[19][20] In 1978, she returned to the National Institute for Medical Research, and following that took up to a Fellowship at Birkbeck College, part of the University of London.

[citation needed] Thornton was Director of the European Bioinformatics Institute (EBI) from 2001 to 2015, on the Wellcome Genome Campus at Hinxton near Cambridge.

[33][32] From 2008 to 2012, she co-ordinated the four-year preparatory phase of the European life sciences data infrastructure ELIXIR.

Thornton has supervised several PhD[36] and postdoctoral researchers including Sarah Teichmann[6] and David Jones.

[39] Thornton's nomination for the Royal Society reads Janet Thornton is distinguished for her contribution to understanding protein three-dimensional structure: her perceptive comparative studies have led to the development of algorithms that are used to analyse and make predictions of supersecondary and tertiary structure.

In the 1970s at Oxford (with M J Sternberg) she established clear and useful rules for the handedness of B-a-B units and demonstrated valid methods for prediction of the ordering of strands in B-sheets.

At Birkbeck she developed this work to define families of conformations in B-hairpins and aB-links where the structures had previously been assumed at random.