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Cell Systems|November 18, 2025
Learning the language of phylogeny with MSA TransformerRuyi Chen, Gabriel Foley, Mikael BodénBriefings in Bioinformatics|February 23, 2025
Do protein language models learn phylogeny?Sanjana Tule, Gabriel Foley, Mikael BodénBioinformatics (Oxford, England)|June 28, 2024
Optimal phylogenetic reconstruction of insertion and deletion eventsSanjana Tule, Gabriel Foley, Chongting Zhao, et al.Biotechniques|June 21, 2019
SeqScrub: a web tool for automatic cleaning and annotation of FASTA file headers for bioinformatic applicationsGabriel Foley, Leander Sützl, Stephlina A D'Cunha, et al.Biotechnology for Biofuels|June 7, 2019
The GMC superfamily of oxidoreductases revisited: analysis and evolution of fungal GMC oxidoreductasesLeander Sützl, Gabriel Foley, Elizabeth M J Gillam, et al.Journal of Bioinformatics and Computational Biology|March 29, 2006
Detecting and sorting targeting peptides with neural networks and support vector machinesJohn Hawkins, Mikael BodénIEEE Transactions on Neural Networks|March 25, 2005
Improved access to sequential motifs: a note on the architectural bias of recurrent networksMikael Bodén, John HawkinsBioinformatics (Oxford, England)|March 5, 2005
Prediction of subcellular localization using sequence-biased recurrent networksMikael Bodén, John HawkinsIEEE/ACM Transactions on Computational Biology and Bioinformatics|October 19, 2006
The applicability of recurrent neural networks for biological sequence analysisJohn Hawkins, Mikael BodénBMC Systems Biology|April 15, 2010
The proteins of intra-nuclear bodies: a data-driven analysis of sequence, interaction and expressionNurul Mohamad, Mikael BodénPageof 15