[3] During his PhD, he worked with Simon Laughlin, who is an experimentalist, and Allan Snyder, who is a theoretician, on the optics and electrophysiological properties of the fly compound eye.

During his postdoc with A. James Hudspeth at University of California, San Francisco, he made several major contributions to the understanding of hair cells and motor proteins.

In 1989, Howard set up his own lab at the University of Washington, where his research focused on how motor proteins convert chemical energy derived from the hydrolysis of ATP into mechanical work used to drive cell motility.

His research contributes to our understanding of motor protein and microtubule in the following ways:[7] his group In 2000, Howard moved to Germany, where he played a key role, as Director, in establishing the Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG) in Dresden, one of the foremost biological research institutes in Europe.

[18] At Yale, he has continued his interest in the biophysics of the microtubule skeleton, including studies of the microtubule-severing proteins Spastin, spindle localization in the C. elegans embryo,[19] ciliary beating in Chlamydomonas,[20] physical bioenergetics during Zebrafish embryogenesis[21] and branching morphogenesis of neuronal dendrites.