Survey of Technologies for Molecular Biology

Course Number: 
CONJ 546
Course Type: 
Methods
Currently Offered: 
Yes
Credits: 
1.5
Quarter: 
Autumn
Weeks: 
1-5
Meeting Time: 
TTh 100-220
Location: 
UW
Instructor (MCB Faculty): 
Bumgarner, Roger
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:

  1. Understand what technologies are in existence for DNA sequencing and genotyping, gene expression measurements, proteomics and metabolomics.
  2. Understand the applications of each technology and why some technologies may be better applied to a certain subset of problems.
  3. Understand the underlying sources of error that may be present in a dataset produced by a given technology.
  4. 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
Required Text: 
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.

Course web page: http://faculty.washington.edu/rogerb/Conj546_2011WebSite/index.html

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

Genotyping technologies

Array and sequence based methods and tools for genotyping

Bumgarner

emPCR, polonies, pyrosequecing and Ion Torrent sequencing

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

Technologies and Methods for Metabolomics

mass spectrometric and NMR methods for proteomics

experimental design and workflow, methods for data analysis

Ka Yee Yeung-Rhee

Systems Biology: Methods for Network Inference

Types of networks and pathways

Information available in ‘omics data

Bayesian and regression based methods for network inference

Areas of Interest: 
Cancer Biology
Areas of Interest: 
Gene Expression, Cell Cycle & Chromosome Biology
Areas of Interest: 
Genetics, Genomics & Evolution
Methods Area: 
Cancer Biology
Cell Signaling & Cell/Environment Interactions
Gene Expression, Cell Cycle & Chromosome Biology
Genetics, Genomics & Evolution
Microbiology, Infection & Immunity
Molecular Structure & Computational Biology