Mauno Vihinen is well-known for his experience and interest in investigating variations and their effects whether they emerge at molecular levels (DNA, RNA protein), in structural context or in the cellular networks and pathways. He is the Professor of Medical Structural Biology at Lund University. 

He has published numerous original ideas and reports, established standards and guidelines for variations and variation databases and developed tools and performed analyses for the interpretation of variations in several diseases. The major part of his production relates to variations ranging from protein engineering to effects and mechanisms of variations in protein structures, genes and diseases. He has contributed significantly to the state-of-the-art by frequently presenting novel ideas, methods and results and have pioneered several important proof-of-concepts relevant for the project, including the conceptualization of DNA, RNA and protein variation to Variation Ontology (Vihinen, Genome Res. 2014); the definition of systematic and practical concept for pathogenicity in general (Vihinen, Hum. Mutat. 2017); and the development of several most reliable prediction methods for variations and effect PON-P2 for amino acid substitution tolerance/pathogenicity (Niroula and Vihinen, Hum Mutat 2016), protein specific prediction for Bruton tyrosine kinase kinase domain (PON- BTK, Väliaho et al. Hum. Mutat. 2015), mismatch repair system variants in cancers (POIN-MMR, Niroula and Vihinen,  Hum. Mutat. 2015), protein mechanism specific predictions for stability (Yang  et al. Amino Acids 2013), disorder (PON-dis Ali  et al. Hum. Mutat. 2015) and solubility (PON-sol Yang et al. Bioinf. 2016), as well as a method for mitochondrial tRNA variants (PON-mt-tRNA Niroula and Vihinen, Nucleic Acids Res. 2016). In addition, Vihinen has introduced widely followed guidelines, recommendations and policies, he has founded a new sub-discipline of immunome, and introduced systematics to biological prediction methods and their assessment.

Vihinen was the first professor in bioinformatics in Nordic countries when appointed 1998 to University of Tampere, Finland. Throughout his career, his aim has been to combine experimental, theoretical and data analysis methods to obtain holistic understanding of biological and medical problems.

In the field of systems biology Vihinen and his team has founded immunome, a new sub-discipline about immunity-related genes and proteins including defining the entirety of immunome (Ortutay et al. Immunogenet. 2007) and its properties including e.g. evolution, interactions and networks in immunity. His group has developed a method for revealing networks from experimental data and investigated with systematic computational perturbations effects of T-cell primary immunodeficiencies on the central signaling pathways.

Current studies are devoted into analysis of variations and their effects, including prediction method development, and systems biological studies. The group is interested in many medical applications, especially in the fields of immunology and cancer.