Yinyin Yuan

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Yinyin Yuan

Professor

 https://orcid.org/0000-0002-8556-4707
    Calculated based on number of publications stored in Pure and citations from Scopus
    20042024

    Research activity per year

    Search results

    • 2024

      Deep Learning Enables Spatial Mapping of the Mosaic Microenvironment of Myeloma Bone Marrow Trephine Biopsies

      Hagos, Y. B., Lecat, C. S. Y., Patel, D., Mikolajczak, A., Castillo, S. P., Lyon, E. J., Foster, K., Tran, T. A., Lee, L. S. H., Rodriguez-Justo, M., Yong, K. L. & Yuan, Y., Feb 2024, In: Cancer Research. 84, 3, p. 493-508 16 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access

    • Image-based multiplex immune profiling of cancer tissues: translational implications. A report of the International Immuno-oncology Biomarker Working Group on Breast Cancer

      Jahangir, C. A., Page, D. B., Broeckx, G., Gonzalez, C. A., Burke, C., Murphy, C., Reis-Filho, J. S., Ly, A., Harms, P. W., Gupta, R. R., Vieth, M., Hida, A. I., Kahila, M., Kos, Z., van Diest, P. J., Verbandt, S., Thagaard, J., Khiroya, R., Abduljabbar, K., Acosta Haab, G., & 117 othersAcs, B., Adams, S., Almeida, J. S., Alvarado-Cabrero, I., Azmoudeh-Ardalan, F., Badve, S., Baharun, N. B., Bellolio, E. R., Bheemaraju, V., Blenman, K. R. M., Botinelly Mendonça Fujimoto, L., Burgues, O., Chardas, A., Cheang, M. C. U., Ciompi, F., Cooper, L. A. D., Coosemans, A., Corredor, G., Dantas Portela, F. L., Deman, F., Demaria, S., Dudgeon, S. N., Elghazawy, M., Fernandez-Martín, C., Fineberg, S., Fox, S. B., Giltnane, J. M., Gnjatic, S., Gonzalez-Ericsson, P. I., Grigoriadis, A., Halama, N., Hanna, M. G., Harbhajanka, A., Hart, S. N., Hartman, J., Hewitt, S., Horlings, H. M., Husain, Z., Irshad, S., Janssen, E. A. M., Kataoka, T. R., Kawaguchi, K., Khramtsov, A. I., Kiraz, U., Kirtani, P., Kodach, L. L., Korski, K., Akturk, G., Scott, E., Kovács, A., Lænkholm, A. V., Lang-Schwarz, C., Larsimont, D., Lennerz, J. K., Lerousseau, M., Li, X., Madabhushi, A., Maley, S. K., Manur Narasimhamurthy, V., Marks, D. K., McDonald, E. S., Mehrotra, R., Michiels, S., Kharidehal, D., Minhas, F. U. A. A., Mittal, S., Moore, D. A., Mushtaq, S., Nighat, H., Papathomas, T., Penault-Llorca, F., Perera, R. D., Pinard, C. J., Pinto-Cardenas, J. C., Pruneri, G., Pusztai, L., Rajpoot, N. M., Rapoport, B. L., Rau, T. T., Ribeiro, J. M., Rimm, D., Vincent-Salomon, A., Saltz, J., Sayed, S., Hytopoulos, E., Mahon, S., Siziopikou, K. P., Sotiriou, C., Stenzinger, A., Sughayer, M., Sur, D., Symmans, F., Tanaka, S., Taxter, T., Tejpar, S., Teuwen, J., Thompson, E. A., Tramm, T., Tran, W. T., van der Laak, J., Verghese, G. E., Viale, G., Wahab, N., Walter, T., Waumans, Y., Wen, H. Y., Yang, W., Yuan, Y., Bartlett, J., Loibl, S., Denkert, C., Savas, P., Loi, S., Specht Stovgaard, E., Salgado, R., Gallagher, W. M. & Rahman, A., Mar 2024, In: Journal of Pathology. 262, 3, p. 271-288 18 p.

      Research output: Contribution to journal › Review article › peer-review

      Open Access

    • The artificial intelligence-based model ANORAK improves histopathological grading of lung adenocarcinoma

      Pan, X., AbdulJabbar, K., Coelho-Lima, J., Grapa, A. I., Zhang, H., Cheung, A. H. K., Baena, J., Karasaki, T., Wilson, C. R., Sereno, M., Veeriah, S., Aitken, S. J., Hackshaw, A., Nicholson, A. G., Jamal-Hanjani, M., Le Quesne, J., Janes, S. M., Hacker, A. M., Sharp, A., Smith, S., & 259 othersDhanda, H. K., Chan, K., Pilotti, C., Leslie, R., Chuter, D., MacKenzie, M., Chee, S., Alzetani, A., Lim, E., De Sousa, P., Jordan, S., Rice, A., Raubenheimer, H., Bhayani, H., Ambrose, L., Devaraj, A., Chavan, H., Begum, S., Buderi, S. I., Kaniu, D., Malima, M., Booth, S., Fernandes, N., Shah, P., Proli, C., Hewish, M., Danson, S., Shackcloth, M. J., Robinson, L., Russell, P., Blyth, K. G., Kidd, A., Kirk, A., Asif, M., Bilancia, R., Kostoulas, N., Thomas, M., Dick, C., Lester, J. F., Bajaj, A., Nakas, A., Sodha-Ramdeen, A., Tufail, M., Scotland, M., Boyles, R., Rathinam, S., Fennell, D. A., Wilson, C., Marrone, D., Dulloo, S., Matharu, G., Shaw, J. A., Riley, J., Primrose, L., Boleti, E., Cheyne, H., Khalil, M., Richardson, S., Cruickshank, T., Price, G., Kerr, K. M., Benafif, S., Papadatos-Pastos, D., Wilson, J., Ahmad, T., French, J., Gilbert, K., Naidu, B., Patel, A. J., Osman, A., Lacson, C., Langman, G., Shackleford, H., Djearaman, M., Kadiri, S., Middleton, G., Leek, A., Hodgkinson, J. D., Totten, N., Montero, A., Smith, E., Fontaine, E., Granato, F., Novasio, J., Rammohan, K., Joseph, L., Bishop, P., Shah, R., Moss, S., Joshi, V., Crosbie, P., Paiva-Correia, A., Chaturvedi, A., Priest, L., Oliveira, P., Gomes, F., Brown, K., Carter, M., Lindsay, C. R., Blackhall, F. H., Krebs, M. G., Summers, Y., Clipson, A., Tugwood, J., Kerr, A., Rothwell, D. G., Dive, C., Aerts, H. J. W. L., Schwarz, R. F., Kaufmann, T. L., Van Loo, P., Wilson, G. A., Rosenthal, R., Rowan, A., Bailey, C., Lee, C., Colliver, E., Enfield, K. S. S., Hill, M. S., Angelova, M., Pich, O., Leung, M., Frankell, A. M., Hiley, C. T., Lim, E. L., Zhai, H., Bakir, M. A., Birkbak, N. J., Lucas, O., Huebner, A., Puttick, C., Grigoriadis, K., Dietzen, M., Biswas, D., Athanasopoulou, F., Ward, S., Demeulemeester, J., Castignani, C., Cadieux, E. L., Kisistok, J., Sokac, M., Szallasi, Z., Diossy, M., Salgado, R., Stewart, A., Magness, A., Weeden, C. E., Levi, D., Grönroos, E., Noorani, I., Goldman, J., Escudero, M., Hobson, P., Vendramin, R., Boeing, S., Denner, T., Barbè, V., Lu, W. T., Hill, W., Naito, Y., Ramsden, Z., Kassiotis, G., Dwornik, A., Karamani, A., Chain, B., Pearce, D. R., Karagianni, D., Gálvez-Cancino, F., Stavrou, G., Mastrokalos, G., Lowe, H. L., Matos, I. G., Reading, J. L., Hartley, J. A., Selvaraju, K., Chen, K., Ensell, L., Shah, M., Litovchenko, M., Chervova, O., Pawlik, P., Hynds, R. E., Gamble, S., Ung, S. K. A., Bola, S. K., Spanswick, V., Wu, Y., Al-Sawaf, O., Jones, T. P., Beck, S., Tanic, M., Marafioti, T., Borg, E., Falzon, M., Khiroya, R., Toncheva, A., Abbosh, C., Richard, C., Naceur-Lombardelli, C., Gimeno-Valiente, F., Thakkar, K., Sunderland, M. W., Sivakumar, M., Kanu, N., Prymas, P., Saghafinia, S., Vanloo, S., Lam, J. M., Liu, W. K., Bunkum, A., Hessey, S., Zaccaria, S., Martínez-Ruiz, C., Black, J. R. M., Thol, K., Bentham, R., Litchfield, K., McGranahan, N., Quezada, S. A., Forster, M. D., Lee, S. M., Herrero, J., Nye, E., Stone, R. K., Nicod, J., Rane, J. K., Peggs, K. S., Ng, K. W., Dijkstra, K., Huska, M. R., Hoogenboom, E. M., Monk, F., Holding, J. W., Choudhary, J., Bhakhri, K., Scarci, M., Gorman, P., Stephens, R. C. M., Wong, Y. N. S., Kaplar, Z., Bandula, S., Watkins, T. B. K., Veiga, C., Royle, G., Collins-Fekete, C. A., Fraioli, F., Ashford, P., Procter, A. J., Ahmed, A., Taylor, M. N., Nair, A., Lawrence, D., Patrini, D., Navani, N., Thakrar, R. M., Swanton, C., Yuan, Y., Le Quesne, J. & Moore, D. A., 2024, (Accepted/In press) In: Nature Cancer.

      Research output: Contribution to journal › Article › peer-review

      Open Access
    • 2023

      Antibodies against endogenous retroviruses promote lung cancer immunotherapy

      TRACERx Consortium & CAPTURE Consortium, Apr 20 2023, In: Nature. 616, 7957, p. 563-573 11 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      56 Scopus citations

    • Body composition and lung cancer-associated cachexia in TRACERx

      TRACERx Consortium, Apr 2023, In: Nature medicine. 29, 4, p. 846-858 13 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      10 Scopus citations

    • Bridging clinic and wildlife care with AI-powered pan-species computational pathology

      AbdulJabbar, K., Castillo, S. P., Hughes, K., Davidson, H., Boddy, A. M., Abegglen, L. M., Minoli, L., Iussich, S., Murchison, E. P., Graham, T. A., Spiro, S., Maley, C. C., Aresu, L., Palmieri, C. & Yuan, Y., Dec 2023, In: Nature communications. 14, 1, 2408.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      2 Scopus citations

    • Evolutionary characterization of lung adenocarcinoma morphology in TRACERx

      TRACERx Consortium, 2023, (Accepted/In press) In: Nature medicine.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      21 Scopus citations

    • Genomic–transcriptomic evolution in lung cancer and metastasis

      TRACERx Consortium, Apr 20 2023, In: Nature. 616, 7957, p. 543-552 10 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      36 Scopus citations

    • Glioblastoma cell fate is differentially regulated by the microenvironments of the tumor bulk and infiltrative margin

      Garcia-Diaz, C., Pöysti, A., Mereu, E., Clements, M. P., Brooks, L. J., Galvez-Cancino, F., Castillo, S. P., Tang, W., Beattie, G., Courtot, L., Ruiz, S., Roncaroli, F., Yuan, Y., Marguerat, S., Quezada, S. A., Heyn, H. & Parrinello, S., May 30 2023, In: Cell Reports. 42, 5, 112472.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      5 Scopus citations

    • Lung adenocarcinoma promotion by air pollutants

      TRACERx Consortium, Apr 6 2023, In: Nature. 616, 7955, p. 159-167 9 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      128 Scopus citations

    • Pitfalls in machine learning-based assessment of tumor-infiltrating lymphocytes in breast cancer: a report of the international immuno-oncology biomarker working group

      Thagaard, J., Broeckx, G., Page, D. B., Jahangir, C. A., Verbandt, S., Kos, Z., Gupta, R., Khiroya, R., Abduljabbar, K., Acosta Haab, G., Acs, B., Akturk, G., Almeida, J. S., Alvarado-Cabrero, I., Amgad, M., Azmoudeh-Ardalan, F., Badve, S., Baharun, N. B., Balslev, E., Bellolio, E. R., & 122 othersBheemaraju, V., Blenman, K. R. M., Botinelly Mendonça Fujimoto, L., Bouchmaa, N., Burgues, O., Chardas, A., Chon U Cheang, M., Ciompi, F., Cooper, L. A. D., Coosemans, A., Corredor, G., Dahl, A. B., Dantas Portela, F. L., Deman, F., Demaria, S., Doré Hansen, J., Dudgeon, S. N., Ebstrup, T., Elghazawy, M., Fernandez-Martín, C., Fox, S. B., Gallagher, W. M., Giltnane, J. M., Gnjatic, S., Gonzalez-Ericsson, P. I., Grigoriadis, A., Halama, N., Hanna, M. G., Harbhajanka, A., Hart, S. N., Hartman, J., Hauberg, S., Hewitt, S., Hida, A. I., Horlings, H. M., Husain, Z., Hytopoulos, E., Irshad, S., Janssen, E. A. M., Kahila, M., Kataoka, T. R., Kawaguchi, K., Kharidehal, D., Khramtsov, A. I., Kiraz, U., Kirtani, P., Kodach, L. L., Korski, K., Kovács, A., Laenkholm, A. V., Lang-Schwarz, C., Larsimont, D., Lennerz, J. K., Lerousseau, M., Li, X., Ly, A., Madabhushi, A., Maley, S. K., Manur Narasimhamurthy, V., Marks, D. K., McDonald, E. S., Mehrotra, R., Michiels, S., Minhas, F. U. A. A., Mittal, S., Moore, D. A., Mushtaq, S., Nighat, H., Papathomas, T., Penault-Llorca, F., Perera, R. D., Pinard, C. J., Pinto-Cardenas, J. C., Pruneri, G., Pusztai, L., Rahman, A., Rajpoot, N. M., Rapoport, B. L., Rau, T. T., Reis-Filho, J. S., Ribeiro, J. M., Rimm, D., Roslind, A., Vincent-Salomon, A., Salto-Tellez, M., Saltz, J., Sayed, S., Scott, E., Siziopikou, K. P., Sotiriou, C., Stenzinger, A., Sughayer, M. A., Sur, D., Fineberg, S., Symmans, F., Tanaka, S., Taxter, T., Tejpar, S., Teuwen, J., Thompson, E. A., Tramm, T., Tran, W. T., van der Laak, J., van Diest, P. J., Verghese, G. E., Viale, G., Vieth, M., Wahab, N., Walter, T., Waumans, Y., Wen, H. Y., Yang, W., Yuan, Y., Zin, R. M., Adams, S., Bartlett, J., Loibl, S., Denkert, C., Savas, P., Loi, S., Salgado, R. & Specht Stovgaard, E., Aug 2023, In: Journal of Pathology. 260, 5, p. 498-513 16 p.

      Research output: Contribution to journal › Review article › peer-review

      Open Access
      5 Scopus citations

    • Self-supervised deep learning for highly efficient spatial immunophenotyping

      Zhang, H., AbdulJabbar, K., Grunewald, T., Akarca, A. U., Hagos, Y., Sobhani, F., Lecat, C. S. Y., Patel, D., Lee, L., Rodriguez-Justo, M., Yong, K., Ledermann, J. A., Le Quesne, J., Hwang, E. S., Marafioti, T. & Yuan, Y., Sep 2023, In: EBioMedicine. 95, 104769.

      Research output: Contribution to journal › Article › peer-review

      Open Access

    • 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

      Page, D. B., Broeckx, G., Jahangir, C. A., Verbandt, S., Gupta, R. R., Thagaard, J., Khiroya, R., Kos, Z., Abduljabbar, K., Acosta Haab, G., Acs, B., Akturk, G., Almeida, J. S., Alvarado-Cabrero, I., Azmoudeh-Ardalan, F., Badve, S., Baharun, N. B., Bellolio, E. R., Bheemaraju, V., Blenman, K. R. M., & 114 othersBotinelly Mendonça Fujimoto, L., Bouchmaa, N., Burgues, O., Cheang, M. C. U., Ciompi, F., Cooper, L. A. D., Coosemans, A., Corredor, G., Dantas Portela, F. L., Deman, F., Demaria, S., Dudgeon, S. N., Elghazawy, M., Ely, S., Fernandez-Martín, C., Fineberg, S., Fox, S. B., Gallagher, W. M., Giltnane, J. M., Gnjatic, S., Gonzalez-Ericsson, P. I., Grigoriadis, A., Halama, N., Hanna, M. G., Harbhajanka, A., Hardas, A., Hart, S. N., Hartman, J., Hewitt, S., Hida, A. I., Horlings, H. M., Husain, Z., Hytopoulos, E., Irshad, S., Janssen, E. A. M., Kahila, M., Kataoka, T. R., Kawaguchi, K., Kharidehal, D., Khramtsov, A. I., Kiraz, U., Kirtani, P., Kodach, L. L., Korski, K., Kovács, A., Laenkholm, A. V., Lang-Schwarz, C., Larsimont, D., Lennerz, J. K., Lerousseau, M., Li, X., Ly, A., Madabhushi, A., Maley, S. K., Manur Narasimhamurthy, V., Marks, D. K., McDonald, E. S., Mehrotra, R., Michiels, S., Minhas, F. U. A. A., Mittal, S., Moore, D. A., Mushtaq, S., Nighat, H., Papathomas, T., Penault-Llorca, F., Perera, R. D., Pinard, C. J., Pinto-Cardenas, J. C., Pruneri, G., Pusztai, L., Rahman, A., Rajpoot, N. M., Rapoport, B. L., Rau, T. T., Reis-Filho, J. S., Ribeiro, J. M., Rimm, D., Vincent-Salomon, A., Salto-Tellez, M., Saltz, J., Sayed, S., Siziopikou, K. P., Sotiriou, C., Stenzinger, A., Sughayer, M. A., Sur, D., Symmans, F., Tanaka, S., Taxter, T., Tejpar, S., Teuwen, J., Thompson, E. A., Tramm, T., Tran, W. T., van der Laak, J., van Diest, P. J., Verghese, G. E., Viale, G., Vieth, M., Wahab, N., Walter, T., Waumans, Y., Wen, H. Y., Yang, W., Yuan, Y., Adams, S., Bartlett, J. M. S., Loibl, S., Denkert, C., Savas, P., Loi, S., Salgado, R. & Specht Stovgaard, E., Aug 2023, In: Journal of Pathology. 260, 5, p. 514-532 19 p.

      Research output: Contribution to journal › Review article › peer-review

      Open Access
      3 Scopus citations

    • Spatial Positioning of Immune Hotspots Reflects the Interplay between B and T Cells in Lung Squamous Cell Carcinoma

      Zhang, H., AbdulJabbar, K., Moore, D. A., Akarca, A., Enfield, K. S. S., Jamal-Hanjani, M., Raza, S. E. A., Veeriah, S., Salgado, R., McGranahan, N., Le Quesne, J., Swanton, C., Marafioti, T. & Yuan, Y., May 2 2023, In: Cancer Research. 83, 9, p. 1410-1425 16 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      8 Scopus citations

    • The evolution of lung cancer and impact of subclonal selection in TRACERx

      TRACERx Consortium, Apr 20 2023, In: Nature. 616, 7957, p. 525-533 9 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      50 Scopus citations

    • The evolution of non-small cell lung cancer metastases in TRACERx

      TRACERx Consortium, Apr 20 2023, In: Nature. 616, 7957, p. 534-542 9 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      39 Scopus citations

    • The tumour ecology of quiescence: Niches across scales of complexity

      Castillo, S. P., Galvez-Cancino, F., Liu, J., Pollard, S. M., Quezada, S. A. & Yuan, Y., Jul 2023, In: Seminars in cancer biology. 92, p. 139-149 11 p.

      Research output: Contribution to journal › Review article › peer-review

      Open Access
      1 Scopus citations

    • Tracking early lung cancer metastatic dissemination in TRACERx using ctDNA

      TRACERx Consortium, Apr 20 2023, In: Nature. 616, 7957, p. 553-562 10 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      52 Scopus citations
    • 2022

      Automated Dcis Identification From Multiplex Immunohistochemistry Using Generative Adversarial Networks

      Sobhani, F., Hamidinekoo, A., Hall, A. H., King, L., Marks, J. R., Maley, C., Horlings, H. M., Shelley Hwang, E. & Yuan, Y., 2022, ISBI 2022 - Proceedings: 2022 IEEE International Symposium on Biomedical Imaging. IEEE Computer Society, (Proceedings - International Symposium on Biomedical Imaging; vol. 2022-March).

      Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    • Comparative Evaluation of Tumor-Infiltrating Lymphocytes in Companion Animals: Immuno-Oncology as a Relevant Translational Model for Cancer Therapy

      on behalf of the International Immuno-Oncology Biomarker Working Group, Oct 2022, In: Cancers. 14, 20, 5008.

      Research output: Contribution to journal › Review article › peer-review

      Open Access
      4 Scopus citations

    • Cross-Stream Interactions: Segmentation of Lung Adenocarcinoma Growth Patterns

      Pan, X., Zhang, H., Grapa, A. I., AbdulJabbar, K., Raza, S. E. A., Cheung, H. K. A., Karasaki, T., Quesne, J. L., Moore, D. A., Swanton, C. & Yuan, Y., 2022, Computational Mathematics Modeling in Cancer Analysis - 1st International Workshop, CMMCA 2022, Held in Conjunction with MICCAI 2022, Proceedings. Qin, W., Zaki, N., Zhang, F., Wu, J. & Yang, F. (eds.). Springer Science and Business Media Deutschland GmbH, p. 78-90 13 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 13574 LNCS).

      Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    • DCIS AI-TIL: Ductal Carcinoma In Situ Tumour Infiltrating Lymphocyte Scoring Using Artificial Intelligence

      Hagos, Y. B., Sobhani, F., Castillo, S. P., Hall, A. H., AbdulJabbar, K., Salgado, R., Harmon, B., Gallagher, K., Kilgore, M., King, L. M., Marks, J. R., Maley, C., Horlings, H. M., West, R., Hwang, E. S. & Yuan, Y., 2022, Artificial Intelligence over Infrared Images for Medical Applications and Medical Image Assisted Biomarker Discovery - 1st MICCAI Workshop, AIIIMA 2022, and 1st MICCAI Workshop, MIABID 2022, Held in Conjunction with MICCAI 2022, Proceedings. Kakileti, S. T., Manjunath, G., Gabrani, M., Rosen-Zvi, M., Braman, N., Schwartz, R. G., Frangi, A. F., Chung, P-C., Weight, C. & Jagadish, V. (eds.). Springer Science and Business Media Deutschland GmbH, p. 164-175 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 13602 LNCS).

      Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    • DeepMIF: Deep Learning Based Cell Profiling for Multispectral Immunofluorescence Images with Graphical User Interface

      Hagos, Y. B., Akarca, A. U., Ramsay, A., Rossi, R. L., Pomplun, S., Moioli, A., Gianatti, A., Mcnamara, C., Rambaldi, A., Quezada, S. A., Linch, D., Gritti, G., Marafioti, T. & Yuan, Y., 2022, Medical Image Computing and Computer Assisted Intervention – MICCAI 2022 - 25th International Conference, Proceedings. Wang, L., Dou, Q., Fletcher, P. T., Speidel, S. & Li, S. (eds.). Springer Science and Business Media Deutschland GmbH, p. 140-149 10 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 13434 LNCS).

      Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    • Emerging technologies and their impact on regulatory science

      Anklam, E., Bahl, M. I., Ball, R., Beger, R. D., Cohen, J., Fitzpatrick, S., Girard, P., Halamoda-Kenzaoui, B., Hinton, D., Hirose, A., Hoeveler, A., Honma, M., Hugas, M., Ishida, S., Kass, G. E. N., Kojima, H., Krefting, I., Liachenko, S., Liu, Y., Masters, S., & 28 othersMarx, U., McCarthy, T., Mercer, T., Patri, A., Pelaez, C., Pirmohamed, M., Platz, S., Ribeiro, A. J. S., Rodricks, J. V., Rusyn, I., Salek, R. M., Schoonjans, R., Silva, P., Svendsen, C. N., Sumner, S., Sung, K., Tagle, D., Tong, L., Tong, W., Eijnden-van-Raaij, J. V. D., Vary, N., Wang, T., Waterton, J., Wang, M., Wen, H., Wishart, D., Yuan, Y. & Slikker, W., Jan 2022, In: Experimental Biology and Medicine. 247, 1, p. 1-75 75 p.

      Research output: Contribution to journal › Review article › peer-review

      Open Access
      19 Scopus citations

    • High inter-follicular spatial co-localization of CD8+FOXP3+ with CD4+CD8+ cells predicts favorable outcome in follicular lymphoma

      Hagos, Y. B., Akarca, A. U., Ramsay, A., Rossi, R. L., Pomplun, S., Ngai, V., Moioli, A., Gianatti, A., Mcnamara, C., Rambaldi, A., Quezada, S. A., Linch, D., Gritti, G., Yuan, Y. & Marafioti, T., Oct 2022, In: Hematological Oncology. 40, 4, p. 541-553 13 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      4 Scopus citations

    • Report on computational assessment of Tumor Infiltrating Lymphocytes from the International Immuno-Oncology Biomarker Working Group

      International Immuno-Oncology Biomarker Working Group, Dec 2022, In: npj Breast Cancer. 6, 1, 16.

      Research output: Contribution to journal › Review article › peer-review

      Open Access
      86 Scopus citations

    • Self-supervised Antigen Detection Artificial Intelligence (SANDI)

      Zhang, H., AbdulJabbar, K., Grunewald, T., Akarca, A., Hagos, Y., Lecat, C., Pate, D., Lee, L., Rodriguez-Justo, M., Yong, K., Ledermann, J., Le Quesne, J., Marafioti, T. & Yuan, Y., 2022, Resource-Efficient Medical Image Analysis - 1st MICCAI Workshop, REMIA 2022, Proceedings. Xu, X., Li, X., Mahapatra, D., Cheng, L., Petitjean, C. & Fu, H. (eds.). Springer Science and Business Media Deutschland GmbH, p. 12-21 10 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 13543 LNCS).

      Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

    • Spatial interplay of lymphocytes and fibroblasts in estrogen receptor-positive HER2-negative breast cancer

      Nederlof, I., Hajizadeh, S., Sobhani, F., Raza, S. E. A., AbdulJabbar, K., Harkes, R., van de Vijver, M. J., Salgado, R., Desmedt, C., Kok, M., Yuan, Y. & Horlings, H. M., Dec 2022, In: npj Breast Cancer. 8, 1, 56.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      2 Scopus citations

    • Spatial interplay of tissue hypoxia and T-cell regulation in ductal carcinoma in situ

      Sobhani, F., Muralidhar, S., Hamidinekoo, A., Hall, A. H., King, L. M., Marks, J. R., Maley, C., Horlings, H. M., Hwang, E. S. & Yuan, Y., Dec 2022, In: npj Breast Cancer. 8, 1, 105.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      3 Scopus citations
    • 2021

      Artificial intelligence and digital pathology: Opportunities and implications for immuno-oncology

      Sobhani, F., Robinson, R., Hamidinekoo, A., Roxanis, I., Somaiah, N. & Yuan, Y., Apr 2021, In: Biochimica et Biophysica Acta - Reviews on Cancer. 1875, 2, 188520.

      Research output: Contribution to journal › Review article › peer-review

      Open Access
      17 Scopus citations

    • Automated Quantification Of Blood Microvessels In Hematoxylin And Eosin Whole Slide Images

      Hamidinekoo, A., Kelsey, A., Trahearn, N., Selfe, J., Shipley, J. & Yuan, Y., 2021, In: Proceedings of Machine Learning Research. 156, p. 94-104 11 p.

      Research output: Contribution to journal › Conference article › peer-review

      1 Scopus citations

    • Biomarkers for site-specific response to neoadjuvant chemotherapy in epithelial ovarian cancer: relating MRI changes to tumour cell load and necrosis

      Winfield, J. M., Wakefield, J. C., Brenton, J. D., AbdulJabbar, K., Savio, A., Freeman, S., Pace, E., Lutchman-Singh, K., Vroobel, K. M., Yuan, Y., Banerjee, S., Porta, N., Ahmed Raza, S. E. & deSouza, N. M., Mar 16 2021, In: British journal of cancer. 124, 6, p. 1130-1137 8 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      10 Scopus citations

    • Cell abundance aware deep learning for cell detection on highly imbalanced pathological data

      Hagos, Y. B., Lecat, C. S. Y., Patel, D., Lee, L., Tran, T. A., Justo, M. R., Yong, K. & Yuan, Y., Apr 13 2021, 2021 IEEE 18th International Symposium on Biomedical Imaging, ISBI 2021. IEEE Computer Society, p. 1438-1442 5 p. 9433994. (Proceedings - International Symposium on Biomedical Imaging; vol. 2021-April).

      Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

      Open Access
      4 Scopus citations

    • Glioma Classification Using Multimodal Radiology and Histology Data

      Hamidinekoo, A., Pieciak, T., Afzali, M., Akanyeti, O. & Yuan, Y., 2021, Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries - 6th International Workshop, BrainLes 2020, Held in Conjunction with MICCAI 2020, Revised Selected Papers. Crimi, A. & Bakas, S. (eds.). Springer Science and Business Media Deutschland GmbH, p. 508-518 11 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 12659 LNCS).

      Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

      4 Scopus citations

    • MoNuSAC2020: A Multi-Organ Nuclei Segmentation and Classification Challenge

      Verma, R., Kumar, N., Patil, A., Kurian, N. C., Rane, S., Graham, S., Vu, Q. D., Zwager, M., Raza, S. E. A., Rajpoot, N., Wu, X., Chen, H., Huang, Y., Wang, L., Jung, H., Thomas Brown, G., Liu, Y., Liu, S., Jahromi, S. A. F., Khani, A. A., & 38 othersMontahaei, E., Baghshah, M. S., Behroozi, H., Semkin, P., Rassadin, A., Dutande, P., Lodaya, R., Baid, U., Baheti, B., Talbar, S., Mahbod, A., Ecker, R., Ellinger, I., Luo, Z., Dong, B., Xu, Z., Yao, Y., Lv, S., Feng, M., Xu, K., Zunair, H., Hamza, A. B., Smiley, S., Yin, T. K., Fang, Q. R., Srivastava, S., Mahapatra, D., Trnavska, L., Zhang, H., Narayanan, P. L., Law, J., Yuan, Y., Tejomay, A., Mitkari, A., Koka, D., Ramachandra, V., Kini, L. & Sethi, A., Dec 1 2021, In: IEEE Transactions on Medical Imaging. 40, 12, p. 3413-3423 11 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      76 Scopus citations

    • Noninvasive MRI native T1 mapping detects response to MYCN-targeted therapies in the Th-MYCN model of neuroblastoma

      Zormpas-Petridis, K., Poon, E., Clarke, M., Jerome, N. P., Boult, J. K. R., Blackledge, M. D., Carceller, F., Koers, A., Barone, G., Pearson, A. D. J., Moreno, L., Anderson, J., Sebire, N., McHugh, K., Koh, D. M., Chesler, L., Yuan, Y., Robinson, S. P. & Jamin, Y., Aug 15 2021, In: Cancer Research. 80, 16, p. 3424-3435 12 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      15 Scopus citations

    • SuperHistopath: A Deep Learning Pipeline for Mapping Tumor Heterogeneity on Low-Resolution Whole-Slide Digital Histopathology Images

      Zormpas-Petridis, K., Noguera, R., Ivankovic, D. K., Roxanis, I., Jamin, Y. & Yuan, Y., Jan 20 2021, In: Frontiers in Oncology. 10, 586292.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      21 Scopus citations

    • Symmetric Dense Inception Network for Simultaneous Cell Detection and Classification in Multiplex Immunohistochemistry Images

      Zhang, H., Grunewald, T., Akarca, A. U., Ledermann, J. A., Marafioti, T. & Yuan, Y., 2021, In: Proceedings of Machine Learning Research. 156, p. 246-257 12 p.

      Research output: Contribution to journal › Conference article › peer-review

      2 Scopus citations

    • The tale of TILs in breast cancer: A report from The International Immuno-Oncology Biomarker Working Group

      the International Immuno-Oncology Biomarker Working Group, Dec 1 2021, In: npj Breast Cancer. 7, 1, 150.

      Research output: Contribution to journal › Review article › peer-review

      Open Access
      101 Scopus citations

    • Unmasking the immune microecology of ductal carcinoma in situ with deep learning

      Narayanan, P. L., Raza, S. E. A., Hall, A. H., Marks, J. R., King, L., West, R. B., Hernandez, L., Guppy, N., Dowsett, M., Gusterson, B., Maley, C., Hwang, E. S. & Yuan, Y., Dec 2021, In: npj Breast Cancer. 7, 1, 19.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      13 Scopus citations

    • Wisdom of the crowd for early detection in barrett's esophagus

      Law, J., Paulson, T. G., Sanchez, C. A., Galipeau, P. C., Jansen, M., Stachler, M. D., Maley, C. C. & Yuan, Y., Apr 13 2021, 2021 IEEE 18th International Symposium on Biomedical Imaging, ISBI 2021. IEEE Computer Society, p. 531-535 5 p. 9433763. (Proceedings - International Symposium on Biomedical Imaging; vol. 2021-April).

      Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

      2 Scopus citations
    • 2020

      Application of a risk-management framework for integration of stromal tumor-infiltrating lymphocytes in clinical trials

      International Immuno-Oncology Biomarker Working Group, Dec 1 2020, In: npj Breast Cancer. 6, 1, 15.

      Research output: Contribution to journal › Review article › peer-review

      Open Access
      12 Scopus citations

    • Geospatial immune variability illuminates differential evolution of lung adenocarcinoma

      TRACERx Consortium, Jul 1 2020, In: Nature medicine. 26, 7, p. 1054-1062 9 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      163 Scopus citations

    • Immune surveillance in clinical regression of preinvasive squamous cell lung cancer

      Pennycuick, A., Teixeira, V. H., Abduljabbar, K., Ahmed Raza, S. E., Lund, T., Akarca, A. U., Rosenthal, R., Kalinke, L., Chandrasekharan, D. P., Pipinikas, C. P., Lee-Six, H., Hynds, R. E., Gowers, K. H. C., Henry, J. Y., Millar, F. R., Hagos, Y. B., Denais, C., Falzon, M., Moore, D. A., Antoniou, S., & 18 othersDurrenberger, P. F., Furness, A. J., Carroll, B., Marceaux, C., Asselin-Labat, M. L., Larson, W., Betts, C., Coussens, L. M., Thakrar, R. M., George, J., Swanton, C., Thirlwell, C., Campbell, P. J., Marafioti, T., Yuan, Y., Quezada, S. A., McGranahan, N. & Janes, S. M., Oct 2020, In: Cancer discovery. 10, 10, p. 1489-1499 11 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      53 Scopus citations

    • Pitfalls in assessing stromal tumor infiltrating lymphocytes (sTILs) in breast cancer

      the International Immuno-Oncology Biomarker Working Group, Dec 1 2020, In: npj Breast Cancer. 6, 1, 17.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      97 Scopus citations

    • The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution

      Human Tumor Atlas Network, Apr 16 2020, In: Cell. 181, 2, p. 236-249 14 p.

      Research output: Contribution to journal › Review article › peer-review

      Open Access
      248 Scopus citations

    • The T cell differentiation landscape is shaped by tumour mutations in lung cancer

      Ghorani, E., Reading, J. L., Henry, J. Y., de Massy, M. R., Rosenthal, R., Turati, V., Joshi, K., Furness, A. J. S., Aissa, A. B., Saini, S. K., Ramskov, S., Georgiou, A., Sunderland, M. W., Wong, Y. N. S., De Mucha, M. V., Day, W., Galvez-Cancino, F., Becker, P. D., Uddin, I., Ismail, M., & 30 othersRonel, T., Woolston, A., Jamal-Hanjani, M., Veeriah, S., Birkbak, N. J., Wilson, G. A., Litchfield, K., Conde, L., Guerra-Assunção, J. A., Blighe, K., Biswas, D., Salgado, R., Lund, T., Al Bakir, M., Moore, D. A., Hiley, C. T., Loi, S., Sun, Y., Yuan, Y., AbdulJabbar, K., Turajilic, S., Herrero, J., Enver, T., Hadrup, S. R., Hackshaw, A., Peggs, K. S., McGranahan, N., Chain, B., Swanton, C. & Quezada, S. A., May 1 2020, In: Nature Cancer. 1, 5, p. 546-561 16 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      63 Scopus citations

    • Topological tumor graphs: A graph-based spatial model to infer stromal recruitment for immunosuppression in melanoma histology a C

      Failmezger, H., Muralidhar, S., Rullan, A., de Andrea, C. E., Sahai, E. & Yuan, Y., Mar 1 2020, In: Cancer Research. 256, 4, p. 1199-1209 11 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      39 Scopus citations
    • 2019

      Analysis of tumour ecological balance reveals resource-dependent adaptive strategies of ovarian cancer

      Nawaz, S., Trahearn, N. A., Heindl, A., Banerjee, S., Maley, C. C., Sottoriva, A. & Yuan, Y., Oct 2019, In: EBioMedicine. 48, p. 224-235 12 p.

      Research output: Contribution to journal › Article › peer-review

      Open Access
      7 Scopus citations

    • ConCORDe-net: Cell count regularized convolutional neural network for cell detection in multiplex immunohistochemistry images

      Hagos, Y. B., Narayanan, P. L., Akarca, A. U., Marafioti, T. & Yuan, Y., 2019, Medical Image Computing and Computer Assisted Intervention – MICCAI 2019 - 22nd International Conference, Proceedings. Shen, D., Yap, P-T., Liu, T., Peters, T. M., Khan, A., Staib, L. H., Essert, C. & Zhou, S. (eds.). Springer Science and Business Media Deutschland GmbH, p. 667-675 9 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 11764 LNCS).

      Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

      Open Access
      18 Scopus citations