Vorolign - fast structural alignment using Voronoi contacts. - Fabian Birzele; Jan E. Gewehr; Gergely Csaba; Ralf Zimmer (Bioinform., 2007)

Protein structure alignment considering phenotypic plasticity. - Gergely Csaba; Fabian Birzele; Ralf Zimmer (ECCB, 2008)

Algorithmische Systembiologie mit Petrinetzen - Von qualitativen zu quantitativen Systemmodellen. - Fabian Birzele; Gergely Csaba; Florian Erhard; Caroline C. Friedel; Robert Küffner; Tobias Petri; Lukas Windhager; Ralf Zimmer (Inform. Spektrum, 2009)

Vorescore - fold recognition improved by rescoring of protein structure models. - Gergely Csaba; Ralf Zimmer (Bioinform., 2010)

miRSel: Automated extraction of associations between microRNAs and genes from the biomedical literature. - Haroon Naeem; Robert Küffner; Gergely Csaba; Ralf Zimmer (BMC Bioinform., 2010)

From sets to graphs: towards a realistic enrichment analysis of transcriptomic systems. - Ludwig Geistlinger; Gergely Csaba; Robert Küffner; Nicola J. Mulder; Ralf Zimmer (Bioinform., 2011)

A context-based approach to identify the most likely mapping for RNA-seq experiments. - Thomas Bonfert; Gergely Csaba; Ralf Zimmer; Caroline C. Friedel (BMC Bioinform., 2012)

Context based bioinformatics. - Gergely Csaba (2013)

ContextMap 2: fast and accurate context-based RNA-seq mapping. - Thomas Bonfert; Evelyn Kirner; Gergely Csaba; Ralf Zimmer; Caroline C. Friedel (BMC Bioinform., 2015)

Bioconductor's EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis. - Ludwig Geistlinger; Gergely Csaba; Ralf Zimmer (BMC Bioinform., 2016)

RelExplain - integrating data and networks to explain biological processes. - Evi Berchtold; Gergely Csaba; Ralf Zimmer (Bioinform., 2017)

YESdb: integrative analysis of environmental stress in yeast. - Evi Berchtold; Gergely Csaba; Ralf Zimmer (Database J. Biol. Databases Curation, 2019)

Comparison of six breast cancer classifiers using qPCR. - Evi Berchtold; Martina Vetter; Melanie Gündert; Gergely Csaba; Christine Fathke; Susanne E. Ulbrich; Christoph Thomssen; Ralf Zimmer; Eva J. Kantelhardt (Bioinform., 2019)

Toward a gold standard for benchmarking gene set enrichment analysis. - Ludwig Geistlinger; Gergely Csaba; Mara Santarelli; Marcel Ramos; Lucas Schiffer; Nitesh Turaga; Charity W. Law; Sean Davis 001; Vincent J. Carey; Martin Morgan; Ralf Zimmer; Levi Waldron (Briefings Bioinform., 2021)