Information for prospective Ph.D. students in Computational Biology or Bioinformatics

Note: every year, many students send applications directly to faculty members, but faculty members cannot accept students directly in any of our programs at Hopkins. You must apply to the Ph.D. programs through the Department websites given below.

The Ph.D. programs in Computational Biology at Johns Hopkins University span four Departments and a wide range of research topics. Our programs provide interdisciplinary training in computational and quantitative approaches to scientific problems that include questions in genomics, medicine, genome engineering, sequencing technology, molecular biology, genetics, and others.

Our students are actively involved in high-profile research, and have developed very widely-used bioinformatics software systems such as Bowtie, Tophat, and Cufflinks. and the more-recent systems HISAT and Stringtie (for RNA-seq alignment and assembly) and Kraken (for metagenomic sequence analysis). The work they do with Hopkins faculty prepares them to go on to postdoctoral and tenure track faculty positions at top-ranked universities including (in recent years) Harvard, the University of Washington, Carnegie Mellon, the University of Maryland, and Brown.

Students in computational biology at Hopkins can enroll in one of four different Ph.D. programs. These include Biomedical Engineering, ranked #1 in the nation; Biostatistics, also ranked #1 in the nation; Biology, ranked #6 in the nation; and the rapidly growing Computer Science Department, ranked #23 in the nation. Hopkins is also ranked #4 in the nation in Bioinformatics, a ranking that just started appearing in 2022.

CCB faculty have appointments in each of these programs, and some of us maintain appointments in multiple programs. To determine which program fits your interests and background, browse the course lists below. Each program has a separate application process; please apply specifically to the departments you're interested in. Applications to multiple programs are permitted, but if you're not certain, we encourage you to contact potential faculty advisors before you apply. Wherever you apply, make it clear that your interest is Computational Biology.

Sample Course Offerings for Ph.D. students in Computational Biology

See this page for a list of current courses in computational biology offered by our faculty across multiple departments. Many of these courses count towards the Ph.D. programs in BME, CS, Biology, and others

Department of Biomedical Engineering, Whiting School of Engineering

The Johns Hopkins Department of Biomedical Engineering (BME), widely regarded as the top program of its kind in the world and ranked #1 in the nation by U.S. News, is dedicated to solving important scientific problems at the intersection of multiple disciplines and that have the potential to make a significant impact on medicine and health. At the intersection of inquiry and discovery, the department integrates biology, medicine, and engineering and draws upon the considerable strengths and talents of the Johns Hopkins Schools of Engineering and Medicine. See the BME Ph.D. program website for many details.

A unique feature of the Hopkins BME program is that students may also opt to take the 1st-year Medical School curriculum to satisfy most of their course requirements. Many students choose this option, in which they sit side by side with the students in Hopkins' highly-ranked M.D. program.

Department of Computer Science, Whiting School of Engineering

Computer Science at Johns Hopkins University is a diverse, collaborative, and intensely research-focused department. In 2015, the Department moved into a brand new, state-of-the-art research building, Malone Hall, designed around the needs of students and faculty. See the video highlighting the new building and some of our students here.

The Department was recently ranked 20th in the nation among Computer Science programs.

The faculty represent a broad spectrum of disciplines encompassing core computer science and many cross-disciplinary areas including Computational Biology and Medicine, Information Security, Machine Learning, Data Intensive Computing, Computer-Integrated Surgery, and Natural Language Processing.

Ph.D. program

A total of 8 courses are required, and a typical load is 3 courses per semester. See the CS Department website for details. For a look at courses that might be included in Ph.D. training, see this page, though note that it is not a comprehensive list. For the Computer Science Ph.D., 2 out of the required 8 classes can be taken outside the Department. These may include any of the courses in the BME, Biostatistics, and Biology programs listed on this page.

Department of Biostatistics, Bloomberg School of Public Health

Johns Hopkins Biostatistics is the oldest department of its kind in the world and has long been considered as one of the best. In 2022, it was ranked #1 in the nation by U.S. News.

Ph.D. program

At least 18 credits required outside the Dept of Biostatistics, at least 9 of these in the School of Public Health. See the Department website for details.

All students in the Biostatistics Ph.D. program have to complete the core requirements:

In addition, students in computational biology might take:

Further courses might include 2-3 courses in Computer Science, BME, or Biology listed on this page.

Department of Biology, Krieger School of Arts and Sciences

The Hopkins Biology Graduate Program, founded in 1876, is the oldest Biology graduate school in the country. People like Thomas Morgan, E. B. Wilson, Edwin Conklin and Ross Harrison, were part of the initial graduate classes when the program was first founded. Hopkins is ranked #6 in the nation in Biological Sciences by U.S. News

Quantitative and computational biology are an integral part of the CMDB training program. During the first semester students attend Quantitative Biology Bootcamp, a one week intensive course in using computational tools and programming for biological data analysis. Two of our core courses - Graduate Biophysical Chemistry and Genomes and Development - each have an associated computational lab component.

Ph.D. in Cell, Molecular, Developmental Biology, and Biophysics (CMDB):

The CMDB core includes the following courses:

Electives include courses such as:

Students in computational biology can use their electives to take more computationally intensive courses. You have considerable flexibility to design a program of study with your Ph.D. advisor.