Masters in Translational Biomedical Informatics

Masters in Translational Biomedical Informatics

Keck’s MS in Translational Biomedical Informatics can be your career at the intersection of health, science, and informatics. Whether you are a lab technician hoping to take your career to the next level, or a recent graduate looking for an alternative career in the biomedical sciences, our hands-on learning program can help you find your path. You’ll learn how to apply and use existing biomedical informatics tools to solve complex biomedical problems. You’ll learn how to work within complex regulatory environments developing solutions to improve human health and disease from datasets that are both small and massive.

Students in this program will gain an understanding of:

  • Best practices for using existing tools and bioinformatics datasets together to better understand biomedical problems;
  • Analysis of next-generation sequencing (NGS) including whole-genome, exome, and transcriptome sequencing (RNA-seq), as well as emerging methods in single-cell sequencing;
  • Project management and requirements in bioinformatics gathering skills to allow them to interface and interact with computational and engineering expertise to help design solutions;
  • Experience and training utilizing modern frameworks for rapid prototyping, and how to extract information from a wide variety of databases;
  • Core responsibilities towards data security, privacy, and data sharing spanning open access frameworks to restricted and regulated frameworks;

About

Bridging the Gap

USC's Department of Translational Genomics at Keck's School of Medicine is offering an intensive two-year MS program in biomedical informatics focusing on bioinformatics within health-related fields. The goal of this program is to train applied bioinformaticians, providing students with the training, skillsets, and best practices for applying and integrating existing bioinformatics tools in the study of human health and disease.

Translational: Translating laboratory data to bedside or clinic

Biomedical: Relating to human biology, medicine, and disease

Informatics: Applied processing and analysis of data

This program uses both traditional class-room based teaching and applied in silico laboratory coupled for an integrated learning experience. This program is tailored for individuals with laboratory-based biomedical experience, biomedical sciences, or biomedical engineering. This program focuses on tool application and integration along pipelines, will scripting emphasized over coding. Graduates will have the analytical capabilities for analyzing datasets across molecular biology, systems biology, structural biology, and genomic sequencing datasets. A major emphasis is on data analysis and data processing associated with next-generation sequencing (NGS) data, understanding that the goal is to build core skill sets that remain relevant as new technologies emerge and change.

Training in Applied Bioinformatics

This program uses both traditional class-room based teaching and applied in silico laboratory for assignments that are coupled with additional on-line materials. Bioinformatics after all is about working mostly on computers with a community that spans the world for help!

Courses alternate between online interactions with faculty followed by in-class lectures and laboratories. Class is often focused on helping students apply concepts that were made available outside of the classroom. Fundamentally, this is an applied program where the focus is on learning to become independent and solve new problems as they emerge. It teaches processes, though in a way that is effectively learning by example. For example, several courses have a strong inclusion of R, R-markdown, and R-shiny, where students develop web- applications to complete homework by submission via GitHub. These applications may include biomedical research or clinical problem commonly seen in the field. Classroom time is often used for working with teams of students on their solutions and suggesting paths through obstacles. In-person classes are often interactive with students and lectures engaged in an ongoing dialogue where lecture materials were already made available and reviewed prior to the course. Students who succeed use both online resources and in-person classroom time.

Career Paths

Biomedical Informatics is an exploding field that can lead to careers in hospitals, clinical labs, research institutes & companies, and biotechnology companies.

Bioinformatic hiring initiatives can be found in such as Illumina, AstraZeneca, Covance, Eli Lilly, Genentech, Invitae, Johnson and Johnson, Loreal, Pfizer, Roche.

Bioinformaticians are in high demand in most research institutes and medical schools with focuses on life sciences. Hospitals and clinical labs – particularly those introducing high-complexity molecular testing – are part of a new opportunity supplementing existing tracks within hospital laboratory IT tracks.

Ideal Candidates

- Biologists - Biomedical engineers - Medical students - Industry professionals

This program is tailored for individuals with laboratory-based biomedical experience and who have bachelors in biomedical sciences or biomedical engineering. This program focuses on tool application and integration along pipelines, will scripting emphasized over coding. This program is not for existing software engineers, computational biologists interesting in developing novel algorithms, but rather on the use and application of existing tools and standards within human health and disease. Graduates will have the analytical capabilities for analyzing datasets across molecular biology, systems biology, structural biology, and genomic datasets. They’ll understand complex regulatory environments and the unique requirements for working in a biomedical setting.

Empowering users through genomics and bioinformatics

The plating prowess and bioinformatic brains in the halls of Norris are available for the entire Keck academic and clinical community. “We want to leverage our strengths to increase the research potential of departments in a variety of disciplines, and to assist patients across the disease spectrum,” says Director John D. Carpten.

One of the ways this will be achieved is through the newly launched Keck Genomics Platform. Under the direction of Zarko Manojlovic, Ph.D., the service offers a range of high-tech, high-throughput sequencing, as well as the bioinformatic backbone and support to be able to interpret the data generated. Technicians at the center also have expertise in preparing complex and fragile samples, allowing researchers and physicians to test materials that have previously been considered unusable.

Together with David W. Craig, his team is working to create a cradle-to-grave next-generation sequencing data management and bioinformatics platform that focuses on downstream interpretation and accelerates discovery through close collaborations between experimental and informatic groups.

Time Commitment

A total of 28 units is needed to graduate. Most students take about 1.5 years, though it is possible to finish in 1 year whereas others take 2 years. A major distinction between the timelines is the extent that a student becomes involved in a lab or internships that go beyond the 4 units of a capstone project. These internships and laboratory-based opportunities provide real-world training environments facilitating transitions to Ph.D. programs or industry positions.

Capstone projects are a key part of the experience - courses can provide a foundation but really becoming emersed in a focus real sets students apart. A wide variety of laboratories inside and outside of the department provide capstone experiences. These can include internships at USC, but many students leverage and work within the program such that their capstone includes industry experience.

To facilitate capstone experiences, most courses are synchronized to be on Tuesday/Thursdays, allowing Monday/Wednesday/Friday for course work and becoming involved in capstone projects.

Two Examples

A 1 Year Intensive Plan

Fall
  • TRGN510 Foundations (4 Units)
  • TRGN514 Genomic Analysis I (4 Units)
  • TRGN524 Genome Methods I (4 Units)
Spring
  • TRGN515 Genomic Analysis II (4 Units)
  • TRGN516  Databases and Datastructures (4 Units)
  • Elective (4 Units)
Summer
  • TRGN520 Capstone

This path is often preferred by those who already have their foot in the door in bioinformatics and are looking for a formal degree.

A 2 Year Deep Dive Plan

Fall
  • TRGN510 Foundations (4 Units)
  • TRGN514 Genomic Analysis I (4 Units)
Spring
  • TRGN515 Genomic Analysis II (4 Units)
  • TRGN516  Databases and Data structures (4 Units)
Fall
  • TRGN525 Genomic Methods (4 Units)
  • TRGN520 Capstone (2 Units)
Spring
  • Elective (4 Units)
  • TRGN520 Capstone (2 Units)

In this preferred path, students are often involved in laboratories that lead to papers or other industry internships. 

Learning Objectives

Upon graduation, students will:

  • Understand best practices for putting existing tools and bioinformatics datasets together to better understand biomedical problems;
  • Be able to analyze next-generation sequencing (NGS) including whole-genome, exome, and transcriptome sequencing (RNA-seq), as well as emerging methods in single-cell sequencing;
  • Understand project management and requirements in bioinformatics gathering skills to allow them to interface and interact with computational and engineering expertise to help design solutions;
  • Have experience and training utilizing modern frameworks for rapid prototyping, and how to extract information from a wide variety of databases;
  • Understand core responsibilities towards data security, privacy, and data sharing spanning open access frameworks to restricted and regulated frameworks;

Courses

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.

ADMISSION

Admission requirements include a minimum GPA of 3.0 and an undergraduate major in biological sciences, or at least 6 bioscience courses in the molecular, cellular, genetics and biochemistry topics.

Formal application via USC Office of Graduate Admission’s online portal is required.

  • Completed online application.
  • Statement of purpose (approximately 500 words): Tell us where you came from, where you are going to, and how enrolling in the Translational Biotechnology Program may help you reach your academic or career goals.
  • Resume or CV: There is no specific format requirement for a Resume or CV.
  • Letters of recommendation (minimum three): We accept letters from both academic and professional evaluators.  At least two of the letters should address your bioscience aptitude.   All letters must be on the letterhead of the organization or department.
  • Transcripts from ALL previously attended post-secondary institutions regardless of whether a degree was obtained.
  • Standardized test score (waved for 2021): A minimum score of 300 on the Graduate Record Examinations (GRE) General Test is required. In lieu of GRE, DAT (minimum 18), MCAT (minimum 28 pre-2015 or 505 post-2015) or USMLE may be submitted.  Applicants beneath these standardized test score requirements or have not yet taken the exam are asked to consult with program director for advisement.
  • International students whose first language is not English are required to provide evidence of English Proficiency: TOEFL (iBT) 90, with no less than 20 on each section, or IELTS 6.5, with 6 or above on each band.
  • Students with strong bioscience preparation but with lower language proficiency scores could consider applying to USC’s International Academy Pre-master’s programs.
  • Applicants considered for admission may be interviewed (in person or via video conferencing) with the program director and/or other faculty.

Ready to Apply?

COST OF ATTENDANCE AND FINANCIAL AID

Estimated budgets for tuition, fees, books, supplies, room, board, and other living expenses can be found here.  Tuition is charged at the same rate for both in-state and out-of-state residents.

Students may apply for financial aid through USC Financial Aid Office, which provides additional information for federally backed student loans, private financing and a federal work-study program.  Limited funding opportunities can be found at the Office of Academic Honors and Fellowships and USC Graduate School.

USC OFFICE OF INTERNATIONAL SERVICES

The Office of International Services (OIS) provides continuing support services for international students. Professionally trained counselors and student peer counselors are available to advise international students on important issues such as immigration regulations, academic progress, financial concerns, housing and cross-cultural adjustment. Through this office, students can receive information about social and cultural activities.

Applications Due April 1st, 2020. Early Notifications for those applying before April 1st, 2021.

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Contact

MS In Translational Biomedical Informatics

Keck School of Medicine of USC
1450. Biggy Street, 2nd Floor
Los Angeles, CA 90033

Program Director

David W Craig, Ph.D.

David W Craig, Ph.D.
Professor and Co-Director
USC Institute for Translational Genomics

Phone: 323.442.7784
Email: davidwcr@usc.edu