Prof. Dr. med. Viktor Kölzer

van den Berg, Nikki, Schoenpflug, Lydia, Horeweg, Nanda, Volinsky-Fremond, Sarah, Barkey-Wolf, Jurriaan, Andani, Sonali, Lafarge, Maxime W, Oertft, Gitte, Jobsen, Jan J., Razack, Rubina, Gerestein, Kees, Jonges, Trudy, de Kroon, Cor D., Nout, Remi, Tseng, Dorine, Kuijsters, Nienke, Powell, Melanie E., Khaw, Pearly, Shepherd, Lois, et al. (2026). Deep Learning-Based Screening for POLE mutations on Histopathology Slides in Endometrial Cancer [Posted-content]. In medRxiv. https://doi.org/10.64898/2026.02.06.26345335

Bräutigam, Konstantin, Baker, Ann‐Marie, Koelzer, Viktor H, Kather, Jakob N, & Graham, Trevor A. (2026). Integrating artificial intelligence ( AI ) into colorectal cancer reporting. Journal of Pathology. https://doi.org/10.1002/path.70029

Chen, Boqi, Vincent-Cuaz, Cédric, Schoenpflug, Lydia A., Madeira, Manuel, Fournier, Lisa, Subramanian, Vaishnavi, Andani, Sonali, Ruiperez-Campillo, Samuel, Vogt, Julia E., Luisier, Raphaëlle, Thanou, Dorina, Koelzer, Viktor H., Frossard, Pascal, Campanella, Gabriele, & Rätsch, Gunnar. (2026). Revisiting Automatic Data Curation for Vision Foundation Models in Digital Pathology. In Lecture Notes in Computer Science: Vol. 15965 LNCS (pp. 554–564). Springer Science and Business Media Deutschland GmbH. https://doi.org/10.1007/978-3-032-04978-0_53

Gosztonyi, Benedict, Mehra, Tarun, Gut, Gabriele, Miglino, Nicola, Ring, Alexander, Martínez Gómez, Julia M., Ramelyte, Egle, Sobottka, Bettina, Koelzer, Viktor Hendrik, Moch, Holger, Levesque, Mitchell P., Mangana, Joanna, Dummer, Reinhard, Boos, Laura, Wicki, Andreas, Aebersold, Rudolf, Ak, Melike, Al-Quaddoomi, Faisal S., Albert, Silvana I., et al. (2026). Safety of Multi-Omics–Guided Therapy in Advanced Melanoma: A Matched Comparative Cohort Analysis [Journal-article]. JCO Precision Oncology, 10(1). https://doi.org/10.1200/po-25-00896

Pnev, S., Wolleb, J., Fuller, J. C., Rammelt, P., Koelzer, V. H., & Cattin, P. C. (2026). Scheduled Cross-Domain Multi-center DINO for Robust High-Content Screening Representation Learning [Book-chapter]. In Lecture Notes in Computer Science: Vol. 16241 LNCS (pp. 432–441). Springer Science and Business Media Deutschland GmbH. https://doi.org/10.1007/978-3-032-09513-8_42

Frei, Céline Arlette, Litchfield, Cassandra, Mihic, Alanna, Prutek, Fabiola, Fitsche, André, Wiesmann, Fabius, Wanner, Miriam, Sobottka, Bettina, Mihic-Probst, Daniela, Aebersold, Rudolf, Ak, Melike, Al-Quaddoomi, Faisal S., Albert, Silvana I., Albinus, Jonas, Alborelli, Ilaria, Andani, Sonali, Attinger, Per-Olof, Bacac, Marina, Baciu-Drăgan, Monica-Andreea, et al. (2025). The chromatin guardian ATRX is a strong prognostic biomarker in melanoma. Scientific Reports, 16(1). https://doi.org/10.1038/s41598-025-30842-4

Mehra, Tarun, Menges, Dominik, Gosztonyi, Benedict, Miglino, Nicola, Ring, Alexander, Boos, Laura, Sobottka, Bettina, Aebersold, Rudolf, Ak, Melike, Al-Quaddoomi, Faisal S., Albert, Silvana I., Albinus, Jonas, Alborelli, Ilaria, Andani, Sonali, Attinger, Per-Olof, Bacac, Marina, Baciu-Drăgan, Monica-Andreea, Baumhoer, Daniel, Beck-Schimmer, Beatrice, et al. (2025). Comparative cost analysis of a diagnostic multi-omics platform for decision support in advanced cancer – results from the Tumor Profiler Melanoma project. npj Precision Oncology, 10(1). https://doi.org/10.1038/s41698-025-01229-5

Shin, JaeWoong, Ryu, Jeongun, Puche, Aaron Valero, Lee, Jinhee, Brattoli, Biagio, Jung, Wonkyung, Cho, Soo Ick, Paeng, Kyunghyun, Ock, Chan-Young, Yoo, Donggeun, Li, Zhaoyang, Li, Wangkai, Mai, Huayu, Millward, Joshua, He, Zhen, Nibali, Aiden, Schoenpflug, Lydia Anette, Koelzer, Viktor Hendrik, Shuoyu, Xu, et al. (2025). OCELOT 2023: Cell detection from cell–tissue interaction challenge. Medical Image Analysis, 106. https://doi.org/10.1016/j.media.2025.103751

Schmid, Dominic, Sobottka, Bettina, Manzo, Massimiliano, Trüb, Marta, Leonards, Katharina, Herzig, Petra, Oyewole, Oluwaseun Rume-Abiola, Jermann, Philip, Hayoz, Stefanie, Savic Prince, Spasenija, Tochtermann, Giulia, Natoli, Marina, Pless, Miklos, Bettini, Adrienne, Früh, Martin, Mauti, Laetitia A., Britschgi, Christian, Peters, Solange, Mark, Michael, et al. (2025). Tumor immune dynamics and long-term clinical outcome of stage IIIA NSCLC patients treated with neoadjuvant chemoimmunotherapy. Nature Communications, 16(1). https://doi.org/10.1038/s41467-025-63696-5

Nonchev, K., Manaiev, G., Koelzer, V. H., & Rätsch, G. (2025). DeepSpot2Cell: Predicting Virtual Single-Cell Spatial Transcriptomics from H&E images using Spot-Level Supervision [Posted-content]. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2025.09.23.678121

Wiesmann, F., Litchfield, C., Mayoux, M., Consortium, T. P., Wicki, A., Becher, B., Koelzer, V. H., Moch, H., Buljan, M., Tugues, S., & Sobottka, B. (2025). RIPPLET: Mutation-Only Gene and Pathway Profiling for Precision Oncology [Posted-content]. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2025.09.17.676675

Fusi, Irene, Serger, Clara, Herzig, Petra, Germann, Markus, Sandholzer, Michael T., Oelgarth, Nicole, Schwalie, Petra C., Don, Leyla, Vetter, Viola K., Koelzer, Viktor H., Lardinois, Didier, Kao, Henry, Deak, Laura Codarri, Umaña, Pablo, Klein, Christian, Hojski, Aljaz, Natoli, Marina, & Zippelius, Alfred. (2025). PD-1–targeted cis-delivery of an IL-2 variant induces a multifaceted antitumoral T cell response in human lung cancer. Science Translational Medicine, 17(816). https://doi.org/10.1126/scitranslmed.adr3718

Bräutigam, Konstantin, Zens, Philipp, Reinhard, Stefan, Rohrbach, Jessica L., Leedham, Simon J., Wenning, Anna S., Gloor, Beat, Koelzer, Viktor H., & Wartenberg, Martin. (2025). Spatially resolved analysis of TGF/BMP signalling in pancreatic ductal adenocarcinoma by digital pathology identifies patient subgroups with adverse outcome. BMC Cancer, 25(1). https://doi.org/10.1186/s12885-025-14751-3

Andani, Sonali, Chen, Boqi, Ficek-Pascual, Joanna, Heinke, Simon, Casanova, Ruben, Hild, Bernard Friedrich, Sobottka, Bettina, Bodenmiller, Bernd, Aebersold, Rudolf, Ak, Melike, Al-Quaddoomi, Faisal S., Albert, Silvana I., Albinus, Jonas, Alborelli, Ilaria, Andani, Sonali, Attinger, Per-Olof, Bacac, Marina, Baumhoer, Daniel, Beck-Schimmer, Beatrice, et al. (2025). Histopathology-based protein multiplex generation using deep learning. Nature Machine Intelligence, 7(8), 1292–1307. https://doi.org/10.1038/s42256-025-01074-y

Litchfield, Cassandra, Nienhold, Ronny, Wicki, Andreas, Schmid, Michael, Aguilera-Garcia, Domingo, Koelzer, Viktor Hendrik, Aebersold, Rudolf, Ak, Melike, Al-Quaddoomi, Faisal S., Albert, Silvana I., Albinus, Jonas, Alborelli, Ilaria, Andani, Sonali, Attinger, Per-Olof, Bacac, Marina, Baciu-Drăgan, Monica-Andreea, Baumhoer, Daniel, Beck-Schimmer, Beatrice, Beerenwinkel, Niko, et al. (2025). Integrating Formalin-Fixed, Paraffin-Embedded–Derived Whole-Genome Sequencing into Routine Molecular Pathology: Validation and First Experiences in Metastatic Melanoma. Journal of Molecular Diagnostics, 27, 722–735. https://doi.org/10.1016/j.jmoldx.2025.04.011

Schoenpflug, Lydia A., Bagan Benavides, Ruben, Nowak, Marta, Sheikhzadeh, Fahime, Moayyedi, Arash, Wasag, Kamil, Reimers, Jacob, Zhou, Michael, Venugopal, Raghavan, Sobottka, Bettina, Koeller, Yasmin, Rivers, Michael, Moch, Holger, Nie, Yao, & Koelzer, Viktor H. (2025). Navigating real-world challenges: A case study on federated learning in computational pathology. Journal of Pathology Informatics, 18. https://doi.org/10.1016/j.jpi.2025.100464

Berg, I., Wu, J., & Koelzer, V. H. (2025). Generative cerebral vasculature visualization using spatial transcriptomic data [Posted-content]. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2025.07.10.664153

Miglino, Nicola, Toussaint, Nora C., Ring, Alexander, Bonilla, Ximena, Tusup, Marina, Gosztonyi, Benedict, Mehra, Tarun, Gut, Gabriele, Jacob, Francis, Chevrier, Stephane, Lehmann, Kjong-Van, Casanova, Ruben, Jacobs, Andrea, Sivapatham, Sujana, Boos, Laura, Rahimzadeh, Parisa, Schuerch, Manuel, Sobottka, Bettina, Chicherova, Natalia, et al. (2025). Feasibility of multiomics tumor profiling for guiding treatment of melanoma. Nature Medicine, 31, 2430–2441. https://doi.org/10.1038/s41591-025-03715-6

Rubin, David T, Kubassova, Olga, Weber, Christopher R, Adsul, Shashi, Freire, Marcelo, Biedermann, Luc, Koelzer, Viktor H, Bressler, Brian, Xiong, Wei, Niess, Jan H, Matter, Matthias S, Kopylov, Uri, Barshack, Iris, Mayer, Chen, Magro, Fernando, Carneiro, Fatima, Maharshak, Nitsan, Greenberg, Ariel, Hart, Simon, et al. (2025). Deployment of an Artificial Intelligence Histology Tool to Aid Qualitative Assessment of Histopathology Using the Nancy Histopathology Index in Ulcerative Colitis. Inflammatory Bowel Diseases, 31(6), 1630–1636. https://doi.org/10.1093/ibd/izae204

Nonchev, Kalin, Dawo, Sebastian, Silina, Karina, Moch, Holger, Andani, Sonali, Koelzer, Viktor H, & Rätsch, Gunnar. (2025). DeepSpot: Leveraging Spatial Context for Enhanced Spatial Transcriptomics Prediction from H&E Images [Posted-content]. Neural Information Processing Systems (NeurIPS), 1–10. https://doi.org/10.1101/2025.02.09.25321567

Schoenpflug, Lydia A, Chatzipli, Aikaterini, Sirinukunwattana, Korsuk, Richman, Susan, Blake, Andrew, Robineau, James, Mertz, Kirsten D, Verrill, Clare, Leedham, Simon, Hardy, Claire, Whalley, Celina, Redmond, Keara, Dunne, Philip, Walker, Steven, Beggs, Andrew, McDermott, Ultan, Murray, Graeme, Samuel, Les, Seymour, Matt, et al. (2025). Tumour purity assessment with deep learning in colorectal cancer and impact on molecular analysis. Journal of Pathology, 265(2), 184–197. https://doi.org/10.1002/path.6376

Palles, Claire, Freeman-Mills, Luke, Arbe-Barnes, Edward, Feeley, Nathalie, Chegwidden, Laura, Curley, Helen, Galavotti, Sara, Woolley, Connor, Cheadle, Jeremy, Mouradov, Dmitri, Sieber, Oliver, Salatino, Silvia, Thorn, Steve, Goel, Anshita, Fernandez-Tajes, Juan, Omwenga, Sulochana, Biswas, Sujata, Maughan, Timothy, Leedham, Simon J, et al. (2025). Comparison between germline and somatic loss-of-function RNF43 mutations reveals different genotype-phenotype associations and provides insights into the genetic mechanisms of colorectal tumourigenesis. Gut. https://doi.org/10.1136/gutjnl-2025-337030

Vledder, Annegé, Paijens, Sterre T., Loiero, Dominik, Maagdenberg, Alexis, Duiker, Evelien W., Bart, Joost, Hendriks, Anne M., Jalving, Mathilde, Werner, Naomi, van Rooij, Nienke, Plat, Annechien, Wisman, G. Bea A., Yigit, Refika, Roelofsen, Thijs, Kruse, Arnold J., de Lange, Nastascha M., Koelzer, Viktor H., de Bruyn, Marco, & Nijman, Hans W. (2024). B cells critical for outcome in high grade serous ovarian carcinoma. International Journal of Cancer, 155(12), 2265–2276. https://doi.org/10.1002/ijc.35149

Eerkens, Anneke L., Brummel, Koen, Vledder, Annegé, Paijens, Sterre T., Requesens, Marta, Loiero, Dominik, van Rooij, Nienke, Plat, Annechien, Haan, Floris-Jan, Klok, Patty, Yigit, Refika, Roelofsen, Thijs, de Lange, Natascha M., Klomp, Rie, Church, David, ter Elst, Arja, Wardenaar, René, Spierings, Diana, Foijer, Floris, et al. (2024). Neoadjuvant immune checkpoint blockade in women with mismatch repair deficient endometrial cancer: a phase I study. Nature Communications , 15(1). https://doi.org/10.1038/s41467-024-52098-8

Fan, Fan, Martinez, Georgia, DeSilvio, Thomas, Shin, John, Chen, Yijiang, Jacobs, Jackson, Wang, Bangchen, Ozeki, Takaya, Lafarge, Maxime W., Koelzer, Viktor H., Barisoni, Laura, Madabhushi, Anant, Viswanath, Satish E., & Janowczyk, Andrew. (2024). CohortFinder: an open-source tool for data-driven partitioning of digital pathology and imaging cohorts to yield robust machine-learning models. npj Imaging, 2(1). https://doi.org/10.1038/s44303-024-00018-2

Lafarge, Maxime W., Domingo, Enric, Sirinukunwattana, Korsuk, Wood, Ruby, Samuel, Leslie, Murray, Graeme, Richman, Susan D., Blake, Andrew, Sebag-Montefiore, David, Gollins, Simon, Klieser, Eckhard, Neureiter, Daniel, Huemer, Florian, Greil, Richard, Dunne, Philip, Quirke, Philip, Weiss, Lukas, Rittscher, Jens, Maughan, Tim, & Koelzer, Viktor H. (2024). Image-based consensus molecular subtyping in rectal cancer biopsies and response to neoadjuvant chemoradiotherapy. Npj Precision Oncology, 8(1). https://doi.org/10.1038/s41698-024-00580-3

Schoenpflug, Lydia A., Nie, Yao, Sheikhzadeh, Fahime, & Koelzer, Viktor H. (2024). A review on federated learning in computational pathology. Computational and Structural Biotechnology Journal, 23, 3938–3945. https://doi.org/10.1016/j.csbj.2024.10.037

Wegmann, Rebekka, Bonilla, Ximena, Casanova, Ruben, Chevrier, Stéphane, Coelho, Ricardo, Esposito, Cinzia, Ficek-Pascual, Joanna, Goetze, Sandra, Gut, Gabriele, Jacob, Francis, Jacobs, Andrea, Kuipers, Jack, Lischetti, Ulrike, Mena, Julien, Milani, Emanuela S., Prummer, Michael, del Castillo, Jacobo Sarabia, Singer, Franziska, Sivapatham, Sujana, et al. (2024). Single-cell landscape of innate and acquired drug resistance in acute myeloid leukemia. Nature Communications , 15(1). https://doi.org/10.1038/s41467-024-53535-4

Wu, Jiqing, & Koelzer, Viktor H. (2024). Towards generative digital twins in biomedical research. Computational and Structural Biotechnology Journal, 23, 3481–3488. https://doi.org/10.1016/j.csbj.2024.09.030

Sobottka, Bettina, Vetter, Viola, Banaei-Esfahani, Amir, Nowak, Marta, Lorch, Anja, Sirek, Andrej, Mertz, Kirsten D., Brunelli, Matteo, Berthold, Dominik, de Leval, Laurence, Kahraman, Abdullah, Koelzer, Viktor Hendrik, & Moch, Holger. (2024). Immune Phenotype-Genotype Associations in Primary Clear Cell Renal Cell Carcinoma and Matched Metastatic Tissue. Modern Pathology, 37(10). https://doi.org/10.1016/j.modpat.2024.100558

Roth, Lilian, Huynh-Russo, Linda, Heeb, Laura, Ulugöl, Sima, Freire Dos Santos, Rafael, Breuer, Eva, Ungethüm, Udo, Haberecker, Martina, Pauli, Chantal, Koelzer, Viktor, Lehmann, Kuno, & Gupta, Anurag. (2024). CD8 + T-cells restrict the development of peritoneal metastasis and support the efficacy of hyperthermic intraperitoneal chemotherapy (HIPEC). Scientific Reports, 14(1). https://doi.org/10.1038/s41598-024-72826-w

Nowak, Marta, Jabbar, Faiz, Rodewald, Ann-Katrin, Gneo, Luciana, Tomasevic, Tijana, Harkin, Andrea, Iveson, Tim, Saunders, Mark, Kerr, Rachel, Oein, Karin, Maka, Noori, Hay, Jennifer, Edwards, Joanne, Tomlinson, Ian, Sansom, Owen, Kelly, Caroline, Pezzella, Francesco, Kerr, David, Easton, Alistair, et al. (2024). Single-cell AI-based detection and prognostic and predictive value of DNA mismatch repair deficiency in colorectal cancer. Cell Reports Medicine, 5(9). https://doi.org/10.1016/j.xcrm.2024.101727

Huellner, M. W., Bühler, M. M., Kölzer, V. H., Limani, P., & Rösler, W. (2024). Distinct [18F]FDG-PET imaging features of a newly recognized and yet uncharacterized RDD-ECD overlap disease entity. European Journal of Nuclear Medicine and Molecular Imaging, 51(11), 3465–3466. https://doi.org/10.1007/s00259-024-06751-5

Wu, Jiqing, & Koelzer, Viktor H. (2024). GILEA: In silico phenome profiling and editing using GAN Inversion. Computers in Biology and Medicine, 179. https://doi.org/10.1016/j.compbiomed.2024.108825

Domingo, Enric, Rathee, Sanjay, Blake, Andrew, Samuel, Leslie, Murray, Graeme, Sebag-Montefiore, David, Gollins, Simon, West, Nicholas, Begum, Rubina, Richman, Susan, Quirke, Phil, Redmond, Keara, Chatzipli, Aikaterini, Barberis, Alessandro, Hassanieh, Sylvana, Mahmood, Umair, Youdell, Michael, McDermott, Ultan, Koelzer, Viktor, et al. (2024). Identification and validation of a machine learning model of complete response to radiation in rectal cancer reveals immune infiltrate and TGFβ as key predictors. eBioMedicine, 106. https://doi.org/10.1016/j.ebiom.2024.105228

Immer, Alexander, Stark, Stefan G, Jacob, Francis, Bonilla, Ximena, Thomas, Tinu, Kahles, André, Goetze, Sandra, Milani, Emanuela S, Wollscheid, Bernd, Aebersold, Rudolf, Ak, Melike, Al-Quaddoomi, Faisal S, Albert, Silvana I, Albinus, Jonas, Alborelli, Ilaria, Andani, Sonali, Attinger, Per-Olof, Bacac, Marina, Baumhoer, Daniel, et al. (2024). Probabilistic pathway-based multimodal factor analysis. Bioinformatics, 40(Supplement_1), i189–i198. https://doi.org/10.1093/bioinformatics/btae216

Janowczyk, Andrew, Zlobec, Inti, Walker, Cedric, Berezowska, Sabina, Huschauer, Viola, Tinguely, Marianne, Kupferschmid, Joel, Mallet, Thomas, Merkler, Doron, Kreutzfeldt, Mario, Gasic, Radivoje, Rau, Tilman T., Mazzucchelli, Luca, Eyberg, Isgard, Cathomas, Gieri, Mertz, Kirsten D., Koelzer, Viktor H., Soldini, Davide, Jochum, Wolfram, et al. (2024). Swiss digital pathology recommendations: results from a Delphi process conducted by the Swiss Digital Pathology Consortium of the Swiss Society of Pathology. Virchows Archiv, 485(1), 13–30. https://doi.org/10.1007/s00428-023-03712-5

Mahmood, Umair, Blake, Andrew, Rathee, Sanjay, Samuel, Leslie, Murray, Graeme, Sebag-Montefiore, David, Gollins, Simon, West, Nicholas P., Begum, Rubina, Bach, Simon P., Richman, Susan D., Quirke, Phil, Redmond, Keara L., Salto-Tellez, Manuel, Koelzer, Viktor H., Leedham, Simon J., Tomlinson, Ian, Dunne, Philip D., Buffa, Francesca M., et al. (2024). Stratification to Neoadjuvant Radiotherapy in Rectal Cancer by Regimen and Transcriptional Signatures. Cancer Research Communications, 4(7), 1765–1776. https://doi.org/10.1158/2767-9764.crc-23-0502

Mahmood ,Umair, Blake, Andrew, Rathee, Sanjay, Samuel, Leslie, Murray ,Graeme, Sebag-Montefiore, David, Gollins, Simon, West, Nicholas P, Begum, Rubina, Bach, Simon P, Richman, Susan D, Quirke, Phil, Redmond Keara L, Salto-Tellez, Manuel, Koelzer, Viktor H, Leedham, Simon J, Tomlinson, Ian, Dunne, Philip D, Buffa, Francesca M, et al. (2024). Stratification to Neoadjuvant Radiotherapy in Rectal Cancer by Regimen and Transcriptional Signatures. Cancer Research Communications, 4(7), 1765–1776. https://doi.org/10.1158/2767-9764.CRC-23-0502

Volinsky-Fremond, Sarah, Horeweg, Nanda, Andani, Sonali, Barkey Wolf, Jurriaan, Lafarge, Maxime W., de Kroon, Cor D., Ørtoft, Gitte, Høgdall, Estrid, Dijkstra, Jouke, Jobsen, Jan J., Lutgens, Ludy C. H. W., Powell, Melanie E., Mileshkin, Linda R., Mackay, Helen, Leary, Alexandra, Katsaros, Dionyssios, Nijman, Hans W., de Boer, Stephanie M., Nout, Remi A., et al. (2024). Author Correction: Prediction of recurrence risk in endometrial cancer with multimodal deep learning (Nature Medicine, (2024), 30, 7, (1962-1973), 10.1038/s41591-024-02993-w). Nature Medicine, 30(7), 2092. https://doi.org/10.1038/s41591-024-03126-z

Volinsky-Fremond, Sarah, Horeweg, Nanda, Andani, Sonali, Barkey Wolf, Jurriaan, Lafarge, Maxime W., de Kroon, Cor D., Ørtoft, Gitte, Høgdall, Estrid, Dijkstra, Jouke, Jobsen, Jan J., Lutgens, Ludy C. H. W., Powell, Melanie E., Mileshkin, Linda R., Mackay, Helen, Leary, Alexandra, Katsaros, Dionyssios, Nijman, Hans W., de Boer, Stephanie M., Nout, Remi A., et al. (2024). Prediction of recurrence risk in endometrial cancer with multimodal deep learning. Nature Medicine, 30(7), 1962–1973. https://doi.org/10.1038/s41591-024-02993-w

Domingo, Enric, Kelly, Caroline, Hay, Jennifer, Sansom, Owen, Maka, Noori, Oien, Karin, Iveson, Tim, Saunders, Mark, Kerr, Rachel, Tomlinson, Ian, Edwards, Joanne, Harkin, Andrea, Nowak, Marta, Koelzer, Viktor, Easton, Alistair, Boukovinas, Ioannis, Moustou, Eleni, Messaritakis, Ippokratis, Chondrozoumaki, Maria, et al. (2024). Prognostic and Predictive Value of Immunoscore in Stage III Colorectal Cancer: Pooled Analysis of Cases From the SCOT and IDEA-HORG Studies. Journal of Clinical Oncology, 42(18), 2207–2218. https://doi.org/10.1200/jco.23.01648

Malla, Sudhir B., Byrne, Ryan M., Lafarge, Maxime W., Corry, Shania M., Fisher, Natalie C., Tsantoulis, Petros K., Mills, Megan L., Ridgway, Rachel A., Lannagan, Tamsin R. M., Najumudeen, Arafath K., Gilroy, Kathryn L., Amirkhah, Raheleh, Maguire, Sarah L., Mulholland, Eoghan J., Belnoue-Davis, Hayley L., Grassi, Elena, Viviani, Marco, Rogan, Emily, Redmond, Keara L., et al. (2024). Correction to: Pathway level subtyping identifies a slow-cycling biological phenotype associated with poor clinical outcomes in colorectal cancer (Nature Genetics, (2024), 56, 3, (458-472), 10.1038/s41588-024-01654-5). Nature Genetics, 56(6), 1321. https://doi.org/10.1038/s41588-024-01809-4

Wakkerman, Famke C, Wu, Jiqing, Putter, Hein, Jürgenliemk-Schulz, Ina M, Jobsen, Jan J, Lutgens, Ludy C H W, Haverkort, Marie A D, de Jong, Marianne A, Mens, Jan Willem M, Wortman, Bastiaan G, Nout, Remi A, Léon-Castillo, Alicia, Powell, Melanie E, Mileshkin, Linda R, Katsaros, Dionyssios, Alfieri, Joanne, Leary, Alexandra, Singh, Naveena, de Boer, Stephanie M, et al. (2024). Prognostic impact and causality of age on oncological outcomes in women with endometrial cancer: a multimethod analysis of the randomised PORTEC-1, PORTEC-2, and PORTEC-3 trials. The Lancet Oncology, 25(6), 779–789. https://doi.org/10.1016/s1470-2045(24)00142-6

Aubreville, Marc, Stathonikos, Nikolas, Donovan, Taryn A., Klopfleisch, Robert, Ammeling, Jonas, Ganz, Jonathan, Wilm, Frauke, Veta, Mitko, Jabari, Samir, Eckstein, Markus, Annuscheit, Jonas, Krumnow, Christian, Bozaba, Engin, Çayır, Sercan, Gu, Hongyan, Chen, Xiang ‘Anthony’, Jahanifar, Mostafa, Shephard, Adam, Kondo, Satoshi, et al. (2024). Domain generalization across tumor types, laboratories, and species — Insights from the 2022 edition of the Mitosis Domain Generalization Challenge. Medical Image Analysis, 94. https://doi.org/10.1016/j.media.2024.103155

Malla, Sudhir B., Byrne, Ryan M., Lafarge, Maxime W., Corry, Shania M., Fisher, Natalie C., Tsantoulis, Petros K., Mills, Megan L., Ridgway, Rachel A., Lannagan, Tamsin R. M., Najumudeen, Arafath K., Gilroy, Kathryn L., Amirkhah, Raheleh, Maguire, Sarah L., Mulholland, Eoghan J., Belnoue-Davis, Hayley L., Grassi, Elena, Viviani, Marco, Rogan, Emily, Redmond, Keara L., et al. (2024). Pathway level subtyping identifies a slow-cycling biological phenotype associated with poor clinical outcomes in colorectal cancer. Nature Genetics, 56(3), 458–472. https://doi.org/10.1038/s41588-024-01654-5

Nasreddin, Nadia, Jansen, Marnix, Loughrey, Maurice B., Wang, Lai Mun, Koelzer, Viktor H., Rodriguez-Justo, Manuel, Novelli, Marco, Fisher, Jennifer, Brown, Matthew W., Al Bakir, Ibrahim, Hart, Ailsa L., Dunne, Philip, Graham, Trevor A., & Leedham, Simon J. (2024). Poor Diagnostic Reproducibility in the Identification of Nonconventional Dysplasia in Colitis Impacts the Application of Histologic Stratification Tools. Modern Pathology, 37(3). https://doi.org/10.1016/j.modpat.2023.100419

Wu, Jiqing, & Koelzer, Viktor H. (2024). SST-editing: in silico spatial transcriptomic editing at single-cell resolution. Bioinformatics, 40(3). https://doi.org/10.1093/bioinformatics/btae077

Frei, Anja L, McGuigan, Anthony, Sinha, Ritik R A K, Jabbar, Faiz, Gneo, Luciana, Tomasevic, Tijana, Harkin, Andrea, Iveson, Timothy, Saunders, Mark P, Oien, Karin A, Maka, Noori, Pezzella, Francesco, Campo, Leticia, Browne, Molly, Glaire, Mark, Kildal, Wanja, Danielsen, Havard E, Hay, Jen, Edwards, Joanne, et al. (2024). Multiplex analysis of intratumoural immune infiltrate and prognosis in patients with stage II–III colorectal cancer from the SCOT and QUASAR 2 trials: a retrospective analysis. The Lancet Oncology, 25(2), 198–211. https://doi.org/10.1016/s1470-2045(23)00560-0

Frei, Anja L, McGuigan, Anthony, Sinha, Ritik R A K, Jabbar, Faiz, Gneo, Luciana, Tomasevic, Tijana, Harkin, Andrea, Iveson, Tim, Saunders, Mark P, Oien, Karin A, Maka, Noori, Pezzella, Francesco, Campo, Leticia, Browne, Molly, Glaire, Mark, Kildal, Wanja, Danielsen, Harvard E, Hay, Jennifer, Edwards, Joanne, et al. (2024). Multiplex analysis of intratumoural immune infiltrate and prognosis in patients with stage II-III colorectal cancer from the SCOT and QUASAR 2 trials: a retrospective analysis. The Lancet Oncology, 25(2), 198–211. https://doi.org/10.1016/S1470-2045(23)00560-0

Jiqing, Wu, Ingrid, Berg, & Viktor Koelzer. (2024, January 1). IST-editing: Infinite spatial transcriptomic editing in a generated gigapixel mouse pup. Medical Imaging with Deep Learning 2024.

Lafarge, Maxime W., & Koelzer, Viktor Hendrik. (2024). Detecting Cells in Histopathology Images with a ResNet Ensemble Model. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 14373 LNCS, 123–129. https://doi.org/10.1007/978-3-031-55088-1_11

Wakkerman, Famke C, Wu, Jiqing, Putter, Hein, Jürgenliemk-Schulz, Ina M, Jobsen, Jan J, Lutgens, Ludy C H W, Haverkort, Marie A D, de Jong, Marianne A, Mens, Jan Willem M, Wortman, Bastiaan G, Nout, Remi A, Léon-Castillo, Alicia, Powell, Melanie E, Mileshkin, Linda R, Katsaros, Dionyssios, Alfieri ,Joanne, Leary, Alexandra, Singh, Naveena, de Boer, Stephanie M, Nijman, Hans W, Smit, Vincent T H B M, et al. (2024). Prognostic impact and causality of age on oncological outcomes in women with endometrial cancer: a multimethod analysis of the randomised PORTEC-1, PORTEC-2, and PORTEC-3 trials. The Lancet Oncology, 779–789. https://doi.org/10.1016/S1470-2045(24)00142-6

Wood, Ruby, Domingo, Enric, Koelzer, Viktor Hendrik, Maughan, Timothy S., & Rittscher, Jens. (2024). Cluster Triplet Loss for Unsupervised Domain Adaptation on Histology Images. IEEE Computer Society Conference on Computer Vision and Pattern Recognition Workshops, 5122–5131. https://doi.org/10.1109/cvprw63382.2024.00519

Brouwer, Nelleke PM, Webbink, Loth, Haddad, Tariq S, Rutgers, Natasja, van Vliet, Shannon, Wood, Colin S, Jansen, Pascal WTC, Lafarge, Maxime W, de Wilt, Johannes HW, Hugen, Niek, Simmer, Femke, Jamieson, Nigel B, Tauriello, Daniele VF, Kölzer, Viktor H, Vermeulen, Michiel, & Nagtegaal, Iris D. (2023). Transcriptomics and proteomics reveal distinct biology for lymph node metastases and tumour deposits in colorectal cancer. Journal of Pathology, 261(4), 401–412. https://doi.org/10.1002/path.6196

Dondi, Arthur, Lischetti, Ulrike, Jacob, Francis, Singer, Franziska, Borgsmüller, Nico, Coelho, Ricardo, Aebersold, Rudolf, Ak, Melike, Al-Quaddoomi, Faisal S., Albert, Silvana I., Albinus, Jonas, Alborelli, Ilaria, Andani, Sonali, Attinger, Per-Olof, Bacac, Marina, Baumhoer, Daniel, Beck-Schimmer, Beatrice, Beisel, Christian, Bernasconi, Lara, et al. (2023). Detection of isoforms and genomic alterations by high-throughput full-length single-cell RNA sequencing in ovarian cancer. Nature Communications, 14(1). https://doi.org/10.1038/s41467-023-43387-9

Grobholz, Rainer, Janowczyk, Andrew, Frei, Ana Leni, Kreutzfeldt, Mario, Koelzer, Viktor H., & Zlobec, Inti. (2023). National digital pathology projects in Switzerland: A 2023 update. Pathologie, 44, 225–228. https://doi.org/10.1007/s00292-023-01259-5

Frei, Anja L, McGuigan, Anthony, Sinha, Ritik RAK, Glaire, Mark A, Jabbar, Faiz, Gneo, Luciana, Tomasevic, Tijana, Harkin, Andrea, Iveson, Tim J, Saunders, Mark, Oein, Karin, Maka, Noori, Pezella, Francesco, Campo, Leticia, Hay, Jennifer, Edwards, Joanne, Sansom, Owen J, Kelly, Caroline, Tomlinson, Ian, et al. (2023). Accounting for intensity variation in image analysis of large-scale multiplexed clinical trial datasets. Journal of Pathology: Clinical Research, 9(6), 449–463. https://doi.org/10.1002/cjp2.342

Marques-Maggio, Ewerton, Maccio, Umberto, Marx, Alexandra, Galli, Serena, Schwab, Nathalie, Frank, Angela, Hamelin, Baptiste, Varga, Zsuzsanna, Nombela-Arrieta, César, Mertz, Kirsten D, Theocharides, Alexandre PA, & Koelzer, Viktor H. (2023). Bone marrow haematopoiesis in patients with COVID-19. Histopathology, 83(4), 582–590. https://doi.org/10.1111/his.14969

Wagner, Sophia J., Reisenbüchler, Daniel, West, Nicholas P., Niehues, Jan Moritz, Zhu, Jiefu, Foersch, Sebastian, Veldhuizen, Gregory Patrick, Quirke, Philip, Grabsch, Heike I., van den Brandt, Piet A., Hutchins, Gordon G.A., Richman, Susan D., Yuan, Tanwei, Langer, Rupert, Jenniskens, Josien C.A., Offermans, Kelly, Mueller, Wolfram, Gray, Richard, Gruber, Stephen B., et al. (2023). Transformer-based biomarker prediction from colorectal cancer histology: A large-scale multicentric study. Cancer Cell, 41(9), 1650–1661. https://doi.org/10.1016/j.ccell.2023.08.002

Kleeman, Sam O., Thakir, Tuba Mansoor, Demestichas, Breanna, Mourikis, Nicholas, Loiero, Dominik, Ferrer, Miriam, Bankier, Sean, Riazat-Kesh, Yosef J.R.A., Lee, Hassal, Chantzichristos, Dimitrios, Regan, Claire, Preall, Jonathan, Sinha, Sarthak, Rosin, Nicole, Yipp, Bryan, de Almeida, Luiz G.N., Biernaskie, Jeff, Dufour, Antoine, Tober-Lau, Pinkus, et al. (2023). Cystatin C is glucocorticoid responsive, directs recruitment of Trem2+ macrophages, and predicts failure of cancer immunotherapy. Cell Genomics, 3(8). https://doi.org/10.1016/j.xgen.2023.100347

Freiberger, Sandra N., Holzmann, David, Morand, Grégoire B., Hüllner, Martin, Levesque, Mitchell P., Dummer, Reinhard, Koelzer, Viktor H., & Rupp, Niels J. (2023). Combinational expression of tumor testis antigens NY-ESO-1, MAGE-A3, and MAGE-A4 predicts response to immunotherapy in mucosal melanoma patients. Journal of Cancer Research and Clinical Oncology, 149(9), 5645–5653. https://doi.org/10.1007/s00432-022-04514-z

Pinto Couto, Joana, Vulin, Milica, Jehanno, Charly, Coissieux, Marie-May, Hamelin, Baptiste, Schmidt, Alexander, Ivanek, Robert, Sethi, Atul, Bräutigam, Konstantin, Frei, Anja L, Hager, Carolina, Manivannan, Madhuri, Gómez-Miragaya, Jorge, Obradović, Milan MS, Varga, Zsuzsanna, Koelzer, Viktor H, Mertz, Kirsten D, & Bentires-Alj, Mohamed. (2023). Nicotinamide N-methyltransferase sustains a core epigenetic program that promotes metastatic colonization in breast cancer. EMBO Journal, 42(13). https://doi.org/10.15252/embj.2022112559

Prummer, Michael, Bertolini, Anne, Bosshard, Lars, Barkmann, Florian, Yates, Josephine, Boeva, Valentina, The Tumor Profiler Consortium, Stekhoven, Daniel, & Singer, Franziska. (2023). scROSHI: robust supervised hierarchical identification of single cells. NAR Genomics and Bioinformatics, 5(2). https://doi.org/10.1093/nargab/lqad058

Eichhoff, Ossia M., Stoffel, Corinne I., Käsler, Jan, Briker, Luzia, Turko, Patrick, Karsai, Gergely, Zila, Nina, Paulitschke, Verena, Cheng, Phil F., Leitner, Alexander, Bileck, Andrea, Zamboni, Nicola, Irmisch, Anja, Balazs, Zsolt, Tastanova, Aizhan, Pascoal, Susana, Johansen, Pal, Wegmann, Rebekka, Mena, Julien, et al. (2023). ROS Induction Targets Persister Cancer Cells with Low Metabolic Activity in NRAS-Mutated Melanoma. Cancer Research, 83(7), 1128–1146. https://doi.org/10.1158/0008-5472.can-22-1826

Aubreville, Marc, Stathonikos, Nikolas, Bertram, Christof A., Klopfleisch, Robert, ter Hoeve, Natalie, Ciompi, Francesco, Wilm, Frauke, Marzahl, Christian, Donovan, Taryn A., Maier, Andreas, Breen, Jack, Ravikumar, Nishant, Chung, Youjin, Park, Jinah, Nateghi, Ramin, Pourakpour, Fattaneh, Fick, Rutger H.J., Ben Hadj, Saima, Jahanifar, Mostafa, et al. (2023). Mitosis domain generalization in histopathology images — The MIDOG challenge. Medical Image Analysis, 84. https://doi.org/10.1016/j.media.2022.102699

Fremond, Sarah, Andani, Sonali, Barkey Wolf, Jurriaan, Dijkstra, Jouke, Melsbach, Sinéad, Jobsen, Jan J, Brinkhuis, Mariel, Roothaan, Suzan, Jurgenliemk-Schulz, Ina, Lutgens, Ludy C H W, Nout, Remi A, van der Steen-Banasik, Elzbieta M, de Boer, Stephanie M, Powell, Melanie E, Singh, Naveena, Mileshkin, Linda R, Mackay, Helen J, Leary, Alexandra, Nijman, Hans W, et al. (2023). Interpretable deep learning model to predict the molecular classification of endometrial cancer from haematoxylin and eosin-stained whole-slide images: a combined analysis of the PORTEC randomised trials and clinical cohorts. The Lancet Digital Health, 5(2), e71–e82. https://doi.org/10.1016/s2589-7500(22)00210-2

Lafarge, Maxime W., & Koelzer, Viktor H. (2023). Fine-Grained Hard-Negative Mining: Generalizing Mitosis Detection with a Fifth of the MIDOG 2022 Dataset. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 13597 LNCS, 226–233. https://doi.org/10.1007/978-3-031-33658-4_24

Bosse, T., Creutzberg, C.L., Crosbie, E.J., Han, K., Horeweg, N., Leary, A., Kroep, J.R., McAlpine, J.N., Powell, M.E., Blanc-Durand, F., Bosse, T., De Bruyn, M., Church, D.N., Horeweg, N., Koelzer, V.H., Kommoss, S., Leary, A., McAlpine, J.N., Singh, N., et al. (2022). Refining adjuvant treatment in endometrial cancer based on molecular features: The RAINBO clinical trial program. International Journal of Gynecological Cancer, 33(1), 109–117. https://doi.org/10.1136/ijgc-2022-004039

Horeweg, Nanda, Workel, Hagma H., Loiero, Dominik, Church, David N., Vermij, Lisa, Léon-Castillo, Alicia, Krog, Ricki T., de Boer, Stephanie M., Nout, Remi A., Powell, Melanie E., Mileshkin, Linda R., MacKay, Helen, Leary, Alexandra, Singh, Naveena, Jürgenliemk-Schulz, Ina M., Smit, Vincent T. H. B. M., Creutzberg, Carien L., Koelzer, Viktor H., Nijman, Hans W., et al. (2022). Tertiary lymphoid structures critical for prognosis in endometrial cancer patients. Nature Communications, 13(1). https://doi.org/10.1038/s41467-022-29040-x

Gil Vazquez, Ester, Nasreddin, Nadia, Valbuena, Gabriel N., Mulholland, Eoghan J., Belnoue-Davis, Hayley L., Eggington, Holly R., Schenck, Ryan O., Wouters, Valérie M., Wirapati, Pratyaksha, Gilroy, Kathryn, Lannagan, Tamsin R.M., Flanagan, Dustin J., Najumudeen, Arafath K., Omwenga, Sulochana, McCorry, Amy M.B., Easton, Alistair, Koelzer, Viktor H., East, James E., Morton, Dion, et al. (2022). Erratum: Dynamic and adaptive cancer stem cell population admixture in colorectal neoplasia (Cell Stem Cell (2022) 29(8) (1213–1228.e8), (S1934590922003034), (10.1016/j.stem.2022.07.008)). Cell Stem Cell, 29(11), 1612. https://doi.org/10.1016/j.stem.2022.09.005

Janowczyk, Andrew, Baumhoer, Daniel, Dirnhofer, Stefan, Grobholz, Rainer, Kipar, Anja, de Leval, Laurence, Merkler, Doron, Michielin, Olivier, Moch, Holger, Perren, Aurel, Rottenberg, Sven, Rubbia-Brandt, Laura, Rubin, Mark A., Sempoux, Christine, Tolnay, Markus, Zlobec, Inti, & Koelzer, Viktor Hendrik. (2022). Towards a national strategy for digital pathology in Switzerland. Virchows Archiv, 481(4), 647–652. https://doi.org/10.1007/s00428-022-03345-0

Fisher, Natalie C., Byrne, Ryan M., Leslie, Holly, Wood, Colin, Legrini, Assya, Cameron, Andrew J., Ahmaderaghi, Baharak, Corry, Shania M., Malla, Sudhir B., Amirkhah, Raheleh, McCooey, Aoife J., Rogan, Emily, Redmond, Keara L., Sakhnevych, Svetlana, Domingo, Enric, Jackson, James, Loughrey, Maurice B., Leedham, Simon, Maughan, Tim, et al. (2022). Biological Misinterpretation of Transcriptional Signatures in Tumor Samples Can Unknowingly Undermine Mechanistic Understanding and Faithful Alignment with Preclinical Data. Clinical Cancer Research, 28(18), 4056–4069. https://doi.org/10.1158/1078-0432.ccr-22-1102

Schumacher, Jonathan, Gutschow, Christian Alexander, Inci, Ilhan, Koelzer, Viktor H., & Opitz, Isabelle. (2022). Case report: Surgical repair of a large tracheo-esophageal fistula in a patient with post-transplant esophageal lymphoproliferative disorder. International Journal of Surgery Case Reports, 98. https://doi.org/10.1016/j.ijscr.2022.107537

Fremond, Sarah, Koelzer, Viktor Hendrik, Horeweg, Nanda, & Bosse, Tjalling. (2022). The evolving role of morphology in endometrial cancer diagnostics: From histopathology and molecular testing towards integrative data analysis by deep learning. Frontiers in Oncology, 12. https://doi.org/10.3389/fonc.2022.928977

Vasquez, Ester Gil, Nasreddin, Nadia, Valbuena, Gabriel N., Mulholland, Eoghan J., Belnoue-Davis, Hayley L., Eggington, Holly R., Schenck, Ryan O., Wouters, Valérie M., Wirapati, Pratyaksha, Gilroy, Kathryn, Lannagan, Tamsin R.M., Flanagan, Dustin J., Najumudeen, Arafath K., Omwenga, Sulochana, McCorry, Amy M.B., Easton, Alistair, Koelzer, Viktor H., East, James E., Morton, Dion, et al. (2022). Dynamic and adaptive cancer stem cell population admixture in colorectal neoplasia. Cell Stem Cell, 29(8), 1213–1228. https://doi.org/10.1016/j.stem.2022.07.008

Bertolini, Anne, Prummer, Michael, Tuncel, Mustafa Anil, Menzel, Ulrike, Rosano-González, María Lourdes, Kuipers, Jack, Stekhoven, Daniel Johannes, Beerenwinkel, Niko, Singer, Franziska, Aebersold, Rudolf, Ak, Melike, Al-Quaddoomi, Faisal S., Albinus, Jonas, Alborelli, Ilaria, Andani, Sonali, Attinger, Per-Olof, Bacac, Marina, Baumhoer, Daniel, Beck-Schimmer, Beatrice, et al. (2022). scAmpi—A versatile pipeline for single-cell RNA-seq analysis from basics to clinics. PLoS Computational Biology, 18(6). https://doi.org/10.1371/journal.pcbi.1010097

Quintavalle, Cristina, Meyer-Schaller, Nathalie, Roessler, Stephanie, Calabrese, Diego, Marone, Romina, Riedl, Tobias, Picco-Rey, Silvia, Panagiotou, Orestis A., Uzun, Sarp, Piscuoglio, Salvatore, Boldanova, Tuyana, Bian, Chaoran B., Semela, David, Jochum, Wolfram, Cathomas, Gieri, Mertz, Kirsten D., Diebold, Joachim, Mazzucchelli, Luca, Koelzer, Viktor H., et al. (2022). miR-579-3p Controls Hepatocellular Carcinoma Formation by Regulating the Phosphoinositide 3-Kinase–Protein Kinase B Pathway in Chronically Inflamed Liver. Hepatology Communications, 6(6), 1467–1481. https://doi.org/10.1002/hep4.1894

Palles, Claire, West, Hannah D., Chew, Edward, Galavotti, Sara, Flensburg, Christoffer, Grolleman, Judith E., Jansen, Erik A.M., Curley, Helen, Chegwidden, Laura, Arbe-Barnes, Edward H., Lander, Nicola, Truscott, Rebekah, Pagan, Judith, Bajel, Ashish, Sherwood, Kitty, Martin, Lynn, Thomas, Huw, Georgiou, Demetra, Fostira, Florentia, et al. (2022). Germline MBD4 deficiency causes a multi-tumor predisposition syndrome. American Journal of Human Genetics, 109(5), 953–960. https://doi.org/10.1016/j.ajhg.2022.03.018

Wu, Ji Q., Horeweg, Nanda, de Bruyn, Marco, Nout, Remi A., Jürgenliemk-Schulz, Ina M., Lutgens, Ludy C. H. W., Jobsen, Jan J., van der Steen-Banasik, Elzbieta M., Nijman, Hans W., Smit, Vincent T. H. B. M., Bosse, Tjalling, Creutzberg, Carien L., & Koelzer, Viktor H. (2022). Automated causal inference in application to randomized controlled clinical trials. Nature Machine Intelligence, 4(5), 436–444. https://doi.org/10.1038/s42256-022-00470-y

Lafarge, Maxime W., & Koelzer, Viktor H. (2022). Rotation Invariance and Extensive Data Augmentation: A Strategy for the MItosis DOmain Generalization (MIDOG) Challenge. Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 13166 LNCS, 62–67. https://doi.org/10.1007/978-3-030-97281-3_9

Sobottka, Bettina, Nienhold, Ronny, Nowak, Marta, Hench, Juergen, Haeuptle, Pirmin, Frank, Angela, Sachs, Melanie, Kahraman, Abdullah, Moch, Holger, Koelzer, Viktor H., & Mertz, Kirsten D. (2022). Integrated analysis of immunotherapy treated clear cell renal cell carcinomas: An exploratory study. Journal of Immunotherapy, 45(1), 35–42. https://doi.org/10.1097/cji.0000000000000387

Wu, Jiqing, Zlobec, Inti, Lafarge, Maxime, He, Yukun, & Koelzer, Viktor H. (2022). Towards IID representation learning and its application on biomedical data. Proceedings of Machine Learning Research, 172, 1375–1402.

Koppens, Martijn A.J., Davis, Hayley, Valbuena, Gabriel N., Mulholland, Eoghan J., Nasreddin, Nadia, Colombe, Mathilde, Antanaviciute, Agne, Biswas, Sujata, Friedrich, Matthias, Lee, Lennard, Wang, Lai Mun, Koelzer, Viktor H., East, James E., Simmons, Alison, Winton, Douglas J., & Leedham, Simon J. (2021). Bone Morphogenetic Protein Pathway Antagonism by Grem1 Regulates Epithelial Cell Fate in Intestinal Regeneration. Gastroenterology, 161(1), 239–254. https://doi.org/10.1053/j.gastro.2021.03.052

Leach, Joshua D. G., Vlahov, Nikola, Tsantoulis, Petros, Ridgway, Rachel A., Flanagan, Dustin J., Gilroy, Kathryn, Sphyris, Nathalie, Vázquez, Ester G., Vincent, David F., Faller, William J., Hodder, Michael C., Raven, Alexander, Fey, Sigrid, Najumudeen, Arafath K., Strathdee, Douglas, Nixon, Colin, Hughes, Mark, Clark, William, Shaw, Robin, et al. (2021). Oncogenic BRAF, unrestrained by TGFβ-receptor signalling, drives right-sided colonic tumorigenesis. Nature Communications, 12(1). https://doi.org/10.1038/s41467-021-23717-5

Jones, Helen J S, Cunningham, Chris, Askautrud Hanne A, Danielsen, Harvard E, Kerr, David J, Domingo Enric, Maughan, Tim, Leedham, Simon J, & Koelzer Viktor H. (2021). Stromal composition predicts recurrence of early rectal cancer after local excision. Histopathology 79(6), 947–956. https://doi.org/10.1111/his.14438

Logan, GE, Chatzipli, A, Amirkhah, R, Humphries, MP, Craig, SG, McDermott, U, Seymour, MT, Morton, DG, Quirke, P, West,NP, Salto-Tellez, M, Kennedy, RD, Johnston, PG, Tomlinson, I, Koelzer, Viktor H, Campo, L, Kaplan, RS, Longley, DB, Lawler, M, et al. (2021). In-depth Clinical and Biological Exploration of DNA Damage Immune Response as a Biomarker for Oxaliplatin Use in Colorectal Cancer. Clin Cancer Res. 27(1), 288–300. https://doi.org/10.1158/1078-0432.CCR-20-3237

Paijens ST, Vledder A, Loiero D, Duiker EW, Bart J, Hendriks AM, Jalving, M, Workel, HH, Hollema, H, Werner, N, Plat, A, Wisman, GBA, Yigit, R, Arts, H, Kruse, AJ, de Lange, NM, Koelzer, Viktor H, de Bruyn, M, & Nijman, HW. (2021). Prognostic image-based quantification of CD8CD103 T cell subsets in high-grade serous ovarian cancer patients. Oncoimmunology 10(1):1935104. https://doi.org/10.1080/2162402X.2021.1935104

Horeweg, Nanda, de Bruyn, Marco, Nout, Remi A., Stelloo, Ellen, Kedziersza, Katarzyna, León-Castillo, Alicia, Plat, Annechien, Mertz, Kirsten D., Osse, Michelle, Jürgenliemk-Schulz, Ina M., Lutgens, Ludy C.H.W., Jobsen, Jan J., van der Steen-Banasik, Elzbieta M., Smit, Vincent T., Creutzberg, Carien L., Bosse, Tjalling, Nijman, Hans W., Koelzer, Viktor H., & Church, David N. (2020). Prognostic integrated image-based immune and molecular profiling in early-stage endometrial cancer. Cancer Immunology Research, 8(12), 1508–1519. https://doi.org/10.1158/2326-6066.cir-20-0149

Stark, Stefan G., Ficek, Joanna, Locatello, Francesco, Bonilla, Ximena, Chevrier, Stéphane, Singer, Franziska, Rätsch, Gunnar, Lehmann, Kjong-Van, Rudolf, Aebersold, Al-Quaddoomi Faisal, S., Jonas, Albinus, Ilaria, Alborelli, Sonali, Andani, Per-Olof, Attinger, Marina, Bacac, Daniel, Baumhoer, Beatrice, Beck-Schimmer, Niko, Beerenwinkel, Christian, Beisel, et al. (2020). SCIM: Universal single-cell matching with unpaired feature sets. Bioinformatics, 36, I919–I927. https://doi.org/10.1093/bioinformatics/btaa843

McCuaig S, Barras D, Mann EH, Friedrich M, Bullers SJ, Janney A, Garner LC, Domingo E, Koelzer VH, Delorenzi M, Tejpar S, Maughan TS, West NR, & Powrie F. (2020). The Interleukin 22 Pathway Interacts with Mutant KRAS to Promote Poor Prognosis in Colon Cancer. Clinical Cancer Research, 26(16), 4313–4325. https://doi.org/10.1158/1078-0432.CCR-19-1086

Kleeman, Sam O., Koelzer, Viktor H., Jones, Helen J.S., Vazquez, Ester Gil, Davis, Hayley, East, James E., Arnold, Roland, Koppens, Martijn A.J., Blake, Andrew, Domingo, Enric, Cunningham, Chris, Beggs, Andrew D., Pestinger, Valerie, Loughrey, Maurice B., Wang, Lai-Mun, Lannagan, Tamsin R.M., Woods, Susan L., Worthley, Daniel, Consortium, Scort, et al. (2020). Exploiting differential Wnt target gene expression to generate a molecular biomarker for colorectal cancer stratification. Gut, 69(6), 1092–1103. https://doi.org/10.1136/gutjnl-2019-319126

Frei, Anja Laura, Merki, Samuel, Henkel, Maurice Johannes, Wey, Norbert, Moch, Holger, Mertz, Kirsten Diana, & Koelzer, Viktor Hendrik. (2019). Future medicine: Digital pathology. Therapeutische Umschau, 76, 404–408. https://doi.org/10.1024/0040-5930/a001108

Läubli, Heinz, Koelzer, Viktor H., Matter, Matthias S., Herzig, Petra, Dolder Schlienger, Beatrice, Wiese, Mark Nikolaj, Lardinois, Didier, Mertz, Kirsten D., & Zippelius, Alfred. (2018). The T cell repertoire in tumors overlaps with pulmonary inflammatory lesions in patients treated with checkpoint inhibitors. OncoImmunology, 7(2). https://doi.org/10.1080/2162402x.2017.1386362

Mager, Lukas Franz, Koelzer, Viktor Hendrik, Stuber, Regula, Thoo, Lester, Keller, Irene, Koeck, Ivonne, Langenegger, Maya, Simillion, Cedric, Pfister, Simona P., Faderl, Martin, Genitsch, Vera, Tcymbarevich, Irina, Juillerat, Pascal, Li, Xiaohong, Xia, Yu, Karamitopoulou, Eva, Lyck, Ruth, Zlobec, Inti, Hapfelmeier, Siegfried, Bruggmann, Rémy, McCoy, Kathy D., Macpherson, Andrew J., Müller, Christoph, Beutler, Bruce, & Krebs, Philippe. (2017). The ESRP1-GPR137 axis contributes to intestinal pathogenesis. eLife, 6. https://doi.org/10.7554/eLife.28366

Koelzer, V.H., Glatz, K., Bubendorf, L., Weber, A., Gaspert, A., Cathomas, G., Lugli, A., Zippelius, A., Kempf, W., & Mertz, K.D. (2017). Pathologie der Nebenwirkungen von Immune-Checkpoint-Inhibitoren. Pathologe, 38(3), 197–208. https://doi.org/10.1007/s00292-017-0281-1

Koelzer, Viktor H., Sokol, Lena, Zahnd, Stefan, Christe, Lucine, Dawson, Heather, Berger, Martin D., Inderbitzin, Daniel, Zlobec, Inti, & Lugli, Alessandro. (2017). Digital analysis and epigenetic regulation of the signature of rejection in colorectal cancer. OncoImmunology, 6(4). https://doi.org/10.1080/2162402x.2017.1288330

Haller, S., Kölzer, V., Fux, C.A., Glaser, C., & Cathomas, G. (2017). Lower right abdominal pain in a young woman: An ordinary appendicitis. Chirurg, 88(2), 155–157. https://doi.org/10.1007/s00104-016-0260-8

Malesci, Alberto, Bianchi, Paolo, Celesti, Giuseppe, Basso, Gianluca, Marchesi, Federica, Grizzi, Fabio, Di Caro, Giuseppe, Cavalleri, Tommaso, Rimassa, Lorenza, Palmqvist, Richard, Lugli, Alessandro, Koelzer, Viktor H., Roncalli, Massimo, Mantovani, Alberto, Ogino, Shuji, & Laghi, Luigi. (2017). Tumor-associated macrophages and response to 5-fluorouracil adjuvant therapy in stage III colorectal cancer. OncoImmunology, 6(12). https://doi.org/10.1080/2162402X.2017.1342918

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