João Carneiro is specialized in bioinformatics applied to the study of different biological questions. He was part of the team of six projects that received funding from FCT and one from the European Union. He is currently principal investigator of one FCT project (Understanding non-B mtDNA conformations using molecular dynamics simulations), and participates in the team that won a project in the 2022 FCT Call for R&D Projects. His main investigation lines are:

- Detection of non-B conformations that occur in mtDNA and are related to human diseases.

- Study of highly infectious viruses (SARS-CoV-2, Influenza, Ebola, HIV, RHDV).

- Study and development of machine learning models applied to biochemical databases (biofilms and cyanobacteria bioactive compounds).