Collaborating and learning from other fields - that is what bioinformatician Hannah Augustijn enjoys most about doing research. During her PhD at Leiden University, she developed new ways to search within bacteria for the antibiotics of the future.
For Augustijn, that search begins with the genetic on-off switches known as transcription factors. 'We currently know around twenty of them in actinobacteria, even though these bacteria have more than seven hundred in total,' Augustijn explains, who conducted her doctoral research at the Institute of Biology (IBL). 'If we can already find something interesting in that tiny fraction, it says a lot about their potential.'
Mapping binding sites
Using a specialised method called the DAP-seq assay, Augustijn mapped many more transcription factors than before. 'Instead of studying them inside the cell, we let the transcription factors bind to DNA outside the cell. That allowed us to see exactly where they attach.'
Working with the Joint Genome Institute in Berkeley, she managed to chart 40% of the transcription factors and their binding sites. 'The great thing is that you can not only look at a single bacterium, but also compare how this regulation works in other species.'
'As a bioinformatician, you can connect those worlds and make sure that computer tools are genuinely useful in the field.'
Smarter searching with antiSMASH
She is currently adding this large amount of data to antiSMASH, a computer programme that predicts gene clusters: groups of genes that work together to produce compounds such as antibiotics. 'This means any researcher can now see how a gene cluster is regulated and how it might be activated,' she says. 'With those predictions, you can prioritise promising gene clusters for further lab work - saving a huge amount of time and resources.'
'I enjoy learning which language people speak'
Augustijn started out as a lab technician, moved into bioinformatics and is now a postdoctoral researcher at Harvard University, working on combining both worlds. 'The group I'm in is very chemistry-focused, while I'm a biologist. So I'm constantly learning. What I enjoy is figuring out which "language" people speak - a biologist talks differently from a chemist. As a bioinformatician, you can connect those worlds and make sure that computer tools are genuinely useful in the field.'
Digging through mammoth poop
Her early papers show just how many ways there are to discover new bioactive compounds. Two colleagues travelled to Siberia to isolate bacteria from 28,000-year-old mammoth poop. 'The bacteria turned out to be so different from the ones we know. It shows how much untapped potential still exists in nature.'
A bridge between Leiden and Wageningen
With positions in both Leiden and Wageningen, Augustijn acted as a bridge between experimental researchers and bioinformaticians. Her PhD supervisors, Gilles van Wezel and Marnix Medema, confirm this: 'Hannah supported colleagues with visualisations, designed the cover of a scientific journal and received recognition for her work during a speech at the Dies Natalis of Wageningen University in 2024.'
Hannah Augustijn will defend her thesis, titled Piecing together the regulatory puzzle: advancing natural product discovery in Actinobacteria, on 3 December 2025 in the Academy Building. Her supervisors are Gilles van Wezel and Marnix Medema.
