Mikael Bodén - RankMe

64 papers A 1B 6C 7Journal 45Unranked 3

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Do protein language models learn phylogeny? Briefings Bioinform. Sanjana Tule, Gabriel Foley, Mikael Bodén
2025	J	`jnl`	TRIAGE: an R package for regulatory gene analysis. Briefings Bioinform. Qiongyi Zhao, Woo Jun Shim, Yuliangzi Sun, Enakshi Sinniah, Sophie Shen, Mikael Bodén, Nathan J. Palpant
2024	J	`jnl`	Optimal phylogenetic reconstruction of insertion and deletion events. Bioinform. Sanjana Tule, Gabriel Foley, Chongting Zhao, Michael Forbes, Mikael Bodén
2022	J	`jnl`	Engineering indel and substitution variants of diverse and ancient enzymes using Graphical Representation of Ancestral Sequence Predictions (GRASP). PLoS Comput. Biol. 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, Ross T. Barnard, Luke Guddat, Gerhard Schenk, Jörg Carsten, Yosephine Gumulya, Burkhard Rost, Dietmar Haltrich, Volker Sieber, Elizabeth M. J. Gillam, Mikael Bodén
2020	J	`jnl`	T-Gene: improved target gene prediction. Bioinform. Timothy O'Connor, Charles E. Grant, Mikael Bodén, Timothy L. Bailey
2019	J	`jnl`	Correction to: Detailed prediction of protein sub-nuclear localization. BMC Bioinform. Maria Littmann, Tatyana Goldberg, Sebastian Seitz, Mikael Bodén, Burkhard Rost
2019	J	`jnl`	Detailed prediction of protein sub-nuclear localization. BMC Bioinform. Maria Littmann, Tatyana Goldberg, Sebastian Seitz, Mikael Bodén, Burkhard Rost
2018	J	`jnl`	Effect of Binding on Enantioselectivity of Epoxide Hydrolase. J. Chem. Inf. Model. Julian Zaugg, Yosephine Gumulya, Mikael Bodén, Alan E. Mark, Alpeshkumar K. Malde
2018	J	`jnl`	NLSdb - major update for database of nuclear localization signals and nuclear export signals. Nucleic Acids Res. Michael Bernhofer, Tatyana Goldberg, Silvana Wolf, Mohamed Ahmed, Julian Zaugg, Mikael Bodén, Burkhard Rost
2018	J	`jnl`	SCRAM: a pipeline for fast index-free small RNA read alignment and visualization. Bioinform. Stephen J. Fletcher, Mikael Bodén, Neena Mitter, Bernard J. Carroll
2017	J	`jnl`	Learning epistatic interactions from sequence-activity data to predict enantioselectivity. J. Comput. Aided Mol. Des. Julian Zaugg, Yosephine Gumulya, Alpeshkumar K. Malde, Mikael Bodén
2017	J	`jnl`	PhosphoPICK-SNP: quantifying the effect of amino acid variants on protein phosphorylation. Bioinform. Ralph Patrick, Bostjan Kobe, Kim-Anh Lê Cao, Mikael Bodén
2015	J	`jnl`	PhosphoPICK: modelling cellular context to map kinase-substrate phosphorylation events. Bioinform. Ralph Patrick, Kim-Anh Lê Cao, Bostjan Kobe, Mikael Bodén
2015	J	`jnl`	Sequencing technologies and tools for short tandem repeat variation detection. Briefings Bioinform. Minh Duc Cao, Sureshkumar Balasubramanian, Mikael Bodén
2014	J	`jnl`	Dimensionality reduction and topographic mapping of binary tensors. Pattern Anal. Appl. Jakub Mazgut, Peter Tiño, Mikael Bodén, Hong Yan
2013	J	`jnl`	DLocalMotif: a discriminative approach for discovering local motifs in protein sequences. Bioinform. Ahmed M. Mehdi, Muhammad Shoaib B. Sehgal, Bostjan Kobe, Timothy L. Bailey, Mikael Bodén
2013	J	`jnl`	PREDIVAC: CD4+ T-cell epitope prediction for vaccine design that covers 95% of HLA class II DR protein diversity. BMC Bioinform. Patricio Oyarzún, Jonathan J. Ellis, Mikael Bodén, Bostjan Kobe
2012	J	`jnl`	Mapping the stabilome: a novel computational method for classifying metabolic protein stability. BMC Syst. Biol. Ralph Patrick, Kim-Anh Lê Cao, Melissa J. Davis, Bostjan Kobe, Mikael Bodén
2012	J	`jnl`	Matching Cavities in G Protein-Coupled Receptors to Infer Ligand-Binding Sites. J. Chem. Inf. Model. Praveen K. Madala, David P. Fairlie, Mikael Bodén
2012	J	`jnl`	NSort/DB: An Intranuclear Compartment Protein Database. Genom. Proteom. Bioinform. Kai Willadsen, Nurul Mohamad, Mikael Bodén
2011	J	`jnl`	A probabilistic model of nuclear import of proteins. Bioinform. Ahmed M. Mehdi, Muhammad Shoaib B. Sehgal, Bostjan Kobe, Timothy L. Bailey, Mikael Bodén
2011	J	`jnl`	Sorting the nuclear proteome. Bioinform. Denis C. Bauer, Kai Willadsen, Fabian A. Buske, Kim-Anh Lê Cao, Timothy L. Bailey, Graham Dellaire, Mikael Bodén
2010	J	`jnl`	A Bayesian Network Model of Proteins' Association with Promyelocytic Leukemia (PML) Nuclear Bodies. J. Comput. Biol. Mikael Bodén, Graham Dellaire, Kevin Burrage, Timothy L. Bailey
2010	J	`jnl`	Assigning roles to DNA regulatory motifs using comparative genomics. Bioinform. Fabian A. Buske, Mikael Bodén, Denis C. Bauer, Timothy L. Bailey
2010	—	`conf`	Multilinear Decomposition and Topographic Mapping of Binary Tensors. ICANN (1) Jakub Mazgut, Peter Tiño, Mikael Bodén, Hong Yan
2010	J	`jnl`	Predicting SUMOylation sites in developmental transcription factors of Drosophila melanogaster. Neurocomputing Denis C. Bauer, Fabian A. Buske, Timothy L. Bailey, Mikael Bodén
2010	J	`jnl`	The proteins of intra-nuclear bodies: a data-driven analysis of sequence, interaction and expression. BMC Syst. Biol. Nurul Mohamad, Mikael Bodén
2010	J	`jnl`	The value of position-specific priors in motif discovery using MEME. BMC Bioinform. Timothy L. Bailey, Mikael Bodén, Tom Whitington, Philip Machanick
2010	J	`jnl`	Using Gaussian Process with Test Rejection to Detect T-Cell Epitopes in Pathogen Genomes. IEEE ACM Trans. Comput. Biol. Bioinform. Liwen You, Vladimir Brusic, Marcus Gallagher, Mikael Bodén
2009	C	`conf`	Detecting sequence and structure homology via an integrative kernel: A case-study in recognizing enzymes. CIBCB Isye Arieshanti, Mikael Bodén, Stefan Maetschke, Fabian A. Buske
2009	J	`jnl`	It's about time: Signal recognition in staged models of protein translocation. Pattern Recognit. Fabian A. Buske, Stefan Maetschke, Mikael Bodén
2009	J	`jnl`	MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. Timothy L. Bailey, Mikael Bodén, Fabian A. Buske, Martin C. Frith, Charles E. Grant, Luca Clementi, Jingyuan Ren, Wilfred W. Li, William Stafford Noble
2008	J	`jnl`	Determining Nucleolar Association from Sequence by Leveraging Protein-Protein Interactions. J. Comput. Biol. Mikael Bodén, Rohan D. Teasdale
2008	B	`conf`	Predicting Nucleolar Proteins Using Support-Vector Machines. APBC Mikael Bodén
2008	—	`conf`	Predicting SUMOylation Sites. PRIB Denis C. Bauer, Fabian A. Buske, Mikael Bodén
2007	C	`conf`	A Comparison of Sequence Kernels for Localization Prediction of Transmembrane Proteins. CIBCB Stefan Maetschke, Marcus Gallagher, Mikael Bodén
2007	J	`jnl`	Computing the Reversal Distance between genomes in the Presence of Multi-gene Families via Binary Integer Programming. J. Bioinform. Comput. Biol. Jakkarin Suksawatchon, Chidchanok Lursinsap, Mikael Bodén
2007	J	`jnl`	Evolving spelling exercises to suit individual student needs. Appl. Soft Comput. Marie Boden, Mikael Bodén
2007	—	`ch.`	Markovian Bias of Neural-based Architectures With Feedback Connections. Perspectives of Neural-Symbolic Integration Peter Tiño, Barbara Hammer, Mikael Bodén
2007	—	`conf`	Understanding Prediction Systems for HLA-Binding Peptides and T-Cell Epitope Identification. PRIB Liwen You, Ping Zhang, Mikael Bodén, Vladimir Brusic
2006	B	`conf`	Evolving discriminative motifs for recognizing proteins imported to the peroxisome via the PTS2 pathway. IEEE Congress on Evolutionary Computation Mikael Bodén, John Hawkins
2006	J	`jnl`	Identifying sequence regions undergoing conformational change via predicted continuum secondary structure. Bioinform. Mikael Bodén, Timothy L. Bailey
2006	J	`jnl`	Prediction of protein continuum secondary structure with probabilistic models based on NMR solved structures. BMC Bioinform. Mikael Bodén, Zheng Yuan, Timothy L. Bailey
2006	J	`jnl`	STAR: predicting recombination sites from amino acid sequence. BMC Bioinform. Denis C. Bauer, Mikael Bodén, Ricarda Thier, Elizabeth M. J. Gillam
2005	B	`conf`	BLOMAP: An encoding of amino acids which improves signal peptide cleavage site prediction. APBC Stefan Maetschke, Michael Towsey, Mikael Bodén
2005	B	`conf`	Detecting residues in targeting peptides. APBC Mikael Bodén, John Hawkins
2005	C	`conf`	Exploiting Sequence Dependencies in the Prediction of Peroxisomal Proteins. IDEAL Mark Wakabayashi, John Hawkins, Stefan Maetschke, Mikael Bodén
2005	C	`conf`	Heuristic Algorithm for Computing Reversal Distance with MultiGene Families via Binary Integer Programming. CIBCB Jakkarin Suksawatchon, Chidchanok Lursinsap, Mikael Bodén
2005	J	`jnl`	Improved access to sequential motifs: a note on the architectural bias of recurrent networks. IEEE Trans. Neural Networks Mikael Bodén, John Hawkins
2005	C	`conf`	Predicting Peroxisomal Proteins. CIBCB John Hawkins, Mikael Bodén
2005	C	`conf`	Predicting Structural Disruption of Proteins Caused by Crossover (based on Amino Acid Sequence). CIBCB Denis C. Bauer, Mikael Bodén, Ricarda Thier, Zheng Yuan
2005	J	`jnl`	Prediction of subcellular localization using sequence-biased recurrent networks. Bioinform. Mikael Bodén, John Hawkins
2005	J	`jnl`	The Applicability of Recurrent Neural Networks for Biological Sequence Analysis. IEEE ACM Trans. Comput. Biol. Bioinform. John Hawkins, Mikael Bodén
2004	J	`jnl`	Generalization by symbolic abstraction in cascaded recurrent networks. Neurocomputing Mikael Bodén
2003	J	`jnl`	Learning the Dynamics of Embedded Clauses. Appl. Intell. Mikael Bodén, Alan D. Blair
2003	B	`conf`	Using evolutionary noise to improve prediction of rapidly evolving targeting peptides. IEEE Congress on Evolutionary Computation Mikael Bodén
2002	B	`conf`	Generalization by structural properties from sparse nested symbolic data. ESANN Mikael Bodén
2002	J	`jnl`	On learning context-free and context-sensitive languages. IEEE Trans. Neural Networks Mikael Bodén, Janet Wiles
2000	J	`jnl`	Context-free and context-sensitive dynamics in recurrent neural networks. Connect. Sci. Mikael Bodén, Janet Wiles
2000	A	`conf`	Evolving context-free language predictors. GECCO Mikael Bodén, Henrik Jacobsson, Tom Ziemke
2000	J	`jnl`	Semantic systematicity and context in connectionist networks. Connect. Sci. Mikael Bodén, Lars Niklasson
1997	—	`—`	Context-sensitive connectionist representations for nonmonotonic inheritance. Mikael Bodén
1996	C	`conf`	A Connectionist Variation of Inheritance. ICANN Mikael Bodén
1993	J	`jnl`	Editorial. Artif. Intell. Rev. Mikael Bodén, Lars Niklasson