Publications

Publications

Pre-Prints

  • GPU-accelerated homology search with MMseqs2 Felix Kallenborn*, Alejandro Chacon*, Christian Hundt, Hassan Sirelkhatim, Kieran Didi, Sooyoung Cha, Christian Dallago, Milot Mirdita, Bertil Schmidt, Martin Steinegger, bioRxiv, 04/2025
  • MotifBench: A standardized protein design benchmark for motif-scaffolding problems Zhuoqi Zheng, Bo Zhang, Kieran Didi, Kevin K. Yang, Jason Yim, Joseph L. Watson, Hai-Feng Chen, Brian L. Trippe, arxiv, 02/2025
  • BioNeMo Framework: a modular, high-performance library for AI model development in drug discovery Peter St. John et al, arxiv, 11/2024
  • 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

Science Journals

  • Structure-based Drug Design with Equivariant Diffusion Models Arne Schneuing*, Yuanqi Du*, Charles Harris*, Kieran Didi, Arian Jamasb, Ilia Igashov, weitao Du, Tom Blundell, Pietro Liò, Carla Gomes, Max Welling, Michael Bronstein, Bruno Correia, Nature Computational Science, 12/2024
  • MISATO: machine learning dataset of protein–ligand complexes for structure-based drug discovery Till Siebenmorgen*, Filipe Menezes*, Sabrina Benassou, Erinc Merdivan, Kieran Didi, André Santos Dias Mourão, Radosław Kitel, Pietro Liò, Stefan Kesselheim, Marie Piraud, Fabian J. Theis, Michael Sattler & Grzegorz M. Popowicz, Nature Computational Science, 05/2024
  • Synsor: a tool for alignment-free detection of engineered DNA sequences Aidan P Tay, Kieran Didi, Anuradha Wickramarachchi, Denis Bauer, Laurence Wilson and Maciej Maselko, Frontiers in Bioengineering and Biotechnology, 04/2024
  • AbNatiV: VQ-VAE-based assessment of antibody and nanobody nativeness for hit selection, humanisation, and engineering Aubin Ramon, Montader Ali, Misha Atkinson, Alessio Saturnino, Kieran Didi, Cristina Visentin, Stefano Ricagno, Xing Xu, Matthew Greenig, Pietro Sormanni, Nature Machine Intelligence, 04/2023
  • 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

ML Conferences (Main Track)

ML Conferences (Workshop Track)

Book Chapters

  • Generative Models in Bioinformatics, Mitchell J O’Brien, Letitia MF Sng, Priya Ramarao-Milne, Kieran Didi, Denis C Bauer, Encyclopedia of Bioinformatics and Computational Biology, 01/2023

Conference Presentations

Reviewing

ICML CompBio 2023, NeurIPS AI4Science 2023, NeurIPS GenBio 2023, MoML@MIT 2023, ICLR GEM 2024

Teaching