CCB Summer Internships

Internship Program Overview

The CCB internship program will provide you with hands-on research experience as part of ongoing projects supervised by faculty in the Departments of Biomedical Engineering, Computer Science, Biostatistics, and Biology, and in the McKusick-Nathans Institute of Genetic Medicine at Hopkins. Current areas of research include analysis of high-throughput DNA sequence data, analysis of RNA sequencing experiments, studies of the human microbiome, assembly of whole-genome shotgun data from various species, and the development of new computational and statistical methods for genome analysis problems. You can browse a list of past internship projects here.

The program involves full-time research for 10 weeks between May and late July. In 2017 the tentative program dates will run from May 22rd to July 28nd, but we can make accommodations if you need to start a bit later. High school students will join the program one month later and intern for 6 weeks. (High schools have varying end dates and we can accomodate students who may need to start slightly earlier or later.) The stipend will be approximately $4500 for the summer for undergraduates and $2500 for high school students. Please note that this is a full-time program to which you will be dedicating 40 hours / week, and therefore we expected that you will not undertake other organized activities that conflict with the times of this appointment, including enrollment in Summer courses.

Summer 2017 news: the CCB internship program is being organized jointly, for the third year in a row, with the the Summer Research Expeditions (SRE) program in the Computer Science Department at JHU. We will use the same applications process, which is described on the SRE site and below on this page.

Program Dates: May 22, 2017 - July 28, 2017
A very small number of slots are available for high school applicants, who will start after their school year ends, approximately mid-June.
Application Deadline: February 15, 2017
Stipend for 10 weeks: $4,500
Note that housing is provided for college students but is optional. Most interns live in the Baltmore area, but students from out of town who can make their own housing arrangements are welcome to apply.
Note for high school applicants:Housing is not provided for these 6-week internship positions. We offer high school internships as an opportunity to Baltimore-area students who can arrange to commute from home, or who can arrange local housing on their own.

When accepted to the program, you will be assigned to a mentor, with whom you will meet frequently beginning with the first day of the program. Your mentor will work with you during the first week to define your summer research project and will help guide you throughout. As part of a research group, you will interact with other students and researchers at JHU, and will participate in group discussions and lab meetings. All interns are invited to at least one regular lab meeting each week. To conclude your research experience at JHU, at the end of the summer you will prepare a report or a poster describing your project and give a brief presentation to the interns and members of CCB.

Required background

The CCB internships are 100\% computational, and we expect that students will have experience with computer programming. In particular, students should have good to excellent programming skills in at least one of these languages: C/C++, Perl, Python, or R. Students with no programming experience will not be considered. In addition, we prefer students who have familiarity with the Unix environment and its command-line interface. If you are an experienced programmer but you don't know Unix, we strongly recommend that you learn the basics of Unix prior to your internship.

Past internship projects

We have been running internship programs since 2012 at Hopkins, and prior to that since 2006 at the University of Maryland's CBCB. You can view a list of past student projects here.

How to apply

The program is open to college undergraduates and to exceptional high school students. Students who graduate from high school in 2015 should apply as high school interns. Participants must be US citizens or permanent residents. You do not need to be a Johns Hopkins University student to apply, and applications from students at other universities are encouraged.

Submit your applications through the Summer Research Expeditions (SRE) program, whose site is site is Note that although this is run by the CS Department, you do not need to be a CS major to apply.

Step 1:: Through SRE, you are asked to choose a project from the list shown at For CCB internships, choose Project 9: Computational Biology Projects. (The SRE site asks you to pick two project choices, but for CCB you may choose just one, Project 9.)

Step 2: Submit your application using the Academic Jobs Online site shown on the SRE page. You will upload the materials below directly on the site, and also provide an email address for the person writing the letter. The website will automatically request the letters using that email.

To apply, you will need the following pieces of information:

  • an up-to-date resume
  • a one page (maximum) statement of interests outlining your goals for this internship.
  • current school transcripts (unofficial transcripts are fine)
  • one letter of recommendation from a teacher or mentor.

Also note that the AcademicJobsOnline site indicates that two letters of recommendation are required, but the CCB internships only require one letter.

Deadline: applications must be submitted by February 15, 2017. Incomplete applications will not be considered.


Funding for the internship program is provided in part by a generous gift from Dr. Jun Wu, Ph.D. 2003, a Hopkins alumnus and member of the Whiting School of Engineering's National Advisory Committee. Additional funding for the internship program by research grants to individual faculty members who serve as mentors in the program.

Faculty mentors

Steven Salzberg, Ben Langmead, Jeff Leek, Liliana Florea, Mihaela Pertea, Alexis Battle, Daehwan Kim, Daniela Puiu, Dan Arking, Geo Pertea, Joel Bader
James Taylor, Steven Salzberg, Ben Langmead, Jeff Leek, Daehwan Kim, Daniela Puiu, Dan Arking, Florian Breitwieser, Liliana Florea

[Steven Salzberg | Liliana Florea | Dan Arking | Joel Bader | Hongkai Ji | Ben Langmead | Andy McCallion | Daniela Puiu | James Taylor ]

[Steven Salzberg | Liliana Florea | Dan Arking | Ben Langmead | Ben Langmead | Daniela Puiu ]

[Steven Salzberg | Liliana Florea | Dan Arking | Hongkai Ji | Tanja Magoc | Daniela Puiu | Rob Scharpf ]

Other information

You can read more about the genomics and bioinformatics research and activities at the JHU Center for Computational Biology on our website here.

Frequent shuttle service is available between Homewood (and Peabody) and JHMI.

Questions? See the Summer Research Expeditions site for more information. If you have questions about the CCB internships in particular, you can contact Ann Vukelich at

Other related opportunities

Summer undergraduate internships in bioinformatics at the University of Maryland's CBCB.