Publications

Charting multicellular tissue structure cell-to-cell. Schrader E, Ali HR. Nat Genet. 2023 Dec 22. doi: 10.1038/s41588-023-01624-3

Spatial predictors of immunotherapy response in triple-negative breast cancer. Wang XQ, Danenberg E, Huang CS, Egle D, Callari M, Bermejo B, Dugo M, Zamagni C, Thill M, Anton A, Zambelli S, Russo S, Ciruelos EM, Greil R, Győrffy B, Semiglazov V, Colleoni M, Kelly CM, Mariani G, Del Mastro L, Biasi O, Seitz RS, Valagussa P, Viale G, Gianni L, Bianchini G & Ali HR. Nature. 2023. doi.org/10.1038/s41586-023-06498-3


Breast tumor microenvironment structures are associated with genomic features and clinical outcome.
Danenberg E, Bardwell H, Zanotelli VRT, Provenzano E, Chin SF, Rueda OM, Green A, Rakha E, Aparicio S, Ellis IO, Bodenmiller B, Caldas C, Ali HR. Nat Genet. 2022 May;54(5):660-669. doi: 10.1038/s41588-022-01041-y

Imaging mass cytometry and multiplatform genomics define the phenogenomic landscape of breast cancer. Ali HR, Jackson HW, Zanotelli VRT, Danenberg E, Fischer JR, Bardwell H, Provenzano E; CRUK IMAXT Grand Challenge Team; Rueda OM, Chin SF, Aparicio S, Caldas C, Bodenmiller B. Nat Cancer. 2020 Feb;1(2):163-175. doi: 10.1038/s43018-020-0026-6.

The single-cell pathology landscape of breast cancer. Hartland W Jackson, Jana R Fischer, Vito RT Zanotelli, H Raza Ali, Robert Mechera, Savas D Soysal, Holger Moch, Simone Muenst, Zsuzsanna Varga, Walter P Weber, Bernd Bodenmiller. Nature 578, 615–620 (2020). https://doi.org/10.1038/s41586-019-1876-x

DNA methylation landscapes of 1538 breast cancers reveal a replication-linked clock, epigenomic instability and cis-regulation. Rajbir Nath Batra, Aviezer Lifshitz, Ana Tufegdzic Vidakovic, Suet-Feung Chin, Ankita Sati-Batra, Stephen-John Sammut, Elena Provenzano, H Raza Ali, Ali Dariush, Alejandra Bruna, Leigh Murphy, Arnie Purushotham, Ian Ellis, Andrew Green, Francine E. Garrett-Bakelman, Chris Mason, Ari Melnick, Samuel A. J. R. Aparicio, Oscar M. Rueda, Amos Tanay & Carlos CaldasNat Commun 12, 5406 (2021). https://doi.org/10.1038/s41467-021-25661-w

Landscapes of cellular phenotypic diversity in breast cancer xenografts and their impact on drug response. Dimitra Georgopoulou, Maurizio Callari, Oscar M Rueda, Abigail Shea, Alistair Martin, Agnese Giovannetti, Fatime Qosaj, Ali Dariush, Suet-Feung Chin, Larissa S Carnevalli, Elena Provenzano, Wendy Greenwood, Giulia Lerda, Elham Esmaeilishirazifard, Martin O’Reilly, Violeta Serra, Dario Bressan, Gordon B Mills, H Raza Ali, Sabina S Cosulich, Gregory J Hannon, Alejandra Bruna, Carlos Caldas. Nat Commun 12, 1998 (2021). https://doi.org/10.1038/s41467-021-22303-z

Cancer-associated fibroblast compositions change with breast cancer progression linking the ratio of S100A4+ and PDPN+ CAFs to clinical outcome. Gil Friedman, Oshrat Levi-Galibov, Eyal David, Chamutal Bornstein, Amir Giladi, Maya Dadiani, Avi Mayo, Coral Halperin, Meirav Pevsner-Fischer, Hagar Lavon, Shimrit Mayer, Reinat Nevo, Yaniv Stein, Nora Balint-Lahat, Iris Barshack, H Raza Ali, Carlos Caldas, Einav Nili-Gal-Yam, Uri Alon, Ido Amit, Ruth Scherz-Shouval. Nat Cancer 1, 692–708 (2020). https://doi.org/10.1038/s43018-020-0082-y

Lymphocyte density determined by computational pathology validated as a predictor of response to neoadjuvant chemotherapy in breast cancer: secondary analysis of the ARTemis trial. H Raza Ali, Aliakbar Dariush, J Thomas, E Provenzano, J Dunn, L Hiller, A-L Vallier, Jean Abraham, T Piper, JMS Bartlett, DA Cameron, L Hayward, JD Brenton, PDP Pharoah, MJ Irwin, NA Walton, HM Earl, C Caldas. Annals of Oncology 28, 1832-1835 (2017). https://doi.org/10.1093/annonc/mdx266

Patterns of immune infiltration in breast cancer and their clinical implications: a gene-expression-based retrospective study. H Raza Ali, Leon Chlon, Paul DP Pharoah, Florian Markowetz, Carlos Caldas. PLoS medicine 13, (2016). https://doi.org/10.1371/journal.pmed.1002194

Computational pathology of pre-treatment biopsies identifies lymphocyte density as a predictor of response to neoadjuvant chemotherapy in breast cancer. H Raza Ali, Aliakbar Dariush, Elena Provenzano, Helen Bardwell, Jean E Abraham, Mahesh Iddawela, Anne-Laure Vallier, Louise Hiller, Janet Dunn, Sarah J Bowden, Tamas Hickish, Karen McAdam, Stephen Houston, Mike J Irwin, Paul DP Pharoah, James D Brenton, Nicholas A Walton, Helena M Earl, Carlos Caldas. Breast Cancer Res 18, 21 (2016). https://doi.org/10.1186/s13058-016-0682-8

Association between CD8+ T-cell infiltration and breast cancer survival in 12439 patients. H Raza Ali, E Provenzano, S-J Dawson, FM Blows, B Liu, M Shah, HM Earl, CJ Poole, L Hiller, JA Dunn, SJ Bowden, C Twelves, JMS Bartlett, SMA Mahmoud, E Rakha, IO Ellis, S Liu, D Gao, TO Nielsen, PDP Pharoah, C Caldas. Annals of oncology 25, 1536-1543 (2014). https://doi.org/10.1093/annonc/mdu191

Astronomical algorithms for automated analysis of tissue protein expression in breast cancer. H Raza Ali, M Irwin, L Morris, SJ Dawson, FM Blows, E Provenzano, B Mahler-Araujo, PD Pharoah, NA Walton, JD Brenton, C Caldas. Br J Cancer 108, 602–612 (2013). https://doi.org/10.1038/bjc.2012.558

Aurora kinase A outperforms Ki67 as a prognostic marker in ER-positive breast cancer. H Raza Ali, SJ Dawson, FM Blows, E Provenzano, PD Pharoah, C Caldas. Br J Cancer 106, 1798–1806 (2012). https://doi.org/10.1038/bjc.2012.167

Cancer stem cell markers in breast cancer: pathological, clinical and prognostic significance. H Raza Ali, Sarah-Jane Dawson, Fiona M Blows, Elena Provenzano, Paul D Pharoah, Carlos Caldas. Breast Cancer Res 13, R118 (2011). https://doi.org/10.1186/bcr3061