Expanding molecular modeling and design tools to non-natural sidechains. - David Gfeller; Olivier Michielin; Vincent Zoete (J. Comput. Chem., 2012)

Beyond the Binding Site: The Role of the β2 - β3 Loop and Extra-Domain Structures in PDZ Domains. - Stefano Mostarda; David Gfeller; Francesco Rao (PLoS Comput. Biol., 2012)

Shaping the interaction landscape of bioactive molecules. - David Gfeller; Olivier Michielin; Vincent Zoete (Bioinform., 2013)

SwissSidechain: a molecular and structural database of non-natural sidechains. - David Gfeller; Olivier Michielin; Vincent Zoete (Nucleic Acids Res., 2013)

SwissTargetPrediction: a web server for target prediction of bioactive small molecules. - David Gfeller; Aurélien Grosdidier; Matthias Wirth; Antoine Daina; Olivier Michielin; Vincent Zoete (Nucleic Acids Res., 2014)

Protein homology reveals new targets for bioactive small molecules. - David Gfeller; Vincent Zoete (Bioinform., 2015)

Deciphering HLA-I motifs across HLA peptidomes improves neo-antigen predictions and identifies allostery regulating HLA specificity. - Michal Bassani-Sternberg; Chloé Chong; Philippe Guillaume; Marthe Solleder; HuiSong Pak; Philippe O. Gannon; Lana E. Kandalaft; George Coukos; David Gfeller (PLoS Comput. Biol., 2017)

Polymorphic sites preferentially avoid co-evolving residues in MHC class I proteins. - Linda Dib; Nicolas Salamin; David Gfeller (PLoS Comput. Biol., 2018)

Computational KIR copy number discovery reveals interaction between inhibitory receptor burden and survival. - Rachel M. Pyke; Raphael Genolet; Alexandre Harari; George Coukos; David Gfeller; Hannah Carter (PSB, 2019)

Metacells untangle large and complex single-cell transcriptome networks. - Mariia Bilous; Loc Tran; Chiara Cianciaruso; Aurélie Gabriel; Hugo Michel; Santiago J. Carmona; Mikael J. Pittet; David Gfeller (BMC Bioinform., 2022)

The MHC Motif Atlas: a database of MHC binding specificities and ligands. - Daniel M. Tadros; Simon Eggenschwiler; Julien Racle; David Gfeller (Nucleic Acids Res., 2023)