Computational Molecular Biology
Doug Brutlag, Rhiju Das, Gavin Sherlock, Mike Snyder, and Peter Karp
Spring Quarter 2012-2013
Doug Brutlag, Rhiju Das, Gavin Sherlock, Mike Snyder, and Peter Karp
Spring Quarter 2012-2013
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 to homework218@cmgm.stanford.edu. A final paper will be required for the course that critically and constructively analyzes any area of computational molecular biology, bioinformatics or genomics. 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 evening June 7, 2013, at midnight. There will be no extensions of this deadline.Examples of Previous Final Projects
The course will be available online only 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
Dan Davison (davisond@stanford.edu) is the teaching assistant for the course and will answer questions about the homework and course content. . 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
Date
Topic
Lecturer
Slides
April 2
Genomics, Bioinformatics and Molecular Biology
April 4
Systematic Literature Search
April 9
Human Genome Project
April 11
Genome and Sequence Databases
April 16
Protein Sequence and Motif Databases
April 18
Sequence Alignment
April 23
Sequence Similarity Search
April 25
Multiple Sequence Alignment
April 30
Distance based Phylogenies
May 2
Building Protein Motifs and Models
May 7
Ab initio Protein Structure Prediction
May 9
Clustering Coordinately Regulated Genes
May 14
Discovering Gene Regulatory Signals
May 16
Gene Regulatory Modules and Networks
May 21
MicroRNA Regulatory Networks
May 23
Simple Nucleotide Polymorphisms (SNPs)
May 28
Genome Variations
May 30
Genome-Wide Association Studies
June 4
Metabolic Pathways and Analyses I
June 6
Metabolic Pathways and Analyses II
The video links in this table let you download quicktime videos of the lectures. Please right click on Video link and dowload the videos before viewing. You should also download the PDF file containing the slides by right clicking on the Slides link. You should have both files (Video and Slides) open when you watch the class video. The Video presents the video and audio, the Slide PDF gives you a high resolution version of the slides which are sometimes difficult to see in the video. Also, the URL links on the PDF file are all active so you can follow along the lecture more easily.
If you have a fast Intenet connection you may watch streaming videos from the SCPD site given below. This site requires a Stanford ID. Again, it is very useful to have the Slide PDF open in a separate window while you watch.
You may also download the course videos on the EdTech Server Web site (SUNET ID Required).
You may watch streaming videos on the SCPD Web site (SUNET ID Required). The SCPD Videos run on both Windows and Macs but require Flip4Mac media components to be viewed on a Macintosh).
Homework Assignments
Number |
Date Assigned |
Homework |
Date Due |
1 |
April 2 | Introduction and short resumé | April 9 |
2 |
April 11 | Human Gene Analysis | April 18 |
3 |
April 18 | Protein Functional Analysis | April 25 |
4 |
April 25 | Sequence Alignment and Search | May 2 |
5 |
May 2 | UPGMA and Neighbor Joining Phylogenies | May 9 |
6 |
May 9 | BLAST, PSI-BLAST and HMM Protein Families | May 16 |
7 |
April 2 | Final Project for course (see Course Requirements above) | June 7 |
Disclaimer for use of this web resource
** Last Updated March 18, 2013**
