List of works - Mikael Bodén

A Bayesian network model of proteins' association with promyelocytic leukemia (PML) nuclear bodies

scientific article published in April 2010

A bioinformatics tool for epitope-based vaccine design that accounts for human ethnic diversity: application to emerging infectious diseases

scientific article published on 25 January 2015

A probabilistic model of nuclear import of proteins

scientific article

Bioinformatics approaches to predict target genes from transcription factor binding data

scientific article published on 7 September 2017

Cell-type-specific expression of NFIX in the developing and adult cerebellum

scientific article published on 23 November 2016

Common Regulatory Targets of NFIA, NFIX and NFIB during Postnatal Cerebellar Development

scientific article published on 01 February 2020

Computational Modelling of Linear Motif-Mediated Protein Interactions ⬇️

scientific article published on January 1, 2012

Computational tools for directed evolution: a comparison of prospective and retrospective strategies.

scientific article

Computing the reversal distance between genomes in the presence of multi-gene families via binary integer programming

scientific article published in February 2007

Correction to: Detailed prediction of protein sub-nuclear localization

scientific article published on 20 December 2019

Crystal Structure of Rice Importin- and Structural Basis of Its Interaction with Plant-Specific Nuclear Localization Signals

scientific article

DLocalMotif: a discriminative approach for discovering local motifs in protein sequences

scientific article published on 9 November 2012

Detailed prediction of protein sub-nuclear localization

scientific article published on 23 April 2019

Detecting and sorting targeting peptides with neural networks and support vector machines

scientific article published in February 2006

Determining nucleolar association from sequence by leveraging protein-protein interactions

scientific article

Distinctive Conformation of Minor Site-Specific Nuclear Localization Signals Bound to Importin-α

Distinctive conformation of minor site-specific nuclear localization signals bound to importin-α

scientific article

Dynamics of re-constitution of the human nuclear proteome after cell division is regulated by NLS-adjacent phosphorylation

scientific article published on January 2014

Engineering indel and substitution variants of diverse and ancient enzymes using Graphical Representation of Ancestral Sequence Predictions (GRASP)

Engineering thermostable CYP2D enzymes for biocatalysis using combinatorial libraries of ancestors for directed evolution (CLADE)

Evolutionary model of protein secondary structure capable of revealing new biological relationships

scientific article published on 11 May 2020

Granule neuron precursor cell proliferation is regulated by NFIX and intersectin 1 during postnatal cerebellar development

scientific article published on 03 December 2018

Identifying novel peroxisomal proteins

scientific article

Identifying sequence regions undergoing conformational change via predicted continuum secondary structure

scientific article published on 23 May 2006

Improved access to sequential motifs: a note on the architectural bias of recurrent networks.

scientific article

In silico characterization of protein chimeras: relating sequence and function within the same fold.

scientific article

Inferring short tandem repeat variation from paired-end short reads

scientific article published on 17 December 2013

Learning epistatic interactions from sequence-activity data to predict enantioselectivity.

scientific article published on 12 December 2017

MEME SUITE: tools for motif discovery and searching

scientific article (publication date: July 2009)

Matching cavities in g protein-coupled receptors to infer ligand-binding sites

scientific article published on 30 April 2012

Molecular basis for specificity of nuclear import and prediction of nuclear localization

scientific article

NAD+ cleavage activity by animal and plant TIR domains in cell death pathways

scientific article published on 01 August 2019

NLSdb-major update for database of nuclear localization signals and nuclear export signals

scientific article published on 2 November 2017

NSort/DB: an intranuclear compartment protein database.

scientific article published on 25 July 2012

On learning context-free and context-sensitive languages

scientific article published in January 2002

PREDIVAC: CD4+ T-cell epitope prediction for vaccine design that covers 95% of HLA class II DR protein diversity

scientific article

PhosphoPICK-SNP: quantifying the effect of amino acid variants on protein phosphorylation

scientific article

PhosphoPICK: modelling cellular context to map kinase-substrate phosphorylation events

scientific article published on 9 October 2014

Predicting SUMOylation sites in developmental transcription factors of Drosophila melanogaster

Predicting nuclear localization

scientific article published on 24 February 2007

Predicting the dynamics of protein abundance

scientific article

Predicting the solvent accessibility of transmembrane residues from protein sequence

scientific article

Prediction of subcellular localization using sequence-biased recurrent networks

scientific article published on 3 March 2005

ReX: A suite of computational tools for the design, visualization, and analysis of chimeric protein libraries.

scientific article

Repeat-encoded poly-Q tracts show statistical commonalities across species.

scientific article

Robust Estimation of Evolutionary Distances with Information Theory.

scientific article

SCRAM: a pipeline for fast index-free small RNA read alignment and visualization.

scientific article published on 15 March 2018

STAR: predicting recombination sites from amino acid sequence

scientific article

SeqScrub: a web tool for automatic cleaning and annotation of FASTA file headers for bioinformatic applications

scientific article published on 20 June 2019

Sequencing technologies and tools for short tandem repeat variation detection.

scientific article published on 06 February 2014

Sorting the nuclear proteome

scientific article published on July 2011

Statistical Enrichment of Epigenetic States Around Triplet Repeats that Can Undergo Expansions

scientific article published on 8 March 2016

Structure and Function of the TIR Domain from the Grape NLR Protein RPV1.

scientific article published on 08 December 2016

The Effect of Binding on the Enantioselectivity of an Epoxide Hydrolase

scientific article published on 9 February 2018

The GMC superfamily of oxidoreductases revisited: analysis and evolution of fungal GMC oxidoreductases

scientific article published on 10 May 2019

The applicability of recurrent neural networks for biological sequence analysis.

scientific article

The distribution of different classes of nuclear localization signals (NLSs) in diverse organisms and the utilization of the minor NLS-binding site inplantnuclear import factor importin-α.

scientific article

The proteins of intra-nuclear bodies: a data-driven analysis of sequence, interaction and expression

scientific article

The value of position-specific priors in motif discovery using MEME.

scientific article

Using Gaussian process with test rejection to detect T-cell epitopes in pathogen genomes.

scientific article published in October 2010

Variational autoencoding of gene landscapes during mouse CNS development uncovers layered roles of Polycomb Repressor Complex 2

scientific article published on 06 January 2022

List of works by Mikael Bodén

A Bayesian network model of proteins' association with promyelocytic leukemia (PML) nuclear bodies

A bioinformatics tool for epitope-based vaccine design that accounts for human ethnic diversity: application to emerging infectious diseases

A probabilistic model of nuclear import of proteins

Bioinformatics approaches to predict target genes from transcription factor binding data

Cell-type-specific expression of NFIX in the developing and adult cerebellum

Common Regulatory Targets of NFIA, NFIX and NFIB during Postnatal Cerebellar Development

Computational Modelling of Linear Motif-Mediated Protein Interactions ⬇️

Computational tools for directed evolution: a comparison of prospective and retrospective strategies.

Computing the reversal distance between genomes in the presence of multi-gene families via binary integer programming

Correction to: Detailed prediction of protein sub-nuclear localization

Crystal Structure of Rice Importin- and Structural Basis of Its Interaction with Plant-Specific Nuclear Localization Signals

DLocalMotif: a discriminative approach for discovering local motifs in protein sequences

Detailed prediction of protein sub-nuclear localization

Detecting and sorting targeting peptides with neural networks and support vector machines

Determining nucleolar association from sequence by leveraging protein-protein interactions

Distinctive Conformation of Minor Site-Specific Nuclear Localization Signals Bound to Importin-α

Distinctive conformation of minor site-specific nuclear localization signals bound to importin-α

Dynamics of re-constitution of the human nuclear proteome after cell division is regulated by NLS-adjacent phosphorylation

Engineering indel and substitution variants of diverse and ancient enzymes using Graphical Representation of Ancestral Sequence Predictions (GRASP)

Engineering thermostable CYP2D enzymes for biocatalysis using combinatorial libraries of ancestors for directed evolution (CLADE)

Evolutionary model of protein secondary structure capable of revealing new biological relationships

Granule neuron precursor cell proliferation is regulated by NFIX and intersectin 1 during postnatal cerebellar development

Identifying novel peroxisomal proteins

Identifying sequence regions undergoing conformational change via predicted continuum secondary structure

Improved access to sequential motifs: a note on the architectural bias of recurrent networks.

In silico characterization of protein chimeras: relating sequence and function within the same fold.

Inferring short tandem repeat variation from paired-end short reads

Learning epistatic interactions from sequence-activity data to predict enantioselectivity.

MEME SUITE: tools for motif discovery and searching

Matching cavities in g protein-coupled receptors to infer ligand-binding sites

Molecular basis for specificity of nuclear import and prediction of nuclear localization

NAD+ cleavage activity by animal and plant TIR domains in cell death pathways

NLSdb-major update for database of nuclear localization signals and nuclear export signals

NSort/DB: an intranuclear compartment protein database.

On learning context-free and context-sensitive languages

PREDIVAC: CD4+ T-cell epitope prediction for vaccine design that covers 95% of HLA class II DR protein diversity

PhosphoPICK-SNP: quantifying the effect of amino acid variants on protein phosphorylation

PhosphoPICK: modelling cellular context to map kinase-substrate phosphorylation events

Predicting SUMOylation sites in developmental transcription factors of Drosophila melanogaster

Predicting nuclear localization

Predicting the dynamics of protein abundance

Predicting the solvent accessibility of transmembrane residues from protein sequence

Prediction of subcellular localization using sequence-biased recurrent networks

ReX: A suite of computational tools for the design, visualization, and analysis of chimeric protein libraries.

Repeat-encoded poly-Q tracts show statistical commonalities across species.

Robust Estimation of Evolutionary Distances with Information Theory.

SCRAM: a pipeline for fast index-free small RNA read alignment and visualization.

STAR: predicting recombination sites from amino acid sequence

SeqScrub: a web tool for automatic cleaning and annotation of FASTA file headers for bioinformatic applications

Sequencing technologies and tools for short tandem repeat variation detection.

Sorting the nuclear proteome

Statistical Enrichment of Epigenetic States Around Triplet Repeats that Can Undergo Expansions

Structure and Function of the TIR Domain from the Grape NLR Protein RPV1.

The Effect of Binding on the Enantioselectivity of an Epoxide Hydrolase

The GMC superfamily of oxidoreductases revisited: analysis and evolution of fungal GMC oxidoreductases

The applicability of recurrent neural networks for biological sequence analysis.

The distribution of different classes of nuclear localization signals (NLSs) in diverse organisms and the utilization of the minor NLS-binding site inplantnuclear import factor importin-α.

The proteins of intra-nuclear bodies: a data-driven analysis of sequence, interaction and expression

The value of position-specific priors in motif discovery using MEME.

Using Gaussian process with test rejection to detect T-cell epitopes in pathogen genomes.

Variational autoencoding of gene landscapes during mouse CNS development uncovers layered roles of Polycomb Repressor Complex 2