Publications

Markus Bauer, and Christoph Augenstein. Self-supervised learning in histopathology: New perspectives for prostate cancer grading. Lecture Notes in Computer Science, 348--360, Springer Nature Switzerland, Cham, 2024. [PUMA: cancer grading histopathology learning prostate self-supervised topic_lifescience yaff]

Raghava Vinaykanth Mushunuri, Matthias Choschzick, Ulf-Dietrich Braumann, and Jürgen Hess. An ensemble approach for histopathological classification of vulvar cancer. In John E Tomaszewski, and Aaron D Ward (Eds.), Medical Imaging 2023: Digital and Computational Pathology, 40, SPIE, April 2023. [PUMA: approach cancer classification ensemble histopathological nopdf vulvar]

Katharina Beyer, Vera Straten, Sebastiaan Remmers, Steven MacLennan, Sara MacLennan, Giorgio Gandaglia, Peter-Paul M. Willemse, Ronald Herrera, Muhammad Imran Omar, Beth Russell, Johannes Huber, Markus Kreuz, Alex Asiimwe, Tom Abbott, Alberto Briganti, Mieke Van Hemelrijck, and Monique J. Roobol. Secondary Treatment for Men with Localized Prostate Cancer: A Pooled Analysis of PRIAS and ERSPC-Rotterdam Data within the PIONEER Data Platform. Journal of Personalized Medicine, (12)5:751, MDPI AG, May 2022. [PUMA: Cancer ERSPC-Rotterdam Localized Men PIONEER PRIAS Prostate Secondary Treatment zno] URL

Mika Katalinic, Martin Schenk, Stefan Franke, Alexander Katalinic, Thomas Neumuth, Andreas Dietz, Matthaeus Stoehr, and Jan Gaebel. Generation of a Realistic Synthetic Laryngeal Cancer Cohort for AI Applications. Cancers, (16)3:639, MDPI AG, February 2024. [PUMA: AI Applications Cancer Cohort Generation Laryngeal Realistic Synthetic zno] URL

Michael Rade, Markus Kreuz, Angelika Borkowetz, Ulrich Sommer, Conny Blumert, Susanne Füssel, Catharina Bertram, Dennis Löffler, Dominik J. Otto, Livia A. Wöller, Carolin Schimmelpfennig, Ulrike Köhl, Ann-Cathrin Gottschling, Pia Hönscheid, Gustavo B. Baretton, Manfred Wirth, Christian Thomas, Friedemann Horn, and Kristin Reiche. A reliable transcriptomic risk-score applicable to formalin-fixed paraffin-embedded biopsies improves outcome prediction in localized prostate cancer. Molecular Medicine, (30)1Springer Science and Business Media LLC, February 2024. [PUMA: applicable biopsies cancer formalin-fixed paraffin-embedded predictionprostate risk-score transcriptomic yaff] URL

Markus Bauer, Lennart Schneider, Marit Bernhardt, Christoph Augenstein, Glen Kristiansen, and Bogdan Franczyk. An Open-Source Approach for Digital Prostate Cancer Histopathology: Bringing AI into Practice. Proceedings of the 26th International Conference on Enterprise Information Systems - Volume 1: ICEIS, 729-738, SciTePress, 2024. [PUMA: AI Cancer Digital Histopatholog Open-Source Prostate nopdf]

Ali Al-Fatlawi, Negin Malekian, Sebastián Garc\'ıa, Andreas Henschel, Ilwook Kim, Andreas Dahl, Beatrix Jahnke, Peter Bailey, Sarah Naomi Bolz, Anna R Poetsch, Sandra Mahler, Robert Grützmann, Christian Pilarsky, and Michael Schroeder. Deep learning improves pancreatic cancer diagnosis using RNA-based variants. Cancers (Basel), (13)11:2654, MDPI AG, May 2021. [PUMA: association cancer chronic deep learning pancreatic pancreatitis study topic_lifescience transcriptome-wide zno]

Lucas Schneider, Sara Laiouar-Pedari, Sara Kuntz, Eva Krieghoff-Henning, Achim Hekler, Jakob N Kather, Timo Gaiser, Stefan Fröhling, and Titus J Brinker. Integration of deep learning-based image analysis and genomic data in cancer pathology: A systematic review. Eur. J. Cancer, (160):80--91, Elsevier BV, January 2022. [PUMA: Biomarker Cancer Convolutional Multimodal Omics fusion identification networks neural topic_lifescience zno]

Chiara Maria Lavinia Loeffler, Nadina Ortiz Bruechle, Max Jung, Lancelot Seillier, Michael Rose, Narmin Ghaffari Laleh, Ruth Knuechel, Titus J Brinker, Christian Trautwein, Nadine T Gaisa, and Jakob N Kather. Artificial intelligence-based detection of FGFR3 mutational status directly from routine histology in bladder cancer: A possible preselection for molecular testing?. Eur. Urol. Focus, (8)2:472--479, Elsevier BV, March 2022. [PUMA: Bladder FGFR3 Molecular cancer factor fibroblast for growth intelligence learning mutations receptor testing therapy topic_lifescience zno artificial deep]

Scarlet Brockmoeller, Amelie Echle, Narmin Ghaffari Laleh, Susanne Eiholm, Marie Louise Malmstrøm, Tine Plato Kuhlmann, Katarina Levic, Heike Irmgard Grabsch, Nicholas P West, Oliver Lester Saldanha, Katerina Kouvidi, Aurora Bono, Lara R Heij, Titus J Brinker, Ismayil Gögenür, Philip Quirke, and Jakob Nikolas Kather. Deep learning identifies inflamed fat as a risk factor for lymph node metastasis in early colorectal cancer. J. Pathol., (256)3:269--281, Wiley, March 2022. [PUMA: AI; LNM adipose and artificial bowel colorectal deep digital early inflamed metastasis; new pT1 pT2 prediction predictive tissue; topic_lifescience zno learning intelligence pathology biomarker cancer]

Peter Leonard Schrammen, Narmin Ghaffari Laleh, Amelie Echle, Daniel Truhn, Volkmar Schulz, Titus J Brinker, Hermann Brenner, Jenny Chang-Claude, Elizabeth Alwers, Alexander Brobeil, Matthias Kloor, Lara R Heij, Dirk Jäger, Christian Trautwein, Heike I Grabsch, Philip Quirke, Nicholas P West, Michael Hoffmeister, and Jakob Nikolas Kather. Weakly supervised annotation-free cancer detection and prediction of genotype in routine histopathology. J. Pathol., (256)1:50--60, Wiley, January 2022. [PUMA: Lynch artificial colorectal computational deep digital instability microsatellite syndrome; topic_lifescience zno learning intelligence pathology cancer]

Julien Calderaro, Luca Di Tommaso, Pascale Maillé, Aurélie Beaufrère, Cong Trung Nguyen, Lara Heij, Viviane Gnemmi, Rondell P Graham, Frédéric Charlotte, Suzanne Chartier, Dominique Wendum, Mukul Vij, Daniela Allende, Alba Diaz, Carla Fuster, Benjamin Rivière, Astrid Herrero, Jérémy Augustin, Katja Evert, Diego Francesco Calvisi, Wei Qiang Leow, Howard Ho Wai Leung, Jan Bednarsch, Emmanuel Boleslawski, Mohamed Rela, Anthony Wing-Hung Chan, Alejandro Forner, Maria Reig, Ana\"ıs Pujals, Loetitia Favre, Manon Allaire, Olivier Scatton, Arnaud Uguen, Eric Trépo, Lukas Otero Sanchez, Denis Chatelain, Myriam Remmelink, Camille Boulagnon-Rombi, Céline Bazille, Nathalie Sturm, Benjamin Menahem, Eric Frouin, David Tougeron, Christophe Tournigand, Emmanuelle Kempf, Haeryoung Kim, Massih Ningarhari, Sophie Michalak-Provost, Jakob Nikolas Kather, Annette S H Gouw, Purva Gopal, Raffaele Brustia, Eric Vibert, Kornelius Schulze, Darius F Rüther, Sören A Weidemann, Rami Rhaiem, Jean-Charles Nault, Alexis Laurent, Giuliana Amaddeo, Hélène Regnault, Eleonora de Martin, Christine Sempoux, Pooja Navale, Jayendra Shinde, Ketan Bacchuwar, Maria Westerhoff, Regina Cheuk-Lam Lo, Mylène Sebbagh, Catherine Guettier, Marie Lequoy, Mina Komuta, Marianne Ziol, Valérie Paradis, Jeanne Shen, and Stefano Caruso. Nestin as a diagnostic and prognostic marker for combined hepatocellular-cholangiocarcinoma. J. Hepatol., (77)6:1586--1597, Elsevier BV, December 2022. [PUMA: carcinoma; cholangiocarcinoma; combined hepatocellular hepatocellular-cholangiocarcinoma; liver; nestin topic_lifescience zno cancer]

Chiara Maria Lavinia Loeffler, Nadine T Gaisa, Hannah Sophie Muti, Marko van Treeck, Amelie Echle, Narmin Ghaffari Laleh, Christian Trautwein, Lara R Heij, Heike I Grabsch, Nadina Ortiz Bruechle, and Jakob Nikolas Kather. Predicting mutational status of driver and suppressor genes directly from histopathology with Deep Learning: A systematic study across 23 solid tumor types. Front. Genet., (12):806386, 2021. [PUMA: (AI); TCGA; artificail cancer deep genes; genetic intelligence pathway pathway; zno learning]

Markus Kreuz, Dominik J Otto, Susanne Fuessel, Conny Blumert, Catharina Bertram, Sophie Bartsch, Dennis Loeffler, Sven-Holger Puppel, Michael Rade, Tilo Buschmann, Sabina Christ, Kati Erdmann, Maik Friedrich, Michael Froehner, Michael H Muders, Stephan Schreiber, Michael Specht, Marieta I Toma, Fabio Benigni, Massimo Freschi, Giorgio Gandaglia, Alberto Briganti, Gustavo B Baretton, Markus Loeffler, Jörg Hackermüller, Kristin Reiche, Manfred Wirth, and Friedemann Horn. ProstaTrend-A multivariable prognostic RNA expression score for aggressive prostate cancer. Eur. Urol., (78)3:452--459, Elsevier BV, September 2020. [PUMA: Biomarker; Molecular Next-generation Personalized Prostate Transcriptome diagnostic medicine; sequencing; testing; zno pathology biomarker cancer]

Mariia Tkachenko, Claire Chalopin, Boris Jansen-Winkeln, Thomas Neumuth, Ines Gockel, and Marianne Maktabi. Impact of pre- and post-processing steps for supervised classification of colorectal cancer in hyperspectral images. Cancers (Basel), (15)7April 2023. [PUMA: cancer classification colorectal convolutional filter hyperspectral imaging learning machine median networks post-processing pre-processing topic_lifescience yaff]