Course Information (28 Units Total)
General requirements include at least 28 units of required courses as follows:
Core Lecture Courses (Required: 24 Units)
TRGN-510. Basic Foundations in Translational Biomedical Informatics (4 Units).
The goal of this introductory platform course is to teach core fundamentals that will allow a someone trained in biology or medicine how to use modern computing and bioinformatics tools to rapidly and reproducibly answer biological questions within an applied setting. The focus is significant on how researchers can use existing tools together to explore novel biomedical questions in ways that retain reproducibility. This course is for all students to have the core fundamentals for the rest of the program and will have bridge together courses that form the Masters in Translational Biomedical Informatics program. Please be aware the students are expected to have a Mac laptop with Sierra or later operating system installed for enrollment.
This course is a core requirement but may be substituted with INF 510 Principles of Programming for Informatics. The INF510 course provides a more focused training specific to python whereas the TRGN510 focuses more on the use of R, bash, and other scripting languages including python in the context of biomedical applications. For more information on INF510, please see https://classes.usc.edu/term-20161/course/inf-510/
TRGN-514. Introduction to Human Genomic Analysis Methods (4 Units).
This course is part of a two-course series and complements courses offered as part of a master's in biomedical informatics. This course is necessary to both teach modern genomics analysis, but to provide students with the broader skillset to adapt and grow in the field as technologies change. More than most fields, they will frequently change tools and frequently build single-use solutions. This course will focus on implementing, versioning, best practices, planning, and delivery specific to translational research by example using a series of emerging methodologies. Please be aware the students are expected to have a Mac laptop with Sierra or later operating system installed for enrollment.
This course is a core requirement
TRGN-515. Advanced Human Genomic Analysis Methods (4 Units).
This course is part two of a two-course series and complements courses offered as part of a master's in biomedical informatics. This course will continue the process of both teaching modern genomics analysis while providing students with the broader skillset to adapt and grow in the field as technologies change. Students will learn the fundamentals of genomics, transcriptomics, proteomics, and epigenomics technologies and will learn how their application and use drive analytical problems. Students will be expected to be familiar with and now experienced with many foundational skillsets introduced in earlier courses that are necessary for biomedical informatics. This course continues to build those by reinforcement with an increased focus on timeliness and flexibility within the more complex analysis. Please be aware the students are expected to have a Mac laptop with Sierra or later operating system installed for enrollment.
This course is a core requirement
TRGN-516. Translational Genomics, Applied Databases and Data Structures (4 Units)
The objective of this course is to provide advanced bioinformatics training in the use of databases and development of databases for sharing results and tracking information. The course will cover how to work with databases and understanding the regulatory environment around their use. A major part of this course will be on applied projects wherein teams students will be asked to use a case-study based approach to identify appropriate datasets, use analytic tools to analyze data, evaluating hypotheses, and interpret results. The first major foci are the current standards and key resources in human annotation and gene ontology. Please be aware the students are expected to have a Mac laptop with Sierra or later operating system installed for enrollment.
This course is a core requirement but may be substituted with INF 550 Overview of Data Informatics in Large Data Environment with prior permission. The TRGN516 course is focused on biomedical applications and the management of biomedical data, particularly within a healthcare context. INF550 provides a deeper technical view using applications that are much broader. In that context, TRGN has a narrower focus on healthcare applications and the associated regulated frameworks, whereas INF550 provides a deeper technical basis within databases and data structures.
TRGN-524. Applications of Genomic Technology in Biomedical Research I (4 Units)
This course is an introductory level course and necessary for Masters of Science (MS) degrees in both Biomedical Informatics and Translational Biotechnology. This course is necessary to build a foundational understanding of modern molecular genetic technologies and the evolution of next-generation technologies. At its core, this course teaches the principles of conducting large-scale data analysis and appreciating how the nature and type of data impact the analysis approach. Next-generation sequencing data is at its nature pseudo-single molecule and analysis approaches treat error differently, and this has implications towards interpretation. Through these courses, students will understand the inherent challenges and opportunities by bridging analysis together to uncover new discoveries, through integration across genomics, transcriptomics, proteomics and epigenomics technologies. Students will learn how these tools are developed and how they are impacting both the laboratory and the clinical setting. Through this course, students will also learn how biotechnology leads to commercialization and gain an understanding of governmental regulations and ethics surrounding hot topic issues such as cloning, stem cells, and genome sequencing.
TRGN-525. Applications of Genomic Technology in Biomedical Research II
This is the second of two courses with the objective to train and provide individuals with strong backgrounds and interests in biological or medical sciences the theoretical and applied knowledge of modern-day biotechnology. It will introduce students to tools and applications that will be instrumental throughout the Biomedical Bioinformatics and Translational Biotechnology Masters programs. This course targets those who have some previous training in biomedical sciences, and aims to provide them with the foundations, basic principles, and core concepts in biotechnology and its applications to basic science, health, and disease. Students will learn how biotechnology leads to commercialization and gain an understanding of governmental regulations and ethics surrounding hot topic issues such as cloning, stem cells, and genome sequencing.
This course is a recommended elective, but may be substituted for one of the electives below
TRGN-520. Translational Biomedical Informatics Capstone Portfolio
This course will provide students the opportunity to build a portfolio in the form of a web-based application that can capture the projects developed and completed through this course, and also show-cases one larger cap-stone project. The overall objective is to provide students provides the culminating, integrative curricular experience and an overarching project tailored to the career direction they are targeting and build a reactive widely accessible “WebApp” that showcases their project.
Electives (At Least 4)
- TRGN 525. Foundations, Concepts, Core Principles In Biotechnology II
- PM 570 Statistical Methods in Human Genetics.
- PM 538 Introduction to Biomedical Informatics.
- BME 528 Medical Diagnostics, Therapeutics and Informatics.
- PM 570 Statistical Methods in Human Genetics.
- INF 510 Principles of Programming for Informatics.
- INF 550 Overview of Data Informatics in Large Data Environments.
- NIIN 500 Neuroimaging and Systems Neuroscience.
- NIIN 540 Neuroimaging Data Processing Methods.
TRGN-520. Clinical Bioinformatics in Genomic Testing
Typically Fall 2 Units
This course aims to provide students with an understanding implementing, versioning, best practices, planning, and bioinformatics within clinical settings. Clinical testing is a highly regulated environment and specific skills in using emerging methodologies are required within these environments. This course will focus on implementing pipelines in a more mature and regulated environment such as in a clinical laboratory. In these cases, we will train by example with a focus on both new genomic analysis methods and the foundational skills to remain relevant as the field changes.