Editorial. - Mikael Bodén; Lars Niklasson (Artif. Intell. Rev., 1993)

A Connectionist Variation of Inheritance. - Mikael Bodén (ICANN, 1996)

Context-sensitive connectionist representations for nonmonotonic inheritance. - Mikael Bodén (1997)

Evolving context-free language predictors. - Mikael Bodén; Henrik Jacobsson; Tom Ziemke (GECCO, 2000)

Semantic systematicity and context in connectionist networks. - Mikael Bodén; Lars Niklasson (Connect. Sci., 2000)

Context-free and context-sensitive dynamics in recurrent neural networks. - Mikael Bodén; Janet Wiles (Connect. Sci., 2000)

Generalization by structural properties from sparse nested symbolic data. - Mikael Bodén (ESANN, 2002)

On learning context-free and context-sensitive languages. - Mikael Bodén; Janet Wiles (IEEE Trans. Neural Networks, 2002)

Using evolutionary noise to improve prediction of rapidly evolving targeting peptides. - Mikael Bodén (IEEE Congress on Evolutionary Computation, 2003)

Learning the Dynamics of Embedded Clauses. - Mikael Bodén; Alan D. Blair (Appl. Intell., 2003)

Generalization by symbolic abstraction in cascaded recurrent networks. - Mikael Bodén (Neurocomputing, 2004)

Detecting residues in targeting peptides. - Mikael Bodén; John Hawkins (APBC, 2005)

BLOMAP: An encoding of amino acids which improves signal peptide cleavage site prediction. - Stefan Maetschke; Michael Towsey; Mikael Bodén (APBC, 2005)

Predicting Structural Disruption of Proteins Caused by Crossover (based on Amino Acid Sequence). - Denis C. Bauer; Mikael Bodén; Ricarda Thier; Zheng Yuan (CIBCB, 2005)

Predicting Peroxisomal Proteins. - John Hawkins; Mikael Bodén (CIBCB, 2005)

Heuristic Algorithm for Computing Reversal Distance with MultiGene Families via Binary Integer Programming. - Jakkarin Suksawatchon; Chidchanok Lursinsap; Mikael Bodén (CIBCB, 2005)

Exploiting Sequence Dependencies in the Prediction of Peroxisomal Proteins. - Mark Wakabayashi; John Hawkins; Stefan Maetschke; Mikael Bodén (IDEAL, 2005)

Prediction of subcellular localization using sequence-biased recurrent networks. - Mikael Bodén; John Hawkins (Bioinform., 2005)

The Applicability of Recurrent Neural Networks for Biological Sequence Analysis. - John Hawkins; Mikael Bodén (IEEE ACM Trans. Comput. Biol. Bioinform., 2005)

Improved access to sequential motifs: a note on the architectural bias of recurrent networks. - Mikael Bodén; John Hawkins (IEEE Trans. Neural Networks, 2005)

Evolving discriminative motifs for recognizing proteins imported to the peroxisome via the PTS2 pathway. - Mikael Bodén; John Hawkins (IEEE Congress on Evolutionary Computation, 2006)

Identifying sequence regions undergoing conformational change via predicted continuum secondary structure. - Mikael Bodén; Timothy L. Bailey (Bioinform., 2006)

STAR: predicting recombination sites from amino acid sequence. - Denis C. Bauer; Mikael Bodén; Ricarda Thier; Elizabeth M. J. Gillam (BMC Bioinform., 2006)

Prediction of protein continuum secondary structure with probabilistic models based on NMR solved structures. - Mikael Bodén; Zheng Yuan; Timothy L. Bailey (BMC Bioinform., 2006)

A Comparison of Sequence Kernels for Localization Prediction of Transmembrane Proteins. - Stefan Maetschke; Marcus Gallagher; Mikael Bodén (CIBCB, 2007)

Understanding Prediction Systems for HLA-Binding Peptides and T-Cell Epitope Identification. - Liwen You; Ping Zhang 008; Mikael Bodén; Vladimir Brusic (PRIB, 2007)

Evolving spelling exercises to suit individual student needs. - Marie Boden; Mikael Bodén (Appl. Soft Comput., 2007)

Computing the Reversal Distance between genomes in the Presence of Multi-gene Families via Binary Integer Programming. - Jakkarin Suksawatchon; Chidchanok Lursinsap; Mikael Bodén (J. Bioinform. Comput. Biol., 2007)

Markovian Bias of Neural-based Architectures With Feedback Connections. - Peter Tiño; Barbara Hammer; Mikael Bodén (Perspectives of Neural-Symbolic Integration, 2007)

Predicting Nucleolar Proteins Using Support-Vector Machines. - Mikael Bodén (APBC, 2008)

Predicting SUMOylation Sites. - Denis C. Bauer; Fabian A. Buske; Mikael Bodén (PRIB, 2008)

Determining Nucleolar Association from Sequence by Leveraging Protein-Protein Interactions. - Mikael Bodén; Rohan D. Teasdale (J. Comput. Biol., 2008)

Detecting sequence and structure homology via an integrative kernel: A case-study in recognizing enzymes. - Isye Arieshanti; Mikael Bodén; Stefan Maetschke; Fabian A. Buske (CIBCB, 2009)

MEME SUITE: tools for motif discovery and searching. - Timothy L. Bailey; Mikael Bodén; Fabian A. Buske; Martin C. Frith; Charles E. Grant; Luca Clementi; Jingyuan Ren; Wilfred W. Li; William Stafford Noble (Nucleic Acids Res., 2009)

It's about time: Signal recognition in staged models of protein translocation. - Fabian A. Buske; Stefan Maetschke; Mikael Bodén (Pattern Recognit., 2009)

Multilinear Decomposition and Topographic Mapping of Binary Tensors. - Jakub Mazgut; Peter Tiño; Mikael Bodén; Hong Yan 001 (ICANN (1), 2010)

Assigning roles to DNA regulatory motifs using comparative genomics. - Fabian A. Buske; Mikael Bodén; Denis C. Bauer; Timothy L. Bailey (Bioinform., 2010)

The value of position-specific priors in motif discovery using MEME. - Timothy L. Bailey; Mikael Bodén; Tom Whitington; Philip Machanick (BMC Bioinform., 2010)

The proteins of intra-nuclear bodies: a data-driven analysis of sequence, interaction and expression. - Nurul Mohamad; Mikael Bodén (BMC Syst. Biol., 2010)

Predicting SUMOylation sites in developmental transcription factors of Drosophila melanogaster. - Denis C. Bauer; Fabian A. Buske; Timothy L. Bailey; Mikael Bodén (Neurocomputing, 2010)

A Bayesian Network Model of Proteins' Association with Promyelocytic Leukemia (PML) Nuclear Bodies. - Mikael Bodén; Graham Dellaire; Kevin Burrage; Timothy L. Bailey (J. Comput. Biol., 2010)

Using Gaussian Process with Test Rejection to Detect T-Cell Epitopes in Pathogen Genomes. - Liwen You; Vladimir Brusic; Marcus Gallagher; Mikael Bodén (IEEE ACM Trans. Comput. Biol. Bioinform., 2010)

Sorting the nuclear proteome. - Denis C. Bauer; Kai Willadsen; Fabian A. Buske; Kim-Anh Lê Cao; Timothy L. Bailey; Graham Dellaire; Mikael Bodén (Bioinform., 2011)

A probabilistic model of nuclear import of proteins. - Ahmed M. Mehdi; Muhammad Shoaib B. Sehgal; Bostjan Kobe; Timothy L. Bailey; Mikael Bodén (Bioinform., 2011)

Mapping the stabilome: a novel computational method for classifying metabolic protein stability. - Ralph Patrick; Kim-Anh Lê Cao; Melissa J. Davis; Bostjan Kobe; Mikael Bodén (BMC Syst. Biol., 2012)

NSort/DB: An Intranuclear Compartment Protein Database. - Kai Willadsen; Nurul Mohamad; Mikael Bodén (Genom. Proteom. Bioinform., 2012)

Matching Cavities in G Protein-Coupled Receptors to Infer Ligand-Binding Sites. - Praveen K. Madala; David P. Fairlie; Mikael Bodén (J. Chem. Inf. Model., 2012)

DLocalMotif: a discriminative approach for discovering local motifs in protein sequences. - Ahmed M. Mehdi; Muhammad Shoaib B. Sehgal; Bostjan Kobe; Timothy L. Bailey; Mikael Bodén (Bioinform., 2013)

PREDIVAC: CD4+ T-cell epitope prediction for vaccine design that covers 95% of HLA class II DR protein diversity. - Patricio Oyarzún; Jonathan J. Ellis; Mikael Bodén; Bostjan Kobe (BMC Bioinform., 2013)

Dimensionality reduction and topographic mapping of binary tensors. - Jakub Mazgut; Peter Tiño; Mikael Bodén; Hong Yan 001 (Pattern Anal. Appl., 2014)

Sequencing technologies and tools for short tandem repeat variation detection. - Minh Duc Cao; Sureshkumar Balasubramanian; Mikael Bodén (Briefings Bioinform., 2015)

PhosphoPICK: modelling cellular context to map kinase-substrate phosphorylation events. - Ralph Patrick; Kim-Anh Lê Cao; Bostjan Kobe; Mikael Bodén (Bioinform., 2015)

PhosphoPICK-SNP: quantifying the effect of amino acid variants on protein phosphorylation. - Ralph Patrick; Bostjan Kobe; Kim-Anh Lê Cao; Mikael Bodén (Bioinform., 2017)

Learning epistatic interactions from sequence-activity data to predict enantioselectivity. - Julian Zaugg; Yosephine Gumulya; Alpeshkumar K. Malde; Mikael Bodén (J. Comput. Aided Mol. Des., 2017)

SCRAM: a pipeline for fast index-free small RNA read alignment and visualization. - Stephen J. Fletcher; Mikael Bodén; Neena Mitter; Bernard J. Carroll (Bioinform., 2018)

Effect of Binding on Enantioselectivity of Epoxide Hydrolase. - Julian Zaugg; Yosephine Gumulya; Mikael Bodén; Alan E. Mark; Alpeshkumar K. Malde (J. Chem. Inf. Model., 2018)

NLSdb - major update for database of nuclear localization signals and nuclear export signals. - Michael Bernhofer; Tatyana Goldberg; Silvana Wolf; Mohamed Ahmed; Julian Zaugg; Mikael Bodén; Burkhard Rost (Nucleic Acids Res., 2018)

Detailed prediction of protein sub-nuclear localization. - Maria Littmann; Tatyana Goldberg; Sebastian Seitz; Mikael Bodén; Burkhard Rost (BMC Bioinform., 2019)

Correction to: Detailed prediction of protein sub-nuclear localization. - Maria Littmann; Tatyana Goldberg; Sebastian Seitz; Mikael Bodén; Burkhard Rost (BMC Bioinform., 2019)

T-Gene: improved target gene prediction. - Timothy O'Connor; Charles E. Grant; Mikael Bodén; Timothy L. Bailey (Bioinform., 2020)

Engineering indel and substitution variants of diverse and ancient enzymes using Graphical Representation of Ancestral Sequence Predictions (GRASP). - Gabriel Foley; Ariane Mora; Connie M. Ross; Scott Bottoms; Leander Sützl; Marnie L. Lamprecht; Julian Zaugg; Alexandra Essebier; Brad Balderson; Rhys Newell; Raine E. S. Thomson; Bostjan Kobe; et al. (PLoS Comput. Biol., 2022)

Do protein language models learn phylogeny? - Sanjana Tule; Gabriel Foley; Mikael Bodén (Briefings Bioinform., 2024)

TRIAGE: an R package for regulatory gene analysis. - Qiongyi Zhao; Woo Jun Shim; Yuliangzi Sun; Enakshi Sinniah; Sophie Shen; Mikael Bodén; Nathan J. Palpant (Briefings Bioinform., 2024)

Optimal phylogenetic reconstruction of insertion and deletion events. - Sanjana Tule; Gabriel Foley; Chongting Zhao; Michael Forbes; Mikael Bodén (Bioinform., 2024)