Course Descriptions (Undergraduate)
The following courses were created for the Bioinformatics Undergraduate Program. Please consult the course catalog and your department for the full list of requirements for each department.
Lower Division
BILD 94. Professional Issues in Bioinformatics (1 unit)
This seminar will introduce undergraduate students, especially freshmen and sophomores, to a variety of issues and topics in the field of bioinformatics.
Upper Division
BENG/BIMM/CSE 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. This course open to bioinformatics majors only.
Prerequisites: CSE 100 or Math. 176, CSE 101 or Math. 188, BIMM 100 or Chem. 114C.BENG/BIMM/CHEM/CSE 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 databases, ontologies, data modeling and description, survey of current biological database with respect to above, implementation of database focused on a biological topic. This course open to bioinformatics majors only.
Prerequisite: CSE 100 or Math 176.BENG 183. Applied Genomic Technologies (4 units)
Principles and technologies for using genomic information for biomedical applications. Technologies will be introduced progressively, from DNA to RNA to protein to whole cell systems. The integration of biology, chemistry, engineering, and computation will be stressed. Topics include: Technology for the Genome, DNA Chips, RNA Technologies, Proteomic Technologies, Physiomic and Phenomic Technologies, Analysis of Cell Function.
Prerequisites: grade of C– or better in BIMM 100 or Chem 114C; BICD 110; Bioinformatics majors only. (F)BENG/BIMM/CHEM/CSE 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 or proteins, functional genomics/proteomics, metabolic pathways/gene networks. This course open to bioinformatics majors only.
Prerequisite: BIMM 181 or BENG 181 or CSE 181, BIMM 182 or BENG 182 or CSE 182 or Chem. 182. Bioinformatics majors only.BIMM 185. Bioinformatics Laboratory (Advanced) (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 anaylysis, computational proteomics. This course open to bioinformatics majors only.
Prerequisite: two courses out of: BIMM 181 or BENG 181 or CSE 181, BIMM 182 or BENG 182 or CSE 182, BENG 183, BIMM 184 or BENG 184 or CSE 184.MATH 186. Probability Statistics for Bioinformatics (4 units)
This course will cover discrete and random variables, data analysis and inferential statistics, likelihood estimators and scoring matrices with applications to biological problems. Introduction to Binomial, Poisson, and Gaussian distributions, central limit theorem, applications to sequence and functional analysis of genomes and genetic epidemiology. (Credit not offered for Math. 186 if Econ. 120A, ECE 109, Math. 180A, Math. 181A, or Math. 183 previously or concurrently.)
Prerequisites: Math. 20C (21C) with a grade of C– or better, or consent of instructor.
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Bioinformatics and Systems Biology Graduate Program
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