The hedgehog signaling pathway is a mechanism that regulates cell growth and differentiation during embryonic development, called embryogenesis, in animals. The hedgehog signaling pathway works both between cells and within individual cells.

In 2011, Sonja Vernes and Simon Fisher performed a series of experiments to determine which developmental processes are controlled by the mouse protein Foxp2. Previous research showed that altering the Foxp2 protein changed how neurons grew, so Vernes and Fisher hypothesized that Foxp2 would affect gene networks that involved in the development of neurons, or nerve cells. Their results confirmed that Foxp2 affected the development of gene networks involved in the growth of neurons, as well as networks that are involved in cell specialization and cell communication. The researchers determined that Foxp2 is important for a variety of developmental processes such as motor control, language acquisition, and cognition.

The crystal jellyfish, Aequorea victoria, produces and emits light, called bioluminescence. Its DNA codes for sequence of 238 amino acids that forms a protein called Green Fluorescent Protein (GFP). FP is folded so that a part of the protein, called the chromophore, is located in the center of the protein. The chemical structure of the chromophore emits a green fluorescence when exposed to light in the range of blue to ultraviolet.

The Protein Information Resource, or PIR, is an online, publicly available resource that contains databases of protein sequences and computer programs that support the study of proteins, their functions, evolutionary histories, and interactions with other biomolecules in living organisms. A non-profit research institution called the National Biomedical Research Foundation, or NBRF, established the PIR in 1984. Since proteins were first sequenced in the late 1950s, scientists have used protein sequence data to understand biological functions, interactions, and pathways. Protein sequences contribute to many kinds of research, including genomics, proteomics, and systems biology. From 1984 to 2004, the PIR housed one of the first, free online protein sequence databases and computer programs that allowed searching and comparison of those sequences. During that twenty-year period, scientists could use the PIR to identify an unknown protein and determine its evolutionary history and function, including its role in embryological development.