Prof. Dr. Frederick Klauschen

Selected publications

Decoding pan-cancer treatment outcomes using multimodal real-world data and explainable artificial intelligence. Keyl J, Keyl P, Montavon G, Hosch R, Brehmer A, Mochmann L, Jurmeister P, Dernbach G, Kim M, Koitka S, Bauer S, Bechrakis N, Forsting M, Führer-Sakel D, Glas M, Grünwald V, Hadaschik B, Haubold J, Herrmann K, Kasper S, Kimmig R, Lang S, Rassaf T, Roesch A, Schadendorf D, Siveke JT, Stuschke M, Sure U, Totzeck M, Welt A, Wiesweg M, Baba HA, Nensa F, Egger J, Müller KR*, Schuler M*, Klauschen F*, Kleesiek J*. Nature Cancer. 2025 Jan 30. *equal contribution

Combining spatial transcriptomics and ECM imaging in 3D for mapping cellular interactions in the tumor microenvironment. Pentimalli TM, Schallenberg S, León-Periñán D, Legnini I, Theurillat I, Thomas G, Boltengagen A, Fritzsche S, Nimo J, Ruff L, Dernbach G, Jurmeister P, Murphy S, Gregory MT, Liang Y, Cordenonsi M, Piccolo S, Coscia F, Woehler A, Karaiskos N, Klauschen F, Rajewsky N. Cell Syst. 2025 May 21;16(5):101261.

AI-based Anomaly Detection for Clinical-Grade Histopathological Diagnostics. Dippel J, Prenißl N, Hense J, Liznerski P, Winterhoff T, Schallenberg S, Kloft M, Buchstab O, Horst D, Alber M, Ruff L, Müller KR, Klauschen F. NEJM AI. 2024.

Forget lung, breast or prostate cancer? Why we shouldn't abandon tumour names yet. Stenzinger A, Klauschen F. Nature. 2024 Mar;627(8002):38.

Toward Explainable Artificial Intelligence for Precision Pathology. Klauschen F, Dippel J, Keyl P, Jurmeister P, Bockmayr M, Mock A, Buchstab O, Alber M, Ruff L, Montavon G, Müller KR. Annual Reviews of Pathology. 2024 Jan 24;19:541-570.

Single-cell gene regulatory network prediction by explainable AI. Keyl P, Bischoff P, Dernbach G, Bockmayr M, Fritz R, Horst D, Blüthgen N, Montavon G, Müller KR, Klauschen F. Nucleic Acids Res. 2023 Feb 28;51(4):e20.

DNA methylation-based classification of sinonasal tumors. Jurmeister P, Glöß S, Roller R, …, Howitt BE, Mertins P, Klauschen F*, Capper D*. Nature Communications. 2022 Nov 28;13(1):7148. *equal contribution.

Artificial intelligence and pathology: From principles to practice and future applications in histomorphology and molecular profiling. Stenzinger A, Alber M, Allgäuer M, Jurmeister P, Bockmayr M, Budczies J, Lennerz J, Eschrich J, Kazdal D, Schirmacher P, Wagner AH, Tacke F, Capper D, Müller KR, Klauschen F. Seminars in Cancer Biology. 2022 Sep;84:129-143.

Comprehensive micro-scaled proteome and phosphoproteome characterization of archived retrospective cancer repositories. Friedrich C, Schallenberg S, Kirchner M, Ziehm M, Niquet S, Haji M, Beier C, Neudecker J, Klauschen F*, Mertins P*. Nature Communications. 2021 Jun 11;12(1):3576. *equal contribution.

Single-cell RNA sequencing reveals distinct tumor microenvironmental patterns in lung adenocarcinoma. Bischoff P, Trinks A, Obermayer B, Pett JP, Wiederspahn J, Uhlitz F, Liang X, Lehmann A, Jurmeister P, Elsner A, Dziodzio T, Rückert JC, Neudecker J, Falk C, Beule D, Sers C, Morkel M, Horst D, Blüthgen N, Klauschen F. Oncogene. 2021 Dec;40(50):6748-6758.

Morphological and molecular breast cancer profiling through explainable machine learning. Binder A, Bockmayr M, Hagele M, Wienert S, Heim D, Hellweg K, Ishii M, Stenzinger A, Hocke A, Denkert C, Muller KR & Klauschen F. Nature Machine Intelligence, 2021.

Machine learning analysis of DNA methylation profiles distinguishes primary lung squamous cell carcinomas from head and neck metastases. Jurmeister P, Bockmayr M, Seegerer P, Bockmayr T, Treue D, Montavon G, Vollbrecht C, Arnold A, Teichmann D, Bressem K, Schüller U, von Laffert M, Müller KR, Capper D, Klauschen F. Science Translational Medicine. 2019 Sep 11;11(509).

Tissue clonality of dendritic cell subsets and emergency DCpoiesis revealed by multicolor fate mapping of DC progenitors. Cabeza-Cabrerizo M, van Blijswijk J, Wienert S, Heim D, Jenkins RP, Chakravarty P, Rogers N, Frederico B, Acton S, Beerling E, van Rheenen J, Clevers H, Schraml BU, Bajénoff M, Gerner M, Germain RN, Sahai E, Klauschen F*, Reis e Sousa C*. Science Immunology. 2019 Mar 1;4(33):eaaw1941.

Computational analysis reveals histotype-dependent molecular profile and actionable mutation effects across cancers. Heim D, Montavon G, Hufnagl P, Müller KR, Klauschen F. Genome Med. 2018 Nov 15;10(1):83.

Clonal Proliferation and Stochastic Pruning Orchestrate Lymph Node Vasculature Remodeling. Mondor I, Jorquera A, Sene C, Adriouch S, Adams RH, Zhou B, Wienert S, Klauschen F, Bajénoff M. Immunity. 2016 Oct 18;45(4):877-888.

Robust Anti-viral Immunity Requires Multiple Distinct T Cell-Dendritic Cell Interactions. Eickhoff S, Brewitz A, Gerner MY, Klauschen F, Komander K, Hemmi H, Garbi N, Kaisho T, Germain RN, Kastenmüller W. Cell. 2015 Sep 10;162(6):1322-37.

Standardized Ki67 Diagnostics Using Automated Scoring--Clinical Validation in the GeparTrio Breast Cancer Study. Klauschen F, Wienert S, Schmitt WD, Loibl S, Gerber B, Blohmer JU, Huober J, Rüdiger T, Erbstößer E, Mehta K, Lederer B, Dietel M, Denkert C, von Minckwitz G. Clin Cancer Res. 2015 Aug 15;21(16):3651-7.

T-cell-receptor-dependent signal intensity dominantly controls CD4(+) T cell polarization In Vivo. van Panhuys N, Klauschen F, Germain RN. Immunity. 2014 Jul 17;41(1):63-74.

Fate mapping reveals origin and dynamics of lymph node follicular dendritic cells. Jarjour M, Jorquera A, Mondor I, Wienert S, Narang P, Coles MC, Klauschen F, Bajénoff M. J Exp Med. 2014 Jun 2;211(6):1109-22.

Multicolor fate mapping of Langerhans cell homeostasis. Ghigo C, Mondor I, Jorquera A, Nowak J, Wienert S, Zahner SP, Clausen BE, Luche H, Malissen B, Klauschen F*, Bajénoff M*. J Exp Med. 2013 Aug 26;210(9):1657-64.

A systems analysis identifies a feedforward inflammatory circuit leading to lethal influenza infection. Brandes M, Klauschen F, Kuchen S, Germain RN. Cell. 2013 Jul 3;154(1):197-212.

Computational modeling of cellular signaling processes embedded into dynamic spatial contexts. Angermann BR*, Klauschen F*, Garcia AD, Prustel T, Zhang F, Germain RN, Meier-Schellersheim M. Nature Methods. 2012 Jan 29;9(3):283-9.

Quantifying cellular interaction dynamics in 3D fluorescence microscopy data. Klauschen F, Ishii M, Qi H, Bajénoff M, Egen JG, Germain RN, Meier-Schellersheim M. Nature Protoc. 2009;4(9):1305-11.

Sphingosine-1-phosphate mobilizes osteoclast precursors and regulates bone homeostasis. Ishii M, Egen JG, Klauschen F, Meier-Schellersheim M, Saeki Y, Vacher J, Proia RL, Germain RN. Nature. 2009 Mar 26;458(7237):524-8.

Computational reconstruction of cell and tissue surfaces for modeling and data analysis. Klauschen F, Qi H, Egen JG, Germain RN, Meier-Schellersheim M. Nature Protoc. 2009;4(7):1006-12.

SAP-controlled T-B cell interactions underlie germinal centre formation. Qi H, Cannons JL, Klauschen F, Schwartzberg PL, Germain RN. Nature. 2008 Oct 9;455(7214):764-9.