His group develops integrative analytics to study large-scale brain organization, connectivity, and neurodevelopment. One focus is the study of individual differences in connectome architecture in developing and adult populations, and the relation to variability in high-level cognition and socio-affective competences. His team studies healthy and diseased populations, notably drug-resistant epilepsy and autism spectrum disorders, two common and persistent conditions of early onset.

Bernhardt's research is funded by NSERC, FRQS, SickKids Foundation and CIHR. He serves as Academic Editor for PLoS One and Frontiers in Psychiatry. His contributions to neuroimaging and connectome analysis of healthy and diseased brains were recognized by several awards, including the 2017 Michael Prize of the International League Against Epilepsy.