring proteins (Quantitative proteomics) | MacCoss and Matthews | |||
| Nov 3 | (JS) | Genetic variation . | Basics of SNPs & their detection. Genetic variation at the nucleotide level. Illumina beadarray and array-based SNP detection | |||
| Applied technology: | Mapping disease genes using whole genome association studies | |||||
| Nov 5 | (JS) | Microarrays II: | RNA profiling in disease; Genomic Annotation with tiling microarrays | Armstrong et al.
Bullinger et al. Golub et al. |
||
| Nov 7 | (MM) | Top-down proteoms | ||||
| Applied technology: | Genomic changes in mental retardation | |||||
| Nov 10 | (MM) | Top Down vs Bottom up Proteomics The amazing world of GFP | GFP Review 1 GFP Review 2 |
|||
| Nov 12 | (JS) | Genetic variation | ||||
| Nov 14 | (JS) | Structural Genomics | Mental Retardation Review of Sturctural Variation Lecture Slides |
|||
| Nov 17 | (MM) | Protein arrays and Activity based proteomics | ||||
| Nov 19 | (JS) | Epigenomics | Basics of chromatin and DNA methylation in relation to genome sequence | Chromatin Review How to Study Chromatin |
||
| Nov 21 | (MM) | Pathway and targeted proteomics | Lecture Notes | |||
| Nov 24 | (MM) | Protein Biomarkers | Basics of Protein Biomakers | Cancer Biomarkers | ||
| Applied technology: | Cancer biomarkers | |||||
| Nov 26 | (MM) | Statistical problems in proteomics | ||||
| Dec 1 | (JS) | Neurogenomics | Neurogenomics |
|||
| Dec 3 | (JS) | Personal Genomics | Upcoming technologies, likely future directions | Next Gen Sequencing Whole Genome Sequencing hapmap 100genomes personal genomes GINA |
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| Dec 5 | (MM) | The Future of Proteomics | Upcoming technologies, likely future directions | |||
Tests:
Oct 19 Midterm
Oct 19 Final
Class Grades:
Mid Term: 25%
Problem Sets/Quiz Section Assignments: 25%
Take Home Final: 40%
Class Participation: 10%
Quiz Sections:
Oct 2 Intro
to Bioinformatics
Oct 9 Sanger Method
DNA Sequencing
Oct 16 De
novo sequencing of peptide MS/MS spectra
Oct 23 Shotgun
proteomics, computational analysis of mass spectrometry data
Oct 30 Gene
Finding
Nov 6 Genetic
expression
Nov 13 Intact
protein analysis and protein structure
Nov 20 Protein
Complexes and Chromatin Structure
Dec 4 Review for final