Genome-wide Analysis of Functions Regulated by Sets of Transcription Factors. - Szymon M. Kielbasa; Nils Blüthgen; Hanspeter Herzel (German Conference on Bioinformatics, 2004)

HOMGL - comparing genelists across species and with different accession numbers. - Nils Blüthgen; Szymon M. Kielbasa; Branka Cajavec; Hanspeter Herzel (Bioinform., 2004)

Ultrasensitization: Switch-Like Regulation of Cellular Signaling by Transcriptional Induction. - Stefan Legewie; Nils Blüthgen; Reinhold Schäfer; Hanspeter Herzel (PLoS Comput. Biol., 2005)

Mathematical Modeling Identifies Inhibitors of Apoptosis as Mediators of Positive Feedback and Bistability. - Stefan Legewie; Nils Blüthgen; Hanspeter Herzel (PLoS Comput. Biol., 2006)

Noise Management by Molecular Networks. - Frank J. Bruggeman; Nils Blüthgen; Hans V. Westerhoff (PLoS Comput. Biol., 2009)

Targetfinder.org: a resource for systematic discovery of transcription factor target genes. - Szymon M. Kielbasa; Nils Blüthgen; Michael Fähling; Ralf Mrowka (Nucleic Acids Res., 2010)

TransFind - predicting transcriptional regulators for gene sets. - Szymon M. Kielbasa; Holger Klein; Helge G. Roider; Martin Vingron; Nils Blüthgen (Nucleic Acids Res., 2010)

Discovering causal signaling pathways through gene-expression patterns. - Jignesh R. Parikh; Bertram Klinger; Yu Xia 002; Jarrod A. Marto; Nils Blüthgen (Nucleic Acids Res., 2010)

Computer-assisted curation of a human regulatory core network from the biological literature. - Philippe Thomas 002; Pawel Durek; Illés Solt; Bertram Klinger; Franziska Witzel; Pascal Schulthess; Yvonne Mayer; Domonkos Tikk; Nils Blüthgen; Ulf Leser (Bioinform., 2015)

Analysis of impedance-based cellular growth assays. - Franziska Witzel; Raphaela Fritsche-Guenther; Nadine Lehmann; Anja Sieber; Nils Blüthgen (Bioinform., 2015)

Sorting sums of binary decision summands. - Torsten Gross; Nils Blüthgen (CoRR, 2017)

Comparative Network Reconstruction using mixed integer programming. - Evert Bosdriesz; Anirudh Prahallad; Bertram Klinger; Anja Sieber; Astrid Bosma; René Bernards; Nils Blüthgen; Lodewyk F. A. Wessels (Bioinform., 2018)

Modelling signalling networks from perturbation data. - Mathurin Dorel; Bertram Klinger; Torsten Gross; Anja Sieber; Anirudh Prahallad; Evert Bosdriesz; Lodewyk F. A. Wessels; Nils Blüthgen (Bioinform., 2018)

Robust network inference using response logic. - Torsten Gross; Matthew Wongchenko; Yibing Yan; Nils Blüthgen (Bioinform., 2019)

Identifiability and experimental design in perturbation studies. - Torsten Gross; Nils Blüthgen (Bioinform., 2020)

SPEED2: inferring upstream pathway activity from differential gene expression. - Mattias Rydenfelt; Bertram Klinger; Martina Klünemann; Nils Blüthgen (Nucleic Acids Res., 2020)

Neuroblastoma signalling models unveil combination therapies targeting feedback-mediated resistance. - Mathurin Dorel; Bertram Klinger; Tommaso Mari; Joern Toedling; Eric Blanc; Clemens Messerschmidt; Michal Nadler-Holly; Matthias Ziehm; Anja Sieber; Falk Hertwig; Dieter Beule; Angelika Eggert; et al. (PLoS Comput. Biol., 2021)

Quantitative modeling of signaling in aggressive B cell lymphoma unveils conserved core network. - Bertram Klinger; Isabel Rausch; Anja Sieber; Helmut Kutz; Vanessa Kruse; Marieluise Kirchner; Philipp Mertins; Arnd Kieser; Nils Blüthgen; Dieter Kube (PLoS Comput. Biol., 2024)