Stefan Verhoeven

14 papers Journal 12Unranked 2
YearRankTypeTitle / Venue / Authors
2025 J jnl
HADDOCK3: A Modular and Versatile Platform for Integrative Modeling of Biomolecular Complexes.
J. Chem. Inf. Model.
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
2025 J jnl
Towards an open soil-plant digital twin based on STEMMUS-SCOPE model following open science.
Comput. Geosci.
Yijian Zeng, Fakhereh Alidoost, Bart Schilperoort, Yang Liu, Stefan Verhoeven, Meiert W. Grootes, Yunfei Wang, Zengjing Song, Danyang Yu, Enting Tang, Qianqian Han, Lianyu Yu, Mostafa Gomaa Daoud, Prajwal Khanal, Yunfei Chen, Christiaan van der Tol, Raúl Zurita-Milla, Serkan Girgin, Bas Retsios, Niels Drost, Yifat Dzigan, Zhongbo Su
2021 J jnl
Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships.
PLoS Comput. Biol.
Florian Huber, Lars Ridder, Stefan Verhoeven, Jurriaan H. Spaaks, Faruk Diblen, Simon Rogers, Justin J. J. van der Hooft
2020 J jnl
matchms - processing and similarity evaluation of mass spectrometry data.
J. Open Source Softw.
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
2018 — conf
A Portable and Scalable Workflow for Detecting Structural Variants in Whole-Genome Sequencing Data.
eScience
Arnold Kuzniar, Jason Maassen, Stefan Verhoeven, Luca Santuari, Carl Shneider, Wigard Kloosterman, Jeroen de Ridder
2018 — conf
Painting the Picture of Software Impact with the Research Software Directory.
eScience
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
2017 J jnl
3D-e-Chem-VM: Structural Cheminformatics Research Infrastructure in a Freely Available Virtual Machine.
J. Chem. Inf. Model.
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
2016 J jnl
Using modular 3D digital earth applications based on point clouds for the study of complex sites.
Int. J. Digit. Earth
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, Pjotr Svetachov
2013 J jnl
Identification of new biomarker candidates for glucocorticoid induced insulin resistance using literature mining.
BioData Min.
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
2011 J jnl
CoPub update: CoPub 5.0 a text mining system to answer biological questions.
Nucleic Acids Res.
Wilco W. M. Fleuren, Stefan Verhoeven, Raoul Frijters, Bart Heupers, Jan Polman, René C. van Schaik, Jacob de Vlieg, Wynand Alkema
2011 J jnl
GPCRDB: information system for G protein-coupled receptors.
Nucleic Acids Res.
Bas Vroling, Marijn P. A. Sanders, Coos Baakman, Annika Borrmann, Stefan Verhoeven, Jan P. G. Klomp, Laerte Oliveira, Jacob de Vlieg, Gert Vriend
2011 J jnl
Snooker: A Structure-Based Pharmacophore Generation Tool Applied to Class A GPCRs.
J. Chem. Inf. Model.
Marijn P. A. Sanders, Stefan Verhoeven, Chris de Graaf, Luc Roumen, Bas Vroling, Sander B. Nabuurs, Jacob de Vlieg, Jan P. G. Klomp
2011 J jnl
ss-TEA: Entropy based identification of receptor specific ligand binding residues from a multiple sequence alignment of class A GPCRs.
BMC Bioinform.
Marijn P. A. Sanders, Wilco W. M. Fleuren, Stefan Verhoeven, Sven van den Beld, Wynand Alkema, Jacob de Vlieg, Jan P. G. Klomp
2005 J jnl
CoPub Mapper: mining MEDLINE based on search term co-publication.
BMC Bioinform.
Blaise T. F. Alako, Antoine Veldhoven, Sjozef van Baal, Rob Jelier, Stefan Verhoeven, Ton Rullmann, Jan Polman, Guido Jenster