Stegemann began his professional career at the Ontario Cancer Institute studying molecular modeling and dynamics. He then worked briefly in engineering research and development at Lurgi GmbH in Frankfurt, Germany, where he studied chemical process design. In 1990, Stegemann returned to the University of Toronto to pursue a master's degree in bioengineering. He then spent five years working for Boston-based W.R. Grace & Co. (later called Circe Biomedical), where his work focused on cell-based bioartificial organs. In 1997, he returned to academia to earn his doctorate degree from the Department of Biomedical Engineering at the Georgia Institute of Technology in Atlanta. Stegemann joined Rensselaer's biomedical engineering department following his graduation in 2002.

In 2004, Stegemann earned a James D. Watson Investigator Program award from the New York State Office of Science, Technology, and Academic Research (NYSTAR). He also received the Young Investigator Award from the International Society for Applied Cardiovascular Biology in 2002.

An active member of Committee F04 - Tissue Engineered Medical Products of the American Society for Testing and Materials since 1998, Stegemann also has served as Chair of Subcommittee F04.43 on Cells and Tissue Engineered Constructs and on other subcommittees. His professional contributions also include serving as a manuscript/grant reviewer for chemical and biomaterial publications, as well as for the National Science Foundation, NASA, and Singapore Biomedical Research Council (A*STAR).

Stegemann is a member of the American Association for the Advancement of Science (AAAS), the American Chemical Society (ACS), the Biomedical Engineering Society (BMES), and the Society for Biomaterials (SFB).

Stegemann's research involves the study of the structure and the function of living tissues, with the aim of recreating these tissues in the laboratory. Such engineered tissues could then be used to replace damaged body parts or to study complex biological problems in a controlled environment. The field is highly multidisciplinary, drawing on expertise in the areas of biology, physiology, computational modeling, transport phenomena, mechanics, and many others.

A key issue in functional tissue engineering is the ability to control cell function in three-dimensional engineered tissues. This is a requirement in order to promote appropriate tissue development in vitro, as well as to ensure physiological tissue function in vivo. A variety of strategies have been developed to achieve these ends, including the application of biochemical and mechanical stimulation, as well as the use of genetic modification to control cell function.

Current research in Stegemann's laboratory focuses on the use of extracellular environments to control cell function and the development of engineered tissues. In particular, his group is interested in naturally derived hydrogels for use as scaffolds in tissue engineering, and their effects on cell phenotype and function. One focus of this work is to create better matrices for tissue engineering applications by creating composite materials of natural polymers and nanoparticles. His group also studies how cell function, and in particular cell signaling, is affected by 3-D matrices of collagen, fibrin, and other polymers.