2022-2023 Course Catalog

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Systems Biology (SYSB)

SYSB 2024 - Fundamentals of Systems Biology (3 credits) 

Introduction to fundamental concepts of systems biology: biological systems, molecular regulatory networks, modeling approaches in systems biology with case studies, high-throughput data generation and bioinformatics data processing.

Prerequisite(s): MATH 1226 and (BIOL 1105 or ISC 1106H) and (CHEM 1036 or CHEM 1056 or CHEM 1056H or ISC 1106H) 
SYSB 2034 - Mathematical Methods in Systems Biology (3 credits) 

Fundamental mathematical methods in systems biology, including differential equations, graph theory, Boolean mathematics, and concepts of probability. Applications of these methods to developing models of biological regulatory networks and dynamical systems. Software tools for Systems Biology.

Prerequisite(s): SYSB 2024 and MATH 1226 and (MATH 1114 or MATH 2114 or MATH 2114H or ISC 2105) and (CS 1064 or CS 1114) 
SYSB 2984 - Special Study (1-19 credits) 
SYSB 2994 - Undergraduate Research (1-19 credits) 
SYSB 3035 - Genomics and Bioinformatics (4 credits) 

Bioinformatic approaches in omics, namely genomics and transcriptomics. 3035: Genomic architecture and evolution. Gene expression and post-translational regulation. Structure and function of genes and other genetic elements. Experimental techniques for generating genomic and transcriptomic data. 3036: Statistical, evolutionary, and computational models and methods to analyze omics data. Techniques for visualization and biological interpretation of omics data derived from experiments. Application of Python and R to bioinformatics. Case studies and specific applications in molecular biology, including comparative genomics, cancer, and infectious diseases.

Prerequisite(s): BIOL 2004 
SYSB 3036 - Genomics and Bioinformatics (4 credits) 

Bioinformatic approaches in omics, namely genomics and transcriptomics. 3035: Genomic architecture and evolution. Gene expression and post-translational regulation. Structure and function of genes and other genetic elements. Experimental techniques for generating genomic and transcriptomic data. 3036: Statistical, evolutionary, and computational models and methods to analyze omics data. Techniques for visualization and biological interpretation of omics data derived from experiments. Application of Python and R to bioinformatics. Case studies and specific applications in molecular biology, including comparative genomics, cancer, and infectious diseases.

Prerequisite(s): SYSB 3035 
SYSB 3115 - Network Dynamics and Cell Physiology (4 credits) 

In-depth study of how molecular regulatory networks determine the physiological properties of prokaryotic and eukaryotic cells. 3115: Biochemical reaction networks, nonlinear dynamical systems, parameter estimation, bifurcation theory, switches and oscillators, gene regulatory networks, signaling pathways, metabolic networks, neural networks, applications. 3116: Stochastic effects, cell cycle and cancer, spatial effects, motility, development, tissue dynamics, applications.

Prerequisite(s): SYSB 2034 
SYSB 3116 - Network Dynamics and Cell Physiology (4 credits) 

In-depth study of how molecular regulatory networks determine the physiological properties of prokaryotic and eukaryotic cells. 3115: Biochemical reaction networks, nonlinear dynamical systems, parameter estimation, bifurcation theory, switches and oscillators, gene regulatory networks, signaling pathways, metabolic networks, neural networks, applications. 3116: Stochastic effects, cell cycle and cancer, spatial effects, motility, development, tissue dynamics, applications.

Prerequisite(s): SYSB 3115 
SYSB 4024 - Careers and Professionalism in Systems Biology (2 credits) 

Career planning, interviewing skills, and training in written and oral communication in systems biology. Critical evaluation of research, effective communication of scientific results, ethical standards in science, societal trends.

Prerequisite(s): SYSB 3036 and SYSB 3116 
Corequisite(s): SYSB 4065 
SYSB 4065 - Research Experience in Systems Biology (2 credits) 

Training and practical experience in the conduct of systems biology research. 4065: Plan a research project, develop a research hypothesis, and perform preliminary testing and analysis. 4066: Execute, refine, complete, and document the projects results.

Prerequisite(s): SYSB 3036 and SYSB 3116 
Corequisite(s): SYSB 4135 
SYSB 4066 - Research Experience in Systems Biology (2 credits) 

Training and practical experience in the conduct of systems biology research. 4065: Plan a research project, develop a research hypothesis, and perform preliminary testing and analysis. 4066: Execute, refine, complete, and document the projects results.

Prerequisite(s): SYSB 4065 
Corequisite(s): SYSB 4136 
SYSB 4114 - Applied Models of Gene Regulatory Networks (3 credits) 

Dynamic modeling of gene regulatory networks. Gene regulatory networks with oscillatory and switch-like dynamic behavior. Design of synthetic genetic switches and oscillators. Modeling gene regulation controlling cell fate, cell differentiation, cell-to-cell communication, synchronization and developmental processes. Real-world research problems and applications.

Prerequisite(s): SYSB 2034 and SYSB 3116 
SYSB 4994 - Undergraduate Research (1-19 credits)