Department of Translational Genomics Lab Pages, Student Resources, and Web Applications

Capstone Project

The capstone project is the culmination of your master’s degree in translational biomedical informatics.

There are four aspects:

  1. Identifying a Lab 
  2. Proposal
  3. Capstone Enrollment
  4. Presentation/Delivery

Importantly, it is the vehicle to gain applied experience working within the research field, and ideally, it will aid in future career steps.  There is flexibility in the format and deliverables, though a requirement of a capstone proposal is required to enroll in the course. 

Tools for Identifying A Lab

There is no single best way to find a mentor, though it is recommended you start the process after becoming nominally proficient in basic bioinformatic and computing tools.  For many students, this will be after there the first semester, though for some it may be sooner depending on their individual backgrounds. Your department will be able to give some advice on this topic, and the process can vary tremendously depending on your long term goals.  While for most the mentor will be a USC faculty member, it is possible for the mentor to be an outside individual to be considered on a case-by-case if certain requirements can be made (such as the ability to share openly your work and work product).

The starting point for many emails to prospective labs.  You will want to introduce yourself and have a short 1 to 2 paragraph query and introduction.  You will want to mention some of your bioinformatics expertise or focus (R/R Shiny, Databases, Unix, Next-generation Sequencing). 

Department

There is no single way to identify a mentor, but utilizing colleagues, the internet and going to presentations are foundational. Clearly, starting by looking at the research and faculty within the Department of Translational Genomics is a great starting point. The research faculty are:

Keck School of Medicine

There are many faculty that work closely with the department and many faculty at USC who would make excellent mentors.  Collaboration is at the heart of translational genomics.  Departments indicating strong interest in Translational Biomedical Informatics Students:

  • Department of Medicine
    • Best initial contact is Matthew Salomon who leads informatics and is aware of different groups who have needs
  • Department of Psychiatry
    • Specific requests for those interested in databasing with genomics by Steven Siegel
  • Stem Cell
    • Various individuals, but Andrew McMahon has opportunities both in his lab and in others. RNA-seq, ChIP-seq, ATAC-seq, single-cell RNA-seq, single-cell-ATAC-seq, and Hi-C to identify the molecular mechanisms regulating maintenance and commitment of stem/progenitor populations in generation and repair of the mouse and human kidney
  • Zilka Institute
    • Berislav V. Zlokovic or individual labs may be the best approach
  • CHLA
    • Xiaowu Gai is a great contact who may be aware of many opportunities

Faculty Collaborators

Faculty who have expressed interest in bioinformatic students:

Faculty/Link Department Position
Adam de Smith, PhD Genetic Epidemiology Assistant Professor
Andrew P. McMahon, PhD Stem Cell Professor
Caryn Lerman Cancer Center Professor
Dana Goldman, PhD Public Policy Professor
Daniel J. Weisenberger, PhD Medicine Associate Professor
Daniella Meeker, PhD Preventive Medicine Assistant Professor
Darcy Spicer, MD Medicine Associate Professor
Darryl Shibata, MD Pathology Professor
Jaclyn A. Biegel, PhD Pediatrics Professor
Jerry SH Lee, PhD Medicine Associate Professor
Jonathan David Buckley, MD, PhD Preventive Medicine Professor
Juan Pablo Lewinger, PhD Preventive Medicine Assistant Professor
Julie E. Lang, MD Surgery Associate Professor
Juliet Ann Emamaullee Surgery Assistant Professor
Justin Ichida, PhD Stem Cell Biology Assistant Professor
Kimberly Siegmund, PhD Preventive Medicine Professor
Linda Michelle Polfus, PhD Genetic Epidemiology Assistant Professor
Matthew Salomon Medicine Assistant Professor
Michael Anthony Bonaguidi, PhD Stem Cell Biology Assistant Professor
Michael R. Lieber, MD, PhD Pathology Professor
Paul Marjoram, PhD Preventive Medicine Professor
Peter Kuhn, PhD Broad CIRM Center Professor
Pinchas Cohen, MD Gerontology Professor
Rangasamy Ramanathan, MD Pediatrics Professor
Ricky Bluthenthal, PhD Institute for Health Associate Professor
Sarah Hamm-Alvarez, PhD Ophthalmology Associate Professor
Shahab Asgharzadeh, MD Pediatrics Associate Professor
Steve Kay, PhD Zilkha Neurogenetic  Professor
Steven Siegel, MD, PhD Psychiatry Chair
Timothy J Triche, MD, PhD Pediatrics Professor
W. Martin Kast, PhD Molecular Microbiology Professor
Wendy Cozen, DO, MPH Preventive Medicine Professor

USC Health Science Profiles - Learn about Keck Faculty

 An automated tool that has information about each faculty. This tool is great for doing searches within areas!

NIH Reporter:  Identifies labs with funding

Often the labs with the greatest opportunities have NIH grants.  This database is great - remember to limit to USC to see all the different labs with substantial NIH funding.

Proposal

After working some time in your lab or research environment, you'll want to start defining what will be your Capstone deliverable. Remember, in the beginning, you want to learn and develop from the lab. The right capstone deliverable will typically be pretty clear after a few months, but it should be something that really showcases what you are learning and the experience you are gaining.

Your proposal will be turned in as a Github titled “capstone” in markdown format as the initiating Readme.md.  You will create the course PI as a collaborator. There is purposeful flexibility in the type of capstone projects  & its deliverable. In the end, they should be done with a mentor. The experience of working within a lab is critical and the deliverable may vary. There will be some back-and-forth on the proposal to make sure expectations are clear. You will be notified by the program director by email when the proposal is accepted.

It is important to understand that the deliverable and timing of the capstone course can capture your entire time within the master’s program. For example, if you are presenting at a conference, you would include work done in all the semesters within the program.

Example deliverables include:

  • Publications (e.g. Journal)
  • Scientific Poster at a Major Conference
  • Technical White Paper, e.g. Biorxv
  • GitHub Repositories
  • Web-sites

There is not a requirement for a traditional academic style presentation, and various forms can be used including video, websites, the publication (PDF), and other media.  Ideally, the presentation can be done in a way that retains your ability to show people the work in the future.

Readme.MD

#Title
Proposed Title
#Student
#Mentor
John Doe, Ph.D.
john.doe@usc.edu#Proposed Work
150 to 250 Words
#Proposed Deliverable
150 to 250 Words