Research is focused in the general areas of biomedical imaging, computational genomics, computational medicine, data intensive biomedical science, genomic-epigenomic engineering, neuroengineering, regenerative and immune engineering, systems biology, and medical technologies.

[8] This founding era gave rise to some of the earliest works in computational neuroscience, exemplified by the application of control theory to the neural basis of eye movements,[9] understanding the control of the strength of heart muscle contractions,[10][11] Johns' articulation of what has come to be known as Systems Biology, the early neural codes of complex auditory stimuli forming the basis for modern cochlear implants,[12] and somatosensory codes forming the basis for modern tactile prostheses.

In 2000, Johns Hopkins University received an award from the Whitaker Foundation, enabling the hiring of 10 tenure line faculty with principal appointments in the Whiting School of Engineering.

With the Whitaker foundation award, the new Clark Hall was constructed at the Homewood campus.

For 30 years, the Johns Hopkins Department of Biomedical Engineering was continuously ranked as the number one undergraduate and graduate Biomedical Engineering program in the United States by U.S. News & World Report.