Seán O’Donoghue in based in Sydney, Australia, where he is a Laboratory Head at the Garvan Institute of Medical Research and a Conjoint Professor in the School of Biotechnology and Biomolecular Science (BABS), University of New South Wales (UNSW). Formerly, he was an OCE Science Leader and a Chief Research Scientist at Data61 in Australia's Commonwealth Scientific and Industrial Research Organisation (CSIRO). He received his B.Sc. (Hons) and PhD in biophysics from the University of Sydney, Australia. Much of his career was spent in Heidelberg, Germany, where he worked in the Structural and Computational Biology research unit at the European Molecular Biology Laboratory (EMBL), and at Lion Bioscience AG - then the world's largest bioinformatics company - where he was Director of Scientific Visualisation. Since returning to Australia in 2011, he has served on the EMBL-Australia council and chaired the EMBL-Australia Bioinformatics Advisory Committee.

His research career has focused on using computational methods to advance the life sciences. His early work was on improving how bimolecular structures are calculated from NMR data. Today, he is well known in the bioinformatics community as co-founder and chair of the 'VIZBI' initiative, which aims to raise the global standard of data visualisation in computational biology. His team create bioinformatics resources used by tens of thousands of life scientists worldwide. The team also produce informative and inspirational biomedical animations that have been seen by over half a million people.

His current research interests centre on using bioinformatics and data visualisation to better understand (1) the spatial organisation of the genome, (2) dynamic changes in the epiproteome, and (3) the 'dark' proteome of structural biology.