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.
Education & Training
Degree-Granting Education
| 2009 | University of Warwick, Warwick, GBR, PHD, Computer Science |
| 2004 | University of Warwick, Warwick, GBR, MS, Computer Science |
| 2003 | University of Science & Technology of China, China, CHN, BS, Computer Science |
Experience & Service
Academic Appointments
Professor, Department of Translational Molecular Pathology, Division of Pathology/Lab Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 2022 - Present
Professor, The Institute of Cancer Research, London, London, 2021 - 2022
Associate Professor, The Institute of Cancer Research, London, London, 2017 - 2021
Assistant Professor, The Institute of Cancer Research, London, London, 2012 - 2017
Administrative Appointments/Responsibilities
Co-Lead, Focus Area #1, Institute for Data Science in Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 2022 - Present
Director of Computational Pathology Research Program, The University of Texas MD Anderson Cancer Center, Houston, TX, 2022 - Present
Honors & Awards
| 2016 | Cancer Research UK (CRUK) Career Establishment Award |
Selected Publications
Peer-Reviewed Articles
- Hagos YB, Akarca AU, Ramsay A, Rossi RL, Pomplun S, Ngai V, Moioli A, Gianatti A, Mcnamara C, Rambaldi A, Quezada SA, Linch D, Gritti G, Yuan Y, Marafioti T. High inter-follicular spatial co-localization of CD8+FOXP3+ with CD4+CD8+ cells predicts favorable outcome in follicular lymphoma. Hematol Oncol 40(4):541-553, 2022. e-Pub 2022. PMID: 35451108.
- Pinard CJ, International Immuno-Oncology Biomarker Working Group, Lagree A, Lu FI, Klein J, Oblak ML, Salgado R, Cardenas JCP, Brunetti B, Muscatello LV, Sarli G, Foschini MP, Hardas A, Castillo SP, AbdulJabbar K, Yuan Y, Moore DA, Tran WT. Comparative Evaluation of Tumor-Infiltrating Lymphocytes in Companion Animals: Immuno-Oncology as a Relevant Translational Model for Cancer Therapy. Cancers (Basel) 14(20), 2022. e-Pub 2022. PMID: 36291791.
- 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.
- Anklam E, Bahl MI, Ball R, Beger RD, Cohen J, Fitzpatrick S, Girard P, Halamoda-Kenzaoui B, Hinton D, Hirose A, Hoeveler A, Honma M, Hugas M, Ishida S, Kass GE, Kojima H, Krefting I, Liachenko S, Liu Y, Masters S, Marx U, McCarthy T, Mercer T, Patri A, Pelaez C, Pirmohamed M, Platz S, Ribeiro AJ, Rodricks JV, Rusyn I, Salek RM, Schoonjans R, Silva P, Svendsen CN, Sumner S, Sung K, Tagle D, Tong L, Tong W, Eijnden-van-Raaij JVD, Vary N, Wang T, Waterton J, Wang M, Wen H, Wishart D, Yuan Y, Slikker W. Emerging technologies and their impact on regulatory science. Exp Biol Med (Maywood) 247(1):1-75, 2022. e-Pub 2021. PMID: 34783606.
- 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.
- 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.
- Pennycuick A, Teixeira VH, AbdulJabbar K, Raza SEA, Lund T, Akarca AU, Rosenthal R, Kalinke L, Chandrasekharan DP, Pipinikas CP, Lee-Six H, Hynds RE, Gowers KHC, Henry JY, Millar FR, Hagos YB, Denais C, Falzon M, Moore DA, Antoniou S, Durrenberger PF, Furness AJ, Carroll B, Marceaux C, Asselin-Labat ML, Larson W, Betts C, Coussens LM, Thakrar RM, George J, Swanton C, Thirlwell C, Campbell PJ, Marafioti T, Yuan Y, Quezada SA, McGranahan N, Janes SM. Immune Surveillance in Clinical Regression of Preinvasive Squamous Cell Lung Cancer. Cancer Discov 10(10):1489-1499, 2020. e-Pub 2020. PMID: 32690541.
- 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, TRACERx Consortium, 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.
- Ghorani E, Reading JL, Henry JY, Massy MR, Rosenthal R, Turati V, Joshi K, Furness AJS, Ben Aissa A, Saini SK, Ramskov S, Georgiou A, Sunderland MW, Wong YNS, Mucha MV, Day W, Galvez-Cancino F, Becker PD, Uddin I, Oakes T, Ismail M, Ronel T, Woolston A, Jamal-Hanjani M, Veeriah S, Birkbak NJ, Wilson GA, Litchfield K, Conde L, Guerra-Assunção JA, Blighe K, Biswas D, Salgado R, Lund T, Bakir MA, Moore DA, Hiley CT, Loi S, Sun Y, Yuan Y, AbdulJabbar K, Turajilic S, Herrero J, Enver T, Hadrup SR, Hackshaw A, Peggs KS, McGranahan N, Chain B, TRACERx Consortium, Swanton C, Quezada SA. The T cell differentiation landscape is shaped by tumour mutations in lung cancer. Nat Cancer 1(5):546-561, 2020. e-Pub 2020. PMID: 32803172.
- 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 2019. PMID: 31874858.
- 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.
- 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. PMID: 28859291.
- Maley CC, Aktipis A, Graham TA, Sottoriva A, Boddy AM, Janiszewska M, Silva AS, Gerlinger M, Yuan Y, Pienta KJ, Anderson KS, Gatenby R, Swanton C, Posada D, Wu CI, Schiffman JD, Hwang ES, Polyak K, Anderson ARA, Brown JS, Greaves M, Shibata D. Classifying the evolutionary and ecological features of neoplasms. Nat Rev Cancer 17(10):605-619, 2017. e-Pub 2017. PMID: 28912577.
- Yuan Y. Spatial Heterogeneity in the Tumor Microenvironment. Cold Spring Harb Perspect Med 6(8), 2016. e-Pub 2016. PMID: 27481837.
- Mardakheh FK, Paul A, Kümper S, Sadok A, Paterson H, Mccarthy A, Yuan Y, Marshall CJ. Global Analysis of mRNA, Translation, and Protein Localization: Local Translation Is a Key Regulator of Cell Protrusions. Dev Cell 35(3):344-57, 2015. PMID: 26555054.
- 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. PMID: 25505134.
- Worboys JD, Sinclair J, Yuan Y, Jørgensen C. Systematic evaluation of quantotypic peptides for targeted analysis of the human kinome. Nat Methods 11(10):1041-4, 2014. e-Pub 2014. PMID: 25152083.
- Yuan Y, Failmezger H, Rueda OM, Ali HR, Gräf S, Chin SF, Schwarz RF, Curtis C, Dunning MJ, Bardwell H, Johnson N, Doyle S, Turashvili G, Provenzano E, Aparicio S, Caldas C, Markowetz F. Quantitative image analysis of cellular heterogeneity in breast tumors complements genomic profiling. Sci Transl Med 4(157):157ra143, 2012. PMID: 23100629.
- Curtis C, Shah SP, Chin SF, Turashvili G, Rueda OM, Dunning MJ, Speed D, Lynch AG, Samarajiwa S, Yuan Y, Gräf S, Ha G, Haffari G, Bashashati A, Russell R, McKinney S, METABRIC Group, Langerød A, Green A, Provenzano E, Wishart G, Pinder S, Watson P, Markowetz F, Murphy L, Ellis I, Purushotham A, Børresen-Dale AL, Brenton JD, Tavaré S, Caldas C, Aparicio S. The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature 486(7403):346-52, 2012. e-Pub 2012. PMID: 22522925.
- Yuan Y, Curtis C, Caldas C, Markowetz F. A sparse regulatory network of copy-number driven gene expression reveals putative breast cancer oncogenes. IEEE/ACM Trans Comput Biol Bioinform 9(4):947-54, 2012. PMID: 21788678.
- Yuan Y, Savage RS, Markowetz F. Patient-specific data fusion defines prognostic cancer subtypes. PLoS Comput Biol 7(10):e1002227, 2011. e-Pub 2011. PMID: 22028636.
- Yuan Y, Li CT, Wilson R. Partial mixture model for tight clustering of gene expression time-course. BMC Bioinformatics 9:287, 2008. e-Pub 2008. PMID: 18564420.
Grant & Contract Support
| Title: | Lung Cancer Evolution |
| Funding Source: | CRUK Fellowship |
| Role: | Principal Investigator |
| Title: | Improving Neoadjuvant Therapy in Sarcomas |
| Funding Source: | CRUK Accelerator |
| Role: | Principal Investigator |
| Title: | Targeting Biological Vulnerabilities of Glioblastoma |
| Funding Source: | CRUK Program |
| Role: | Principal Investigator |
| Title: | Arizona Cancer Evolution Center |
| Funding Source: | NIH/CSBC |
| Role: | Principal Investigator |
| Title: | Early Detection of Multiple Myeloma |
| Funding Source: | CRUK Program |
| Role: | Principal Investigator |