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Journal Articles

Failmezger, H. Muralidhar, S. Rullan, A. de Andrea, C.E. Sahai, E. Yuan, Y. (2020). Topological Tumor Graphs: A Graph-Based Spatial Model to Infer Stromal Recruitment for Immunosuppression in Melanoma Histology. Cancer research, Vol.80 (5), pp. 1199-1209.

Ghorani, E. Reading, J.L. Henry, J.Y. Massy, M.R. Rosenthal, R. Turati, V. Joshi, K. Furness, A.J. Ben Aissa, A. Saini, S.K. Ramskov, S. Georgiou, A. Sunderland, M.W. Wong, Y.N. Mucha, M.V. Day, W. Galvez-Cancino, F. Becker, P.D. Uddin, I. Oakes, T. Ismail, M. Ronel, 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. Bakir, M.A. 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. (2020). The T cell differentiation landscape is shaped by tumour mutations in lung cancer. Nature cancer, Vol.1 (5), pp. 546-561.

AbdulJabbar, K. Raza, S.E. Rosenthal, R. Jamal-Hanjani, M. Veeriah, S. Akarca, A. Lund, T. Moore, D.A. Salgado, R. Al Bakir, M. Zapata, L. Hiley, C.T. Officer, L. Sereno, M. Smith, C.R. Loi, S. Hackshaw, A. Marafioti, T. Quezada, S.A. McGranahan, N. Le Quesne, J. TRACERx Consortium, Swanton, C. Yuan, Y. (2020). Geospatial immune variability illuminates differential evolution of lung adenocarcinoma. Nat med, Vol.26 (7), pp. 1054-1062.  show abstract

Pennycuick, A. Teixeira, V.H. AbdulJabbar, K. 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. Henry, J.Y. Millar, F.R. Hagos, Y.B. Denais, C. Falzon, M. Moore, D.A. Antoniou, S. Durrenberger, P.F. Furness, A.J. Carroll, B. Marceaux, C. Asselin-Labat, M.-. 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. (2020). Immune Surveillance in Clinical Regression of Preinvasive Squamous Cell Lung Cancer. Cancer discovery, Vol.10 (10), pp. 1489-1499.

Amgad, M. Stovgaard, E.S. Balslev, E. Thagaard, J. Chen, W. Dudgeon, S. Sharma, A. Kerner, J.K. Denkert, C. Yuan, Y. AbdulJabbar, K. Wienert, S. Savas, P. Voorwerk, L. Beck, A.H. Madabhushi, A. Hartman, J. Sebastian, M.M. Horlings, H.M. Hudeček, J. Ciompi, F. Moore, D.A. Singh, R. Roblin, E. Balancin, M.L. Mathieu, M.-. Lennerz, J.K. Kirtani, P. Chen, I.-. Braybrooke, J.P. Pruneri, G. Demaria, S. Adams, S. Schnitt, S.J. Lakhani, S.R. Rojo, F. Comerma, L. Badve, S.S. Khojasteh, M. Symmans, W.F. Sotiriou, C. Gonzalez-Ericsson, P. Pogue-Geile, K.L. Kim, R.S. Rimm, D.L. Viale, G. Hewitt, S.M. Bartlett, J.M. Penault-Llorca, F. Goel, S. Lien, H.-. Loibl, S. Kos, Z. Loi, S. Hanna, M.G. Michiels, S. Kok, M. Nielsen, T.O. Lazar, A.J. Bago-Horvath, Z. Kooreman, L.F. van der Laak, J.A. Saltz, J. Gallas, B.D. Kurkure, U. Barnes, M. Salgado, R. Cooper, L.A. (2020). Report on computational assessment of Tumor Infiltrating Lymphocytes from the International Immuno-Oncology Biomarker Working Group. Npj breast cancer, Vol.6 (1).

Zormpas-Petridis, K. Poon, E. Clarke, M. Jerome, N.P. Boult, J.K. Blackledge, M.D. Carceller, F. Koers, A. Barone, G. Pearson, A.D. Moreno, L. Anderson, J. Sebire, N. McHugh, K. Koh, D.-. Chesler, L. Yuan, Y. Robinson, S.P. Jamin, Y. (2020). Noninvasive MRI Native T1 Mapping Detects Response to MYCN-targeted Therapies in the Th-MYCN Model of Neuroblastoma. Cancer res, Vol.80, pp. 3424-3435.  show abstract

Zormpas-Petridis, K. Jerome, N.P. Blackledge, M.D. Carceller, F. Poon, E. Clarke, M. McErlean, C.M. Barone, G. Koers, A. Vaidya, S.J. Marshall, L.V. Pearson, A.D. Moreno, L. Anderson, J. Sebire, N. McHugh, K. Koh, D.-. Yuan, Y. Chesler, L. Robinson, S.P. Jamin, Y. (2019). MRI Imaging of the Hemodynamic Vasculature of Neuroblastoma Predicts Response to Antiangiogenic Treatment. Cancer res, Vol.79, pp. 2978-2991.  show abstract

Nawaz, S. Trahearn, N.A. Heindl, A. Banerjee, S. Maley, C.C. Sottoriva, A. Yuan, Y. (2019). Analysis of tumour ecological balance reveals resource-dependent adaptive strategies of ovarian cancer. Ebiomedicine, Vol.48, pp. 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, Vol.19 (1).

Li, J. Zormpas-Petridis, K. Boult, J.K. Reeves, E.L. Heindl, A. Vinci, M. Lopes, F. Cummings, C. Springer, C.J. Chesler, L. Jones, C. Bamber, J.C. Yuan, Y. Sinkus, R. Jamin, Y. Robinson, S.P. (2019). Investigating the Contribution of Collagen to the Tumor Biomechanical Phenotype with Noninvasive Magnetic Resonance Elastography. Cancer res, Vol.79, pp. 5874-5883.  show abstract

Zormpas-Petridis, K. Failmezger, H. Raza, S.E. 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. Front oncol, Vol.9, pp. 1045-1045.  show abstract

Zhang, A.W. McPherson, A. Milne, K. Kroeger, D.R. Hamilton, P.T. Miranda, A. Funnell, T. Little, N. de Souza, C.P. Laan, S. LeDoux, S. Cochrane, D.R. Lim, J.L. Yang, W. Roth, A. Smith, M.A. Ho, J. Tse, K. Zeng, T. Shlafman, I. Mayo, M.R. Moore, R. Failmezger, H. Heindl, A. Wang, Y.K. Bashashati, A. Grewal, D.S. Brown, S.D. Lai, D. Wan, A.N. Nielsen, C.B. Huebner, C. Tessier-Cloutier, B. Anglesio, M.S. Bouchard-Côté, A. Yuan, Y. Wasserman, W.W. Gilks, C.B. Karnezis, A.N. Aparicio, S. McAlpine, J.N. Huntsman, D.G. Holt, R.A. Nelson, B.H. Shah, S.P. (2018). Interfaces of Malignant and Immunologic Clonal Dynamics in Ovarian Cancer. Cell, Vol.173 (7), pp. 1755-1769.e22.

Heindl, A. Khan, A.M. Rodrigues, D.N. 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, Vol.9 (1).

Maley, C.C. Aktipis, A. Graham, T.A. Sottoriva, A. Boddy, A.M. Janiszewska, M. Silva, A.S. Gerlinger, M. Yuan, Y. Pienta, K.J. Anderson, K.S. Gatenby, R. Swanton, C. Posada, D. Wu, C.-. Schiffman, J.D. Hwang, E.S. Polyak, K. Anderson, A.R. Brown, J.S. Greaves, M. Shibata, D. (2017). Classifying the evolutionary and ecological features of neoplasms. Nat rev cancer, Vol.17 (10), pp. 605-619.  show abstract

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

Booth, T.C. Larkin, T.J. Yuan, Y. Kettunen, M.I. Dawson, S.N. Scoffings, D. Canuto, H.C. Vowler, S.L. Kirschenlohr, H. Hobson, M.P. Markowetz, F. Jefferies, S. Brindle, K.M. (2017). Analysis of heterogeneity in T2-weighted MR images can differentiate pseudoprogression from progression in glioblastoma. Plos one, Vol.12 (5), p. e0176528.  show abstract

Heindl, A. Lan, C. Rodrigues, D.N. Koelble, 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, Vol.7 (44), pp. 71123-71135.

Savage, R.S. Yuan, Y. (2016). Predicting chemoinsensitivity in breast cancer with ’omics/digital pathology data fusion. Royal society open science, Vol.3 (2), pp. 140501-140501.  show abstract

Hill, D.K. Kim, E. Teruel, J.R. Jamin, Y. Widerøe, M. Søgaard, C.D. Størkersen, Ø. Rodrigues, D.N. Heindl, A. Yuan, Y. Bathen, T.F. Moestue, S.A. (2016). Diffusion-weighted MRI for early detection and characterization of prostate cancer in the transgenic adenocarcinoma of the mouse prostate model. Journal of magnetic resonance imaging, Vol.43 (5), pp. 1207-1217.

Yuan, Y. (2016). Spatial Heterogeneity in the Tumor Microenvironment. Cold spring harbor perspectives in medicine, Vol.6 (8), pp. a026583-a026583.

Locard-Paulet, M. Lim, L. Veluscek, G. McMahon, K. Sinclair, J. van Weverwijk, A. Worboys, J.D. Yuan, Y. Isacke, C.M. Jørgensen, C. (2016). Phosphoproteomic analysis of interacting tumor and endothelial cells identifies regulatory mechanisms of transendothelial migration. Science signaling, Vol.9 (414), pp. ra15-ra15.

Nawaz, S. Yuan, Y. (2016). Computational pathology: Exploring the spatial dimension of tumor ecology. Cancer letters, Vol.380 (1), pp. 296-303.

Khan, A.M. Yuan, Y. (2016). Biopsy variability of lymphocytic infiltration in breast cancer subtypes and the ImmunoSkew score. Scientific reports, Vol.6 (1).

Vollan, H.K. Rueda, O.M. Chin, S.-. Curtis, C. Turashvili, G. Shah, S. Lingjærde, O.C. Yuan, Y. Ng, C.K. Dunning, M.J. Dicks, E. Provenzano, E. Sammut, S. McKinney, S. Ellis, I.O. Pinder, S. Purushotham, A. Murphy, L.C. Kristensen, V.N. METABRIC Group, Brenton, J.D. Pharoah, P.D. Børresen-Dale, A.-. Aparicio, S. Caldas, C. (2015). A tumor DNA complex aberration index is an independent predictor of survival in breast and ovarian cancer. Mol oncol, Vol.9 (1), pp. 115-127.  show abstract

Heindl, A. Nawaz, S. Yuan, Y. (2015). Mapping spatial heterogeneity in the tumor microenvironment: a new era for digital pathology. Laboratory investigation, Vol.95 (4), pp. 377-384.

Nawaz, S. Heindl, A. Koelble, K. Yuan, Y. (2015). Beyond immune density: critical role of spatial heterogeneity in estrogen receptor-negative breast cancer. Modern pathology, Vol.28 (6), pp. 766-777.

Yuan, Y. (2015). Modelling the spatial heterogeneity and molecular correlates of lymphocytic infiltration in triple-negative breast cancer. Journal of the royal society interface, Vol.12 (103).

Mardakheh, F.K. Paul, A. Kümper, S. Sadok, A. Paterson, H. Mccarthy, A. Yuan, Y. Marshall, C.J. (2015). Global Analysis of mRNA, Translation, and Protein Localization: Local Translation Is a Key Regulator of Cell Protrusions. Developmental cell, Vol.35 (3), pp. 344-357.

Maley, C.C. 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, Vol.17 (1).

Lan, C. Heindl, A. Huang, X. Xi, S. Banerjee, S. Liu, J. Yuan, Y. (2015). Quantitative histology analysis of the ovarian tumour microenvironment. Scientific reports, Vol.5 (1).

Jäger, R. Migliorini, G. Henrion, M. Kandaswamy, R. Speedy, H.E. Heindl, A. Whiffin, N. Carnicer, M.J. Broome, L. Dryden, N. Nagano, T. Schoenfelder, S. Enge, M. Yuan, Y. Taipale, J. Fraser, P. Fletcher, O. Houlston, R.S. (2015). Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci. Nat commun, Vol.6, p. 6178.  show abstract

Worboys, J.D. Sinclair, J. Yuan, Y. Jorgensen, C. (2014). Systematic evaluation of quantotypic peptides for targeted analysis of the human kinome. Nature methods, Vol.11 (10), pp. 1041-1044.

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 comput biol bioinform, Vol.9 (4), pp. 947-954.  show abstract

Curtis, C. Shah, S.P. Chin, S.-. Turashvili, G. Rueda, O.M. Dunning, M.J. Speed, D. Lynch, A.G. 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, A.-. Brenton, J.D. Tavaré, S. Caldas, C. Aparicio, S. (2012). The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature, Vol.486 (7403), pp. 346-352.  show abstract

Yuan, Y. Failmezger, H. Rueda, O.M. Ali, H.R. Gräf, S. Chin, S.-. Schwarz, R.F. Curtis, C. Dunning, M.J. 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. Sci transl med, Vol.4 (157), p. 157ra143.  show abstract

Yuan, Y. Rueda, O.M. Curtis, C. Markowetz, F. (2011). Penalized regression elucidates aberration hotspots mediating subtype-specific transcriptional responses in breast cancer. Bioinformatics, Vol.27 (19), pp. 2679-2685.  show abstract

Yuan, Y. Li, C.-. Windram, O. (2011). Directed Partial Correlation: Inferring Large-Scale Gene Regulatory Network through Induced Topology Disruptions. Plos one, Vol.6 (4).

Yuan, Y. Savage, R.S. Markowetz, F. (2011). Patient-specific data fusion defines prognostic cancer subtypes. Plos comput biol, Vol.7 (10), p. e1002227.  show abstract

Li, C.-. Yuan, Y. Wilson, R. (2008). An unsupervised conditional random fields approach for clustering gene expression time series. Bioinformatics, Vol.24 (21), pp. 2467-2473.  show abstract

Yuan, Y. Li, C.-. Wilson, R. (2008). Partial mixture model for tight clustering of gene expression time-course. Bmc bioinformatics, Vol.9, p. 287.  show abstract

Yuan, Y. Li, C.-. (2008). A Bayes random field approach for integrative large-scale regulatory network analysis. J integr bioinform, Vol.5 (2).  show abstract

Li, C.-. Yuan, Y. (2006). Digital watermarking scheme exploiting nondeterministic dependence for image authentication. Optical engineering, Vol.45 (12).

Natrajan, R. Sailem, H. Mardakheh, F.K. Arias Garcia, M. Tape, C.J. Dowsett, M. Bakal, C. Yuan, Y. Microenvironmental Heterogeneity Parallels Breast Cancer Progression: A Histology–Genomic Integration Analysis. Plos medicine, Vol.13 (2), pp. e1001961-e1001961.

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. Journal of the national cancer institute, .

Naidoo, K. Wai, P. Maguire, S. Daley, F. Haider, S. Kriplani, D. Campbell, J. Mirza, H. Grigoriadis, A. Tutt, A. Moseley, P. Abdel-Fatah, T. Chan, S. Madhusudan, S. Rhaka, E. Ellis, I. Lord, C. Yuan, Y. Green, A. Natrajan, R. Evaluation of CDK12 Protein Expression as a Potential Novel Biomarker for DNA Damage Response Targeted Therapies in Breast Cancer. Molecular cancer therapeutics, .

Barry, P. Vatsiou, A. Spiteri Sagastume, I. Nichol, D. Cresswell, G. Acar, A. Trahearn, N. Hrebien, S. Garcia-Murillas, I. Chkhaidze, K. Ermini, L. Cottom, H. Zabaglo, L. Koelble, K. Khalique, S. Rusby, J. Muscara, F. Dowsett, M. Maley, C. Natrajan, R. Yuan, Y. Schiavon, G. Turner, N. Sottoriva, A. The spatio-temporal evolution of lymph node spread in early breast cancer. Clinical cancer research, .

Zormpas-Petridis, K. Roxanis, I. Jamin, Y. Yuan, Y. SuperHistopath: A Deep Learning Pipeline for Mapping Tumor Heterogeneity on Low-Resolution Whole-Slide Digital Histopathology Images. Frontiers in oncology, .


Conferences

Raza, S.E.AbdulJabbar, K.Jamal-Hanjani, M.Veeriah, S.Le Quesne, J.Swanton, C.Yuan, Y.IEEE, (2019). DECONVOLVING CONVOLUTIONAL NEURAL NETWORK FOR CELL DETECTION, 2019 IEEE 16TH INTERNATIONAL SYMPOSIUM ON BIOMEDICAL IMAGING (ISBI 2019), , pp.891-894.

Heindl, A.Khan, A.M.Yuan, Y. (2015). Abstract B2-51: SpEeCH: Quantifying Spatial Expression of Clonal Heterogeneity in breast cancer, Presented at Abstracts: AACR Special Conference: Computational and Systems Biology of Cancer; February 8-11, 2015; San Francisco, CA, Tumor Heterogeneity and Plasticity, .

Nawaz, S.Heindl, A.Agostinelli, A.Yuan, Y. (2015). Abstract B2-55: Critical role of immune spatial heterogeneity and the molecular scaffold in estrogen receptor-negative breast cancer, Presented at Abstracts: AACR Special Conference: Computational and Systems Biology of Cancer; February 8-11, 2015; San Francisco, CA, Tumor Heterogeneity and Plasticity, .

Booth, T.C.Larkin, T.Yuan, Y.Kettunen, M.Markowetz, F.Scoffings, D.Jefferies, S.Brindle, K.M. (2012). MINKOWSKI FUNCTIONAL IMAGE ANALYSIS ALLOWS PSEUDOPROGRESSION TO BE DIFFERENTIATED FROM PROGRESSION IN BRAIN TUMOURS, NEURO-ONCOLOGY, Vol.14, p.35.

Yuan, Y.Curtis, C.Caldas, C.Markowetz, F. (2010). A sparse regulatory network of copy-number driven expression reveals putative breast cancer oncogenes, 2010 IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICINE, , pp.473-478.

Yuan, Y.Li, C.-. (2009). Inferring Causal Relations from Multivariate Time Series: A Fast Method for Large-Scale Gene Expression Data., BIBE, , pp.92-99.

Yuan, Y.Li, C.-. (2008). Probabilistic framework for gene expression clustering validation based on gene ontology and graph theory., ICASSP, , pp.625-628.

Yuan, Y.Li, C.-.IEEE, (2007). Unsupervised clustering of gene expression time series with conditional random fields, 2007 INAUGURAL IEEE INTERNATIONAL CONFERENCE ON DIGITAL ECOSYSTEMS AND TECHNOLOGIES, , pp.59-+.

Yuan, Y.Li, C.-. (2007). Partial Mixture Model for Tight Clustering in Exploratory Gene Expression Analysis., BIBE, , pp.1061-1065.

Yuan, Y.Li, C.-. (2004). Fragile Watermarking Scheme Exploiting Non-Deterministic Block-Wise Dependency., ICPR (4), , pp.849-852.