Genome Expression Pathway Analysis Tool - Analysis and visualization of microarray gene expression data under genomic, proteomic and metabolic context. - Markus Weniger; Julia C. Engelmann; Jörg Schultz (BMC Bioinform., 2007)

A statistical approach to virtual cellular experiments: improved causal discovery using accumulation IDA (aIDA). - Franziska Taruttis; Rainer Spang; Julia C. Engelmann (Bioinform., 2015)

miRA: adaptable novel miRNA identification in plants using small RNA sequencing data. - Maurits Evers; Michael Huttner; Anne Dueck; Gunter Meister; Julia C. Engelmann (BMC Bioinform., 2015)

Causal Modeling of Cancer-Stromal Communication Identifies PAPPA as a Novel Stroma-Secreted Factor Activating NFκB Signaling in Hepatocellular Carcinoma. - Julia C. Engelmann; Thomas Amann; Birgitta Ott-Rötzer; Margit Nützel; Yvonne Reinders; Jörg Reinders; Wolfgang E. Thasler; Theresa Kristl; Andreas Teufel; Christian G. Huber; Peter J. Oefner; Rainer Spang; et al. (PLoS Comput. Biol., 2015)

FastqPuri: high-performance preprocessing of RNA-seq data. - Paula Pérez-Rubio; Claudio Lottaz; Julia C. Engelmann (BMC Bioinform., 2019)