CoPub Mapper: mining MEDLINE based on search term co-publication. - Blaise T. F. Alako; Antoine Veldhoven; Sjozef van Baal; Rob Jelier; Stefan Verhoeven; Ton Rullmann; Jan Polman; Guido Jenster (BMC Bioinform., 2005)

ss-TEA: Entropy based identification of receptor specific ligand binding residues from a multiple sequence alignment of class A GPCRs. - Marijn P. A. Sanders; Wilco W. M. Fleuren; Stefan Verhoeven; Sven van den Beld; Wynand Alkema; Jacob de Vlieg; Jan P. G. Klomp (BMC Bioinform., 2011)

Snooker: A Structure-Based Pharmacophore Generation Tool Applied to Class A GPCRs. - Marijn P. A. Sanders; Stefan Verhoeven; Chris de Graaf; Luc Roumen; Bas Vroling; Sander B. Nabuurs; Jacob de Vlieg; Jan P. G. Klomp (J. Chem. Inf. Model., 2011)

CoPub update: CoPub 5.0 a text mining system to answer biological questions. - Wilco W. M. Fleuren; Stefan Verhoeven; Raoul Frijters; Bart Heupers; Jan Polman; René C. van Schaik; Jacob de Vlieg; Wynand Alkema (Nucleic Acids Res., 2011)

GPCRDB: information system for G protein-coupled receptors. - Bas Vroling; Marijn P. A. Sanders; Coos Baakman; Annika Borrmann; Stefan Verhoeven; Jan P. G. Klomp; Laerte Oliveira; Jacob de Vlieg; Gert Vriend (Nucleic Acids Res., 2011)

Identification of new biomarker candidates for glucocorticoid induced insulin resistance using literature mining. - Wilco W. M. Fleuren; Erik J. M. Toonen; Stefan Verhoeven; Raoul Frijters; Tim Hulsen; Ton Rullmann; René C. van Schaik; Jacob de Vlieg; Wynand Alkema (BioData Min., 2013)

Using modular 3D digital earth applications based on point clouds for the study of complex sites. - Oscar Martinez-Rubi; Maurice de Kleijn; Stefan Verhoeven; Niels Drost; Jisk Attema; Maarten A. J. van Meersbergen; Rob van Nieuwpoort; Rens de Hond; Eduardo Dias 001; Pjotr Svetachov (Int. J. Digit. Earth, 2016)

3D-e-Chem-VM: Structural Cheminformatics Research Infrastructure in a Freely Available Virtual Machine. - Ross McGuire; Stefan Verhoeven; Márton Vass; Gerrit Vriend; Iwan J. P. de Esch; Scott J. Lusher; Rob Leurs; Lars Ridder; Albert J. Kooistra; Tina Ritschel; Chris de Graaf (J. Chem. Inf. Model., 2017)

A Portable and Scalable Workflow for Detecting Structural Variants in Whole-Genome Sequencing Data. - Arnold Kuzniar; Jason Maassen; Stefan Verhoeven; Luca Santuari; Carl Shneider; Wigard Kloosterman; Jeroen de Ridder (eScience, 2018)

Painting the Picture of Software Impact with the Research Software Directory. - Jurriaan H. Spaaks; Tom Klaver; Stefan Verhoeven; Jason Maassen; Tom Bakker; Atze van der Ploeg; Ben van Werkhoven; Willem Robert van Hage; Rob V. van Nieuwpoort (eScience, 2018)

matchms - processing and similarity evaluation of mass spectrometry data. - Florian Huber; Stefan Verhoeven; Christiaan Meijer; Hanno Spreeuw; Efraín Castilla; Cunliang Geng; Justin J. J. van der Hooft; Simon Rogers; Adam Belloum; Faruk Diblen; Jurriaan H. Spaaks (J. Open Source Softw., 2020)

Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships. - Florian Huber; Lars Ridder; Stefan Verhoeven; Jurriaan H. Spaaks; Faruk Diblen; Simon Rogers; Justin J. J. van der Hooft (PLoS Comput. Biol., 2021)

HADDOCK3: A Modular and Versatile Platform for Integrative Modeling of Biomolecular Complexes. - Marco Giulini; Victor Reys; João M. C. Teixeira; Brian Jiménez-García; Rodrigo V. Honorato; Anna Kravchenko; Xiaotong Xu; Raphaëlle Versini; Anna Engel; Stefan Verhoeven; Alexandre M. J. J. Bonvin (J. Chem. Inf. Model., 2025)