Doug Brutlag is located in the Biochemistry Department at Stanford University and is also affiliated with the Stanford Center for Biomedical Informatics Research in the Department of Medicine, Stanford Medical School. The primary goal of my research was understanding the meaning of the genomic information and how this information is expressed using computational means. I was interested in the problems of predicting biological function of genes and gene products from their sequence and structure (sometimes known as functional genomics). I was also interested in understanding how and when genes are expressed. My group developed advanced profile and sequence motifs for representing structural and functional aspects of proteins (EMOTIF, EMATRIX, 3MOTIF and 3MATRIX). These methods can be used for assigning functions to unidentified protein sequences.

My group developed accurate and rapid methods for comparing protein structures and structural database search (LOCK2 and FoldMiner). We were also interested in the areas of secondary structure prediction, discovery of promoters and other DNA regulatory sequences, small molecule and protein docking, identifying drug targets, and drug design. We also developed rapid methods for discovering transcription factor binding sites in coregulated genes. Both BioProspector and MDScan can take upstream sequences from co-regulated genes and can find conserved DNA consensus sequences even if they are very short (8bps), poorly coonserved (50%), interrupted, and present in less than 50% of the sequences.

Since I have retired from research, I am no longer accepting applications for graduate or postdoctoral students.

I am currently involved in teaching Computational Molecular Biology and Genomics & Medicine. Computational molecular biology is available both at Stanford and online via the Stanford Center for Professional Development. Genomics & Medicine is only available to Freshmen and Sophomores.

Biochemistry 118: Genomics & Medicine Sophomore Seminar limited to sophomores and freshmen

In this seminar I will discuss the kind of knowledge we hope to gain from sequencing human genomes and the implications of such knowledge for medicine and biomedical research. I will discuss novel diagnoses and treatment of diseases, including stem cells, gene therapy and rational drug design. I will discuss personal genomics and how it can be used to improve health and well being. We will also discuss the social and ethical implications of genetic information such as privacy, discrimination and insurability.

Biochemistry 158/258 Genomics, Bioinformatics and Medicine Lecture based course for Juniors and seniors and (258) for graduate and medical students. Covers same material as Biochem 118Q

This course covers the molecular basis of inherited disease.  I discuss both simple Mendelian diseases and complex, multifactorial diseases.. I 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.

Biochemistry 218 Computational Molecular Biology http://biochem218.stanford.edu/ Designed for seniors and graduate students peforming molecular biology research

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.

Bio 84: Your Genes and Your Health A Stanford Continuing Studies adult education course on personal genomics.

Analyzing your DNA can reveal a lot about your potential health and future well being. Although knowledge of your genetic frailties may suggest a predisposition to a disease, genetics alone does not seal your fate. Most common diseases are affected by your behavior and your environment. Changing one's lifestyle can alleviate or even prevent disease. Hence, understanding genetic indicators can alert one to the importance of being vigilant about lifestyle and medical follow-ups. In this course, we will empower you with tools to learn more about diseases, treatments and genetic tests that will help you to understand any genetic disease. The instructor will use data from his own genome to show you how you can look into your ancestry, family relationships, inherited diseases and response to drugs. You will see how knowing one's genetic profile can lead to reduced health care costs and a new approach to a confident, healthy lifestyle.

 

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