Seminars
Stanford Sophomore Seminar
This course is a Sophomore Seminar Series and only open to Sophomores and Freshmen. We discuss the kinds of information medicine hopes to gain from sequencing human and bacterial genomes and the implications of such information for medicine and biomedical research. We will study novel diagnoses and treatment of diseases, including gene therapy and new drugs, and will discuss the ethical implications of genetic information. The course syllabus is located at: http://cmgm.stanford.edu/biochem118/
Courses
Courses for Stanford and SCPD students
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 representation and analysis of genomes, sequences and proteins. 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. While no computer experience or programming skills are required, prior exposure to personal computers, e-mail, and the Internet are essential. All homework and coursework must 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. This course is also available to industry students through Stanford Center for Professional Development (SCPD).
Computational Genomic Biology is a graduate level course targeted at graduate students or upper level undergraduates desiring an advanced knowledge of the application of computational genomic methods to biological problems. Topics to be covered include assembly of genomic sequences, genome databases, comparative genomics, gene discovery, gene expression analyses including gene clustering by expression, transcription factor binding site discovery, metabolic pathway discovery, functional genomics, gene and genome ontologies, and medical diagnostics using SNPs and gene expression. We will also cover gene regulation via epigenetic and port-transcriptional mechanisms. The course will be based on recent papers from the literature as well as practical hands-on use of these methods. Prerequisites include an introductory course in computational molecular biology or genomics such as Biochem 218, Biomedical Informatics 214 or Genetics 211 or permission of instructor. This course is also available to industry students through Stanford Center for Professional Development (SCPD).
Computational Proteomic Biology is a graduate level or upper undergraduate level course focusing on the application of computational protein analysis to biological problems. The specific areas to be covered include protein sequence analysis and comparison (including protein sequence databases, amino acid composition, protein alignment, protein motifs, protein families and probabilistic models of families) protein structure (structure comparison and superposition methods, structural motifs, structure and domain databases) protein structure prediction (including secondary structure, homology modeling, threading and ab initio structure prediction), protein-protein interaction databases and protein-protein interaction prediction, protein-DNA interaction motifs and protein-ligand docking. Prerequisites for this course would be an introductory course in computational biology such as Biochem 218, Biomedical Informatics 214 or Structural Biology 228. This course is also available to industry students through Stanford Center for Professional Development (SCPD).
Computational Systems Biology (Biochem 248) is currently in development.This course will also be available to industry students through Stanford Center for Professional Development (SCPD).Course Syllabus http://biochem248.stanford.edu/
Certificates:
Computational Genomics Certificate Program:
Genomics is the study of the organization, function and evolution of genetic material at the level of the whole genome rather than individual genes. Modern methods of sequencing and analyzing whole genomes leads to the need to store,model and understand genomic data using computational methods. Topics include: pairwise and multiple sequence alignment, sequence analysis and annotation, SNP's, microarray analysis, modeling and visualization of genetic data, controlled vocabularies (ontologies) for biological data,the impact of genomics on health care, including diagnostics and therapeutic applications.
Relevant Related Links:
Links
to Biomedical Informatics
Courses
Link
to all bioinformatics & bioengineering online programs at
SCPD
Link
to the new Bioinformatics & Computational Genomics Certificate
program
Disclaimer for use of these web resources.