Gepard: a rapid and sensitive tool for creating dotplots on genome scale. - Jan Krumsiek; Roland Arnold; Thomas Rattei (Bioinform., 2007)

ProCope - protein complex prediction and evaluation. - Jan Krumsiek; Caroline C. Friedel; Ralf Zimmer (Bioinform., 2008)

SIMAP - structuring the network of protein similarities. - Thomas Rattei; Patrick Tischler; Roland Arnold; Franz Hamberger; Jörg Krebs; Jan Krumsiek; Benedikt Wachinger; Volker Stümpflen; Hans-Werner Mewes (Nucleic Acids Res., 2008)

Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling. - Dominik M. Wittmann; Jan Krumsiek; Julio Saez-Rodriguez; Douglas A. Lauffenburger; Steffen Klamt; Fabian J. Theis (BMC Syst. Biol., 2009)

Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast. - Caroline C. Friedel; Jan Krumsiek; Ralf Zimmer (J. Comput. Biol., 2009)

Odefy – From discrete to continuous models. - Jan Krumsiek; Sebastian Pölsterl; Dominik M. Wittmann; Fabian J. Theis (BMC Bioinform., 2010)

An ISA algorithm with unknown group sizes identifies meaningful clusters in metabolomics data. - Harold W. Gutch; Jan Krumsiek; Fabian J. Theis (EUSIPCO, 2011)

Gaussian graphical modeling reconstructs pathway reactions from high-throughput metabolomics data. - Jan Krumsiek; Karsten Suhre; Thomas Illig; Jerzy Adamski; Fabian J. Theis (BMC Syst. Biol., 2011)

On the hypothesis-free testing of metabolite ratios in genome-wide and metabolome-wide association studies. - Ann-Kristin Petersen; Jan Krumsiek; Brigitte Wägele; Fabian J. Theis; Heinz-Erich Wichmann; Christian Gieger; Karsten Suhre (BMC Bioinform., 2012)

Unbiased Prediction and Feature Selection in High-Dimensional Survival Regression. - Michael Laimighofer; Jan Krumsiek; Florian A. Büttner; Fabian J. Theis (J. Comput. Biol., 2016)

MoDentify: phenotype-driven module identification in metabolomics networks at different resolutions. - Kieu Trinh Do; David J. N. P. Rasp; Gabi Kastenmüller; Karsten Suhre; Jan Krumsiek (Bioinform., 2019)

SGI: automatic clinical subgroup identification in omics datasets. - Mustafa Buyukozkan; Karsten Suhre; Jan Krumsiek (Bioinform., 2022)

maplet: an extensible R toolbox for modular and reproducible metabolomics pipelines. - Kelsey Chetnik; Elisa Benedetti; Daniel P. Gomari; Annalise Schweickart; Richa Batra; Mustafa Buyukozkan; Zeyu Wang; Matthias Arnold; Jonas Zierer; Karsten Suhre; Jan Krumsiek (Bioinform., 2022)