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Publications

 2023  

Zhang H, AbdulJabbar K, Yuan Y, Self-supervised deep learning for highly efficient spatial immunophenotyping. eBioMedicine, 95: 104769.
AbdulJabbar K*, Castillo SP*, Hughes K, Davidson H, Boddy AM, Abegglen LM, Murchison EP, Graham TA, Spiro S, Palmieri C, Yuan Y. AI-powered pan-species computational pathology: bridging clinic and wildlife care. Nature Communications 14: 2408 PMCID: PMC10133243 (Featured article in Cancer collection of Nature Communication).
Castillo SP, F Galvez-Cancino, J Liu, SM Pollard, SA Quezada, Y Yuan. The tumour ecology of quiescence: niches across scales of complexity. Seminars in Cancer Biology 92: 139-149, PMID: 37037400.

 2022  

Sobhani F, Muralidhar S, Hamidinekoo A, Hall AH, King L, Marks JR, Maley CC, Horlings HM, Hwang ES, Yuan Y* (2022), Spatial interplay of tissue hypoxia and T-cell regulation in ductal carcinoma in situ, NPJ Breast Cancer, 8, 105.

Hagos et al. Yuan Y (2022), “DCIS AI-TIL: Ductal Carcinoma in situ tumour infiltrating lymphocyte scoring using artificial intelligence”, MICCAI workshop on Medical Image Assisted Biomarkers’ Discovery.
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* (2022). High inter-follicular spatial co-localisation of CD8+FOXP3+ with CD4+CD8+ cells predicts favourable outcome in follicular lymphoma. Hematol Oncol. Apr 22. doi: 10.1002/hon.3003.
Sobhani F, Hamidinekoo A, Hall AH, King L, Marks JR, Maley CC, Horlings HM, Hwang ES, Yuan Y (2022). Automated DCIS identification from multiplex immunohistochemistry using generative adversarial networks, IEEE International Symposium on Biomedical Imaging (ISBI).

 

 2021  

Narayanan PL*, Raza SEA, Hall AH, Marks JM, King L, Hernandez, L, Dowsett M, Gusterson B, Carlo Maley, Hwang ES, Yuan Y* (2021). Unmasking the immune microecology of ductal carcinoma in situ with deep learning, NPJ Breast Cancer, 7, 19.
Hamidinekoo A, Kelsey A, Trahearn N, Selfe J, Shipley J, Yuan Y (2021). Automated Quantification of Blood Microvessels in Hematoxylin and Eosin Whole Slide Images. MICCAI Workshop on Computational Pathology (COMPAY).
Zhang HY, Grunewald T, Akarca AU, Ledermann JA, Marafioti T, Yuan Y (2021). Symmetric dense inception network for simultaneous cell detection and classification in multiplex immunohistochemistry images. The MICCAI workshop on Computational Pathology (COMPAY).
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. IEEE International Symposium on Biomedical Imaging (ISBI), DOI:10.1109/ISBI48211.2021.9433994.
Law J, Paulson T, Sanchez C, Galipeau P, Jansen M, Stachler M, Carlo Maley CC, Yuan Y (2021). Wisdom of the Crowd for Early Detection in Barrett's Esophagus, IEEE International Symposium on Biomedical Imaging (ISBI), DOI: 10.1109/ISBI48211.2021.9433763.
Castillo S, Yuan Y (2021). Artificial naturalism: coevolving pathology and AI. Trends in Cancer, Special issue: Quantitative Cancer Biology, DOI: https://doi.org/10.1016/j.trecan.2021.01.011.
Zormpas-Petridis K, Noguera R, Ivankovic DK, Roxanis sI*, 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.
Sobhani F, Robinson R, Hamidinekoo A, Roxanis I, Somaiah N, Yuan Y. Artificial intelligence and digital pathology: Opportunities and implications for immuno-oncology (2021). Biochimica et Biophysica Acta (BBA) - Reviews on Cancer, 1875(2).
Hamidinekoo A, Pieciak P, Maryam Afzali M, Otar Akanyeti O, Yuan Y. Glioma Classification Using Multimodal Radiology and Histology Data. Lecture Notes in Computer Science, Vol.12659, 508-518.

 2020  

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*, TRACERx Consortium, Swanton C*, Yuan Y* (2020). Geospatial immune variability illuminates differential evolution of lung adenocarcinoma, Nature Medicine, 26, 1054–1062.
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, DOI: 10.1158/0008-5472.CAN-19-2268.

 2019  

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.
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.
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.
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).
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).

 2018  

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, 9:3917.
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, 110(2), djx137.
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).

 2016  

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, 16;13(2):e1001961.
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.
Khan AM, Yuan Y* (2016). Biopsy variability of lymphocytic infiltration in breast cancer subtypes and the ImmunoSkew score, Scientific Reports, 6:36231.
Yuan Y* (2016). Spatial Heterogeneity of the Tumor Microenvironment, Cold Spring Harb Perspect Med, 2016 Aug 1;6(8). pii: a026583.
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.

 2015  

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.
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.
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.
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.
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.
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.

 Collaborative Peer-reviewed Research Publications  

Nederlof I^, Hajizadeh S^, Sobhani F, Raza SEA, AbdulJabbar K, Harkes R, van de Vijver MJ, Salgado R, Desmedt C, Kok M, Yuan Y, Horlings HM* (2022). Spatial interplay of lymphocytes and fibroblasts in estrogen receptor-positive HER2-negative breast cancer. NPJ Breast Cancer 8(1):56 28 Apr 2022.
William S, et al. (2022). Emerging Technologies and Their Impact on Regulatory Science: The 10th annual Global Summit on Regulatory Science (GSRS20), Regulatory Toxicology and Pharmacology, Exp Biol Med (Maywood);247(1):1-75. doi: 10.1177/15353702211052280.
Verma R, et al. (2021). "MoNuSAC2020: A Multi-organ Nuclei Segmentation and Classification Challenge," in IEEE Transactions on Medical Imaging, 40(12):3413-3423, doi: 10.1109/TMI.2021.3085712.
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. British Journal of Cancer. doi: 10.1038/s41416-020-01217-5.
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.
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.
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.
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.
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.
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.
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.
 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.
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.
Zhang, AW et al. (2018). Interfaces of Malignant and Immunologic Clonal Dynamics in Ovarian Cancer. Cell, Volume 173, Issue 7, 1755 - 1769.e22.
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, Yuan Y., 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.
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.
Naidoo, K, Wai PT, Maguire SL, Daley F, Haider S, Kriplani D, Campbell J, Mirza H, Grigoriadis A, Tutt A, Moseley PM, Abdel-Fatah TMA, Chan SY, Madhusudan S, Rakha EA, Ellis IO, Lord CJ, Yuan Y, Green AR, and Natrajan R (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.
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.
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.
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.
Savage RS*, Yuan Y (2016). Predicting chemosensitivity in breast cancer with omics/digital pathology data fusion, Royal Society Open Science, 10;3(2).
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.
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.
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.
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.
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