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Applications in florescence
Phycobiliprotein has many applications in fluorescent experiments due to its ability to participate in multi-color detection, as the fluorescent colors derived from it won't overlap and give low background noise. This allows for high sensitivity and a wide range of uses for Fluorescent tag s such as R- and B-Phycoerythrin and Allophycocyanin, all of which are made from phycobiliproteins. One application is in Flow cytometry which measures and detects the different chemical and physical characteristics a large pool. This pool can include cells or particles that are in fluid. Cell sorting by fluorescence is another application, where live cells labeled with different fluorescent tags can be sorted. Histochemistry can also apply this as it is used when trying to find chemicals that are related to different biological structures.

Applications in antioxidants and anti-inflammatory
Phycobiliprotein, specifically phycocyanin has many antioxidant and anti-inflammatory effects which can help treat various human and animal diseases, such as atherosclerosis, liver and cataracts. Phycocyanin is a pigment found in blue-green algae which contains open chain tetrapyrroles with possible scavenging properties. It is categorized as one of the types of phycobiliprotein; along with phycoerythrin and allophycocyanin.

1.	Atherosclerosis
Atherosclerosis begins with the accumulation of low-density lipoprotein (LDL) in the arteries to form plaques. Reactive oxygen species play a role in oxidative modification of low-density lipoprotein and endothelial dysfunction, thereby promoting vascular inflammation. The plaques then grow with proliferation of fibrous tissue which can then lead to atherosclerosis. Phycocyanin from spirulina can increase the level of antioxidant enzymes in the body, and consequently inhibit the production of Reactive Oxygen Species (ROS). This will enhance the plasma antioxidant capacity. Phycocyanin can also reduce expression of NAD oxidase to decrease ROS production and thus treat atherosclerosis that was caused by ROS.

2.	Liver disease
As liver is an important detoxifying organ, it metabolizes many compounds that may produce reactive oxidative species (ROS). Liver diseases such as fatty liver, viral hepatitis and hepatic fibrosis can occur resulting from oxidative stress. In addition, increased ROS can affect oxidation of acetaldehyde which causes acetaldehyde to accumulate in the liver. Acetaldehyde can bind to DNA and inhibit its repair system. This will lead to formation of carcinogenic exocyclic DNA ethenoadducts. A study was conducted by Xia and colleagues to investigate the protective effects of Phycocyanin on alcoholic fatty liver. From the study, the researchers found that Phycocyanin reduced the serum levels of alanine aminotransferase, aspartate aminotransferase, triglycerides, total cholesterol and LDL, increased the content of superoxide dismutase and malondialdehyde in the liver. The results show that phycocyanin able to reduce oxidative stress and protect the liver cells from damage

3.	Cataracts:
Researchers had found the correlation between cataracts and oxidation index, which is due to imbalance between oxidation and antioxidant systems in eyes and can produce an oxidative stress response. A study had used sodium selenite to induce cataracts in rats for phycocyanin treatment. Sodium selenite has been documented to trigger early lenticular epithelial cell damage including loss of calcium homeostasis, crystallin protein breakdown, loss of anti-oxidant enzyme activity, accelerated apoptosis and DNA damage. Based on the study, the researchers learnt that phycocyanin in Spirulina platensis could reduce the oxidative stress response and other related cellular damages by scavenging free radicals and chelating metal ions. Administration of phycocyanin also reduce the cataractogenic process and damage of the eye lens, liver and kidney. The study suggested that the antioxidant properties of phycobiliproteins might provide an effective treatment for cataracts.

Applications in anti-tumor
Phycobiliproteins could have some anti-tumor properties when used on patients suffering from cancer. CPC, C-Phycocyanin, for example, has been shown to stop DNA replication in colon cancer and lung cancer cells; thus, reducing the size of the tumor. CPC is able to induce apoptosis, programmed cell death, in the cancer cells. This is due to CPC’s ability to activate cytochrome C. CPC has also been shown to block the cell cycle in the G0 and G1 phase by blocking DNA synthesis. This can cause cancer cells to lose the ability to rapidly multiply and prevent cancer from spreading. Phycobiliproteins could provide a way to help reduce tumors in patients while also remove the harsh side-effects of other methods that are currently being used to remove tumors and fight cancer. The entire mechanism of how Phycobiliproteins reduce tumors is still unknown and currently being researched.