Publications

BioModelsML: Building a FAIR and reproducible collection of machine learning models in life sciences and medicine for easy reuse, Divyang Deep Tiwari, Nils Hoffmann, Kieran Didi, Sumukh Deshpande, Sucheta Ghosh, Tung V. N. Nguyen, Karthik Raman, Henning Hermjakob, Rahuman S Malik Sheriff, biorxviv, 05/2023
AbNatiV: VQ-VAE-based assessment of antibody and nanobody nativeness for engineering, selection, and computational design, Aubin Ramon, Alessio Saturnino, Kieran Didi, Matthew Greenig, Pietro Sormanni, biorxviv, 04/2023

Generative Models in Bioinformatics, invited book chapter in Encyclopedia of Bioinformatics and Computational Biology, under review, 01/2023
The Art of Molecular Programming, textbook, active as editor

Flexible Small-Molecule Design and Optimization with Equivariant Diffusion Models, Charlie Harris, Kieran Didi, Arne Schneuing, Yuanqi Du, Arian R. Jamasb, Michael Bronstein, Bruno Correia, Pietro Liò, Tom Blundell, ICLR 2023 MLDD workshop, 03/2023
Biomolecular condensate phase diagrams with a combinatorial microdroplet platform, William E. Arter, Runzhang Qi, Nadia A. Erkamp, Georg Krainer, Kieran Didi, Timothy J. Welsh, Julia Acker, Jonathan Nixon-Abell, Seema Qamar, Jordina Guillén-Boixet, Titus M. Franzmann, David Kuster, Anthony A. Hyman, Alexander Borodavka, Peter St George-Hyslop, Simon Alberti & Tuomas P. J. Knowles, Nature Communications, 12/2022

Conference Presentations

Accessible AMR-detection tools for clinicians via cloud-based bioinformatics (oral presentation), Clinical Informatics Symposium Melbourne (Australia), 12/2022
sINSIDER: a cloud-native modular platform for kmer-based genomic analysis (oral presentation), ABACBS Conference Melbourne (Australia), 11/2022
Moving bioinformatics to the cloud (keynote presentation), eSCAMPS Symposium Cambridge (UK), 09/2022
Detecting DNA integration via HPC bioinformatics pipeline (poster),R&I Conference Sydney (Australia), 08/2022
Teaching
Structural Bioinformatics, lecture, Heidelberg University, 10/2023
Advanced Python for Scientists, lecture, Heidelberg University, 06/2023
Algorithms II, supervising course on data structures and graph algorithms, Cambridge University, 03-05/2023
Algorithms I, Cambridge University, 01-03/2023
MLOps with PyTorch Lightning and W&B, conceptualised and lecture workshop, ML Forum CSIRO Australia, 01/2023
Python for Scientists, lecture, Heidelberg University, 11/2022
Python Best Practices, workshop (co-host), Scientific Software Center Heidelberg, 11/2022
Deep Learning with PyTorch, Lunch Time Python workshop, Scientific Software Center Heidelberg, 10/2022
Python for Biochemists, lecture, Heidelberg University, 03/2022