Phoenix read biochemistry at the University of Liverpool followed by completion of a doctorate on amphiphilic membrane protein anchors. He studied part-time to obtain a degree in mathematics from the Open University and moved into the field of molecular engineering. He has published widely on the structure-function relationship of amphiphilic biomolecules, obtaining a Chair in Biochemistry in 2000. His work is multidisciplinary and focuses on the understanding of the structure function relationships used by amphiphilic bioactive molecules. He is especially known for his work on the design of antimicrobial peptides  which led to the award of a Higher Doctorate by Liverpool University. He has held Visiting Chairs in Russia, China, Canada and the UK, including King's College London and Sichuan University.
In addition to peer-reviewed papers, edited collections and research monographs he has also been recognised for publication of undergraduate textbooks and has written widely on the development of technical education and skills. He was elected to the Academy of Social Sciences for this work.
He has an been involved in STEM communication and outreach as Editor in Chief for journals such as Biologist which are aimed at a broader readership and as Vice Chair of the Science Museum Group and Chair of the Museum for Science and Industry.