Course Descriptions (-2008)
Applies to students admitted AY 2007-8 and earlier.
Each student must take the four courses below.
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 (CSE 282/BENG 202). Sequence and Structure Analysis—Methods and Applications (4 units)
(Formerly CSE 257A/BENG 202.) Introduction to methods for sequence analysis. Applications to genome and proteome sequences. Protein structure, sequence-structure analysis.
Prerequisite: Pharm. 201 or consent of instructor.
Annotating genomes, characterizing functional genes, profiling, reconstructing pathways.
Prerequisites: Pharm. 201, BENG 202/CSE 282 or consent of instructor.
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.
Prerequisites: one year of calculus, one statistics course or consent of instructor.
Each student will select from five of the eight 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.
BENG 230A. Biochemistry (4 units)
A graduate course in biochemistry especially tailored to the requirements and background of bioengineering graduate students. It will cover the important macro- and small molecules in cells that are the major constituents, or that function as signaling molecules or molecular machineries. The structures, pathways, interactions, methodologies, and molecular designs using recombinant DNA technology will be covered.
Prerequisites: BIPN 100 and 102 or consent of instructor. (F)
BIBC 100. Structural Biochemistry (4 units)
The structure and function of biomolecules. Includes protein conformation, dynamics, and function; enzymatic catalysis, enzyme kinetics, and allosteric regulation; lipids and membranes; sugars and polysaccarides; and nucleic acids. Three hours of lecture and one hour of recitation.
Prerequisite: Chem. 140A; Chem. 140B may be taken concurrently. (Note: Students may not receive credit for both BIBC 100 and Chem. 114A.)
Introduction to biochemistry from a structural and functional viewpoint.
Prerequisite: elementary organic chemistry (Chem. 140A or equivalent). (Note: Students may not receive credit for both Chem. 114A and BIBC 100.) (F)
(Conjoined with Chem. 113.) A discussion of the structural principles governing biological macromolecules, the techniques used in their study, and how their functional properties depend on three-dimensional structure. Chem. 213 students will be required to complete additional coursework beyond that expected of students in Chem. 113.
Prerequisites: elementary physical and organic chemistry. (May not be offered every year.)
CHEM 218. Macromolecular Biochemistry (4 units)
A comprehensive course in biochemistry emphasizing structural biochemistry.
Prerequisites: physical and organic chemistry; graduate-student standing. (F)
CSE 100. Advanced Data Structures (4 units)
Descriptive and analytical presentation of data structures and algorithms. Lists, tables, priority queues, disjoint subsets, and dictionaries data types. Data structuring techniques include linked lists, arrays, hashing, and trees. Performance evaluation involving worst case, average and expected case, and amortized analysis. Credit not offered for both Math. 176 and CSE 100. Equivalent to Math. 176.
Prerequisites: CSE 21 or Math. 15B, and CSE 30, and CSE 70 or consent of
instructor. Majors only.
CSE 200. Computability and Complexity (4 units)
Computability review, including halting problem, decidable sets, r.e. sets, many-one reductions; TIME(t(n)), SPACE(s(n)) and general relations between these classes; L, P, PSPACE, NP; NP—completeness; hierarchy theorems; RP, BPP.
Prerequisite: CSE 105 or equivalent.
MATH 176. Advanced Data Structures (4 units)
Descriptive and analytical presentation of data structures and algorithms. Lists, tables, priority queues, disjoint subsets, and dictionaries data types. Data structuring techniques include linked lists, arrays, hashing, and trees. Performance evaluation involving worst case, average and expected case, and amortized analysis. Crecit not offered for both Math. 176 and CSE 100. Equivalent to CSE 100.
Prerequisites: CSE 12, CSE 21, or Math. 15B, and CSE 30, or consent of instructor.
Design and analysis of efficient algorithms with emphasis of non-numerical algorithms such as sorting, searching, pattern matching, and graph and network algorithms. Measuring complexity of algorithms, time and storage. NP-complete problems. Credit not offered for both Math. 188 and CSE 101.
Prerequisites: CSE 12, CSE 21 or Math. 15B or Math. 100A or Math. 103A and CSE 100 or Math. 176. Majors only.
Development of high quality mathematical software for the computer solution of mathematical problems. Three lectures, one recitation.
Prerequisites: Math. 170A or Math. 174 and knowledge of FORTRAN. (W)
CSE 132A. Database System Principles (4 units)
Basic concepts of databases, including data modeling, relational databases, query languages, optimization, dependencies, schema design, and concurrency control. Exposure to one or several commercial database systems. Advanced topics such as deductive and object-oriented databases, time allowing.
Prerequisite: CSE 100 or Math. 176. Majors only.
CSE 133. Information Retrieval (4 units)
(Formerly CSE 181.) How to find “relevant” documents (e.g., an electronic mail message or a book) from very large corpora (e.g., all the world's electronic mail or the library.) Students will construct and experimentally evaluate a complete IR system for a modest textual corpus.
Prerequisite: CSE 100 or Math. 176. Majors only.
CSE 254. Statistical Learning (4 units)
Learning algorithms based on statistics. Possible topics include minimum-variance unbiased estimators, maximum likelihood estimation, likelihood ratio tests, resampling methods, linear logistic regression, feature selection, regularization, dimensionality reduction, manifold detection. An upper-division undergraduate course on probability and statistics such as Math. 183 or 186, or any graduate course on statistics, pattern recognition, or machine learning is recommended.
Prerequisite: graduate standing.
BICD 100. Genetics (4 units)
An introduction to the principles of heredity in diploid organisms, fungi, bacteria, and viruses. Mendelian inheritance; population genetics; quantitative genetics; linkage; sex determination; meiotic behavior of chromosome aberrations, gene structure, regulation, and replication; genetic code. Three hours of lecture and one hour of recitation.
Prerequisite: BILD 1 or the equivalent.
BIMM 100. Molecular Biology (4 units)
Molecular basis of biological processes, emphasizing gene action in context of entire genome. Chromosomes and DNA metabolism: chromatin, DNA replication, repair, mutation, recombination, transposition. Transcription, protein synthesis, regulation of gene activity. Procaryotes and eucaryotes
Prerequisites: BIBC 100 or BIBC 102, BICD 100. (Note: Students may not receive credit for both BIMM 100 and Chem. 114C.)
The history of an organism can be found in its genome. Analyses of the primary sequences will be used to recognize families of genes that arose by duplication and divergence. Topics include comparisons of amino acid sequences and three dimensional structures and range from the oldest and most widely distributed proteins to modem mosaics. Where possible, specific motifs and folds will be traced to their ancestral beginnings.
Prerequisites: BIBC 100, BIMM 100.
BGGN 220. Graduate Molecular Biology (6 units)
Provides a broad, advanced-level coverage of modern molecular biology for first-year graduate students. Topics include prokaryotic and eukaryotic gene structure and regulation, chromatin structure, DNA replication, translation, mechanisms of transcription, and an introduction to viruses. OPEN ONLY TO STUDENTS ENROLLED IN A GRADUATE DEGREE PROGRAM. (Letter grades only.) (F)
BGGN 223. Graduate Genetics (6 units)
Provides a broad and extensive advanced-level coverage of molecular and formal aspects of genetics for first-year graduate students. Topics covered include: bacterial genetics, recombination in prokaryotes and eukaryotes, mammalian somatic-cell genetics, developmental genetics, sex determination, dosage compensation, and immunogenetics. Extensive coverage of the use of model systems like Drosophila and C. elegans is included. General and specific aspects of cellular signalling mechanisms will be covered.
Prerequisites: BGGN 220, 221 and 222. OPEN ONLY TO STUDENTS ENROLLED IN A GRADUATE DEGREE PROGRAM. (Letter grades only.) (S)
BICD 110. Cell Biology (4 units)
The structure and function of cells and cell organelles, cell growth and division, motility, cell differentiation and specialization. Three hours of lecture and one hour of recitation.
Prerequisites: BIBC 100 or BIBC 102, and BICD 100.
Developmental biology of animals at the tissue, cellular, and molecular levels. Basic processes of embryogenesis in a variety of invertebrate and vertebrate organisms. Cellular and molecular mechanisms that underlie cell fate determination and cell differentiation. More advanced topics such as pattern formation and sex determination are discussed. Open to upper-division students only. Three hours of lecture and one hour of recitation.
Prerequisites: BICD 100, upper-division standing, BIBC 100 or BIBC 102; BICD 110 strongly recommended, BIMM 100 strongly recommended.
BIOMED 210. Cell Biology (6 units)
The course focuses on fundamentals of the biology of eukaryotic cells. Topics include: Cell structure and cytoskeleton, biosynthesis of macromolecules, transport across cell membranes, receptors and signal transduction, regulation of the cell growth cycle, early development and differentiation. (F)
Topics include: Analysis of ligand-macromolecule interactions, biochemistry and pharmacology of chemical transmission and signal transduction, cellular responses to environmental stress (cyto P-450, P-glycoprotein, etc.), and bases of selective toxicity (viruses, bacteria, insects, mammalian tumor cells). Emphasis is on basic principles, on analysis of recent experimental data, and on integration in mammalian systems. (W)
BGGN 222. Graduate Cell Biology (6 units)
A coverage of modern cell biology for first year graduate students. There is an up-to-date discussion of topics such as: structure and function of membranes; ion pumps, ion channels, transmembrane signalling; receptor mediated endocytosis; protein targeting; the role of RER and Golgi apparatus; the biosynthesis of intracellular organelles in animal and plant cells; the cytoskeleton, motility, molecular motors, cell-cell interactions, mitosis; and the control of cell division. Also included are extensive coverage of cell signalling mechanisms and discussions on molecular approaches to cell biology.
Prerequisites: BGGN 220 and 221. OPEN ONLY TO STUDENTS ENROLLED IN A GRADUATE DEGREE PROGRAM. (Letter grades only.) (W)
BENG 253. Biomedical Transport Phenomena (4 units)
Nonequilibrium thermodynamic analysis of transport phenomena. The osmotic effect. Diffusion and exchange in biological systems.
Prerequisite: consent of instructor. (W)
BENG 275. Computational Bioengineering (4 units)
Finite element and methods for anatomical modeling and boundary value problems in the biomechanics of tissues and biomedical devices. Numerical solution of ordinary differential equations governing biological systems. Finite difference methods for partial differential equations. Nonlinear biodynamics, heat flow, cardiac impulse propagation, anatomic modeling, and biomechanics.
Prerequisite: consent of instructor. (S)
Approach to equilibrium: BBGKY hierarchy; Boltzmann equation; H-theorem. Ensemble theory; thermodynamic potentials. Quantum statistics; Bose condensation. Interacting systems: Cluster expansion; phase transition via mean-field theory; the Ginzburg criterion.
Prerequisites: Physics 140A-B, 152A, 200A-B, or equivalent; concurrent enrollment in Physics 212C. (S)
(Conjoined with Math. 274) Floating point arithmetic, direct and iterative solution of linear equations, iterative solution of nonlinear equations, optimization, approximation theory, interpolation, quadrature, numerical methods for initial and boundary value problems in ordinary differential equations. Students may not receive credit for both Math. 174 and PHYS 105, AMES 153 or 154. Students may not receive credit for Math. 174 if Math. 170A, B, or C has already been taken. Graduate students will do an extra assignment/exam.
Prerequisites: Math. 20D with a grade of C– or better and Math. 20F with a grade of C– or better, or consent of instructor.
MATH 181E. Mathematical Statistics (4 units)
Time Series. Analysis of trends and seasonal effects, autoregressive and moving averages models, forecasting, informal introduction to spectral analysis.
Prerequisites: Math. 181A, 181B previously or concurrently.
MATH 280A-B-C. Probability Theory (4-4-4 units)
(MATH 280A is the Bioinformatics elective; this catalog description applies to the three-quarter Math Department course MATH 280A-B-C.)
Probability measures; Borel fields; conditional probabilities, sums of independent random variables; limit theorems; zero-one laws; stochastic processes.
Prerequisites: advanced calculus and consent of instructor. (F,W,S)