Image-Omics The Yuan Lab Publications Team Projects Contact

Yinyin Yuan

Positions


Team Leader, Computational Pathology & Integrated Genomics, ICR

Specialised in computational pathology and omics data integration, I lead an interdisciplinary team at the Institute of Cancer Research in London to develop impact-driven AI solutions for cancer research and treatment.


Diversity and Equalities champion, Academic Dean’s team, ICR

I believe that to achieve equality, the key is to respect and celebrate our differences and diversity. At ICR I provide an oversight from the ICR-wide equality agendas to the Dean’s team and multiple committees, and provide visible leadership in the area of equality and diversity.

Previous positions and degrees


Junior Research Fellow, Wolfson College, University of Cambridge, 2010-2012

I won a prestigious fellowship at the University of Cambridge and served as part of the governing body at Wolfson College, University of Cambridge.


Postdoctoral fellow, Markowetz Lab, Cambridge Institute, Cancer Research UK & Department of Oncology, University of Cambridge, 2009-2012

I trained in both dry and wet lab during my postdoc, under the supervision and mentorship of Florian Markowetz at Cambridge Institute.


PhD, Computer Science, University of Warwick

MSc by research, Computer Science, University of Warwick

BSc, Computer Science, University of Science & Technology of China (USTC)

Publications


Top 10 Selected Publications

 

High impact biomedicine

1.     AbdulJabbar K^, Raza SEA^, Rosenthal R, Jamal-Hanjani M, Veeriah S, Akarca A, Lund T, Moore D, Salgado R, Bakir MA, Zapata L, Hiley CT, Officer L, Sereno M, Smith CR, Loi S, Hackshaw A, Marafioti T, Quezada SA, McGranahan N, Le Quesne J*, Swanton C*, Yuan Y* (2020). Geospatial immune variability illuminates differential evolution of lung adenocarcinoma, Nature Medicine, IF:35, 26, 1054–1062.

2.     Failmezger H^, Muralidhar S^, Rullan A, de Andrea CE, Sahai E, Yuan Y* (2020). Topological Tumor Graphs: a graph-based spatial model to infer stromal recruitment for immunosuppression in melanoma histology, Cancer Research, IF:9, DOI: 10.1158/0008-5472.CAN-19-2268.

3.     Heindl A, Khan AM, Rodrigues DN, Eason K, Sadanandam A, Orbegoso C, Punta M, Sottoriva A, Lise S, Banerjee S, Yuan Y* (2018). Microenvironmental niche divergence shapes BRCA1-dysregulated ovarian cancer morphological plasticity, Nature Communications, IF:12, 9:3917.

4.     Heindl A, Sestak I, Naidoo R, Cuzick J, Dowsett M, Yuan Y* (2018). Relevance of spatial heterogeneity of immune infiltration for predicting risk of recurrence after endocrine therapy of ER+ breast cancer, JNCI: Journal of the National Cancer Institute, IF:12, 110(2), djx137.

5.     Natrajan R, Sailem H, Mardakheh FM, Arias MG, Dowsett M, Bakal C, Yuan Y* (2016). Microenvironmental heterogeneity parallels breast cancer progression: A histology-genomics integration analysis, PLoS Medicine, IF:11, 16;13(2):e1001961.

Machine learning / deep learning

6.     Hagos YB*, Lecat CSY, Patel D, Lee L, Tran TA, Rodriguez-Justo M, Yong K, Yuan Y* (2021). Cell abundance aware deep learning for cell detection on highly imbalanced pathological data. 2021 IEEE International Symposium on Biomedical Imaging (ISBI 2021).

7.   Zormpas-Petridis K, Noguera R, Ivankovic DK, Roxanis I*, Jamin Y*, Yuan Y* (2021), SuperHistopath: A Deep Learning Pipeline for Mapping Tumor Heterogeneity on Low-Resolution Whole-Slide Digital Histopathology Images, Frontiers in Oncology, 10,3052, DOI=10.3389/fonc.2020.586292.

8.     Hagos YB, Narayanan P, Akarca AU, Marafioti T, Yuan Y* (2019), ConCORDe-Net: Cell Count Regularized Convolutional Neural Network for Cell Detection in Multiplex Immunohistochemistry Images, Medical Image Computing and Computer Assisted Intervention (MICCAI) 2019.

9.     Raza SEA, AbdulJabbar K, Jamal-Hanjani M, Veeriah S, Le Quesne J, Swanton C, Yuan Y* (2019), Deconvolving convolution neural network for cell detection, IEEE International Symposium on Biomedical Imaging (ISBI) 2019.

10.  Narayanan PL*, Dodson A, Gusterson B, Dowsett M, and Yuan Y* (2018), DeepSDCS: Dissecting cancer proliferation heterogeneity in Ki67 digital whole slide images, Medical Imaging in Deep Learning (MIDL 2018).

Other publication/manuscript as (co-)corresponding author

11.  Narayanan PL, Raza SEA, Hall AH, Marks JM, King L, Hernandez, L, Dowsett M, Gusterson B, Carlo Maley, Hwang ES, Yuan Y*, Unmasking the immune microecology of ductal carcinoma in situ with deep learning, NPJ Breast Cancer, in press.

12.     Hamidinekoo A, Pieciak P, Maryam Afzali M, Otar Akanyeti O, Yinyin Yuan Y (2020). Glioma Classification Using Multimodal Radiology and Histology Data. CoRR abs/2011.05410.

13.  Nawaz S, Trahearn NA, Heindl A, Banerjee S, Maley CC, Sottoriva A, Yuan Y* (2019), Analysis of tumour ecological balance reveals resource-dependent adaptive strategies of ovarian cancer, EBioMedicine, 48, 224-235.

14.  Lan C, Li J, Huang X, Heindl A, Wang Y, Yan S, Yuan Y* (2019). Stromal cell ratio based on automated image analysis as a predictor for platinum-resistant recurrent ovarian cancer, BMC Cancer, 19:159.

15.  Zormpas-Petridis K, Failmezger H, Raza SEA, Roxanis I, Jamin Y, Yuan Y* (2019). Superpixel-based Conditional Random Fields (SuperCRF): Incorporating global and local context for enhanced deep learning in melanoma histopathology. Frontiers in Oncology, 9: 1045, doi.org/10.3389/fonc.2019.01045.

16.  Zormpas-Petridis K*, Failmezger H, Roxanis I, Blackledge MD, Jamin Y, Yuan Y* (2018). Capturing global spatial context for accurate cell classification in skin cancer histology, Medical Image Computing and Computer Assisted Intervention (MICCAI) COMPAY workshop 2018.

17.  Khan AM, Yuan Y* (2016). Biopsy variability of lymphocytic infiltration in breast cancer subtypes and the ImmunoSkew score, Scientific Reports, 6:36231.

18.  Heindl A, Lan C, Rodrigues DN, Koelbel K, Yuan Y* (2016). 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, Nov 1;7(44):71123-71135.

19.  Nawaz S, Heindl A, Koelble K, Yuan Y* (2015). Beyond immune density: critical role of spatial heterogeneity in oestrogen-receptor negative breast cancer, Modern Pathology, doi:10.1038/ modpathol.2015.37.

20.  Maley CC, Koelble K, Natrajan R, Aktipis A, Yuan Y* (2015). An ecological measure of immune-cancer colocalization as a prognostic factor for breast cancer, Breast Cancer Research, 17(1):131.

21.  Yuan Y* (2015). Modelling the Spatial Heterogeneity and Molecular Correlates of Lymphocytic Infiltration in Triple-Negative Breast Cancer. Journal of the Royal Society Interface, 12 20141153.

22.  Lan C^, Heindl A^, Huang X, Xi S, Banerjee S, Liu J*, Yuan Y* (2015). Quantitative histology analysis of the ovarian tumor microenvironment, Scientific Reports, 5:16317.

23.  Yuan Y*, Failmezger H, Rueda OM, Ali HR, Graf S, Chin S-FF, Schwarz RF, Curtis C, Dunning MJ, Bardwell H, Johnson N, Doyle S, Turashvili G, Provenzano E, Aparicio S, Caldas C, Markowetz F* (2012). Quantitative image analysis of cellular heterogeneity in breast tumors complements genomic profiling. Science Translational Medicine, 4(157): 157ra143.

24.  Yuan Y*, Curtis C, Caldas C & Markowetz F (2012). A sparse regulatory network of copy-number driven gene expression reveals putative breast cancer oncogenes. IEEE/ACM Trans Computational Biology and Bioinformatics, 9(4): 947-954.  

25.  Yuan Y*, Curtis C, Caldas C & Markowetz F (2012). A sparse regulatory network of copy-number driven gene expression reveals putative breast cancer oncogenes. Proceedings of IEEE International Conference on Bioinformatics and Biomedicine (BIBM Best Paper), 473-478.

26.  Yuan Y*^, Savage RS^ & Markowetz F (2011). Patient-specific data fusion defines prognostic cancer subtypes. PLoS Computational Biology, 7(10): e1002227.

27.  Yuan Y*, Rueda OM, Curtis C & Markowetz F* (2011). Penalized regression elucidates aberration hotspots mediating subtype-specific transcriptional responses in breast cancer. Bioinformatics, 27(19): 2679-2685.

28.  Yuan Y*, Li CT & Windram O (2011). Directed partial correlation: Inferring large-scale gene regulatory network through induced topology disruptions. PLoS ONE, 6(4): e16835.

29.  Yuan Y* & Li CT (2008). A Bayes random fields approach for integrative large-scale regulatory network analysis. Journal of Integrative Bioinformatics, 5(2): 99.

30.  Yuan Y* & Li CT*. Fragile watermarking scheme exploiting non-deterministic block-wise dependency. Proceedings of the 17th International Conference on Pattern Recognition (ICPR) 2004, 4: 849-852.

Other research publications

31.  Winfield JM, Wakefield JC, Brenton JD, AbdulJabbar K, Savio A, Freeman S, Pace E, Lutchman-Singh K, Vroobel KM, Yuan Y, Banerjee S, Porta N, Ahmed Raza SE, deSouza NM (2021). Biomarkers for site-specific response to neoadjuvant chemotherapy in epithelial ovarian cancer: relating MRI changes to tumour cell load and necrosis. Br J Cancer. doi: 10.1038/s41416-020-01217-5.

32.  Pennycuick A, et al., Yuan Y, Quezada SA, McGranahan N, Janes SM (2020). Immune Surveillance in Clinical Regression of Preinvasive Squamous Cell Lung Cancer. Cancer Discovery. 10(10):1489-1499. doi: 10.1158/2159-8290.CD-19-1366. Epub 2020 Jul 20. PMID: 32690541.

33.  Ghorani E, et al., Yuan Y, AbdulJabbar K, Turajilic S, Herrero J, Enver T, Hadrup SR, Hackshaw A, Peggs KS, McGranahan N, Chain B, Swanton C, Quezada SA (2020). The T cell differentiation landscape is shaped by tumour mutations in lung cancer. Nature Cancer. 1(5):546-561. doi:10.1038/s43018-020-0066-y.

34.  Zormpas-Petridis K, et al., Yuan Y, Robinson SP, Jamin Y (2020). Noninvasive MRI Native T1 Mapping Detects Response to MYCN-targeted Therapies in the Th-MYCN Model of Neuroblastoma. Cancer Research. 15;80(16):3424-3435. doi: 10.1158/0008-5472.CAN-20-0133.  

35.  Zormpas-Petridis K, Jerome NP, Blackledge MD, Carceller F, Poon E, Clarke M, et al., Yuan Y, Chesler L, Robinson SP and Jamin Y* (2020). Imaging the Hemodynamic Vasculature of Neuroblastoma with MRI - Non-invasive Prediction of Response to Anti-angiogenic Treatment, Cancer Research, DOI: 10.1158/0008-5472.CAN-18-3412.

36.  Kos Z, et al. (2020). Pitfalls in assessing stromal tumor infiltrating lymphocytes (sTILs) in breast cancer. NPJ Breast Cancer. 12;6:17. doi:10.1038/s41523-020-0156-0.  

37.  Amgad M, et al. (2020). Report on computational assessment of Tumor Infiltrating Lymphocytes from the International Immuno-Oncology Biomarker Working Group. NPJ Breast Cancer. 12;6:16. doi:10.1038/s41523-020-0154-2.

38.  Li J, Zormpas-Petridis K, Boult JKR, Reeves EL, Heindl A, Vinci M, Lopes F, Cummings C, Springer CJ, Chesler L, Jones C, Bamber JC, Yuan Y, Sinkus R, Jamin Y, Robinson SP (2019). Investigating the Contribution of Collagen to the Tumor Biomechanical Phenotype with Noninvasive Magnetic Resonance Elastography. Cancer Research. 15;79(22):5874-5883. doi: 10.1158/0008-5472.CAN-19-1595.  

39.  Zormpas-Petridis K, Jerome NP, Blackledge MD, Carceller F, Poon E, Clarke M, McErlean CM, Barone G, Koers A, Vaidya SJ, Marshall LV, Pearson ADJ, Moreno L, Anderson J, Sebire N, McHugh K, Koh DM, Yuan Y, Chesler L, Robinson SP, Jamin Y (2019). MRI Imaging of the Hemodynamic Vasculature of Neuroblastoma Predicts Response to Antiangiogenic Treatment. Cancer Research. 1;79(11):2978-2991. doi: 10.1158/0008-5472.CAN-18-3412.

40.   Barry P, Vatsiou A, et al. Yuan Y, Schiavon G, Turner N, & Sottoriva A (2018). The spatio-temporal evolution of lymph node spread in early breast cancer, Clinical Cancer Research, 10.1158/1078-0432.CCR-17-3374.

41.  Zhang, AW et al. (2018). Interfaces of Malignant and Immunologic Clonal Dynamics in Ovarian Cancer. Cell, Volume 173, Issue 7, 1755 - 1769.e22.

42.  Hill, D.K., A. Heindl, K. Zormpas-Petridis, D.J. Collins, L.R. Euceda, D.N. Rodrigues, S.A. Moestue, Y. Jamin, D.M. Koh, Y. Yuan, T.F. Bathen, M.O. Leach, and M.D. Blackledge (2017). Non-Invasive Prostate Cancer Characterization with Diffusion-Weighted MRI: Insight from In silico Studies of a Transgenic Mouse Model. Frontiers in oncology, 7:290.

43.  Naidoo, K., P.T. Wai, S.L. Maguire, F. Daley, S. Haider, D. Kriplani, J. Campbell, H. Mirza, A. Grigoriadis, A. Tutt, P.M. Moseley, T.M.A. Abdel-Fatah, S.Y. Chan, S. Madhusudan, E.A. Rakha, I.O. Ellis, C.J. Lord, Y. Yuan, A.R. Green, and R. Natrajan (2017). Evaluation of CDK12 Protein Expression as a Potential Novel Biomarker for DNA Damage Response Targeted Therapies in Breast Cancer. Molecular cancer therapeutics, 17(1): 306–315.

44.  Booth, T., Larkin, T., Yuan, Y, Kettunen, M., Dawson, S., Scoffings, D., Canuto, H., et al. (2017) Analysis of Heterogeneity in T2-Weighted MR Images Can Differentiate Pseudoprogression from Progression in Glioblastoma. PLoS ONE, 12(5):e0176528.

45.  Todd JR, Ryall KA, Vyse S, Wong JP, Natrajan RC, Yuan Y, Tan AC, Huang PH. (2016) Systematic analysis of tumour cell-extracellular matrix adhesion identifies independent prognostic factors in breast cancer. Oncotarget, 7(39):62939-62953.

46.  Locard-Paulet M, Lim L, Veluscek G, McMahon K, Sinclair J, Weverwijk A, Worboys JD, Yuan Y, Isacke CM, Jørgensen C* (2016). Phosphoproteomic analysis of tumor endothelial signaling identifies EPHA2 as a negative regulator of transendothelial migration, Science Signaling, 9;9(414):ra15–ra15.

47.  Savage RS*, Yuan Y (2016). Predicting chemosensitivity in breast cancer with omics/digital pathology data fusion, Royal Society Open Science, 10;3(2).

48.  Mardakheh FK, Paul A, Kumper S, Sadok, A, Paterson, H, Mccarthy A, Yuan Y & Marshall CJ* (2015). Global Analysis of mRNA, Translation, and Protein Localization: Local Translation Is a Key Regulator of Cell Protrusions, Developmental Cell, 35:3, 344-357.

49.  Hill DK, Kim E, Teruel J, Jamin Y, Widerøe M, Søgaard CD, Størkersen Ø, Rodrigues DN, Heindl A, Yuan Y, Bathen T, and Moestue S* (2015). Characterisation of Cancer Onset and Development in the TRAMP Model of Prostate Cancer using Diffusion-Weighted Magnetic Resonance Imaging, Journal of Magnetic Resonance Imaging, DOI: 10.1002/jmri.25087.

50.  Jäger R, Migliorini G, Henrion M, Kandaswamy R, Speedy HE, Heindl A, Whiffin N, Carnicer MJ, Broome L, Dryden N, Nagano T, Schoenfelder S, Enge M, Yuan Y, Taipale J, Fraser P, Fletcher O & Houlston R* (2015).  Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci, Nature Communications, 6:6178.

51.  Moen Vollan HK, Vollan HKM, Rueda OM, Chin S-F, Curtis C, Turashvili G, Shah S, Lingjærde OC, Yuan Y, Ng CK, Dunning MJ, Dicks E, Provenzano E, Sammut S, McKinney S, Ellis IO, Pinder S, Purushotham A, Murphy LC, Kristensen VN, Group M, Brenton JD, Pharoah PDP, Børresen-Dale A-L, Aparicio S*, Caldas C* (2015). A tumor DNA complex aberration index is an independent predictor of survival in breast and ovarian cancer, Molecular Oncology, 9(1):115-27.

52.  Worboys J, Sinclair J, Yuan Y & Jorgensen C* (2014). Systematic empirical evaluation of proteotypic and quantotypic peptides for targeted analysis of the human kinome, Nature Methods, 11: 1041-1044.

53.  Curtis C, Shah SP, Chin SF, Turashvili G, Rueda OM, Dunning MJ, Speed D, Lynch AG, Samarajiwa S, Yuan Y, Graf S, Ha G, Haffari G, Bashashati A, Russell R, McKinney S, Langerod A, Green A, Provenzano E, Wishart G, Pinder S, Watson P, Markowetz F, Murphy L, Ellis I, Purushotham A, Borresen-Dale AL, Brenton JD, Tavare S, Caldas C*, Aparicio S*. (2012). The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups, Nature, 486(7403): 346-352.

54.  Booth T, Larkin T, Yuan Y, Kettunen M, Markowetz F, Scoffings D, Jefferies S, Brindle KM* (2012). Minkowski functional image analysis allows pseudoprogression to be differentiated from progression in brain tumours, Neuro-Oncology, 14: 35-35.

55.  Yuan Y, Li CT* & Wilson R (2008). Partial mixture model for tight clustering of gene expression time-course, BMC Bioinformatics, 9: 287.

56.  Li CT*, Yuan Y & Wilson R (2008). An unsupervised conditional random fields approach for clustering gene expression time series, Bioinformatics, 24(21): 2467-2473.

57.  Yuan Y & Li CT (2008). Probabilistic framework for gene expression clustering validation based on gene ontology and graph theory, Proceedings of International Conference of Acoustics, Speech, and Signal Processing (ICASSP), 625-628.

58.  Yuan Y & Li CT (2007). Unsupervised clustering of gene expression time series with conditional random fields, Proceedings of IEEE International Conference on Digital Ecosystems and Technologies (IEEE DEST) , 59-64.

59.  Yuan Y & Li CT (2007). Partial mixture model for tight clustering in exploratory gene expression analysis, Proceedings of International Symposium on BioInformatics and BioEngineering (BIBE), 1061-1065.

60.  Li CT* & Yuan Y (2006). Digital watermarking scheme exploiting nondeterministic dependence for image authentication, Optical Engineering, 45(12).

Invited reviews

61.  Maley C, Aktipis A, Graham T, Sottoriva A, Boddy A, Janiszewska M, Silva A, Gerlinger M, Yuan Y, Pienta K, Anderson K, Gatenby R, Swanton C, Posada D, Wu C, Schiffman J, Hwang E, Polyak K, Anderson A, Brown J, Greaves M, Shibata D (2017). Classifying the Evolutionary and Ecological Features of Neoplasms, Nature Reviews Cancer, 17(10):605-619.

62.  Yuan Y* (2016). Spatial Heterogeneity of the Tumor Microenvironment, Cold Spring Harb Perspect Med, 2016 Aug 1;6(8). pii: a026583.

63.  Nawaz S, Yuan Y* (2015). Computational pathology: Exploring the spatial dimension of tumor ecology. Special issue on “Tumor Microenvironment”, Cancer Letters, doi: 10.1016/ j.canlet.2015.11.018.

64.  Heindl A, Nawaz S, Yuan Y* (2015).  Mapping Spatial Heterogeneity of the Tumour Microenvironment: A New Era for Digital Pathology, Laboratory Investigation, 95(4):377-84.


* Corresponding author; ^ Joint first author;    

Outside work

Outside work my passion is in travelling, sports, and music/gigs. My favourite sport is rock climbing (see my dedicated page), followed by hiking, skiing and diving (PADI advanced). I believe that climbing is one of the best sports for scientists, in which persistence, problem solving, and confidence are the key to success.

Copyright © Yinyin Yuan's Lab, the Institute of Cancer Research, London. All Rights Reserved.