Bioinformatics

Research:

Graduate Studies in Bioinformatics

BME 200: Research and Teaching in Bioinformatics (3 credits).F

Basic teaching techniques for teaching assistants, including responsibilities and rights of teaching assistants, resource materials, computer security, leading discussion or lab sessions, presentation techniques, maintaining class records, electronic handling of homework, and grading. Examines research and professional training, including use of library and online databases, technical typesetting, writing journal and conference papers, publishing in bioinformatics, giving talks in seminars and conferences, and ethical issues in science and engineering. Required for all teaching assistants. Enrollment restricted to graduate students. T. Lowe, K. Karplus

BME 205: Bioinformatics Models and Algorithms. F

Covers bioinformatics models and algorithms: the use of computational techniques to convert the masses of information from biochemical experiments (DNA sequencing, DNA chips, and other high-throughput experimental methods) into useful information. Emphasis is on DNA and protein sequence alignment and analysis. Enrollment restricted to graduate students. Undergraduates may enroll with prerequisite(s): Computer Science 12B; and Computer Engineering 107 or Applied Math and Statistics 131; and Biology 20A; and concurrent enrollment in Biochemistry 100A. K. Karplus

BME 210: Experimental Systems Biology. S

Topics include, but are not limited to, microarray production techniques, experimental strategies using microarrays, extraction and analysis of microarray data, DNA and protein arrays, SNP analysis, gene expression analysis, materials analysis, and advanced analysis of data using bioinformatic techniques. (FormerlyApplication and Analysis of Microarrays.) (Also offered as Biology 210. Students cannot receive credit for both courses.) Enrollment restricted to graduate students; undergraduates by permission of instructor. T. Lowe

BME 211: Computational Systems Biology. S

Teaches machine-learning methods relevant for the analysis of high-throughput molecular biology experiments. Students should be fluent in a programming language and should have taken basic molecular biology courses. Prerequisite(s): course 205. Enrollment restricted to graduate students; undergraduates may enroll if they have completed course 205, Computer Science 101, and any upper-division molecular biology or biochemistry course, such as Biochemistry 100 or 100A. J. Stuart

BME 220: Protein Bioinformatics. W

Covers the application of bioinformatics techniques to protein sequences and structures. Topics include protein sequence analysis, protein structure prediction, and sources of experimental data about proteins. Prerequisite(s): course 205, or Chemistry 200B; concurrent enrollment in course 220L, 296, or 297 is required. Enrollment restricted to graduate students; undergraduates may enroll if they have completed course 205, CMPS 101, and BIOC 100A. K. Karplus

BME 220L: Protein Bioinformatics Laboratory (1 credit).W

Project in protein bioinformatics. Prerequisite(s): course 205; concurrent enrollment in course 220 is required. K. Karplus

BME 225: Protein Function in Biology and Bioinformatics. F

Reviews functional roles of proteins and computational methods used to predict functional aspects of proteins. Focus is on molecular function and structure-function relationships. Wider-reaching notions of function (pathways, interaction networks) are considered peripherally, as the context in which molecular function occurs. Course includes lectures, (computational) lab work, and discussions of topical publications. Prerequisite(s): Biochemistry and Molecular Biology 100A (or equivalent knowledge) and courses 205 and 220, or by instructor's permission. Enrollment limited to 15. D. Gerloff

BME 230: Computational Genomics. W

Genomics databases: analysis of high-throughput genomics datasets; BLAST and related sequence comparison methods; pairwise alignment of biosequences by dynamic programming; statistical methods to discover common motifs in biosequences; multiple alignment and database search using motif models; constructing phylogenetic trees; hidden Markov models for finding genes, etc.; discriminative methods for analysis of bioinformatics data, neural networks, and support vector machines; locating genes and predicting gene function, including introduction to linkage analysis and disease association studies using SNPs; and modeling DNA and RNA structures. Prerequisite(s): course 205; concurrent enrollment in course 230L, 296, or 297 is required. Enrollment restricted to graduate students; undergraduates may enroll if they have completed course 205, Computer Science 101, and BIOC 100A. J. Stuart, D. Haussler, T. Lowe

BME 230L: Computational Genomics Laboratory (1 credit).W

Project in computational genomics. Prerequisite(s): course 205; concurrent enrollment in course 230 is required. J. Stuart, D. Haussler, T. Lowe

BME 247: Stem Cell Research: Scientific, Ethical, Social, and Legal Issues. W

Scientific, ethical, social, and legal dimensions of human embryonic stem-cell research, including the moral status of the embryo; the concept of respect for life; ethical constraints on oocyte procurement; creation of embryonic chimeras; federal policies; and political realities. (Also offered as Biology 288. Students cannot receive credit for both courses.) Enrollment restricted to graduate students. E. Suckiel

BME 255: Biotechnology and Drug Development. W

Recommended for students interested in careers in the biopharmaceutical industry. Focuses on recombinant DNA technology and the drug-development process, including discovery research; preclinical testing; clinical trials; and regulatory review, as well as manufacturing and production considerations. Students may not receive credit for this course and course 155. Enrollment limited to graduate students. Enrollment limited to 10. P. Berman

BME 280B: Seminar on Bioinformatics (2 credits).F,W,S

Weekly seminar series covering topics of current research in computational biology or bioinformatics. Current research work and literature in these areas are discussed in weekly meetings. Enrollment restricted to graduate students or permission of instructor. May be repeated for credit. J. Stuart, D. Haussler, T. Lowe, K. Karplus

BME 281B: HIV Vaccine Research (2 credits).F,S

Weekly seminar series covering topics of HIV vaccine research. Current research work and literature in this area are discussed. Students lead some discussions and participate in all meetings. Enrollment restricted to graduate students. Enrollment limited to 10. P. Berman

BME 281G: Seminar on Protein Structure and Function (2 credits).F,W,S

Weekly seminar series covering topics of current computational and experimental research in protein structure prediction and design, structure-function relationships and protein evolution. Current research work and literature in these areas discussed. Students lead some discussions and participate in all meetings. (Formerly course 281R.) Enrollment restricted to graduate students; qualifed undergraduates may enroll with permission of instructor. May be repeated for credit. D. Gerloff

BME 281H: Seminar in Comparative Genomics (2 credits).F,W,S

Weekly seminar series covering topics of current computational and experimental research in comparative genomics. Current research work and literature in this area discussed. Students lead some discussions and participate in all meetings. Enrollment restricted to graduate students; qualified undergraduates may enroll with permission of instructor. May be repeated for credit. D. Haussler

BME 281K: Seminar on Protein Structure Prediction (2 credits).F,W

Weekly seminar series covering topics of current computational and experimental research in protein structure prediction. Current research work and literature in this area discussed. Students lead some discussions and participate in all meetings. Enrollment restricted to graduate students; qualified undergraduates may enroll with permission of instructor. May be repeated for credit. K. Karplus

BME 281L: Seminar in Computational Genetics (2 credits).F,W,S

Weekly seminar series covering topics and experimental research in computational genetics. Current research work and literature in this area discussed. Students lead some discussions and participate in all meetings. Enrollment restricted to graduate students; qualified undergraduates may enroll with permission of instructor. May be repeated for credit. T. Lowe

BME 281S: Seminar in Computational Functional Genomics (2 credits).F,W,S

Weekly seminar series covering topics of current computational and experimental research in computational functional genomics. Current research work and literature in this area discussed. Students lead some discussions and participate in all meetings. Enrollment restricted to graduate students; qualified undergraduates may enroll with permission of instructor. May be repeated for credit. J. Stuart

BME 293: Seminar in Biomolecular Engineering. *

Weekly seminar series covering topics of bioinformatics and biomolecular engineering research. Current research work and literature in this area discussed. Students lead some discussions and participate in all meetings. Enrollment restricted to graduate students; qualified undergraduates may enroll with permission of instructor. The Staff

BME 296: Research in Bioinformatics. F,W,S

Independent research in bioinformatics under faculty supervision. Although this course may be repeated for credit, not every degree program accepts a repeated course towards degree requirements.Students submit petition to sponsoring agency. May be repeated for credit. The Staff

BME 297: Independent Study or Research. F,W,S

Independent study or research under faculty supervision. Although course may be repeated for credit, not every degree program accepts a repeated course towards degree requirements. Students submit petition to sponsoring agency. May be repeated for credit. The Staff

BME 297F: Independent Study or Research (2 credits).F,W,S

* - Not currently offered.