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Curriculum

 

Our program currently offers the Classical MS track and the Professional Science Master’s (PSM) track. Students in each track must choose a specialization in either bioinformatics or medical informatics. Beyond the required core courses, students choose complementary courses to overcome deficiencies in their academic background. Elective courses are intended to assist students with their research and are best chosen in consultation with their thesis advisor.

Further details and updated course numbers and descriptions can be found in the SDSU graduate bulletin.

Classical MS Professional Science Master
Core Courses 12 units 12 units
Complementary Courses 9 units 12 units
(3 units from Plus Courses)
Electives 6 units 9 units
(3 units from Plus Courses)
Research (BMI)
(including Thesis)
6 units 5 units

Core Courses

CHEM 560 – General Biochemistry (3)

The structure, function, metabolism, and thermodynamic relationships of chemical entities in living systems.

BIOMI 510 – Molecular Evolution (3)

Molecular evolution including concepts of homology and convergence, the nearly neutral theory of evolution, evolution of new protein function, detecting selection, multi-gene family evolution and evolutionary genomics.

BIOMI 568 – Bioinformatics (3)

Bioinformatics analysis methods and programming skills. Practical bioinformatic software for sequence analysis, bioinformatic algorithms and programming fundamentals.

BIOMI 600 – Methods in Bioinformatics, Medical Informatics, and Cheminformatics (3)

Computer, mathematical, and engineering techniques for bioinformatics, cheminformatics, and medical informatics. Techniques used in microarray data analysis, gene and protein sequence alignment, and classification techniques in medical decision making.

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Complementary Courses

STAT 551A – Probability and Mathematical Statistics (3)

Discrete and continuous random variables, probability mass functions and density functions, conditional probability and Bayes’ theorem, moments, properties of expectation and variance, joint and marginal distributions, functions of random variables, moment generating functions. Special distributions and sampling distributions.

STAT 551B – Probability and Mathematical Statistics (3)

Point and interval estimation and hypothesis testing in statistical models with applications to problems in various fields.

STAT 680A-680B – Advanced Biostatistical Methods (3,3)

Design, conduct, and analysis of experimental and observational studies including cohort, survival, case-control studies. Multifactor screening. Biological assays.

BIOMI 609 – Computational Genomics and Bioinformatics (3)

Biological and genomics data. Application of computational algorithms to biological questions. Post-genomics techniques in annotation and comparison of microbial and eukaryotic genome sequences.

BIOL 562 – Ecological Metagenomics (3)

Next generation DNA sequencing technology with emphasis on ecological applications in microbial communities. Metagenomic analysis of taxonomic identification, physiological function, and the ecological role of the microbial community in the broader ecosystem.

BIOL 740 – Phylogenetic Systematics (3)

Theory and methodology of phylogenetic systematics. Includes use of computer algorithms, survey of literature and preparation of a project in phylogenetic systematics.

CS 514 – Database Theory and Implementation (3)

Database systems architecture. Storage structures and access techniques. Relational model, relational algebra and calculus, normalization of relations, hierarchical and network models. Current database systems.

CS 520 – Advanced Programming Languages (3)

Object oriented programming, concurrent programming, logic programming. Implementation issues.

CS 532 – Software Engineering (3)

Theory and methodology of programming complex computer software. Analysis, design, and implementation of programs. Team projects required.

CS 560 – Algorithms and Their Analysis (3)

Algorithms for solving frequently occurring problems. Analysis techniques and solutions to recurrence relations. Searching and sorting algorithms. Graph problems (shortest paths, minimal spanning trees, graph search, etc.). NP complete problems.

CS 615 – Spatial Databases (3)

Strategies for databases in which locations are prominent. Access strategies such as quadtrees and R-trees. Topological and other spatial extensions to query languages. Spatial models like non-intersection. Oracle spatial features. Object and object-oriented databases.

PH 602 – Biostatistics (3)

Statistical reasoning applied to public health; probability, hypothesis testing, regression and correlation, analysis of variance, measurement theory and modeling.

PH 700A – Migration & Global Health Seminar (3)

Investigation of current problems in one of the fields of public health.

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General Electives

 

Statistics

STAT 551A – Probability and Mathematical Statistics (3)

Discrete and continuous random variables, probability mass functions and density functions, conditional probability and Bayes’ theorem, moments, properties of expectation and variance, joint and marginal distributions, functions of random variables, moment generating functions. Special distributions and sampling distributions.

STAT 551B – Probability and Mathematical Statistics (3)

Point and interval estimation and hypothesis testing in statistical models with applications to problems in various fields.

STAT 680A-680B – Advanced Biostatistical Methods (3,3)

Design, conduct, and analysis of experimental and observational studies including cohort, survival, case-control studies. Multifactor screening. Biological assays.

Computer Science

CS 503 – Scientific Database Techniques (3)

Fundamental data models for handling scientific data, including flat file, indexed compressed files, relational databases, and object oriented databases, and their associated query technologies; e.g. file formats, input/output libraries, string searching, structured query language, object-oriented structured query language, hypertext markup language/common gateway interface, and other specialized interfaces. Designed for computational science students. Computer science majors must obtain adviser approval. See Computer Science 514.

CS 514 – Database Theory and Implementation (3)

Database systems architecture. Storage structures and access techniques. Relational model, relational algebra and calculus, normalization of relations, hierarchical and network models. Current database systems.

CS 520 – Advanced Programming Languages (3)

Object oriented programming, concurrent programming, logic programming. Implementation issues.

CS 532 – Software Engineering (3)

Theory and methodology of programming complex computer software. Analysis, design, and implementation of programs. Team projects required.

CS 535 – Object-Oriented Programming and Design (3)

Basic concepts of object-oriented programming; classes, objects, messages, data abstraction, inheritance, encapsulation. Object-oriented design methodology.

CS 560 – Algorithms and Their Analysis (3)

Algorithms for solving frequently occurring problems. Analysis techniques and solutions to recurrence relations. Searching and sorting algorithms. Graph problems (shortest paths, minimal spanning trees, graph search, etc.). NP complete problems.

CS 615 – Spatial Databases (3)

Strategies for databases in which locations are prominent. Access strategies such as quadtrees and R-trees. Topological and other spatial extensions to query languages. Spatial models like non-intersection. Oracle spatial features. Object and object-oriented databases.

CS 653 – Datamining and Knowledge Discovery (3)

Foundations of data mining and knowledge discovery. Diverse methods, algorithms, design techniques and application practice including statistical and Bayesian methods, pattern recognition, clustering, knowledge discovery in data sets, machine learning, neural networks, rough and fuzzy sets.

Biology and Molecular Biology

BIOL 549 – Microbial Genetics and Physiology (3)

Physiology of microbial growth, bacterial structure and function, genetics of bacteriophages and bacteria.

BIOL 584 – Medical Microbiology (3)

Major bacterial and viral pathogens; molecular mechanisms of pathogenesis, microbial toxins and antimicrobial agents; immune response to microbial infections; biochemical and molecular diagnostics.

BIOL 624 – Population Genetics (3)

Theoretical and applied population genetics to include genetic diversity in natural populations, random drift, mutation, gene flow, natural selection, nucleotide variation, and quantitative genetics. Emphasis on data analysis and interpretation.

MBIO 610 – Advanced Topics in Molecular and Cell Biology (3)

Intensive study in specific areas of molecular and cell biology. May be repeated with new content. See Class Schedule for specific content.

BIOL 740 – Phylogenetic Systematics (3)

Theory and methodology of phylogenetic systematics. Includes use of computer algorithms, survey of literature and preparation of a project in phylogenetic systematics.

Chemistry

CHEM 567 – Biochemistry Laboratory (3)

Theory and practice of procedures used in study of life at molecular level. Includes purification and characterization of enzymes, isolation of cell components, and use of radioactive tracer techniques.

Public Health

PH 621 – Epidemiology of Infectious Diseases (3)

Utilizing selected infectious diseases and environmental settings, provides scientific background on which epidemiological investigations and control measures are based.

PH 645 – Health Economics (3)

Economics of health care, including supply and demand factors, efficiency, incentives facing physicians, hospitals, and health plans, economic evaluation of provider performance, health workforce issues, and cost-effectiveness analysis.

PH 649 – Border and Global Public Health Surveillance (3)

Data sources for border and global surveillance, including hospital system syndromic data. Methods of data quality control, data analysis, and alerting and communication of information.

PH 682 – Geographic Information Systems and Public Health Spatial Analysis (3)

Theoretical concepts of geographic information systems (GIS) and applications of GIS in public health. ArcGIS 9 software to illustrate the capabilities and uses of GIS in both academic research and regulatory decision making.

Bioinformatics Electives

BIOMI 609 – Computational Genomics and Bioinformatics (3)

Biological and genomics data. Application of computational algorithms to biological questions. Post-genomics techniques in annotation and comparison of microbial and eukaryotic genome sequences.

BIOL 562 – Ecological Metagenomics (3)

Next generation DNA sequencing technology with emphasis on ecological applications in microbial communities. Metagenomic analysis of taxonomic identification, physiological function, and the ecological role of the microbial community in the broader ecosystem.

Medical Informatics Electives

NURS 684 – Information Systems for Nursing (3)

Information systems and information management in all aspects of nursing practice including client care, administration, research and education. Ethics of computer use and influence of information technology on client care. User skills.

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Professional Science Master’s “Plus Courses”

RWS 508W – Scientific Writing (3)

Scientific writing in academic and research settings to include clear and concise writing style, rhetorical strategies, and writing of research reports, proposals, conference presentations, and articles.

BA 651 – Organizational Behavior (3)

Study of individuals and groups within an organizational context. Topics include leadership, individual differences, organizational design, group processes and characteristics, organizational processes and practices; and influence of these on individual, group, and organizational effectiveness.

BA 653 – Managerial Economics (3)

Microeconomic theory applied to business decision making; optimal resource allocation, market structure and pricing from a business viewpoint. Economics of information.

BA 662 – Operations and Supply Chain Management (3)

Managerial concepts and quantitative methods associated with the design, execution, and management of operations and supply chain systems.

MIS 750 – Project Management (3)

Managing projects. Includes network modeling, defining activities and events, cost estimating and reporting, single and multiple resource allocation and leveling. Computerized project management software will be used. (Formerly numbered Information and Decision Systems 750.)

MIS 691 – Decision Support Systems (3)

Design, implementation, and integration of computerized decision support systems into business management. Problem representation, modeling, and simulation.

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Research

BIOMI 797 – Research (1-3)

Research in one of the fields of bioinformatics and medical informatics.

BIOMI 798 – Special Study (1-3)

Individual study.

BIOMI 799A – Thesis or Project (3)

Preparation of a project or thesis for the master’s degree.

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BMI Events

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