Combining Shapley value and statistics to the analysis of gene expression data in children exposed to air pollution. - Stefano Moretti 001; Danitsja van Leeuwen; Hans Gmuender; Stefano Bonassi; Joost van Delft; Jos Kleinjans; Fioravante Patrone; Domenico Franco Merlo (BMC Bioinform., 2008)

A dictionary to identify small molecules and drugs in free text. - Kristina M. Hettne; Rob H. Stierum; Martijn J. Schuemie; Peter J. M. Hendriksen; Bob J. A. Schijvenaars; Erik M. van Mulligen; Jos Kleinjans; Jan A. Kors (Bioinform., 2009)

Automatic vs. manual curation of a multi-source chemical dictionary: the impact on text mining. - Kristina M. Hettne; Antony J. Williams; Erik M. van Mulligen; Jos Kleinjans; Valery Tkachenko; Jan A. Kors (J. Cheminformatics, 2010)

Automatic vs. manual curation of a multi-source chemical dictionary: the impact on text mining (Correction). - Kristina M. Hettne; Antony J. Williams; Erik M. van Mulligen; Jos Kleinjans; Valery Tkachenko; Jan A. Kors (J. Cheminformatics, 2010)

Integrating transcriptomics and metabonomics to unravel modes-of-action of 2, 3, 7, 8-tetrachlorodibenzo-p-dioxin (TCDD) in HepG2 cells. - Danyel Jennen; Ainhoa Ruiz-Aracama; Christina Magkoufopoulou; Ad Peijnenburg; Arjen Lommen; Joost van Delft; Jos Kleinjans (BMC Syst. Biol., 2011)

diXa: a data infrastructure for chemical safety assessment. - Diana M. Hendrickx; Hugo J. W. L. Aerts; Florian Caiment; Dominic Clark; Timothy M. D. Ebbels; Chris T. A. Evelo; Hans Gmuender; Dennie G. A. J. Hebels; Ralf Herwig; Jürgen Hescheler; Danyel G. J. Jennen; Marlon J. A. Jetten; et al. (Bioinform., 2015)

Pattern recognition methods to relate time profiles of gene expression with phenotypic data: a comparative study. - Diana M. Hendrickx; Danyel G. J. Jennen; Jacob J. Briedé; Rachel Cavill; Theo M. de Kok; Jos C. S. Kleinjans (Bioinform., 2015)

MagiCMicroRna: a web implementation of AgiMicroRna using shiny. - Maarten Coonen; Daniel Theunissen; Jos Kleinjans; Danyel Jennen (Source Code Biol. Medicine, 2015)

Transcriptomic and metabolomic data integration. - Rachel Cavill; Danyel Jennen; Jos Kleinjans; Jacob J. Briedé (Briefings Bioinform., 2016)

ToxDB: pathway-level interpretation of drug-treatment data. - Christopher Hardt; Moritz Emanuel Beber; Axel Rasche; Atanas Kamburov; Dennie G. A. J. Hebels; Jos C. S. Kleinjans; Ralf Herwig (Database J. Biol. Databases Curation, 2016)

DynOVis: a web tool to study dynamic perturbations for capturing dose-over-time effects in biological networks. - T. J. M. Kuijpers; J. E. J. Wolters; Jos C. S. Kleinjans; Danyel G. J. Jennen (BMC Bioinform., 2019)

FuSe: a tool to move RNA-Seq analyses from chromosomal/gene loci to functional grouping of mRNA transcripts. - Rajinder Gupta; Yannick Schrooders; Marcha Verheijen; Adrian Roth; Jos Kleinjans; Florian Caiment (Bioinform., 2021)

A bioinformatics workflow to detect genes with DNA methylation alterations: a case study of analyzing MeDIP-seq data in cardiac microtissue exposed to epirubicin. - Nhan Nguyen; Matthias Lienhard; Ralf Herwig; Jos Kleinjans; Danyel Jennen (ICBBB, 2022)