Schnell's research program departs from the premise that there is a continuum between health and disease; if we are capable of measuring this continuum, we will be in the position of detecting disease earlier and understanding it better to intervene more precisely. His research focuses on two broad areas: (i) the development of standard-methods to obtain high quality measurements in the biomedical sciences and scientometrics, and (ii) the development of mathematical models of complex biomedical systems with the goal of identifying the key mechanisms underlying the behavior of the system as a whole.
Schnell has also focused his research attention on deriving mathematical expressions to estimate enzyme kinetics parameters under different reaction conditions. He has systematically obtained equations to estimate kinetic parameters for the family of Michaelis-Menten reaction mechanisms and determined their region of validity for the initial enzyme and substrate concentrations.  Schnell derived a generic expression, known nowadays as the Schnell-Mendoza equation, to determine the Michaelis constant and maximum velocity for enzyme catalyzed reactions following Michaelis-Menten kinetics using time course data.  He has also systematically investigated for the first time how the rate laws describing intracellular reactions vary as a function of the physico-chemical conditions of the intracellular environments.  His work has focused to resolve the ambiguities in the quantitative analysis and modeling of reactions inside cells.
In addition, Schnell has also extensive experience in developing multiscale models of developmental processes and cancer. His work has been highlighted in popular science magazines, such as American Scientist (USA), Investigación y Ciencia (Spain and Latin-America), Spektrum der Wissenschaft (Germany).