PhyloPat: phylogenetic pattern analysis of eukaryotic genes. - Tim Hulsen; Jacob de Vlieg; Peter M. A. Groenen (BMC Bioinform., 2006)

Testing statistical significance scores of sequence comparison methods with structure similarity. - Tim Hulsen; Jacob de Vlieg; Jack A. M. Leunissen; Peter M. A. Groenen (BMC Bioinform., 2006)

CoPub: a literature-based keyword enrichment tool for microarray data analysis. - Raoul Frijters; Bart Heupers; Pieter van Beek; Maurice Bouwhuis; René C. van Schaik; Jacob de Vlieg; Jan Polman; Wynand Alkema (Nucleic Acids Res., 2008)

PhyloPat: an updated version of the phylogenetic pattern database contains gene neighborhood. - Tim Hulsen; Peter M. A. Groenen; Jacob de Vlieg; Wynand Alkema (Nucleic Acids Res., 2009)

Integrating gene expression and GO classification for PCA by preclustering. - Jorn R. de Haan; Ester Piek; René C. van Schaik; Jacob de Vlieg; Susanne Bauerschmidt; Lutgarde M. C. Buydens; Ron Wehrens (BMC Bioinform., 2010)

Fleksy: a flexible approach to induced fit docking. - Markus Wagener; Sander B. Nabuurs; Jacob de Vlieg (J. Cheminformatics, 2010)

Literature Mining for the Discovery of Hidden Connections between Drugs, Genes and Diseases. - Raoul Frijters; Marianne van Vugt; Ruben Smeets; René C. van Schaik; Jacob de Vlieg; Wynand Alkema (PLoS Comput. Biol., 2010)

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)

Extraction of useful bioisostere replacments from the PDB. - Tina Ritschel; David J. Wood; Jacob de Vlieg; Markus Wagener (J. Cheminformatics, 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)

Quantum mechanical polar surface area. - Gijs Schaftenaar; Jacob de Vlieg (J. Comput. Aided Mol. Des., 2012)

Flexible protein-ligand docking using the Fleksy protocol. - Markus Wagener; Jacob de Vlieg; Sander B. Nabuurs (J. Comput. Chem., 2012)

Integrated Project Views: Decision Support Platform for Drug Discovery Project Teams. - Eric J. Baede; Ernest den Bekker; Jan-Willem Boiten; Deborah Cronin; Rob van Gammeren; Jacob de Vlieg (J. Chem. Inf. Model., 2012)

Comparative Analysis of Pharmacophore Screening Tools. - Marijn P. A. Sanders; Arménio Jorge Moura Barbosa; Barbara Zarzycka; Gerry A. F. Nicolaes; Jan P. G. Klomp; Jacob de Vlieg; Alberto Del Rio 001 (J. Chem. Inf. Model., 2012)

Pharmacophore Fingerprint-Based Approach to Binding Site Subpocket Similarity and Its Application to Bioisostere Replacement. - David J. Wood; Jacob de Vlieg; Markus Wagener; Tina Ritschel (J. Chem. Inf. Model., 2012)

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)