Computational Molecular Biology
Doug Brutlag, Gavin Sherlock, Mike Snyder, Peter Karp and Rhiju Das
Winter Quarter 2010
Tuesdays and Thursdays 2:15 – 3:30 PM
Alway M114
Doug Brutlag, Gavin Sherlock, Mike Snyder, Peter Karp and Rhiju Das
Winter Quarter 2010
Tuesdays and Thursdays 2:15 – 3:30 PM
Alway M114
Computational Molecular Biology (Biochem 218) is a practical, hands-on approach to the field of computational molecular biology. The course is recommended for both molecular biologists and computer scientists desiring to understand the major issues concerning analysis of genomes, sequences and structures. Various existing methods will be critically described and the strengths and limitations of each will be discussed. There will be practical assignments utilizing the tools described. All homework and coursework will be submitted electronically. Prerequisites include an introductory molecular biology course at the level of Biology 41 or permission of the instructor. Students who have not had a course in molecular biology may acquire the necessary background by reading either Stryer's Biochemistry (5th edition by Berg, Tymoczko and Stryer) or Lewin's Genes IX.
Course Requirements
There will be several homework assignments utilizing the tools described in the lectures. All homework and final projects will be submitted in electronic form, as e-mail or e-mail attachments. A final paper will be required for the course that critically and constructively analyzes one of the areas presented in the course. The final project may also present a novel application of existing tools or the development of some new or improved method. The final projects will be due Friday, March 12, at midnight. There will be no extensions of this deadline. The homework will count for 35% of the final grade and the project will count for 65%.Examples of Previous Final Projects
The course will be taught live in the Winter Quarter and available on the internet in the Spring Quarter.
Registration
On campus students must register with the registrar via AXESS. Off campus students must register with the Stanford Center for Professional Development.Students receiving a grade of B or better in this course may use this grade as partial completion towards the Stanford Bioinformatics Certificate program.Teaching Assistants and Staff
Maeve O'Huallachain (maeveo@stanford.edu) and Dan Davison (davisond@stanford.edu) are the teaching assistants for the course and will answer questions about the homework and course content. Lee Kozar (kozar@stanford.edu) is the Director of the Bioinformatics Resource at Stanford and is in charge of the computing facilities including software and databases that will be used for the homework. Questions concerning the programs, databases and other computing resources used in the course should be addressed to him. Doug Brutlag (brutlag@stanford.edu) is the Administrator for the course. You should contact him for all administrative needs such as registration priority, web page problems, student status, etc.Lecture Syllabus Winter 2010
Date
Topic
Lecturer
PDF Slides
Jan 5
Genomics, Bioinformatics and Molecular Biology
Jan 7
Systematic Literature Search
Jan 12
Human Genome Project
Jan 14
Genome and Sequence Databases
Jan 19
Protein Sequence and Motif Databases
Jan 21
Sequence Alignment
Jan 26
Sequence Similarity Search
Jan 28
Multiple Sequence Alignment
Feb 2
Distance based Phylogenies
Feb 4
Building Protein Motifs and Models
Feb 9
Ab initio Protein Structure Prediction
Slides
Feb 11
Clustering Coordinately Regulated Genes
Slides
Feb 16
Discovering Transcriptional Regulatory signals
Slides
Feb 18
Gene regulatory Modules and Networks
Slides
Feb 23
MicroRNA Regulatory Networks
Slides
Feb 25
Genome-Wide Association Studies
Slides
Mar 2
Genome Variations
Slides
Mar 4
Genes and Diseases
Slides
Mar 9
Metabolic Pathways and analyses I
Slides
Mar 11
Metabolic Pathways and analyses II
Slides
Homework Assignments
Number |
Date Assigned |
Homework |
Date Due |
1 |
January 5 | Introduction and short resumé | January 12 |
|
January 14 | Human Gene Analysis | January 21 |
3 |
January 21 | Protein Functional Analysis | January 28 |
4 |
January 28 | Sequence Alignment and Search | February 8 |
5 |
February 4 | UPGMA and Neighbor Joining Phylogenies | February 11 |
You may also access the course videos on the EdTech Server Web site
(SUNET ID Required)
You may also access the class videos on the SCPD Web site
(The SCPD Videos run on both Windows and Macs but require
Flip4Mac media components to be viewed on a Macintosh)
Tutorials
|
Topic |
Lecturer |
|---|---|
Progressive Pairwise Alignment Algorithm and Its Use by the SeqWeb BestFit Program |
|
|
Phylogenetic Analysis - Intro to Distance Methods to Study Evolutionary Relationships |
Bioinformatics Week Videos
https://cmgm.stanford.edu/classes/EBI-NCBI/videos/
Bioinformatics Resource Courses
http://cmgm.stanford.edu/classes/
** Last Updated February 5, 2010**
