Yinyin Yuan
Department of Translational Molecular Pathology, Division of Pathology-Lab Medicine Div
About Yinyin Yuan
Dr. Yinyin Yuan is a professor and the Director of Computational Pathology Research Program at the Department of Translational Molecular Pathology. The mission of the Yuan lab is to design impact-driven strategies and artificial intelligence (AI) engines to accelerate the applications of AI and data science to pathology. The scientific focus is to decipher how the tumor microenvironment shapes the evolution of immune escape and drug resistance. Her team is developing cutting-edge technologies to study the spatial heterogeneity of the tumor microenvironment and how it shapes cancer genetic heterogeneity and clinical outcome.
As a Co-Lead of Focus Area One - Quantitative analysis and insight extraction from imaging and pathology data - in the Institute for Data Science in Oncology, Dr. Yuan is committed to building the computational infrastructure and data science capacity for pathology. This will enable accelerated, rigorous, and actionable approaches for building data science capacity with translational impacts in pathology. The vision is to create a new paradigm of technological advances and multidisciplinary convergences that will lead the way to novel digital biomarkers and ultimately to the new frontier of integrated diagnostics.
Dr. Yuan obtained degrees in computer science from the University of Science and Technology of China (USTC, BSc) and University of Warwick (MSc and PhD), and has won prestigious awards and fellowships including a Junior Research Fellowship from Wolfson College, University of Cambridge and Cancer Research UK Career Establishment Fellowship. From 2012 to 2022, she led the Computational Pathology and Integrative Genomics team at the institute of Cancer Research, London. There she built a pioneering interface between digital pathology, machine learning, and cancer biology with strong clinical applications, and was awarded the title of Professor of Computational Pathology in 2021. Her team currently leads artificial intelligence developments in computational pathology in several international scientific programs and consortiums include the Cancer Research UK-funded TRACERx Lung, Sarcoma Network Accelerator, Early detection for myeloma, Brain Tumour Award Target-GBM, and the NIH-funded Arizona Cancer Evolution Center and Breast Pre-Cancer Atlas.
Present Title & Affiliation
Primary Appointment
Professor, Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
Dual/Joint/Adjunct Appointment
Professor, Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
Research Interests
Dr. Yinyin Yuan is a professor and Director of the Computational Pathology Research Program in the Department of Translational Molecular Pathology. Her research focuses on computational and artificial intelligence (AI) development for digital pathology images and data-driven discovery in cancer biology. Her work introduced spatial and ecology-inspired analysis of the tumor microenvironment using digital pathology, contributing to a shift in the field from density-based analysis toward spatial biology. By grounding AI development in cancer biology, her research provides analytical frameworks to understand how interactions between genetically diverse cancer cells and their microenvironment drive tumor evolution and the emergence of drug resistance.
She co-leads Focus Area One – Quantitative Pathology and Medical Imaging within the Institute for Data Science in Oncology (IDSO), which integrates meaningful data extraction with MD Anderson’s unparalleled clinical expertise to transform the future of cancer. The focus area fosters collaborations to harness large-scale data from digital pathology and radiological imaging to provide accelerated, rigorous and actionable insight for patients.
Dr. Yuan founded and co-directs the SEQUOIA program (Spatial Ecology & Quantitative pathOlogy Image Analytical Platform), an institutional initiative dedicated to building AI and data science capacity for pathology. SEQUOIA integrates data science and clinical pathology expertise, data and computational resources, and research programs across the IDSO, The Strategic Research Initiative Development (STRIDE), and The Pathology and Laboratory Medicine division, to create a collaborative ecosystem in digital pathology. The program aims to advance technological innovation and multidisciplinary collaboration toward digital biomarker discovery, enabling a new frontier in integrated diagnostics.
Dr. Yuan received her BSc in Computer Science from the University of Science and Technology of China and her MSc and PhD in Computer Science from the University of Warwick. She has won prestigious awards and fellowships, including a Junior Research Fellowship from Wolfson College, University of Cambridge, UK. Prior to joining MD Anderson, she led the Computational Pathology and Integrative Genomics research team at The Institute of Cancer Research in London, one of the world’s most influential cancer research organizations. There she built a pioneering interface between digital pathology, machine learning, and cancer biology with strong clinical applications.
Education & Training
Degree-Granting Education
| 2009 | University of Warwick, GB, Computer Science, Ph.D |
| 2004 | University of Warwick, GB, Computer Science, M.Sc |
| 2003 | University of Science & Technology of China, CN, Computer Science, B.Sc |
Postgraduate Training
| 2010-2012 | Junior Research Fellow, University of Cambridge |
| 2009-2012 | Postdoctoral Fellow, University of Cambridge |
Experience & Service
Faculty Academic Appointments
Professor, Computational Pathology, The Institute of Cancer Research, London, 2021 - 2022
Associate Professor, The Institute of Cancer Research, London, 2017 - 2021
Assistant Professor, The Institute of Cancer Research, London, 2012 - 2017
Administrative Appointments/Responsibilities
Co-Lead, Focus Area One – Quantitative Pathology and Medical Imaging, the Institute for Data Science in Oncology, The University of Texas MD Anderson Cancer Center, 2023 - Present
Director of Computational Pathology Research Program, Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 2022 - Present
Honors & Awards
| 2016 | Cancer Research UK Career Establishment Award |
| 2012 | Cancer Research UK Visiting Scholarship Award |
| 2010 | University of Cambridge Wolfson College Fellowship |
Selected Publications
Peer-Reviewed Articles
- Hagos, YB, Lecat, CS, Patel, D, Mikolajczak, A, Castillo, SP, Lyon, EJ, Foster, K, Tran, TA, Lee, L, Rodriguez-Justo, M, Yong, K, Yuan, Y. Deep Learning Enables Spatial Mapping of the Mosaic Microenvironment of Myeloma Bone Marrow Trephine Biopsies. Cancer Research 84(3):493-508, 2024. e-Pub 2024. PMID: 37963212.
- Pan, X, AbdulJabbar, K, Coelho-Lima, J, Grapa, AI, Zhang, H, Cheung, AH, Baena, J, Karasaki, T, Wilson, CR, Sereno, M, Veeriah, S, Aitken, S, Hackshaw, A, Nicholson, A, Jamal-Hanjani, M, Le Quesne, J, Janes, SM, Hacker, AM, Sharp, A, Smith, S, Dhanda, H, Chan, K, Pilotti, C, Leslie, R, Chuter, D, MacKenzie, M, Chee, SJ, Alzetani, A, Lim, E, De Sousa, P, Jordan, S, Rice, A, Raubenheimer, H, Bhayani, H, Ambrose, L, Devaraj, A, Chavan, H, Begum, S, Buderi, SI, Kaniu, D, Malima, M, Booth, S, Fernandes, N, Shah, P, Proli, C, Hewish, M, Danson, S, Shackcloth, M, Robinson, L, Russell, P, Blyth, KG, Kidd, AC, Kirk, A, Asif, M, Bilancia, R, Kostoulas, N, Thomas, M, Dick, C, Lester, JF, Bajaj, A, Nakas, A, Sodha-Ramdeen, A, Tufail, M, Scotland, M, Boyles, R, Rathinam, S, Fennell, D, Wilson, C, Marrone, D, Dulloo, S, Matharu, G, Shaw, J, Riley, J, Primrose, L, Boleti, E, Cheyne, H, Khalil, M, Richardson, S, Cruickshank, T, Price, G, Kerr, K, Benafif, S, Papadatos-Pastos, D, Wilson, JF, Ahmad, T, French, J, Gilbert, K, Naidu, B, Patel, AJ, Osman, A, Lacson, C, Langman, G, Shackleford, H, Djearaman, M, Kadiri, S, Middleton, G, Leek, A, Hodgkinson, JD, 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, CR, Blackhall, FH, Krebs, M, Summers, Y, Clipson, A, Tugwood, J, Kerr, A, Rothwell, DG, Dive, C, Aerts, HJ, Schwarz, R, Kaufmann, TL, Van Loo, P, Wilson, GA, Rosenthal, R, Rowan, AJ, Bailey, C, Lee, C, Colliver, E, Enfield, K, Hill, MS, Angelova, M, Pich, O, Leung, M, Frankell, AM, Hiley, CT, Lim, E, Zhai, H, Bakir, MA, Birkbak, NJ, Lucas, O, Huebner, A, Puttick, C, Grigoriadis, K, Dietzen, M, Biswas, D, Athanasopoulou, F, Ward, S, Demeulemeester, J, Castignani, C, Cadieux, EL, Kisistok, J, Sokac, M, Szallasi, Z, Diossy, M, Salgado, R, Stewart, A, Magness, A, Weeden, CE, Levi, D, Gronroos, E, Noorani, I, Goldman, J, Escudero, M, Hobson, P, Vendramin, R, Boeing, S, Denner, T, Barbe, V, Lu, WT, Hill, W, Naito, Y, Ramsden, Z, Kassiotis, G, Dwornik, A, Karamani, A, Chain, B, Pearce, DR, Karagianni, D, Galvez-Cancino, F, Stavrou, G, Mastrokalos, G, Lowe, HL, Matos, I, Reading, JL, Hartley, JA, Selvaraju, K, Chen, K, Ensell, L, Shah, M, Litovchenko, M, Chervova, O, Pawlik, P, Hynds, RE, Gamble, S, Ung, SK, Bola, SK, Spanswick, V, Wu, Y, Al-Sawaf, O, Jones, TP, Beck, S, Tanić, M, Marafioti, T, Borg, E, Falzon, M, Khiroya, R, Toncheva, A, Abbosh, C, Richard, C, Naceur-Lombardelli, C, Gimeno-Valiente, F, Thakkar, K, Sunderland, MW, Sivakumar, M, Kanu, N, Prymas, P, Saghafinia, S, Vanloo, S, Lam, JM, Liu, WK, Bunkum, A, Hessey, S, Zaccaria, S, Martínez-Ruiz, C, Black, JR, Thol, K, Bentham, R, Litchfield, K, Mcgranahan, N, Quezada, SA, Forster, M, Lee, SM, Herrero, J, Nye, E, Stone, RK, Nicod, J, Rane, J, Peggs, KS, Ng, KW, Dijkstra, K, Huska, M, Hoogenboom, EM, Monk, F, Holding, JW, Choudhary, J, Bhakhri, K, Scarci, M, Gorman, P, Stephens, RC, Wong, YS, Kaplar, Z, Bandula, S, Watkins, TB, Veiga, C, Royle, G, Collins-Fekete, CA, Fraioli, F, Ashford, P, Procter, AJ, Ahmed, A, Taylor, MN, Nair, A, Lawrence, D, Patrini, D, Navani, N, Thakrar, R, Swanton, C, Yuan, Y, Le Quesne, J, Moore, DA. The artificial intelligence-based model ANORAK improves histopathological grading of lung adenocarcinoma. Nature Cancer 5(2):347-363, 2024. e-Pub 2024. PMID: 38200244.
- AbdulJabbar, K, Castillo, SP, Hughes, K, Davidson, H, Boddy, AM, Abegglen, LM, Minoli, L, Iussich, S, Murchison, EP, Graham, TA, Spiro, S, Maley, CC, Aresu, L, Palmieri, C, Yuan, Y. Bridging clinic and wildlife care with AI-powered pan-species computational pathology. Nature communications 14(1), 2023. e-Pub 2023. PMID: 37100774.
- Zhang, H, AbdulJabbar, K, Grunewald, T, Akarca, A, Hagos, YB, Sobhani, F, Lecat, CS, Patel, D, Lee, L, Rodriguez-Justo, M, Yong, K, Ledermann, J, Le Quesne, J, Hwang, ES, Marafioti, T, Yuan, Y. Self-supervised deep learning for highly efficient spatial immunophenotyping. EBioMedicine 95, 2023. e-Pub 2023. PMID: 37672979.
- Zhang, H, AbdulJabbar, K, Moore, DA, Akarca, A, Enfield, K, Jamal-Hanjani, M, Raza, SE, Veeriah, S, Salgado, R, Mcgranahan, N, Le Quesne, J, Swanton, C, Marafioti, T, Yuan, Y. Spatial Positioning of Immune Hotspots Reflects the Interplay between B and T Cells in Lung Squamous Cell Carcinoma. Cancer Research 83(9):1410-1425, 2023. e-Pub 2023. PMID: 36853169.
- Sobhani F, Muralidhar S, Hamidinekoo A, Hall AH, King LM, Marks JR, Maley C, Horlings HM, Hwang ES, Yuan Y. Spatial interplay of tissue hypoxia and T-cell regulation in ductal carcinoma in situ. NPJ Breast Cancer 8(1):105, 2022. e-Pub 2022. PMID: 36109587.
- Narayanan PL, Raza SEA, Hall AH, Marks JR, King L, West RB, Hernandez L, Guppy N, Dowsett M, Gusterson B, Maley C, Hwang ES, Yuan Y. Unmasking the immune microecology of ductal carcinoma in situ with deep learning. NPJ Breast Cancer 7(1):19, 2021. e-Pub 2021. PMID: 33649333.
- AbdulJabbar K, Raza SEA, Rosenthal R, Jamal-Hanjani M, Veeriah S, Akarca A, Lund T, Moore DA, Salgado R, Al Bakir M, Zapata L, Hiley CT, Officer L, Sereno M, Smith CR, Loi S, Hackshaw A, Marafioti T, Quezada SA, McGranahan N, Le Quesne J, Consortium T, Swanton C, Yuan Y. Geospatial immune variability illuminates differential evolution of lung adenocarcinoma. Nat Med 26(7):1054-1062, 2020. e-Pub 2020. PMID: 32461698.
- Failmezger H, Muralidhar S, Rullan A, de Andrea CE, Sahai E, Yuan Y. Topological Tumor Graphs: A Graph-Based Spatial Model to Infer Stromal Recruitment for Immunosuppression in Melanoma Histology. Cancer Res 80(5):1199-1209, 2020. e-Pub 2020. PMID: 31874858.
- Zormpas-Petridis K, Noguera R, Ivankovic DK, Roxanis I, Jamin Y, Yuan Y. SuperHistopath: A Deep Learning Pipeline for Mapping Tumor Heterogeneity on Low-Resolution Whole-Slide Digital Histopathology Images. Front Oncol 10:586292, 2020. e-Pub 2020. PMID: 33552964.
- Nawaz S, Trahearn NA, Heindl A, Banerjee S, Maley CC, Sottoriva A, Yuan Y. Analysis of tumour ecological balance reveals resource-dependent adaptive strategies of ovarian cancer. EBioMedicine 48:224-235, 2019. e-Pub 2019. PMID: 31648981.
- Zormpas-Petridis K, Failmezger H, Raza SEA, Roxanis I, Jamin Y, Yuan Y. Superpixel-Based Conditional Random Fields (SuperCRF): Incorporating Global and Local Context for Enhanced Deep Learning in Melanoma Histopathology. Front Oncol 9:1045, 2019. e-Pub 2019. PMID: 31681583.
- Heindl A, Khan AM, Rodrigues DN, Eason K, Sadanandam A, Orbegoso C, Punta M, Sottoriva A, Lise S, Banerjee S, Yuan Y. Microenvironmental niche divergence shapes BRCA1-dysregulated ovarian cancer morphological plasticity. Nat Commun 9(1):3917, 2018. e-Pub 2018. PMID: 30254278.
- Heindl A, Sestak I, Naidoo K, Cuzick J, Dowsett M, Yuan Y. Relevance of Spatial Heterogeneity of Immune Infiltration for Predicting Risk of Recurrence After Endocrine Therapy of ER+ Breast Cancer. J Natl Cancer Inst 110(2), 2018. e-Pub 2018. PMID: 28859291.
- Khan AM, Yuan Y. Biopsy variability of lymphocytic infiltration in breast cancer subtypes and the ImmunoSkew score. Sci Rep 6:36231, 2016. e-Pub 2016. PMID: 27812028.
- Heindl A, Lan C, Rodrigues DN, Koelble K, Yuan Y. Similarity and diversity of the tumor microenvironment in multiple metastases: critical implications for overall and progression-free survival of high-grade serous ovarian cancer. Oncotarget 7(44):71123-71135, 2016. e-Pub 2016. PMID: 27661102.
- Natrajan R, Sailem H, Mardakheh FK, Arias Garcia M, Tape CJ, Dowsett M, Bakal C, Yuan Y. Microenvironmental Heterogeneity Parallels Breast Cancer Progression: A Histology-Genomic Integration Analysis. PLoS Med 13(2):e1001961, 2016. e-Pub 2016. PMID: 26881778.
- Savage RS, Yuan Y. Predicting chemoinsensitivity in breast cancer with 'omics/digital pathology data fusion. R Soc Open Sci 3(2):140501, 2016. e-Pub 2016. PMID: 26998311.
- Nawaz S, Heindl A, Koelble K, Yuan Y. Beyond immune density: critical role of spatial heterogeneity in estrogen receptor-negative breast cancer. Mod Pathol 28(12):1621, 2015. e-Pub 2015. PMID: 26621491.
- Lan C, Heindl A, Huang X, Xi S, Banerjee S, Liu J, Yuan Y. Quantitative histology analysis of the ovarian tumour microenvironment. Sci Rep 5:16317, 2015. e-Pub 2015. PMID: 26573438.
- Maley CC, Koelble K, Natrajan R, Aktipis A, Yuan Y. An ecological measure of immune-cancer colocalization as a prognostic factor for breast cancer. Breast Cancer Res 17(1):131, 2015. e-Pub 2015. PMID: 26395345.
- Nawaz S, Heindl A, Koelble K, Yuan Y. Beyond immune density: critical role of spatial heterogeneity in estrogen receptor-negative breast cancer. Mod Pathol 28(6):766-77, 2015. e-Pub 2015. PMID: 25720324.
- Yuan Y. Modelling the spatial heterogeneity and molecular correlates of lymphocytic infiltration in triple-negative breast cancer. J R Soc Interface 12(103), 2015. e-Pub 2015. PMID: 25505134.
Review Articles
- Castillo, SP, Galvez-Cancino, F, Liu, J, Pollard, SM, Quezada, SA, Yuan, Y. The tumour ecology of quiescence. Seminars in cancer biology 92:139-149, 2023. e-Pub 2023. PMID: 37037400.
- Sobhani F, Robinson R, Hamidinekoo A, Roxanis I, Somaiah N, Yuan Y. Artificial intelligence and digital pathology: Opportunities and implications for immuno-oncology. Biochim Biophys Acta Rev Cancer 1875(2):188520, 2021. e-Pub 2021. PMID: 33561505.
- Nawaz S, Yuan Y. Computational pathology: Exploring the spatial dimension of tumor ecology. Cancer Lett 380(1):296-303, 2016. e-Pub 2016. PMID: 26592351.
- Yuan Y. Spatial Heterogeneity in the Tumor Microenvironment. Cold Spring Harb Perspect Med 6(8), 2016. e-Pub 2016. PMID: 27481837.
- Heindl A, Nawaz S, Yuan Y. Mapping spatial heterogeneity in the tumor microenvironment: a new era for digital pathology. Lab Invest 95(4):377-84, 2015. e-Pub 2015. PMID: 25599534.
Patents
- Scoring of tumour infiltration by lymphocytes. Patent Number: Yinyin Yuan/WO/2016/083791.
Patient Reviews
CV information above last modified July 22, 2026