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Bioinformatics (Oxford, England)|July 15, 2025
Deep learning models for unbiased sequence-based PPI prediction plateau at an accuracy of 0.65Timo Reim, Anne Hartebrodt, David B Blumenthal, et al.Briefings in Bioinformatics|March 6, 2024
Cracking the black box of deep sequence-based protein-protein interaction predictionJudith Bernett, David B Blumenthal, Markus ListMethods in Molecular Biology (Clifton, N.J.)|October 5, 2019
De Novo Pathway Enrichment with KeyPathwayMinerNicolas Alcaraz, Anne Hartebrodt, Markus ListNature Methods|August 9, 2024
Guiding questions to avoid data leakage in biological machine learning applicationsJudith Bernett, David B Blumenthal, Dominik G Grimm, et al.Bioinformatics (Oxford, England)|January 5, 2022
Robust disease module mining via enumeration of diverse prize-collecting Steiner treesJudith Bernett, Dominik Krupke, Sepideh Sadegh, et al.Briefings in Bioinformatics|March 30, 2021
On the limits of active module identificationOlga Lazareva, Jan Baumbach, Markus List, et al.Nature Communications|May 12, 2026
Critical evaluation of drug response prediction models with DrEvalJudith Bernett, Pascal Iversen, Mario Picciani, et al.NPJ Systems Biology and Applications|December 2, 2024
Spatial cell graph analysis reveals skin tissue organization characteristic for cutaneous T cell lymphomaSuryadipto Sarkar, Anna Möller, Anne Hartebrodt, et al.Bioinformatics (Oxford, England)|November 30, 2020
A framework for modeling epistatic interactionDavid B Blumenthal, Jan Baumbach, Markus Hoffmann, et al.Gigascience|November 9, 2025
NApy: efficient statistics in Python for large-scale heterogeneous data with enhanced support for missing dataFabian Woller, Lis Arend, Christian Fuchsberger, et al.Pageof 16