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:
Michael Hoopmann - hoopmann@u.washington.edu, 206-616-9023
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 |
| Oct 1 | (JS) | What is genomics? | Introduction to genome/gene organization and function | |
| Oct 3 | (MM) | What is proteomics? | Why study many proteins simultaneously? | |
| Oct 5 | (JS) | Tools of molecular biology | PCR, Gels, antibodies, enzymes, fluorescent detection, avidin/biotin, etc… | |
| Tools of bioinformatics | BLAST, Databases, Genome Browsers, etc… | |||
| Oct 8 | (JS) | How are genomes sequenced? | How DNA sequencing works on a small and a large scale | |
| ‘Shotgun’ sequencing | Shotgun sequencing and assembly of genomes | |||
| Oct 10 | (JS) | Finding genes | How genes are identified and annotated | |
| Comparative genomics | Highlights of comparative genomics | |||
| Applied technology: | Finding new genes | |||
| Oct 12 | (MM) | Identifying and measuring proteins – part I | 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 15 | (MM) | Identifying and measuring proteins – part II | Basics of mass spectrometry. Why use mass spectrometry for the analysis of proteins? | Steen and Mann Chapter 8.4 Measuring Proteins |
| Oct 17 | (JS) | Gene transcription into RNA | Basic concepts of gene transcription, splicing. | |
| Oct 19 | (JS) | DNA microarray technology | Basics of microarray design, synthesis, and use | |
| Oct 22 | (MM) | Identifying and measuring proteins – part III | Shotgun proteomics | Washburn et al. Yates |
| Oct 24 | (MM) | Applied technology: | Shotgun proteomics | |
| Oct 26 | (JS) | Functional genomics part I: | Whole-genome array analysis of gene expression DNA microarrays | |
| Oct 29 | (JS) | Functional genomics part I cont’d: | Finding differentially regulated genes | |
| Applied technology: | Breast cancer | |||
| Oct 31 | (JS) | Midterm Examination | Complete list of exam questions Answerkey |
|
| Nov 2 | (JS) | Functional genomics part II | Basics of microRNAs, siRNA | |
| RNA: | more than just protein coding genes | |||
| Functional genomics part III: | Basics of SNPs & their detection. Genetic variation at the nucleotide level. Illumina beadarray and array-based SNP detection. | |||
| Applied technology: | Finding disease genes Diabetes. | |||
| Nov 5 | (JS) | Functional genomics part IV: | CGH technology: not all genomes are the same. Large scale genetic variation | |
| Applied technology: | Genomic disorders Examples of copy #-related diseases (MR, etc.) | |||
| Nov 7 | (JS) | Functional genomics part V: | Basics of transcription factors/complexes | |
| Nov 9 | (MM) | Methods for identifying protein complexes | Pulling down and analyzing protein complexes | Rigaut et al. |
| Nov 14 | (MM) | Identifying and measuring proteins – part IV | Quantitative proteomics | MacCoss and Matthews |
| Nov 16 | (MM) | Identifying and measuring proteins – part V | Intact protein analysis by mass spectrometry | Kelleher |
| Applied technology: | Applications of Top Down mass spectrometry to the identification of histone modifications | |||
| Identifying and measuring proteins – part VI | High throughput approaches for interrogating protein conformation and structure | |||
| Nov 19 | (JS) | Regulation of genes by protein complexes | Chip-Chip | |
| Nov 21 | (JS) | Functional genomics part VI: | Basics of higher order genome function | |
| Nov 26 | (MM) | Identifying and measuring proteins – part VI | High throughput approaches for interrogating protein conformation and structure | Petricoin et al. |
| Identifying and measuring proteins – part VII | Protein Arrays | |||
| Nov 28 | (MM) | Identifying and measuring proteins – part VIII | Activity based proteomics | |
| Identifying and measuring proteins – part VIX | Targeted proteomics | |||
| Applied technology: | Pathway based proteomics | |||
Nov 30 (MM) Protein
Biomarkers Basics
of protein biomarkers
Applied
technology: Cancer biomarkers
Dec 3 (JS) The Future of
Genomics Upcoming
technologies, likely future directions
Dec 7 (MM) The
Future of Proteomics Upcoming
technologies, likely future directions
Class Grades:
Mid Term: 25%
Problem Sets/Quiz Section Assignments: 25%
Take Home Final: 40%
Class Participation: 10%
Quiz Sections:
Oct 4 Intro
to Bioinformatics
Oct 11 Sanger Method
DNA Sequencing
Oct 18 De
novo sequencing of peptide MS/MS spectra
Oct 25 Shotgun
proteomics, computational analysis of mass spectrometry data
Nov 1 Gene
Finding
Nov 8 Genetic
expression