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)

Addressing false discoveries in network inference. - Tobias Petri; Stefan Altmann; Ludwig Geistlinger; Ralf Zimmer; Robert Küffner (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)

Orchestrating a community-developed computational workshop and accompanying training materials. - Sean Davis 001; Marcel Ramos; Lori A. Shepherd; Nitesh Turaga; Ludwig Geistlinger; Martin T. Morgan; Benjamin Haibe-Kains; Levi Waldron (F1000Research, 2018)

CNVRanger: association analysis of CNVs with gene expression and quantitative phenotypes. - Vinícius da Silva; Marcel Ramos; Martien Groenen; Richard Crooijmans; Anna Johansson; Luciana C. A. Regitano; Luiz Coutinho; Ralf Zimmer; Levi Waldron; Ludwig Geistlinger (Bioinform., 2020)

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)

SIMON: Open-Source Knowledge Discovery Platform. - Adriana Tomic; Ivan Tomic; Levi Waldron; Ludwig Geistlinger; Max Kuhn; Rachel L. Spreng; Lindsay C. Dahora; Kelly E. Seaton; Georgia D. Tomaras; Jennifer Hill; Niharika A. Duggal; Ross D. Pollock; et al. (Patterns, 2021)

Curated single cell multimodal landmark datasets for R/Bioconductor. - Kelly B. Eckenrode; Dario Righelli; Marcel Ramos; Ricard Argelaguet; Christophe Vanderaa; Ludwig Geistlinger; Aedín C. Culhane; Laurent Gatto; Vincent J. Carey; Martin Morgan; Davide Risso; Levi Waldron (PLoS Comput. Biol., 2023)

BioPlexR and BioPlexPy: integrated data products for the analysis of human protein interactions. - Ludwig Geistlinger; Roger Vargas; Tyrone Lee; Joshua Pan; Edward L. Huttlin; Robert Gentleman (Bioinform., 2023)

Learning and teaching biological data science in the Bioconductor community. - Jenny Drnevich; Frederick J. Tan; Fabricio Almeida-Silva; Robert Castelo; Aedín C. Culhane; Sean R. Davis; Maria A. Doyle; Ludwig Geistlinger; Andrew R. Ghazi; Susan P. Holmes; Leo Lahti; Alexandru Mahmoud; et al. (PLoS Comput. Biol., 2025)