2024

Nanopore sequencing from formalin-fixed paraffin-embedded specimens for copy-number profiling and methylation-based CNS tumor classification
Afflerbach A, Albers A, Appelt A, Schweizer L, Paulus W, Bockmayr M, Schüller U, Thomas C
ACTA NEUROPATHOL. 2024;147(1):.

Molecular refinement of pilocytic astrocytoma in adult patients
Bode H, Kresbach C, Holdhof D, Dorostkar M, Harter P, Hench J, Frank S, Suwala A, Schweizer L, Eckhardt A, Neyazi S, Bockmayr M, Wefers A, Schüller U
NEUROPATH APPL NEURO. 2024;50(1):e12949.

Impact of molecular classification on prognosis in children and adolescents with spinal ependymoma: Results from the HIT-MED database
Engertsberger L, Benesch M, Mynarek M, Tonn S, Obrecht-Sturm D, Perwein T, Stickan-Verfürth M, Funk A, Timmermann B, Bockmayr M, Eckhardt A, Claviez A, Kortmann R, Riemenschneider M, Pietsch T, Bison B, Warmuth-Metz M, Pajtler K, Rutkowski S, Schüller U
NEURO-ONCOL ADV. 2024;6(1):.

Erklärbare Künstliche Intelligenz in der Pathologie
Klauschen F, Dippel J, Keyl P, Jurmeister P, Bockmayr M, Mock A, Buchstab O, Alber M, Ruff L, Montavon G, Müller K
PATHOLOGIE. 2024;45(2):133-139.

Erklärbare Künstliche Intelligenz in der Pathologie
Klauschen F, Dippel J, Keyl P, Jurmeister P, Bockmayr M, Mock A, Buchstab O, Alber M, Ruff L, Montavon G, Müller K
Forum. 2024;39(4):269-276.

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 K
ANNU REV PATHOL-MECH. 2024;19:541-570.

Transcriptomics-based characterization of the immuno-stromal microenvironment in pediatric low-grade glioma
Körner M, Spohn M, Schüller U, Bockmayr M
ONCOIMMUNOLOGY. 2024;13(1):2386789.

Weakly supervised medulloblastoma tumor classification using domain specific patch-level feature extraction
Maack L, Bhattacharya D, Behrendt F, Bockmayr M, Schlaefer A
2024. Medical Imaging 2024: Digital and Computational Pathology. Tomaszewski J, Ward A (Hrsg.). 1. Aufl. Bellingham, Washington: SPIE , .

Proteomic profiling reveals ACSS2 facilitating metabolic support in acute myeloid leukemia
Mochmann L, Treue D, Bockmayr M, Silva P, Zasada C, Mastrobuoni G, Bayram S, Forbes M, Jurmeister P, Liebig S, Blau O, Schleich K, Splettstoesser B, Nordmann T, von der Heide E, Isaakidis K, Schulze V, Busch C, Siddiq H, Schlee C, Hester S, Fransecky L, Neumann M, Kempa S, Klauschen F, Baldus C
CANCER GENE THER. 2024;31(9):1344-1356.

Transcriptomic and epigenetic dissection of spinal ependymoma (SP-EPN) identifies clinically relevant subtypes enriched for tumors with and without NF2 mutation
Neyazi S, Yamazawa E, Hack K, Tanaka S, Nagae G, Kresbach C, Umeda T, Eckhardt A, Tatsuno K, Pohl L, Hana T, Bockmayr M, Kim P, Dorostkar M, Takami T, Obrecht D, Takai K, Suwala A, Komori T, Godbole S, Wefers A, Otani R, Neumann J, Higuchi F, Schweizer L, Nakanishi Y, Monoranu C, Takami H, Engertsberger L, Yamada K, Ruf V, Nomura M, Mohme T, Mukasa A, Herms J, Takayanagi S, Mynarek M, Matsuura R, Lamszus K, Ishii K, Kluwe L, Imai H, von Deimling A, Koike T, Benesch M, Kushihara Y, Snuderl M, Nambu S, Frank S, Omura T, Hagel C, Kugasawa K, Mautner V, Ichimura K, Rutkowski S, Aburatani H, Saito N, Schüller U
ACTA NEUROPATHOL. 2024;147(1):22.

Molecular characteristics and improved survival prediction in a cohort of 2023 ependymomas
Pohl L, Leitheiser M, Obrecht D, Schweizer L, Wefers A, Eckhardt A, Raffeld M, Sturm D, Pajtler K, Rutkowski S, Fukuoka K, Ichimura K, Bockmayr M, Schüller U
ACTA NEUROPATHOL. 2024;147(1):24.

2023

Rapid Determination of Nutmeg Shell Content in Ground Nutmeg Using FT-NIR Spectroscopy and Machine Learning
Drees A, Bockmayr B, Bockmayr M, Fischer M
FOODS. 2023;12(15):.

Recurrent atypical teratoid/rhabdoid tumors (AT/RT) reveal discrete features of progression on histology, epigenetics, copy number profiling, and transcriptomics
Johann P, Altendorf L, Efremova E, Holsten T, Steinbügl M, Nemes K, Eckhardt A, Kresbach C, Bockmayr M, Koch A, Haberler C, Antonelli M, DeSisto J, Schuhmann M, Hauser P, Siebert R, Bens S, Kool M, Green A, Hasselblatt M, Frühwald M, Schüller U
ACTA NEUROPATHOL. 2023;146(3):527-541.

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 K, Klauschen F
NUCLEIC ACIDS RES. 2023;51(4):e20.

Atypical Neurofibromas reveal distinct epigenetic features with proximity to benign peripheral nerve sheath tumor entities
Kresbach C, Dottermusch M, Eckhardt A, Ristow I, Paplomatas P, Altendorf L, Wefers A, Bockmayr M, Belakhoua S, Tran I, Pohl L, Neyazi S, Bode H, Farschtschi S, Well L, Friedrich R, Reuss D, Snuderl M, Hagel C, Mautner V, Schüller U
NEURO-ONCOLOGY. 2023;25(9):1644-1655.

Identification of low and very high-risk patients with non-WNT/non-SHH medulloblastoma by improved clinico-molecular stratification of the HIT2000 and I-HIT-MED cohorts
Mynarek M, Obrecht D, Sill M, Sturm D, Kloth-Stachnau K, Selt F, Ecker J, von Hoff K, Juhnke B, Goschzik T, Pietsch T, Bockmayr M, Kool M, von Deimling A, Witt O, Schüller U, Benesch M, Gerber N, Sahm F, Jones D, Korshunov A, Pfister S, Rutkowski S, Milde T
ACTA NEUROPATHOL. 2023;145(1):97-112.

Risk prediction in early childhood sonic hedgehog medulloblastoma treated with radiation-avoiding chemotherapy
Tonn S, Korshunov A, Obrecht D, Sill M, Spohn M, von Hoff K, Milde T, Pietsch T, Goschzik T, Bison B, Juhnke B, Struve N, Sturm D, Sahm F, Bockmayr M, Friedrich C, von Bueren A, Gerber N, Benesch M, Jones D, Kool M, Wefers A, Schüller U, Pfister S, Rutkowski S, Mynarek M
NEURO-ONCOLOGY. 2023;25(8):1518-1529.

2022

Comprehensive profiling of myxopapillary ependymomas identifies a distinct molecular subtype with relapsing disease
Bockmayr M, Harnisch K, Pohl L, Schweizer L, Mohme T, Körner M, Alawi M, Suwala A, Dorostkar M, Monoranu C, Hasselblatt M, Wefers A, Capper D, Hench J, Frank S, Richardson T, Tran I, Liu E, Snuderl M, Engertsberger L, Benesch M, von Deimling A, Obrecht D, Mynarek M, Rutkowski S, Glatzel M, Neumann J, Schüller U
NEURO-ONCOLOGY. 2022;24(10):1689-1699.

DNA methylation-based classification of sinonasal tumors
Jurmeister P, Glöß S, Roller R, Leitheiser M, Schmid S, Mochmann L, Payá Capilla E, Fritz R, Dittmayer C, Friedrich C, Thieme A, Keyl P, Jarosch A, Schallenberg S, Bläker H, Hoffmann I, Vollbrecht C, Lehmann A, Hummel M, Heim D, Haji M, Harter P, Englert B, Frank S, Hench J, Paulus W, Hasselblatt M, Hartmann W, Dohmen H, Keber U, Jank P, Denkert C, Stadelmann C, Bremmer F, Richter A, Wefers A, Ribbat-Idel J, Perner S, Idel C, Chiariotti L, Della Monica R, Marinelli A, Schüller U, Bockmayr M, Liu J, Lund V, Forster M, Lechner M, Lorenzo-Guerra S, Hermsen M, Johann P, Agaimy A, Seegerer P, Koch A, Heppner F, Pfister S, Jones D, Sill M, von Deimling A, Snuderl M, Müller K, Forgó E, Howitt B, Mertins P, Klauschen F, Capper D
NAT COMMUN. 2022;13(1):.

Patient-level proteomic network prediction by explainable artificial intelligence
Keyl P, Michael B, Heim D, Dernbach G, Montavon G, Müller K, Klauschen F
NPJ PRECIS ONCOL. 2022;6(1):.

Machine Learning Models Predict the Primary Sites of Head and Neck Squamous Cell Carcinoma Metastases Based on DNA Methylation
Leitheiser M, Capper D, Seegerer P, Lehmann A, Schüller U, Müller K, Klauschen F, Jurmeister P, Michael B
J PATHOL. 2022;256(4):378-387.

Clinical and molecular characterization of isolated M1 disease in pediatric medulloblastoma: experience from the German HIT-MED studies
Obrecht D, Mynarek M, Hagel C, Kwiecien R, Spohn M, Bockmayr M, Bison B, Pfister S, Jones D, Sturm D, von Deimling A, Sahm F, von Hoff K, Juhnke B, Benesch M, Gerber N, Friedrich C, von Bueren A, Kortmann R, Schwarz R, Pietsch T, Fleischhack G, Schüller U, Rutkowski S
J NEURO-ONCOL. 2022;157(1):37-48.

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 A, Tacke F, Capper D, Müller K, Klauschen F
SEMIN CANCER BIOL. 2022;84:129-143.

2021

Medulloblastoma tumor classification using deep transfer learning with multi-scale EfficientNets
Bengs M, Bockmayr M, Schüller U, Schlaefer A
Progress in Biomedical Optics and Imaging - Proceedings of SPIE. 2021.

Multi-Scale Input Strategies for Medulloblastoma Tumor Classification using Deep Transfer Learning
Bengs M, Pant S, Bockmayr M, Schüller U, Schlaefer A
Current Directions in Biomedical Engineering. 2021;7(1):.

Morphological and molecular breast cancer profiling through explainable machine learning
Binder A, Bockmayr M, Hägele M, Wienert S, Heim D, Hellweg K, Ishii M, Stenzinger A, Hocke A, Denkert C, Müller K, Klauschen F
NAT MACH INTELL. 2021;3(4):355-366.

Cauda equina paragangliomas express HOXB13
Bockmayr M, Körner M, Schweizer L, Schüller U
NEUROPATH APPL NEURO. 2021;47(6):889-890.

Atypical teratoid/rhabdoid tumors (ATRTs) with SMARCA4 mutation are molecularly distinct from SMARCB1-deficient cases
Holdhof D, Johann P, Spohn M, Bockmayr M, Safaei S, Joshi P, Masliah-Planchon J, Ho B, Andrianteranagna M, Bourdeaut F, Huang A, Kool M, Upadhyaya S, Bendel A, Indenbirken D, Foulkes W, Bush J, Creytens D, Kordes U, Frühwald M, Hasselblatt M, Schüller U
ACTA NEUROPATHOL. 2021;141(2):291-301.

DIMEimmune: Robust estimation of infiltrating lymphocytes in CNS tumors from DNA methylation profiles
Safaei S, Mohme M, Niesen J, Schüller U, Bockmayr M
ONCOIMMUNOLOGY. 2021;10(1):.

2020

Multiclass cancer classification in fresh frozen and formalin-fixed paraffin-embedded tissue by DigiWest multiplex protein analysis
Bockmayr T, Erdmann G, Treue D, Jurmeister P, Schneider J, Arndt A, Heim D, Bockmayr M, Sachse C, Klauschen F
LAB INVEST. 2020;100(10):1288-1299.

Resolving challenges in deep learning-based analyses of histopathological images using explanation methods
Hägele M, Seegerer P, Lapuschkin S, Bockmayr M, Samek W, Klauschen F, Müller K, Binder A
SCI REP-UK. 2020;10(1):6423.

Glioma escape signature and clonal development under immune pressure
Maire C, Mohme M, Bockmayr M, Fita K, Riecken K, Börnigen D, Alawi M, Failla A, Kolbe K, Zapf S, Holz M, Neumann K, Dührsen L, Lange T, Fehse B, Westphal M, Lamszus K
J CLIN INVEST. 2020;130(10):5257-5271.

Molecular characterization of CNS paragangliomas identifies cauda equina paragangliomas as a distinct tumor entity
Schweizer L, Thierfelder F, Thomas C, Soschinski P, Suwala A, Stichel D, Wefers A, Wessels L, Misch M, Kim H, Jödicke R, Teichmann D, Kaul D, Kahn J, Bockmayr M, Hasselblatt M, Younsi A, Unterberg A, Knie B, Walter J, Al Safatli D, May S, Jödicke A, Ntoulias G, Moskopp D, Vajkoczy P, Heppner F, Capper D, Hartmann W, Hartmann C, von Deimling A, Reuss D, Schöler A, Koch A
ACTA NEUROPATHOL. 2020;140(6):893-906.

Interpretable Deep Neural Network to Predict Estrogen Receptor Status from Haematoxylin-Eosin Images
Seegerer P, Binder A, Saitenmacher R, Bockmayr M, Alber M, Jurmeister P, Klauschen F, Müller K
2020. Artificial Intelligence and Machine Learning for Digital Pathology. Holzinger A, Goebel R, Mengel M, Müller H (Hrsg.). 1. Aufl. Cham: Springer Heidelberg, 16-37.

2019

Immunologic Profiling of Mutational and Transcriptional Subgroups in Pediatric and Adult High-Grade Gliomas
Bockmayr M, Klauschen F, Maire C, Rutkowski S, Westphal M, Lamszus K, Schüller U, Mohme M
CANCER IMMUNOL RES. 2019;7(9):1401-1411.

TCF4 (E2-2) harbors tumor suppressive functions in SHH medulloblastoma
Hellwig M, Lauffer M, Bockmayr M, Spohn M, Merk D, Harrison L, Ahlfeld J, Kitowski A, Neumann J, Ohli J, Holdhof D, Niesen J, Schoof M, Kool M, Kraus C, Zweier C, Holmberg D, Schüller U
ACTA NEUROPATHOL. 2019;137(4):657-673.

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 K, Capper D, Klauschen F
SCI TRANSL MED. 2019;11(509):.

Immunhistochemische Analyse von Bcl-2, nukleärem S100A4, MITF und Ki67 zur Risikostratifizierung von Melanomen im Frühstadium - ein kombinierter immunhistochemischer Score
Jurmeister P, Bockmayr M, Treese C, Stein U, Lenze D, Jöhrens K, Friedling F, Dietel M, Klauschen F, Marsch W, Fiedler E, von Laffert M
J DTSCH DERMATOL GES. 2019;17(8):800-809.

Immunohistochemical analysis of Bcl-2, nuclear S100A4, MITF and Ki67 for risk stratification of early-stage melanoma - A combined IHC score for melanoma risk stratification
Jurmeister P, Bockmayr M, Treese C, Stein U, Lenze D, Jöhrens K, Friedling F, Dietel M, Klauschen F, Marsch W, Fiedler E, von Laffert M
J DTSCH DERMATOL GES. 2019;17(8):800-808.

Food authentication: Multi-elemental analysis of white asparagus for provenance discrimination
Richter B, Gurk S, Wagner D, Bockmayr M, Fischer M
FOOD CHEM. 2019;286:475-482.

Proteogenomic systems analysis identifies targeted therapy resistance mechanisms in EGFR-mutated lung cancer
Treue D, Bockmayr M, Stenzinger A, Heim D, Hester S, Klauschen F
INT J CANCER. 2019;144(3):545-557.

2018

Subgroup-specific immune and stromal microenvironment in medulloblastoma
Bockmayr M, Mohme M, Klauschen F, Winkler B, Budczies J, Rutkowski S, Schüller U
ONCOIMMUNOLOGY. 2018;7(9):e1462430.

Scoring of tumor-infiltrating lymphocytes: from visual estimation to machine learning
Klauschen F, Müller K, Binder A, Bockmayr M, Hägele M, Seegerer P, Wienert S, Pruneri G, de Maria S, Badve S, Michiels S, Nielsen T, Adams S, Savas P, Symmans F, Willis S, Gruosso T, Park M, Haibe-Kains B, Gallas B, Thompson A, Cree I, Sotiriou C, Solinas C, Preusser M, Hewitt S, Rimm D, Viale G, Loi S, Loibl S, Salgado R, Denkert C
SEMIN CANCER BIOL. 2018;52(Pt 2):151-157.

Multilayered omics-based analysis of a head and neck cancer model of cisplatin resistance reveals intratumoral heterogeneity and treatment-induced clonal selection
Niehr F, Eder T, Pilz T, Konschak R, Treue D, Klauschen F, Bockmayr M, Türkmen S, Jöhrens K, Budach V, Tinhofer I
CLIN CANCER RES. 2018;24(1):158-168.

Combined inhibition of receptor tyrosine and p21-activated kinases as a therapeutic strategy in childhood ALL
Siekmann I, Dierck K, Prall S, Klokow M, Strauss J, Buhs S, Wrzeszcz A, Bockmayr M, Beck F, Trochimiuk M, Gottschling K, Martens V, Khosh-Naucke M, Gerull H, Müller J, Behrmann L, Blohm M, Zahedi R, Jeremias I, Sickmann A, Nollau P, Horstmann M
BLOOD ADV. 2018;2(19):2554-2567.

2017

Mutation patterns in genes encoding interferon signaling and antigen presentation: A pan-cancer survey with implications for the use of immune checkpoint inhibitors
Budczies J, Bockmayr M, Klauschen F, Endris V, Fröhling S, Schirmacher P, Denkert C, Stenzinger A
GENE CHROMOSOME CANC. 2017;56(8):651-659.

PD-L1 (CD274) copy number gain, expression, and immune cell infiltration as candidate predictors for response to immune checkpoint inhibitors in soft-tissue sarcoma
Budczies J, Mechtersheimer G, Denkert C, Klauschen F, Mughal S, Chudasama P, Bockmayr M, Jöhrens K, Endris V, Lier A, Lasitschka F, Penzel R, Dietel M, Brors B, Gröschel S, Glimm H, Schirmacher P, Renner M, Fröhling S, Stenzinger A
ONCOIMMUNOLOGY. 2017;6(3):e1279777.

Tubular, lactating, and ductal adenomas are devoid of MED12 Exon2 mutations, and ductal adenomas show recurrent mutations in GNAS and the PI3K-AKT pathway
Volckmar A, Leichsenring J, Flechtenmacher C, Pfarr N, Siebolts U, Kirchner M, Budczies J, Bockmayr M, Ridinger K, Lorenz K, Herpel E, Noske A, Weichert W, Klauschen F, Schirmacher P, Penzel R, Endris V, Stenzinger A
GENE CHROMOSOME CANC. 2017;56(1):11-17.

2016

Pan-cancer analysis of copy number changes in programmed death-ligand 1 (PD-L1, CD274) - associations with gene expression, mutational load, and survival
Budczies J, Bockmayr M, Denkert C, Klauschen F, Gröschel S, Darb-Esfahani S, Pfarr N, Leichsenring J, Onozato M, Lennerz J, Dietel M, Fröhling S, Schirmacher P, Iafrate A, Weichert W, Stenzinger A
GENE CHROMOSOME CANC. 2016;55(8):626-39.

Prognostic impact of programmed cell death-1 (PD-1) and PD-ligand 1 (PD-L1) expression in cancer cells and tumor-infiltrating lymphocytes in ovarian high grade serous carcinoma
Darb-Esfahani S, Kunze C, Kulbe H, Sehouli J, Wienert S, Lindner J, Budczies J, Bockmayr M, Dietel M, Denkert C, Braicu I, Jöhrens K
ONCOTARGET. 2016;7(2):1486-99.

Mutations in genes encoding PI3K-AKT and MAPK signaling define anogenital papillary hidradenoma
Pfarr N, Sinn H, Klauschen F, Flechtenmacher C, Bockmayr M, Ridinger K, von Winterfeld M, Warth A, Lorenz K, Budczies J, Penzel R, Lennerz J, Endris V, Weichert W, Stenzinger A
GENE CHROMOSOME CANC. 2016;55(2):113-9.

2015

Classical pathology and mutational load of breast cancer - integration of two worlds
Budczies J, Bockmayr M, Denkert C, Klauschen F, Lennerz J, Györffy B, Dietel M, Loibl S, Weichert W, Stenzinger A
J PATHOL CLIN RES. 2015;1(4):225-38.

Semiconductor sequencing: how many flows do you need?
Budczies J, Bockmayr M, Treue D, Klauschen F, Denkert C
BIOINFORMATICS. 2015;31(8):1199-203.

The landscape of metastatic progression patterns across major human cancers
Budczies J, von Winterfeld M, Klauschen F, Bockmayr M, Lennerz J, Denkert C, Wolf T, Warth A, Dietel M, Anagnostopoulos I, Weichert W, Wittschieber D, Stenzinger A
ONCOTARGET. 2015;6(1):570-83.

2013

New network topology approaches reveal differential correlation patterns in breast cancer
Bockmayr M, Klauschen F, Györffy B, Denkert C, Budczies J
BMC SYST BIOL. 2013;7:78.

Letzte Aktualisierung aus dem FIS: 01.07.2025 - 00:37 Uhr