Course Requirements (-2008)

Applies to students admitted AY 2007-8 and earlier.

Core Requirements

(Each student must take the four courses below.)

  • Bioinformatics I: Biological Data & Analysis

    Pharmacology (PHAR 201)
    Bioinformatics is driven by the need to understand complex biological systems for which data are accumulating at exponential or near exponential rates. Such an understanding relies of the effective representation of these data and the ability to analyze these data. This is a broad topic and we focus on macromolecular structure data, which is suitably complex, to introduce the principles of formal data representation, reductionism, comparison, classification, visualization and biological inference. As such the course also serves as an introduction to Structural Bioinformatics. For details of what is covered in the course and more, refer to Structural Bioinformatics, 2nd Edition (2009), Editors Jenny Gu and Philip E. Bourne, Wiley & Sons.
     

  • Bioinformatics II: Sequence and Structure Analysis - Methods and Applications

    Bioengineering (BENG 202/CSE 282)
    (Formerly BENG 202/CSE 257A.) Introduction to methods for sequence analysis. Applications to genome and proteome sequences. Protein structure, sequence-structure analysis.
     

  • Bioinformatics III: Functional Genomics

    Bioengineering (BENG 203/CSE 283)
    Annotating genomes, characterizing functional genes, profiling, reconstructing pathways.
     

  • Bioinformatics IV: Statistical Methods for Bioinformatics

    Mathematics (MATH 283)
    This course will cover material related to the analysis of modern genomic data; sequence analysis, gene expression/functional genomics analysis, and gene mapping/applied population genetics. The course will focus on statistical modeling and inference issues and not on database mining techniques.
     

Program Electives

(Each student will select from 5 of the 8 elective fields below. One must be from the Biology field and one from the Computer Science field. For each elective, multiple course options currently available are listed).

Elective 1 - Biochemistry
BENG230A Biochemistry
BIBC100 Structural Biochemistry
CHEM114A Biochemical Structure and Function
CHEM213 Chemistry of Macromolecules
CHEM218 Macromolecular Biochemistry
 
Elective 2 - Data Structures
CSE100 Data Structures
CSE200 Computability and Complexity
MATH176 Advanced Data Structures
 
Elective 3 - Algorithms
CSE101 Design and Analysis of Algorithms
MATH173 Mathematical Software-Scientific Programming
 
Elective 4 - Information Retrieval, Database & Data Mining
CSE132A Database System Principles
CSE133 Information Retrieval
CSE254 Statistical Learning
 
Elective 5 - Molecular Genetics
BICD100 Genetics
BIMM100 Molecular Biology
BIBC116 Evolution of Genes and Proteins
BGGN220 Graduate Molecular Biology
BGGN223 Graduate Genetics
 
Elective 6 - Cell Biology
BICD110 Cellular Biology
BICD130 Embryos, Genes, and Development
BIOM210 Cellular Biology
BIOM212 Cellular and Molecular Pharmacology
BGGN222 Graduate Cell Biology
 
Elective 7 - Physics and Engineering
BENG253 Biomedical Transport Phenomena
BENG275 Computational Biomechanics
PHYS210A Equilibrium Statistical Mechanics
 
Elective 8 - Mathematics and Statistics
MATH174 Numerical Methods for Physical Modeling
MATH181E Mathematical Statistics
MATH280A Probability Theory