Publications

2024

  1. Ordinal Learning: Longitudinal Attention Alignment Model for Predicting Time to Future Breast Cancer Events from Mammograms
    Lecture Notes in Computer Science
    X. Wang, T. Tan, Y. Gao, E. Marcus, L. Han, A. Portaluri, T. Zhang, C. Lu, X. Liang, R. Beets-Tan, J. Teuwen, R. Mann, 2024
    doi
    Abstract
  2. Does “One Size Fits All”? Rethinking FIGO Depth of Invasion Measurements in Vulvar Cancer
    International Journal of Gynecological Pathology
    M. C. Bleeker, T. Bosse, K. K. Van De Vijver, J. Bart, H. Horlings, T. G. Jonges, N. C. Visser, L. F. Kooreman, J. Bulten, P. C. Ewing-Graham, 2024
    doi
    Abstract
  3. Abstract 4951: Integrative multi-omic machine learning model predicts neoadjuvant immunotherapy response using molecular data and deep learning-derived features from digital pathology
    Cancer Research
    L. V. Leek, V. Botha, V. A. Baxi, J. Teuwen, H. M. Horlings, S. D. Chasalow, J. V. D. Haar, L. F. Wessels, A. Debroy, E. E. Voest, 2024, 84;(6_Supplement):4951-4951
    doi
    Abstract
  4. Tumor-Infiltrating Lymphocytes in Patients With Stage I Triple-Negative Breast Cancer Untreated With Chemotherapy
    JAMA Oncology
    V. C. M. Geurts, S. Balduzzi, T. G. Steenbruggen, S. C. Linn, S. Siesling, S. S. Badve, A. Demichele, M. Ignatiadis, R. A. Leon-Ferre, M. P. Goetz, A. C. Wolff, N. Klar, S. Michiels, S. Loi, S. Adams, H. M. Horlings, G. S. Sonke, R. Salgado, M. Kok, 2024
    doi
    Abstract
  5. Image‐based multiplex immune profiling of cancer tissues: translational implications. A report of the International Immuno‐oncology Biomarker Working Group on Breast Cancer
    The Journal of Pathology
    C. A. Jahangir, D. B. Page, G. Broeckx, C. A. Gonzalez, C. Burke, C. Murphy, J. S. Reis‐Filho, A. Ly, P. W. Harms, R. R. Gupta, M. Vieth, A. I. Hida, M. Kahila, Z. Kos, P. J. Van Diest, S. Verbandt, J. Thagaard, R. Khiroya, K. Abduljabbar, G. Acosta Haab, B. Acs, S. Adams, J. S. Almeida, I. Alvarado‐Cabrero, F. Azmoudeh‐Ardalan, S. Badve, N. B. Baharun, E. R. Bellolio, V. Bheemaraju, K. R. Blenman, L. Botinelly Mendonça Fujimoto, O. Burgues, A. Chardas, M. C. U. Cheang, F. Ciompi, L. A. Cooper, A. Coosemans, G. Corredor, F. L. Dantas Portela, F. Deman, S. Demaria, S. N. Dudgeon, M. Elghazawy, C. Fernandez‐Martín, S. Fineberg, S. B. Fox, J. M. Giltnane, S. Gnjatic, P. I. Gonzalez‐Ericsson, A. Grigoriadis, N. Halama, M. G. Hanna, A. Harbhajanka, S. N. Hart, J. Hartman, S. Hewitt, H. M. Horlings, Z. Husain, S. Irshad, E. A. Janssen, T. R. Kataoka, K. Kawaguchi, A. I. Khramtsov, U. Kiraz, P. Kirtani, L. L. Kodach, K. Korski, G. Akturk, E. Scott, A. Kovács, A. Lænkholm, C. Lang‐Schwarz, D. Larsimont, J. K. Lennerz, M. Lerousseau, X. Li, A. Madabhushi, S. K. Maley, V. Manur Narasimhamurthy, D. K. Marks, E. S. Mcdonald, R. Mehrotra, S. Michiels, D. Kharidehal, F. U. A. A. Minhas, S. Mittal, D. A. Moore, S. Mushtaq, H. Nighat, T. Papathomas, F. Penault‐Llorca, R. D. Perera, C. J. Pinard, J. C. Pinto‐Cardenas, G. Pruneri, L. Pusztai, N. M. Rajpoot, B. L. Rapoport, T. T. Rau, J. M. Ribeiro, D. Rimm, A. Vincent‐Salomon, J. Saltz, S. Sayed, E. Hytopoulos, S. Mahon, K. P. Siziopikou, C. Sotiriou, A. Stenzinger, M. A. Sughayer, D. Sur, F. Symmans, S. Tanaka, T. Taxter, S. Tejpar, J. Teuwen, E. A. Thompson, T. Tramm, W. T. Tran, J. Van Der Laak, G. E. Verghese, G. Viale, N. Wahab, T. Walter, Y. Waumans, H. Y. Wen, W. Yang, Y. Yuan, J. Bartlett, S. Loibl, C. Denkert, P. Savas, S. Loi, E. Specht Stovgaard, R. Salgado, W. M. Gallagher, A. Rahman, 2024
    doi paper (open access)
    Abstract

2023

  1. Generalizable biomarker prediction from cancer pathology slides with self-supervised deep learning: A retrospective multi-centric study
    Cell Reports Medicine
    J. M. Niehues, P. Quirke, N. P. West, H. I. Grabsch, M. Van Treeck, Y. Schirris, G. P. Veldhuizen, G. G. Hutchins, S. D. Richman, S. Foersch, T. J. Brinker, J. Fukuoka, A. Bychkov, W. Uegami, D. Truhn, H. Brenner, A. Brobeil, M. Hoffmeister, J. N. Kather, 2023, 4;(4):100980
    doi paper (open access)
    Abstract
  2. 1240P Multi-centric validation of an AI-based sTIL% scoring model for breast cancer H&E whole-slide images
    Annals of Oncology
    Y. Schirris, R. Voorthuis, M. Opdam, E. Gavves, R. De Menezes, S. Linn, H. Horlings, 2023, 34
    doi
    Abstract
  3. PatchSorter: A High Throughput Deep Learning Digital Pathology Tool for Object Labeling
    C. Walker, T. Talawalla, R. Toth, A. Ambekar, K. Rea, O. Chamian, F. Fan, S. Berezowska, S. Rottenberg, A. Madabhushi, M. Maillard, L. Barisoni, H. M. Horlings, A. Janowczyk, 2023
    ArXiv
    Abstract
  4. The prognostic value of tumor-stroma ratio and a newly developed computer-aided quantitative analysis of routine H&E slides in high-grade serous ovarian cancer
    L. V. Wagensveld, C. Walker, K. Hahn, J. Sanders, R. Kruitwagen, M. V. D. Aa, G. Sonke, S. Rottenberg, K. V. De Vijver, A. Janowczyk, H. Horlings, 2023
    doi paper (open access)
    Abstract
  5. Abstract P3-06-01: Unleashing NK- and CD8 T cells by combining monalizumab (anti-NKG2A) and trastuzumab for metastatic HER2+ breast cancer: first results MIMOSA trial
    Cancer Research
    V. Geurts, L. Voorwerk, K. Sikorska, R. Salgado, K. Van De Vijver, M. Van Dongen, I. Kemper, I. A. Mandjes, M. Heuver-Mes, J. Haanen, G. S. Sonke, H. Horlings, M. Kok, 2023, 83;(5_Supplement):P3-06-01-P3-06-01
    doi
    Abstract
  6. PROACTING: predicting pathological complete response to neoadjuvant chemotherapy in breast cancer from routine diagnostic histopathology biopsies with deep learning
    Breast Cancer Research
    W. Aswolinskiy, E. Munari, H. M. Horlings, L. Mulder, G. Bogina, J. Sanders, Y. Liu, A. W. Van Den Belt-Dusebout, L. Tessier, M. Balkenhol, M. Stegeman, J. Hoven, J. Wesseling, J. Van Der Laak, E. H. Lips, F. Ciompi, 2023, 25;(1)
    doi paper (open access)
    Abstract
  7. CMTM6 shapes antitumor T cell response through modulating protein expression of CD58 and PD-L1
    Cancer Cell
    B. Miao, Z. Hu, R. Mezzadra, L. Hoeijmakers, A. Fauster, S. Du, Z. Yang, M. Sator-Schmitt, H. Engel, X. Li, C. Broderick, G. Jin, R. Gomez-Eerland, L. Rozeman, X. Lei, H. Matsuo, C. Yang, I. Hofland, D. Peters, A. Broeks, E. Laport, A. Fitz, X. Zhao, M. A. Mahmoud, X. Ma, S. Sander, H. Liu, G. Cui, Y. Gan, W. Wu, Y. Xiao, A. J. Heck, W. Guan, S. W. Lowe, H. M. Horlings, C. Wang, T. R. Brummelkamp, C. U. Blank, T. N. Schumacher, C. Sun, 2023, 41;(10):1817-1828.e9
    doi paper (open access)
    Abstract
  8. B-cells and regulatory T-cells in the microenvironment of HER2+ breast cancer are associated with decreased survival: a real-world analysis of women with HER2+ metastatic breast cancer
    Breast Cancer Research
    T. G. Steenbruggen, D. M. Wolf, M. J. Campbell, J. Sanders, S. Cornelissen, B. Thijssen, R. A. Salgado, C. Yau, N. O-Grady, A. Basu, R. Bhaskaran, L. Mittempergher, G. L. Hirst, J. Coppe, M. Kok, G. S. Sonke, L. J. Van ‘T Veer, H. M. Horlings, 2023, 25;(1)
    doi paper (open access)
    Abstract
  9. Characterization of the Tumor Microenvironment of De Novo Oligometastatic Breast Cancer in a Nationwide Cohort
    JCO Precision Oncology
    T. G. Steenbruggen, D. M. Wolf, B. Thijssen, J. Sanders, S. Cornelissen, R. Salgado, L. Mittempergher, R. Bhaskaran, A. Broeks, E. H. Lips, S. Siesling, G. S. Sonke, H. M. Horlings, L. J. Van ’T Veer, 2023
    doi
    Abstract
  10. Immune landscape of breast tumors with low and intermediate estrogen receptor expression
    npj Breast Cancer
    L. Voorwerk, J. Sanders, M. S. Keusters, S. Balduzzi, S. Cornelissen, M. Duijst, E. H. Lips, G. S. Sonke, S. C. Linn, H. M. Horlings, M. Kok, 2023, 9;(1)
    doi paper (open access)
    Abstract
  11. PD-L1 blockade in combination with carboplatin as immune induction in metastatic lobular breast cancer: the GELATO trial
    Nature Cancer
    L. Voorwerk, O. I. Isaeva, H. M. Horlings, S. Balduzzi, M. Chelushkin, N. A. M. Bakker, E. Champanhet, H. Garner, K. Sikorska, C. E. Loo, I. Kemper, I. A. M. Mandjes, M. De Maaker, J. J. L. Van Geel, J. Boers, M. De Boer, R. Salgado, M. G. J. Van Dongen, G. S. Sonke, K. E. De Visser, T. N. Schumacher, C. U. Blank, L. F. A. Wessels, A. Jager, V. C. G. Tjan-Heijnen, C. P. Schröder, S. C. Linn, M. Kok, 2023, 4;(4):535-549
    doi paper (open access)
    Abstract
  12. Predicting breast cancer types on and beyond molecular level in a multi-modal fashion
    npj Breast Cancer
    T. Zhang, T. Tan, L. Han, L. Appelman, J. Veltman, R. Wessels, K. M. Duvivier, C. Loo, Y. Gao, X. Wang, H. M. Horlings, R. G. H. Beets-Tan, R. M. Mann, 2023, 9;(1)
    doi paper (open access)
    Abstract
  13. Spatial analyses of immune cell infiltration in cancer: current methods and future directions. A report of the International Immuno‐Oncology Biomarker Working Group on Breast Cancer
    The Journal of Pathology
    D. B. Page, G. Broeckx, C. A. Jahangir, S. Verbandt, R. R. Gupta, J. Thagaard, R. Khiroya, Z. Kos, K. Abduljabbar, G. Acosta Haab, B. Acs, J. S. Almeida, I. Alvarado‐Cabrero, F. Azmoudeh‐Ardalan, S. Badve, N. B. Baharun, E. R. Bellolio, V. Bheemaraju, K. R. Blenman, L. Botinelly Mendonça Fujimoto, O. Burgues, M. C. U. Cheang, F. Ciompi, L. A. Cooper, A. Coosemans, G. Corredor, F. L. Dantas Portela, F. Deman, S. Demaria, S. N. Dudgeon, M. Elghazawy, S. Ely, C. Fernandez‐Martín, S. Fineberg, S. B. Fox, W. M. Gallagher, J. M. Giltnane, S. Gnjatic, P. I. Gonzalez‐Ericsson, A. Grigoriadis, N. Halama, M. G. Hanna, A. Harbhajanka, A. Hardas, S. N. Hart, J. Hartman, S. Hewitt, A. I. Hida, H. M. Horlings, Z. Husain, E. Hytopoulos, S. Irshad, E. A. Janssen, M. Kahila, T. R. Kataoka, K. Kawaguchi, D. Kharidehal, A. I. Khramtsov, U. Kiraz, P. Kirtani, L. L. Kodach, K. Korski, A. Kovács, A. Laenkholm, C. Lang‐Schwarz, D. Larsimont, J. K. Lennerz, M. Lerousseau, X. Li, A. Ly, A. Madabhushi, S. K. Maley, V. Manur Narasimhamurthy, D. K. Marks, E. S. Mcdonald, R. Mehrotra, S. Michiels, F. U. A. A. Minhas, S. Mittal, D. A. Moore, S. Mushtaq, H. Nighat, T. Papathomas, F. Penault‐Llorca, R. D. Perera, C. J. Pinard, J. C. Pinto‐Cardenas, G. Pruneri, L. Pusztai, A. Rahman, N. M. Rajpoot, B. L. Rapoport, T. T. Rau, J. S. Reis‐Filho, J. M. Ribeiro, D. Rimm, A. Salomon, M. Salto‐Tellez, J. Saltz, S. Sayed, K. P. Siziopikou, C. Sotiriou, A. Stenzinger, M. A. Sughayer, D. Sur, F. Symmans, S. Tanaka, T. Taxter, S. Tejpar, J. Teuwen, E. A. Thompson, T. Tramm, W. T. Tran, J. Van Der Laak, P. J. Van Diest, G. E. Verghese, G. Viale, M. Vieth, N. Wahab, T. Walter, Y. Waumans, H. Y. Wen, W. Yang, Y. Yuan, S. Adams, J. M. S. Bartlett, S. Loibl, C. Denkert, P. Savas, S. Loi, R. Salgado, E. Specht Stovgaard, G. Akturk, N. Bouchmaa, 2023
    doi paper (open access)
    Abstract
  14. Pitfalls in machine learning‐based assessment of tumor‐infiltrating lymphocytes in breast cancer: A report of the International Immuno‐Oncology Biomarker Working Group on Breast Cancer
    The Journal of Pathology
    J. Thagaard, G. Broeckx, D. B. Page, C. A. Jahangir, S. Verbandt, Z. Kos, R. Gupta, R. Khiroya, K. Abduljabbar, G. Acosta Haab, B. Acs, G. Akturk, J. S. Almeida, I. Alvarado‐Cabrero, M. Amgad, F. Azmoudeh‐Ardalan, S. Badve, N. B. Baharun, E. Balslev, E. R. Bellolio, V. Bheemaraju, K. R. Blenman, L. Botinelly Mendonça Fujimoto, N. Bouchmaa, O. Burgues, A. Chardas, M. Chon U Cheang, F. Ciompi, L. A. Cooper, A. Coosemans, G. Corredor, A. B. Dahl, F. L. Dantas Portela, F. Deman, S. Demaria, J. Doré Hansen, S. N. Dudgeon, T. Ebstrup, M. Elghazawy, C. Fernandez‐Martín, S. B. Fox, W. M. Gallagher, J. M. Giltnane, S. Gnjatic, P. I. Gonzalez‐Ericsson, A. Grigoriadis, N. Halama, M. G. Hanna, A. Harbhajanka, S. N. Hart, J. Hartman, S. Hauberg, S. Hewitt, A. I. Hida, H. M. Horlings, Z. Husain, E. Hytopoulos, S. Irshad, E. A. Janssen, M. Kahila, T. R. Kataoka, K. Kawaguchi, D. Kharidehal, A. I. Khramtsov, U. Kiraz, P. Kirtani, L. L. Kodach, K. Korski, A. Kovács, A. Laenkholm, C. Lang‐Schwarz, D. Larsimont, J. K. Lennerz, M. Lerousseau, X. Li, A. Ly, A. Madabhushi, S. K. Maley, V. Manur Narasimhamurthy, D. K. Marks, E. S. Mcdonald, R. Mehrotra, S. Michiels, F. U. A. A. Minhas, S. Mittal, D. A. Moore, S. Mushtaq, H. Nighat, T. Papathomas, F. Penault‐Llorca, R. D. Perera, C. J. Pinard, J. C. Pinto‐Cardenas, G. Pruneri, L. Pusztai, A. Rahman, N. M. Rajpoot, B. L. Rapoport, T. T. Rau, J. S. Reis‐Filho, J. M. Ribeiro, D. Rimm, A. Roslind, A. Vincent‐Salomon, M. Salto‐Tellez, J. Saltz, S. Sayed, E. Scott, K. P. Siziopikou, C. Sotiriou, A. Stenzinger, M. A. Sughayer, D. Sur, S. Fineberg, F. Symmans, S. Tanaka, T. Taxter, S. Tejpar, J. Teuwen, E. A. Thompson, T. Tramm, W. T. Tran, J. Van Der Laak, P. J. Van Diest, G. E. Verghese, G. Viale, M. Vieth, N. Wahab, T. Walter, Y. Waumans, H. Y. Wen, W. Yang, Y. Yuan, R. M. Zin, S. Adams, J. Bartlett, S. Loibl, C. Denkert, P. Savas, S. Loi, R. Salgado, E. Specht Stovgaard, 2023, 260;(5):498-513
    doi paper (open access)
    Abstract
  15. 474P ctDNA-based copy number dynamics during anti-PD1 treatment in patients with metastatic triple-negative breast cancer
    Annals of Oncology
    A. Lin, O. Isaeva, D. Vessies, T. Deger, L. Voorwerk, V. Geurts, H. Horlings, J. Martens, L. Wessels, D. Van Den Broek, M. Kok, 2023, 34
    doi
    Abstract
  16. 163MO Single-cell T cell dynamics induced by neoadjuvant nivolumab +/- ipilimumab in early triple negative breast cancer with tumor-infiltrating lymphocytes (BELLINI trial)
    Immuno-Oncology and Technology
    O. Isaeva, I. Nederlof, M. De Graaf, B. Boeckx, J. Traets, I. Mandjes, K. Van De Vijver, M. Chelushkin, C. Drukker, M. Dongen, G. Sonke, S. Linn, C. Blank, K. De Visser, R. Salgado, L. Wessels, T. Schumacher, H. Horlings, D. Lambrechts, M. Kok, 2023, 20
    doi paper (open access)
    Abstract
  17. Unleashing NK- and CD8 T cells by combining monalizumab and trastuzumab for metastatic HER2-positive breast cancer: Results of the MIMOSA trial
    The Breast
    V. Geurts, L. Voorwerk, S. Balduzzi, R. Salgado, K. Van De Vijver, M. Van Dongen, I. Kemper, I. Mandjes, M. Heuver, W. Sparreboom, J. Haanen, G. Sonke, H. Horlings, M. Kok, 2023, 70
    doi paper (open access)
    Abstract
  18. BluePrint molecular subtypes predict response to neoadjuvant pertuzumab in HER2-positive breast cancer
    Breast Cancer Research
    M. C. Liefaard, A. Van Der Voort, M. S. Van Ramshorst, J. Sanders, S. Vonk, H. M. Horlings, S. Siesling, L. De Munck, A. E. Van Leeuwen, M. Kleijn, L. Mittempergher, M. M. Kuilman, A. M. Glas, J. Wesseling, E. H. Lips, G. S. Sonke, 2023, 25;(1)
    doi paper (open access)
    Abstract

2022

  1. WeakSTIL: weak whole-slide image level stromal tumor infiltrating lymphocyte scores are all you need
    Medical Imaging 2022: Digital and Computational Pathology
    Y. Schirris, M. Engelaer, A. Panteli, H. M. Horlings, E. Gavves, J. Teuwen, 2022
    doi preprints
    Abstract
  2. DeepSMILE: Contrastive self-supervised pre-training benefits MSI and HRD classification directly from H&E whole-slide images in colorectal and breast cancer
    Medical Image Analysis
    Y. Schirris, E. Gavves, I. Nederlof, H. M. Horlings, J. Teuwen, 2022, 79
    doi
    Abstract
  3. HRD-related morphology discovery in breast cancer by controlling for confounding factors
    Cell Reports Medicine
    Y. Schirris, H. M. Horlings, 2022, 3;(12):100873
    doi paper (open access)
    Abstract
  4. Establishment of the Dutch Nationwide, Interdisciplinary Infrastructure and Biobank for Fundamental and Translational Ovarian Cancer Research: Archipelago of Ovarian Cancer Research
    Gynecologic and Obstetric Investigation
    H. S. Zelisse, M. D. Van Gent, S. De Ridder, M. A. Van Der Aa, A. M. Van Altena, J. Bart, J. A. Belien, I. A. Boere, S. L. Bosch, A. Broeks, J. Bulten, M. Collée, F. H. Groenendijk, H. M. Horlings, M. P. Jansen, T. G. Jonges, L. F. Kooreman, C. D. De Kroon, S. Lambrechts, C. A. Lok, J. M. Piek, A. K. Reyners, E. Roes, M. Simons, G. B. A. Wisman, R. Yigit, R. P. Zweemer, C. H. Mom, M. J. Van De Vijver, F. Dijk, 2022, 87;(6):389-397
    doi paper (open access)
    Abstract

2021

  1. Sparse-shot learning with exclusive cross-entropy for extremely many localisations
    Proceedings of the IEEE/CVF International Conference on Computer Vision (ICCV)
    A. Panteli, J. Teuwen, H. Horlings, E. Gavves, 2021
    url preprints
    Abstract