Church is known for his professional contributions in the sequencing of genomes and interpreting such data, in synthetic biology and genome engineering, and in an emerging area of neuroscience that proposes to map brain activity and establish a "functional connectome". Church is known for pioneering the specialized fields of personal genomics and synthetic biology. He has co-founded commercial concerns spanning these areas, and others from green and natural products chemistry to infectious agent testing and fuel production, including Knome, LS9, and Joule Unlimited (respectively, human genomics, green chemistry, and solar fuel companies).