Dittami SM, Scornet D, Petit JL, Ségurens B, Da Silva C, Corre E, Dondrup M, Glatting KH, König R, Sterck L, Rouzé P, Van de Peer Y, Cock JM, Boyen C, Tonon T (2009) Global expression analysis of the brown alga Ectocarpus siliculosus (Phaeophyceae) reveals large-scale reprogramming of the transcriptome in response to abiotic stress. Genome Biol 10(6), R66.

Fatumo S, Plaimas K, Mallm JP, Schramm G, Adebiyi E, Oswald M, Eils R, König R (2009) Estimating novel potential drug targets of Plasmodium falciparum by analysing the metabolic network of knock-out strains in silico. Infect Genet Evol 9(3), 351-358.

Plaimas K, Mallm JP, Oswald M, Svara F, Sourjik V, Eils R, König R (2008) Machine learning based analyses on metabolic networks supports high-throughput knockout screens. BMC Syst Biol 2, 67.

Westermann F, Muth D, Benner A, Bauer T, Henrich KO, Oberthuer A, Brors B, Beissbarth T, Vandesompele J, Pattyn F, Hero B, König R, Fischer M, Schwab M (2008) Distinct transcriptional MYCN/c-MYC activities are associated with spontaneous regression or malignant progression in neuroblastomas. Genome Biol 9(10), R150.

Schramm G, Zapatka M, Eils R, König R (2007) Using gene expression data and network topology to detect substantial pathways, clusters and switches during oxygen deprivation of Escherichia coli. BMC Bioinformatics 8, 149.

Westermann F, Henrich KO, Wei JS, Lutz W, Fischer M, König R, Wiedemeyer R, Ehemann V, Brors B, Ernestus K, Leuschner I, Benner A, Khan J, Schwab M (2007) High Skp2 expression characterizes high-risk neuroblastomas independent of MYCN status. Clin Cancer Res 13(16), 4695-4703.

König R, Schramm G, Oswald M, Seitz H, Sager S, Zapatka M, Reinelt G, Eils R (2006) Discovering functional gene expression patterns in the metabolic network of Escherichia coli with wavelets transforms. BMC Bioinformatics 7, 119.

Oberthuer A, Berthold F, Warnat P, Hero B, Kahlert Y, Spitz R, Ernestus K, König R, Haas S, Eils R, Schwab M, Brors B, Westermann F, Fischer M (2006) Customized oligonucleotide microarray gene expression-based classification of neuroblastoma patients outperforms current clinical risk stratification. J Clin Oncol 24(31), 5070-5078.

Vinayagam A, del Val C, Schubert F, Eils R, Glatting KH, Suhai S, König R (2006) GOPET: a tool for automated predictions of Gene Ontology terms. BMC Bioinformatics 7, 161.

Baldessari D, Shin Y, Krebs O, König R, Koide T, Vinayagam A, Fenger U, Mochii M, Terasaka C, Kitayama A, Peiffer D, Ueno N, Eils R, Cho KW, Niehrs C (2005) Global gene expression profiling and cluster analysis in Xenopus laevis. Mech Dev 122(3), 441-475.