The broad focus of my research is discovery of new biology through bioinformatic analyses and prediction of protein function and structure. I'm interested in how computational analyses can be combined with experimental research to reconstruct functional evolution of proteins, and to generate testable hypotheses about unknown aspects of protein function.

We are particularly interested in proteins involved in microbial attack and defence, such as toxin antitoxin systems and other bacteriophage defence mechanisms.

In my group we use and develop bioinformatics tools for analysing molecular sequence data. Read more about what we do and access our preprints here: https://atkinson-lab.com/

We have developed online tools for sequence analyses that are used by researchers around the world. Find our server-based tools (uORF4u, MSA4u, webFlaGs and Netflax) here https://server.atkinson-lab.com/.

I am the founder of LU-Fold, a Lund University infrastructure for high throughput protein structure prediction. Read more here https://www.medicine.lu.se/research/list-research-infrastructures/lu-fold

Ongoing projects in the group and relevant publications:

• Prediction and verification of novel toxin-antitoxin systems and other phage defence systems
  • eg https://pubmed.ncbi.nlm.nih.gov/38821063/ , https://www.nature.com/articles/s41586-022-05444-z , https://pubmed.ncbi.nlm.nih.gov/37556498/ , https://www.pnas.org/doi/full/10.1073/pnas.2102212119
• Development of bioinformatics tools for comparative evolutionary sequence analysis (see our tools page here https://server.atkinson-lab.com/)
  • eg https://pubmed.ncbi.nlm.nih.gov/37556498/ , https://doi.org/10.1093/bioinformatics/btad323 , https://doi.org/10.1093/bioinformatics/btaa788
• High throughput structural and functional prediction of proteins and protein complexes
  • eg https://pubmed.ncbi.nlm.nih.gov/37556498/ and see our infrastructure here https://atkinson-lab.com/lu-fold/
• Evolution and function of ABCF translation and antibiotic resistance factors in eukaryotes and bacteria
  • eg https://www.ncbi.nlm.nih.gov/pubmed/30597160 , https://pubmed.ncbi.nlm.nih.gov/36951104/ , https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gky050/4838057
• Functional diversity of small alarmone (ppGpp) synthetase-like enzymes in bacteria and bacteriophages
  • eg https://pubmed.ncbi.nlm.nih.gov/32345719/ , https://pubmed.ncbi.nlm.nih.gov/38834893/
• Discovery of new ribosome-associating proteins involved in translation, ribosome quality control and antibiotic resistance
  • eg https://pubmed.ncbi.nlm.nih.gov/38183984/ , https://pubmed.ncbi.nlm.nih.gov/38811035/ , https://pubmed.ncbi.nlm.nih.gov/33259810/
• High-throughput AlphaFold predictions of viral proteins and protein-protein interactions