A data-analysis pipeline for large-scale gene expression analysis. - Steffen Hennig; Ralf Herwig; Matthew Clark; Pia Aanstad; A. Musa; John O'Brien; C. Bull; Uwe Radelof; Georgia Panopoulou; Albert J. Poustka; Hans Lehrach (RECOMB, 2000)

Information theoretical probe selection for hybridisation experiments. - Ralf Herwig; Armin Otto Schmitt; Matthias Steinfath; John O'Brien; Henrik Seidel; Sebastian Meier-Ewert; Hans Lehrach; Uwe Radelof (Bioinform., 2000)

Simulation of DNA array hybridization experiments and evaluation of critical parameters during subsequent image and data analysis. - Christoph K. Wierling; Matthias Steinfath; Thorsten Elge; Steffen Schulze-Kremer; Pia Aanstad; Matthew Clark; Hans Lehrach; Ralf Herwig (BMC Bioinform., 2002)

Exploring potential target genes of signaling pathways by predicting conserved transcription factor binding sites. - Christoph Dieterich; Ralf Herwig; Martin Vingron (ECCB, 2003)

Transformation and other factors of the peptide mass spectrometry pairwise peak-list comparison process. - Witold E. Wolski; Maciej Lalowski; Peter Martus; Ralf Herwig; Patrick Giavalisco; Johan Gobom; Albert Sickmann; Hans Lehrach; Knut Reinert (BMC Bioinform., 2005)

T2DM-GeneMiner a web resource for meta-analysis and marker identification for type 2 diabetes mellitus. - Axel Rasche; Ralf Herwig (BMC Bioinform., 2007)

GeNGe: systematic generation of gene regulatory networks. - Hendrik Hache; Christoph K. Wierling; Hans Lehrach; Ralf Herwig (Bioinform., 2009)

Reverse Engineering of Gene Regulatory Networks: A Comparative Study. - Hendrik Hache; Hans Lehrach; Ralf Herwig (EURASIP J. Bioinform. Syst. Biol., 2009)

ConsensusPathDB - a database for integrating human functional interaction networks. - Atanas Kamburov; Christoph K. Wierling; Hans Lehrach; Ralf Herwig (Nucleic Acids Res., 2009)

Evidence mining and novelty assessment of protein-protein interactions with the ConsensusPathDB plugin for Cytoscape. - Konstantin Pentchev; Keiichiro Ono; Ralf Herwig; Trey Ideker; Atanas Kamburov (Bioinform., 2010)

ARH: predicting splice variants from genome-wide data with modified entropy. - Axel Rasche; Ralf Herwig (Bioinform., 2010)

Integrated pathway-level analysis of transcriptomics and metabolomics data with IMPaLA. - Atanas Kamburov; Rachel Cavill; Timothy M. D. Ebbels; Ralf Herwig; Hector C. Keun (Bioinform., 2011)

ConsensusPathDB: toward a more complete picture of cell biology. - Atanas Kamburov; Konstantin Pentchev; Hanna Galicka; Christoph K. Wierling; Hans Lehrach; Ralf Herwig (Nucleic Acids Res., 2011)

Consensus-Phenotype Integration of Transcriptomic and Metabolomic Data Implies a Role for Metabolism in the Chemosensitivity of Tumour Cells. - Rachel Cavill; Atanas Kamburov; James K. Ellis; Toby J. Athersuch; Marcus S. C. Blagrove; Ralf Herwig; Timothy M. D. Ebbels; Hector C. Keun (PLoS Comput. Biol., 2011)

DIPSBC - data integration platform for systems biology collaborations. - Felix Dreher 002; Thomas Kreitler; Christopher Hardt; Atanas Kamburov; Reha Yildirimman; Karl Schellander; Hans Lehrach; Bodo M. H. Lange; Ralf Herwig (BMC Bioinform., 2012)

Cluster-based assessment of protein-protein interaction confidence. - Atanas Kamburov; Arndt Grossmann; Ralf Herwig; Ulrich Stelzl (BMC Bioinform., 2012)

IntScore: a web tool for confidence scoring of biological interactions. - Atanas Kamburov; Ulrich Stelzl; Ralf Herwig (Nucleic Acids Res., 2012)

The ConsensusPathDB interaction database: 2013 update. - Atanas Kamburov; Ulrich Stelzl; Hans Lehrach; Ralf Herwig (Nucleic Acids Res., 2013)

MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments. - Matthias Lienhard; Christina Grimm; Markus Morkel; Ralf Herwig; Lukas Chavez (Bioinform., 2014)

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)

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)

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)

ConsensusPathDB 2022: molecular interactions update as a resource for network biology. - Atanas Kamburov; Ralf Herwig (Nucleic Acids Res., 2022)

Systematic analysis of hepatotoxicity: combining literature mining and AI language models. - Chris Bauer; Long Tran Duc Dang; Twan van den Beucken; Johannes Schuchhardt; Ralf Herwig (Frontiers Artif. Intell., 2025)