Integration of gel-based proteome data with pProRep. - Kris Laukens; Rune Matthiesen; Filip Lemière; Eddy Esmans; Harry Van Onckelen; Ole Nørregaard Jensen; Erwin Witters (Bioinform., 2006)

Prediction of kinase-specific phosphorylation sites using conditional random fields. - Thanh Hai Dang; Koenraad Van Leemput; Alain Verschoren; Kris Laukens (Bioinform., 2008)

Flexible network reconstruction from relational databases with Cytoscape and CytoSQL. - Kris Laukens; Jens Hollunder; Thanh Hai Dang; Geert De Jaeger; Martin Kuiper; Erwin Witters; Alain Verschoren; Koenraad Van Leemput (BMC Bioinform., 2010)

An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data. - Trung-Nghia Vu; Dirk Valkenborg; Koen Smets; Kim A. Verwaest; Roger Dommisse; Filip Lemière; Alain Verschoren; Bart Goethals; Kris Laukens (BMC Bioinform., 2011)

Use of structural DNA properties for the prediction of transcription-factor binding sites in Escherichia coli. - Pieter Meysman; Thanh Hai Dang; Kris Laukens; Riet De Smet; Yan Wu; Kathleen Marchal; Kristof Engelen (Nucleic Acids Res., 2011)

AcoSeeD: An Ant Colony Optimization for Finding Optimal Spaced Seeds in Biological Sequence Search. - Dong Do Duc; Huy Q. Dinh; Thanh Hai Dang; Kris Laukens; Huan Hoang Xuan (ANTS, 2012)

Mining spatially cohesive itemsets in protein molecular structures. - Cheng Zhou; Pieter Meysman; Boris Cule; Kris Laukens; Bart Goethals (BIOKDD, 2013)

COLOMBOS v2.0: an ever expanding collection of bacterial expression compendia. - Pieter Meysman; Paolo Sonego; Luca Bianco; Qiang Fu 009; Daniela Ledezma-Tejeida; Socorro Gama-Castro; Veerle Liebens; Jan Michiels; Kris Laukens; Kathleen Marchal; Julio Collado-Vides; Kristof Engelen (Nucleic Acids Res., 2014)

Discovery of Spatially Cohesive Itemsets in Three-Dimensional Protein Structures. - Cheng Zhou; Pieter Meysman; Boris Cule; Kris Laukens; Bart Goethals (IEEE ACM Trans. Comput. Biol. Bioinform., 2014)

Mining Association Rules in Graphs Based on Frequent Cohesive Itemsets. - Tayena Hendrickx; Boris Cule; Pieter Meysman; Stefan Naulaerts; Kris Laukens; Bart Goethals (PAKDD (2), 2015)

A primer to frequent itemset mining for bioinformatics. - Stefan Naulaerts; Pieter Meysman; Wout Bittremieux; Trung-Nghia Vu; Wim Vanden Berghe; Bart Goethals; Kris Laukens (Briefings Bioinform., 2015)

Mining the entire Protein DataBank for frequent spatially cohesive amino acid patterns. - Pieter Meysman; Cheng Zhou; Boris Cule; Bart Goethals; Kris Laukens (BioData Min., 2015)

Mining the human proteome for conserved mechanisms. - Stefan Naulaerts; Pieter Meysman; Wim Vanden Berghe; Kris Laukens (BMC Bioinform., 2015)

COLOMBOS v3.0: leveraging gene expression compendia for cross-species analyses. - Marco Moretto; Paolo Sonego; Nicolas Dierckxsens; Matteo Brilli; Luca Bianco; Daniela Ledezma-Tejeida; Socorro Gama-Castro; Marco Galardini; Chiara Romualdi; Kris Laukens; Julio Collado-Vides; Pieter Meysman; et al. (Nucleic Acids Res., 2016)

Highlights from the 11th ISCB Student Council Symposium 2015: Dublin, Ireland. 10 July 2015. - Katie Wilkins; Mehedi Hassan; Margherita Francescatto; Jakob B. Jespersen; R. Gonzalo Parra; Bart Cuypers; Dan F. DeBlasio; Alexander Junge; Anupama Jigisha; Farzana Rahman; Griet Laenen; Sander Willems; et al. (BMC Bioinform., 2016)

sfinx: an R package for the elimination of false positives from affinity purification-mass spectrometry datasets. - Kevin Titeca; Pieter Meysman; Kris Laukens; Lennart Martens; Jan Tavernier; Sven Eyckerman (Bioinform., 2017)

Grasping frequent subgraph mining for bioinformatics applications. - Aida Mrzic; Pieter Meysman; Wout Bittremieux; Pieter Moris; Boris Cule; Bart Goethals; Kris Laukens (BioData Min., 2018)

pBRIT: gene prioritization by correlating functional and phenotypic annotations through integrative data fusion. - Ajay Anand Kumar; Lut Van Laer; Maaike Alaerts; Amin Ardeshirdavani; Yves Moreau; Kris Laukens; Bart Loeys; Geert Vandeweyer (Bioinform., 2018)

speaq 2.0: A complete workflow for high-throughput 1D NMR spectra processing and quantification. - Charlie Beirnaert; Pieter Meysman; Trung-Nghia Vu; Nina Hermans; Sandra Apers; Luc Pieters; Adrian Covaci; Kris Laukens (PLoS Comput. Biol., 2018)

On the viability of unsupervised T-cell receptor sequence clustering for epitope preference. - Pieter Meysman; Nicolas De Neuter; Sofie Gielis; Danh Bui Thi; Benson Ogunjimi; Kris Laukens (Bioinform., 2019)

Mining the Enriched Subgraphs for Specific Vertices in a Biological Graph. - Pieter Meysman; Yvan Saeys; Ehsan Sabaghian; Wout Bittremieux; Yves Van de Peer; Bart Goethals; Kris Laukens (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Clustering association rules to build beliefs and discover unexpected patterns. - Danh Bui Thi; Pieter Meysman; Kris Laukens (Appl. Intell., 2020)

MILES: a Java tool to extract node-specific enriched subgraphs in biomolecular networks. - Pieter Moris; Danh Bui Thi; Kris Laukens; Pieter Meysman (Bioinform., 2020)

Current challenges for unseen-epitope TCR interaction prediction and a new perspective derived from image classification. - Pieter Moris; Joey De Pauw; Anna Postovskaya; Sofie Gielis; Nicolas De Neuter; Wout Bittremieux; Benson Ogunjimi; Kris Laukens; Pieter Meysman (Briefings Bioinform., 2021)

ClusTCR: a python interface for rapid clustering of large sets of CDR3 sequences with unknown antigen specificity. - Sebastiaan Valkiers; Marc van Houcke; Kris Laukens; Pieter Meysman (Bioinform., 2021)

MoMAC: Multi-objective optimization to combine multiple association rules into an interpretable classification. - Danh Bui Thi; Pieter Meysman; Kris Laukens (Appl. Intell., 2022)

A treatment recommender clinical decision support system for personalized medicine: method development and proof-of-concept for drug resistant tuberculosis. - Lennert Verboven; Toon Calders; Steven Callens; John Black; Gary Maartens; Kelly E. Dooley; Samantha Potgieter; Robin M. Warren; Kris Laukens; Annelies Van Rie (BMC Medical Informatics Decis. Mak., 2022)

The pitfalls of negative data bias for the T-cell epitope specificity challenge. - Ceder Dens; Kris Laukens; Wout Bittremieux; Pieter Meysman (Nat. Mac. Intell., 2023)

tcrBLOSUM: an amino acid substitution matrix for sensitive alignment of distant epitope-specific TCRs. - Anna Postovskaya; Koen Vercauteren; Pieter Meysman; Kris Laukens (Briefings Bioinform., 2024)

Benchmarking of Small Molecule Feature Representations for hERG, Nav1.5, and Cav1.2 Cardiotoxicity Prediction. - Issar Arab; Kristof Egghe; Kris Laukens; Ke Chen; Khaled H. Barakat; Wout Bittremieux (J. Chem. Inf. Model., 2024)

Semisupervised Learning to Boost hERG, Nav1.5, and Cav1.2 Cardiac Ion Channel Toxicity Prediction by Mining a Large Unlabeled Small Molecule Data Set. - Issar Arab; Kris Laukens; Wout Bittremieux (J. Chem. Inf. Model., 2024)

Correction to "Semisupervised Learning to Boost hERG, Nav1.5, and Cav1.2 Cardiac Ion Channel Toxicity Prediction by Mining a Large Unlabeled Small Molecule Data Set". - Issar Arab; Kris Laukens; Wout Bittremieux (J. Chem. Inf. Model., 2024)

TransExION: a transformer based explainable similarity metric for comparing IONS in tandem mass spectrometry. - Danh Bui Thi; Youzhong Liu; Jennifer L. Lippens; Kris Laukens; Thomas De Vijlder (J. Cheminformatics, 2024)