Survey of Technologies for Molecular Biology
Course web page: http://faculty.washington.edu/rogerb/Conj546_2011WebSite/index.html
Dates, days and times: (10/4 - 11/3; Tues. & Thurs. 1:00-2:20pm)
Location: UW HST T473
Class size: 30
Course description: This course provides a broad overview of modern technologies used in molecular biology with an emphasis on “ ‘omics” technologies – e.g. genomics, transcriptomics, proteomics and metabolomics. In addition to methods and applications for the technologies, the course examines the theoretical basis and underlying instrumentation through which these technologies are implemented. It’s intended to be broadly useful for anyone working in a molecular biology lab where such technologies might be useful.
Learning objectives: At the end of this course, students should:
- Understand what technologies are in existence for DNA sequencing and genotyping, gene expression measurements, proteomics and metabolomics.
- Understand the applications of each technology and why some technologies may be better applied to a certain subset of problems.
- Understand the underlying sources of error that may be present in a dataset produced by a given technology.
- Have an appreciation for where the various technologies are heading and how this might impact future experiments.
Prerequisites: Graduate student status or permission of instructor
Course materials and/or textbooks: No textbooks are used. Selected literature is linked on the course website.
Course requirements, examinations and grading:
30% Attendance - you can't learn if you don't attend.
50% Two homework assignments - Homework will consist of preparing two reviews of articles provided (students will be able to select from a small list of 3-4 articles for each assignment).
20% One midterm and one final quiz - these will be multiple-choice exams and the questions will only cover the assigned reading materials.
Sample syllabus
Notes – The lectures will vary slightly from year to year as new technologies come into fruition and older technologies are replaced. Reading for each lecture is linked from the course web site and will vary slightly from year-to-year.
|
Instructor (optional) |
Lecture topic |
Concepts |
|
Bumgarner |
"First generation" sequencing technologies and genome assembly |
Maxim-Gilbert and Sanger sequencing chemistries, slab gel post run detection, fluorescent DNA sequencing RT detection, sources of errors and noise in data, shotgun sequencing |
|
Bumgarner |
cDNA sequencing, SAGE and microarray analysis
|
Microarray types and methods of fabrication Expression analysis via microarrays and early sequencing methods |
|
Bumgarner |
Array and sequence based methods and tools for genotyping |
|
|
Bumgarner |
Emulsion based PCR and polonies as methods to replace library production, pyrosequencing technology, Ion torrent sequencing technology Error rates, sources of error and read length limitations |
|
|
Bumgarner |
Illumina and the ABI Solid Sequencing technologies
|
Sequencing by synthesis with reversible dye terminators Sequencing by ligation Error rates, sources of error and read length limitations |
|
Bumgarner |
Single Molecule Sequencing Methods and Complete Genomics Technology
|
Current and emerging technologies for single molecule sequencing (PacBio, Oxford Nanopore and other nanopore technologies), Complete genomics’ sequencing technologies Error rates, sources of error and read length limitations Comparison of current 2nd and 3rd gene technologies |
|
Bumgarner |
Applications enabled by 2nd and 3rd generation sequencing technologies (plus a few novel assays that haven’t yet been converted from arrays to sequencing) |
Assays performed by sequencing – RNA seq., methylation assays, genotyping, etc. |
|
Bumgarner |
Proteomics technologies – Mass spectrometry and protein arrays |
2-D gel and mass spectrometric methods for proteomics Protein arrays, antibody arrays Limitations of various technologies |
|
Yvonne Lin |
mass spectrometric and NMR methods for proteomics experimental design and workflow, methods for data analysis |
|
|
Ka Yee Yeung-Rhee |
Types of networks and pathways Information available in ‘omics data Bayesian and regression based methods for network inference |
|
Instructor (optional) |
Lecture topic |
Concepts |
|
Bumgarner |
"First generation" sequencing technologies and genome assembly |
Maxim-Gilbert and Sanger sequencing chemistries, slab gel post run detection, fluorescent DNA sequencing RT detection, sources of errors and noise in data, shotgun sequencing |
|
Bumgarner |
cDNA sequencing, SAGE and microarray analysis
|
Microarray types and methods of fabrication Expression analysis via microarrays and early sequencing methods |
|
Bumgarner |
Array and sequence based methods and tools for genotyping |
|
|
Bumgarner |
Emulsion based PCR and polonies as methods to replace library production, pyrosequencing technology, Ion torrent sequencing technology Error rates, sources of error and read length limitations |
|
|
Bumgarner |
Illumina and the ABI Solid Sequencing technologies
|
Sequencing by synthesis with reversible dye terminators Sequencing by ligation Error rates, sources of error and read length limitations |
|
Bumgarner |
Single Molecule Sequencing Methods and Complete Genomics Technology
|
Current and emerging technologies for single molecule sequencing (PacBio, Oxford Nanopore and other nanopore technologies), Complete genomics’ sequencing technologies Error rates, sources of error and read length limitations Comparison of current 2nd and 3rd gene technologies |
|
Bumgarner |
Applications enabled by 2nd and 3rd generation sequencing technologies (plus a few novel assays that haven’t yet been converted from arrays to sequencing) |
Assays performed by sequencing – RNA seq., methylation assays, genotyping, etc. |
|
Bumgarner |
Proteomics technologies – Mass spectrometry and protein arrays |
2-D gel and mass spectrometric methods for proteomics Protein arrays, antibody arrays Limitations of various technologies |
|
Yvonne Lin |
mass spectrometric and NMR methods for proteomics experimental design and workflow, methods for data analysis |
|
|
Ka Yee Yeung-Rhee |
Types of networks and pathways Information available in ‘omics data Bayesian and regression based methods for network inference |
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