Bioinformatics Course Offerings

CSE Bioinformatics Steering Committee:

• Vineet Bafna, Chair Bioinformatics Steering Committee

• Pavel Pevzner, CSE Faculty

• Ramamohan Paturi, CSE Faculty

• Viera Kair, CSE Undergraduate Advisor

• Patricia Raczka, CSE Undergraduate Program Director and Advisor

Questions about information found on this page may be directed to Patricia Raczka at 858/534-3621 or to raczka@cs.ucsd.edu

Courses for the Bioinformatics Program:

BILD 94 (1 unit): This seminar will introduce undergraduate students, expecially freshmen and sophomores, to a variety of issues and topics in the field of informatics.

CSE 181/ BIMM 181/BENG 181 - Molecular Sequence Analysis (4 units): This course covers the analysis of nucleic acid and protein sequences, with an emphasis on the application of algorithms to biological problems. Topics include sequence alignments, database searching, comparative genomics, and phylogenetic and clustering analyses. Pairwise alignment, Multiple alignment, DNA sequencing, Scoring functions, Fast database search, Comparative genomics, Clustering, Phylogenetic trees, Gene finding/DNA statistics. Prerequisites: CSE 100 or Math 176, CSE 101 or Math 188, BIMM 100 or Chem 114D

CSE 182 /BIMM 182/BENG 182/CHEM 182 - Biological Databases (4 units): This course provides an introduction to the features of biological data, how that data are organized efficiently in databases, and how existing data resources can be utilized to solve a variety of biological problems. Relational databases, Object oriented data bases, Ontologies, Data modeling and description, Survey of current biological database with respect to above, Implementation of a database focused on a biological topic. Prerequisites: CSE 100 or Math 176

BENG 183 - Applied Genomic Technologies (4 units): The goal of this course is to introduce the student to fundamental principles and enabling technologies that will be utilized for harnessing genomic information for biomedical applications. Technologies will be introduced progressively, from DNA to RNA to protein to whole cell platforms. The integration of biology, chemistry, engineering, and computation will be stressed. Topics include: Technology for the Genome, DNA Chips, RNA Technologies, Proteomic Technologies, Cellomic Technologies, Analyzing Cell Function. Prerequisites: BIMM100 or Chem114D, BICD110

CSE 184/BIMM 184/BENG 184 - Computational Molecular Biology (4 units): This advanced course covers the application of machine learning and modeling techniques to biological systems. Topics include gene structure, recognition of DNA and protein sequence patterns, classification, and protein structure prediction. Pattern discovery, Hidden Markov models/Support vector machines/Neural network/profiles, Protein structure prediction, Functional characterization of proteins, Functional genomics/proteomics, Metabolic pathways/gene networks. Prerequisites: BIOINF 181, 182. Bioinformatics majors only.

BIMM 185 - Bioinformatics Lab (4 units): This course emphasizes the hands-on application of bioinformatics methods to biological problems. Students will gain experience in the application of existing software, as well as in combining approaches to answer specific biological questions. Sequence alignment, Fast database search, Profiles and motifs, Comparative genomics, Gene finding , Phylogenetic trees, Protein structure, Functional characterization of proteins, Expression analysis, Computational proteomics. Prerequisites: Two courses out of BIOINF 181, BIOINF 182, BIOINF 183, BIOINF 184. Bioinformatics majors only.

Math 186 - Probability and Statistics (4 units): This course will cover an introduction to probability and statistics, the use of discrete and random variables, different types of distributions, data analysis and inferential statistics, likelihood estimates and scoring matrices with applications to biological problems. Introduction to probability, Discrete and continuous random variables, Binomial, Poisson, and Gaussian distributions, Central limit theorem, Data analysis and inferential statistics, Likelihood estimators and scoring matrices, Applications to sequence and functional analysis of genomes and genetic epidemiology. Prerequisites: Math 20A, Math 20B, Math 21C. Bioinformatics majors only.

Course History

BILD 94

• Spring 2008, Staff, BioEngr Dept.

• Spring 2007, Vineet Bafna, CSE Dept.

• Spring 2006, Vineet Bafna, CSE Dept.

• Spring 2005,William Loomis, Biol Dept.

CSE 181/BIMM 181/BENG 181/CHEM 181

• Spring 2008, Pavel Pevzner, CSE Dept.

• Spring 2007, Pavel Pevzner, CSE Dept.

• Spring 2006, Pavel Pevzner, CSE Dept.

• Spring 2005, Pavel Pevzner, CSE Dept.

• Fall 2005, Phillip Bourne,Chem Dept.

• Spring 2004, Pavel Pevzner, CSE Dept.

• Spring 2003, Pavel Pevzner, CSE Dept.

CSE 182/BIMM 182/BENG 182/CHEM 182

• Fall 2007, Vineet Bafna, CSE Dept.

• Fall 2006, Vineet Bafna, CSE Dept.

• Fall 2005, Vineet Bafna, CSE Dept.

• Fall 2004, Vineet Bafna, CSE Dept.

• Fall 2003, Phillip Bourne as Pharm 201, Pharm Sch

• Spring 2004, Vineet Bafna, CSE Dept.

BENG 183

• Fall 2007, Tre Ideker, Bioengr Dept.

• Fall 2006, Tre Ideker, Bioengr Dept.

• Fall 2005, Tre Ideker, Bioengr Dept.

• Fall 2004, Tre Ideker, Bioengr Dept.

• Winter 2004, Michael Heller, Bioengr Dept.

CSE 184/BIMM 184/BENG 184/CHEM 184

• Winter 2008, Wei Wang,Chem Dept.

• Winter 2007, Wei Wang,Chem Dept.

• Winter 2006, Wei Wang,Chem Dept.

• Winter 2005, Steven Cammer,Chem Dept.

• Winter 2004, Steven Cammer, Chem Dept.

BIMM 185

• Spring 2008, Steven Briggs, Biol Dept.

• Spring 2007, Steven Briggs, Biol Dept.

• Spring 2006, William Loomis, Biol Dept.

• Spring 2004, William Loomis, Biol Dept.

Math 186

• Winter 2008, Glenn Tesler, Math Dept.

• Winter 2007, Glenn Tesler, Math Dept.

• Winter 2006, Glenn Tesler, Math Dept.

• Winter 2004, Glenn Tesler, Math Dept.

• Winter 2003, Leonard Haff, Math Dept.