Biochemistry 158/258 - BioMedical Informatics 258
Genomics, Bioinformatics & Medicine
Spring Quarter 2012-2013
This course covers the molecular basis of inherited disease. We will discuss both simple Mendelian diseases and complex, multifactorial diseases in which both genetics and environmental factors are involved. We will discuss genomics, functional genomics, epigenetics, gene expression, SNPs, copy number and other structural genomic variations involved in disease. In addition to these diagnostic approaches, we will discuss novel therapeutic methods such as stem cell therapy, gene therapy and drug developments that depend on the knowledge of genomics. We will discuss personal genomics, pharmacogenomics and clinical genomics and their role in the future of preventive medicine.
Course Requirements
Students in this course will become familiar with many web resources and will be expected to complete several short research projects during the course (see below). The research projects will include a personal introduction, a case presentation of a Mendelian inherited disease, a functional analysis of a human gene, a review of a genome wide-association study on a multifactorial disease, a description of causal mutants in one disease, a stem cell therapy in a disease and a final paper on a topic of personal interest related to Genomics, Bioinformatics & Medicine.
In the Spring quarter, Biochem 158/258 will be taught online only. The research projects must be submitted to brutlag@stanford.edu. by the dates in the project table below. The methods essential for each assignment and examples of how to perform each assignment is demonstrated in the lectures. Examples of previous final papers in the course appear at:
This course will be of interest to anyone considering a career in genomics, bioinformatics or treatment of disease. It will be especially valuable to premedical, medical or graduate students interested in human genomics. It will also be of value to those interested in health care policy or biotechnology law.
This course is approved as an elective for Biology Majors, and is approved for Natural-Science GER credit for students in other majors.
Prerequisites
Prerequites for the course are Biology 41 or HumBio 2A or consent of the instructor.
Students with credit in Biochem 118 may not take this course for credit.
Videos of the lectures will also be available from the SCPD and CMGM file servers.
A Primer of Genome Science 3rd edition is not required for the course but it provides an excellent introduction to the material discussed including basic genetics and genomics used in medicine and research. Background readings for lecture area will be given from this book. This book would be a good reference book for those continuing to work in this field.
Date |
Topic |
Slide Links |
2012 Videos |
2013 Videos |
April 2 |
Introduction to Genes, Diseases and Preventive Medicine |
Video |
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April 4 |
Diseases and Disease Databases |
Video |
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April 9 |
Sequencing the Human Genome |
Video |
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April 11 |
Finishing the Human Genome & |
Video |
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April 16 |
Next Generation Sequencing |
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April 18 |
Genome Databases & Bibliographic Search |
Video |
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April 23 |
Bioinformatics and Functional Genomics I |
Video |
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April 25 |
Bioinformatics and Functional Genomics II |
Video |
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April 30 |
Sequence Variations in the Human Genome |
Video |
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May 2 |
Structural Variations in the Human Genome |
Video |
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May 7 |
Discovering Variations Associated with Disease |
Video |
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May 9 |
Personal Genomics |
Video |
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May 14 |
Stem Cells |
Video |
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May 16 |
Stem Cell Therapies |
Video |
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May 21 |
Gene Expression and Cancer Diagnostics |
Video |
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May 23 |
MicroRNA Regulatory Networks |
Slides |
Video |
Video |
May 28 |
Epigenetics |
Video |
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May 30 |
Drug Development |
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June 4 |
Pharmacogenomics |
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June 6 |
Bibliographic Search |
Slides |
Video |
Video |
2012 Lecture Videos:: To view these videos you musthave Quicktime installed on your computer. Clicking on the video link will start a streaming video in your browser. Clicking on the Slides will automatically download a PDF file of the slides directly into your browser. You should view the PDF of the slides while watching the video in another window so you can see the slides in higher resolution than visible in the video. Also the Web links in the Slide PDF file are all active so you can more easily follow along the lecture.
2013 Lectue Video Links are for download only. You must right-click (on a Macintosh Control-Click) on the video link and Save the Video file to your computer. Then you may watch the lecture using which ever media viewer you may have on your computer (Quicktime, VLC, Windows Media Player etc.). You should also download the Slide document for that lecture and view it in Adobe Reader so you can see the slides in high resolution.
Short Research Projects
Topic
Date Due
10%
April 11
Mendelian disease case presentation (4 page max)
10%
April 18
Functional analysis of a human gene (4 page max)
10%
May 2
Summary of a genome-wide association study (4 page max)
10%
May 9
Describe the genomic variations known to cause a specific inherited disease (4 page max)
10%
May 16
Describe a disease that could be cured using stem cell therapy (4 page max)
10%
May 23
Final project (10 page max)
40%
June 7
Each assignment is a short research project. Click on each project title to see how to perform the research project and an outline of what is expected. The assignments are due on midnight Pacific time at the end of the due date day (usually a Thursday at midnight except the final paper.). Please submit your assignments in electronic form (Word , text , PDF, postscript, HTML or Google document) to brutlag@stanford.edu. If you are late, you will loose 10% of the grade for that assignment for each day you are late. Please be sure to give web-links (URL pointers) to the disease, gene, GWAS paper and all references and web sites used in your bibliography or footnotes in your paper. Also please be sure to put any copied material in quotes with complete reference or URL ponter to the source of the material copied in your paper. Failure to properly reference source material, even from the Internet, is plagiarism. If you do not get 100% on each of the first six assignments you will be given a description of what you did wrong and then have one week to resubmit for full credit.The final project may only be submitted once
*** Web Page Last Updated March 18, 2013 ***
