Publications

Canadian and Transatlantic Collaborative Guidelines for Implementing Digital Pathology in Clinical Practice: A Comprehensive Framework for Laboratories. Sonal Varma, Andrew Evans, Bich Nguyen, and George M Yousef. Submission in progress to Journal of Pathology Informatics.

Featured Research Highlights

Testing of rapid evaporative mass spectrometry for histological tissue classification and molecular diagnostics in a multi-site study

  • Authors: Kaufmann M, Vaysse PM, Savage A, Kooreman LFS, Janssen N, Varma S, Ren KYM, Merchant S, Engel CJ, Olde Damink SWM, Smidt ML, Shousha S, Chauhan H, Karali E, Kazanc E, Poulogiannis G, Fichtinger G, Tauber B, Leff DR, Pringle SD, Rudan JF, Heeren RMA, Porta Siegel T, Takáts Z, Balog J

  • Journal: British Journal of Cancer (2024)

  • Why it matters: This multi-site international study successfully tests rapid evaporative mass spectrometry (REMS) for automated histological tissue classification. This technology paves the way for near-instantaneous molecular diagnostics and real-time tumor boundary detection during surgeries.

Full article

Efficient self-supervised Barlow Twins from limited tissue slide cohorts for colonic pathology diagnostics. Medical Image Analysis

  • Authors: Cassandre Notton, Vasudev Sharma, Vincent Quoc-Huy Trinh, Lina Chen, Minqi Xu, Sonal Varma, Mahdi S. Hosseini

  • Journal: Medical Image Analysis (2026)
     

  • Why it matters: Introducing "Barlow Twins"—an advanced AI framework capable of highly accurate colonic pathology diagnostics using restricted, smaller tissue slide data sets. This breakthrough removes a massive hurdle in computational pathology, allowing smaller hospitals with limited historical data to deploy reliable diagnostic AI models

Read Full Article on ScienceDirect

Intravital imaging reveals systemic ezrin inhibition impedes cancer cell migration and lymph node metastasis in breast cancer

  • Authors: Ghaffari A, Hoskin V, Turashvili G, Varma S, Mewburn J, Mullins G, Greer PA, Kiefer F, Day AG, Madarnas Y, SenGupta S, Elliott BE

  • Journal: Breast Cancer Research (2019)

  • Why it matters: Utilizing advanced intravital imaging, this study proves that blocking the ezrin protein successfully stops breast cancer cells from migrating and invading the lymph nodes. It highlights a powerful new therapeutic target to halt aggressive tumor metastasis before it spreads throughout the body.

Read Full Article on Springer Nature

 

  1.  A hierarchical histological tissue type-annotated dataset for potential biomarker discovery of colorectal disease. J Pathol Inform.Yang Z, Li K, Ramandi SG, Brassard P, Khellaf A, Trinh VQ, Zhang J, Chen L, Rowsell C, Varma S, Plataniotis K, Hosseini MS. ADPv2: 2025: 23:100537. Full article...
     
  2. MassVision: An open-source end-to-end platform for AI-driven mass spectrometry image analysis. Amoon Jamzad, Ayesha Syeda, Jade Warren, Martin Kaufmann, Natasha Iaboni, Christopher J. B. Nicol, John Rudan, Kevin Y. M. Ren, David Hurlbut, Sonal Varma, Gabor Fichtinger, Parvin Mousavi. Full article...
     
  3. Comparative Analysis of Diffusion Generative Models in Computational Pathology. Denisha Thakkar, Vincent Quoc-Huy Trinh, Sonal Varma, Samira Ebrahimi Kahou, Hassan Rivaz, Mahdi S. Hosseini. Full article...
     
  4. Efficient Self-Supervised Barlow Twins from Limited Tissue Slide Cohorts for Colonic Pathology Diagnostics. Cassandre Notton, Vasudev Sharma, Vincent Quoc-Huy Trinh, Lina Chen, Minqi Xu, Sonal Varma, Mahdi S. Hosseini.Full article... 
     
  5. Fit-for-Purpose Ki-67 Immunohistochemistry Assays for Breast Cancer. Emina E. Torlakovic, Nick Baniak, Penny J. Barnes, … Sonal Varma, Gang Wang, Tao Wang, Bret Wehrli, Gilbert Bigras. 2024 Laboratory Investigation, 104 (7): 102076
     
  6. Jamzad, Amoon, Fooladgar, Fahimeh, Connolly, Laura, Srikanthan, Dilakshan, Syeda, Ayesha, Kaufmann, Martin, Ren, Kevin, Merchant, Shaila, Engel, Cecil, Varma, Sonal, Fichtinger, Gabor, Rudan, John, Mousavi, Parvin. (2023). Bridging Ex-Vivo Training and Intra-operative Deployment for Surgical Margin Assessment with Evidential Graph Transformer. In book: Medical Image Computing and Computer-Assisted Intervention 
    MICCAI 2023 (pp.562-571). 10.1007/978-3-031-43990-2_53.
     
  7. Self-supervised learning and uncertainty estimation for surgical margin detection. Ayesha Syeda, Fahimeh Fooladgar, Amoon Jamzad, Dilakshan Srikanthan, Martin Kaufmann, Kevin Ren, Jay Engel, Ross Walker, Shaila Merchant, Doug McKay, Sonal Varma, Gabor Fichtinger, John Rudan, and Parvin Mousavi. Proc. SPIE 12466, Medical Imaging 2023: Image-Guided Procedures, Robotic Interventions, and Modelling, 124660B (3 April 2023)
     
  8. A retrospective analysis of ezrin protein and mRNA expression in breast cancer: Ezrin expression is associated with patient survival and survival of patients with receptor-positive disease. Storr SJ, Hoskin V, Aiyappa-Maudsley R, Ghaffari A, Varma S, Green A, Rakha E, Ellis IO, Greer PA, Martin SG. Cancer Med. 2023 May;12(9):10908-10916.
     
  9. Metabolically Active Zones Involving Fatty Acid Elongation Delineated by DESI-MSI Correlate with Pathological and Prognostic Features of Colorectal Cancer. Kaufmann M, Iaboni N, Jamzad A, Hurlbut D, Ren KYM, Rudan JF, Mousavi P, Fichtinger G, Varma S, Caycedo-Marulanda A, Nicol CJB. Metabolites. 2023 Mar 31;13(4):508.
     
  10. Targeting the Ezrin Adaptor Protein Sensitizes Metastatic Breast Cancer Cells to Chemotherapy and Reduces Neoadjuvant Therapy-induced Metastasis. Hoskin V, Ghaffari A, Laight BJ, SenGupta S, Madarnas Y, Nicol CJB, Elliott BE, Varma S, Greer PA. Cancer Res Commun. 2022 Jun 17;2(6):456-470
     
  11. HistoKT: Cross Knowledge Transfer in Computational Pathology. Ryan Zhang, Jiadai Zhu, Stephen Yang, Mahdi S. Hosseini, Angelo Genovese, Lina Chen, Corwyn Rowsell, Savvas Damaskinos, Sonal Varma, Konstantinos N. Plataniotis. 2022; ArXiv:2201.11246 
     
  12. Domain Adaptation and Self-Supervised Learning for Surgical Margin Detection. A.M.L. Santilli, A. Jamzad, A. Sedghi, M. Kaufmann, S. Merchant, J. Engel, K. Logan, J. Wallis, N. Janssen, S. Varma, G. Fichtinger, J. Rudan, P. Mousavi. Accepted for IPCAI proceedings. June 2021 and accepted in: Int J Comput Assist Radiol Surg 2021 for publication
     
  13. Metabolomics Patterns of Breast Cancer Tumours Using Mass Spectrometry Imaging. Rachel L. Theriault, Martin Kaufmann, Kevin Y. M. Ren, Sonal Varma, Randy E. Ellis. International Journal of Computer Assisted Radiology and Surgery. 2021; volume 16,1089–1099
     
  14. Probeable DARTS with Application to Computational Pathology. Sheyang Tang, Mahdi S. Hosseini, Lina Chen, Sonal Varma, Corwyn Rowsell, Savvas Damaskinos, Konstantinos N. Plataniotis, Zhou Wang. ArXiv:2108.06859 
     
  15. Self-Supervised Learning for Detection of Breast Cancer in Surgical Margins with Limited Data. A.M.L. Santilli, A. Jamzad, A. Sedghi, M. Kaufmann, S. Merchant, J. Engel, K. Logan, J. Wallis, N. Janssen, S. Varma, G. Fichtinger, J. Rudan, P. Mousavi. Accepted at the IEEE International Symposium on Biomedical Imaging (ISBI) proceedings. April 2021.
     
  16. Lack of definitive presurgical pathological diagnosis is associated with inadequate surgical margins in breast-conserving surgery. Nasute Fauerbach PV, Tyryshkin K, Rodrigo SP, Rudan J, Fichtinger G, Reedijk M, Varma S, Berman DM. Eur J Surg Oncol. 2021 Oct;47(10):2483-2491.
     
  17. Management of Mycobacterium tuberculosis Prosthetic Joint Infection: 2 Cases and Literature Review.Lo CK, Chen L, Varma S, Wood GCA, Grant J, Wilson EW.  Open Forum Infect Dis. 2021
     
  18. Whole-circumference or near whole-circumference endoscopic submucosal dissection specimens: “rolling out” a new specimen preparation technique. Lina Chen, David Hurlbut, Robert Bechara, Sonal Varma. Canadian Journal of Pathology. 2020; 13 ( 1), 34-40
     
  19. Salvage circumferential endoscopic submucosal dissection for refractory dysplastic Barrett’s esophagus. Robert Bechara, Lina Chen, Wiley Chung, Sonal Varma. VIDEOGIE. 2020; Volume 5 (12), 641-642.
     
  20. Detecting Breast Cancer Clusters from Mass Spectrometry Imaging. R. Theriault1, B. Everitt, S. Varma, M. Kaufmann, R. Ellis. Int J CARS (2020) 15 (Suppl 1): S1–S214.(This was later expanded and published as articles in archival journals)
     
  21. STAT5A is regulated by DNA damage via the tumour suppressor p53. Mukhopadhyay UK, Cass J, Raptis L, Craig AW, Bourdeau V, Varma S, SenGupta S, Elliott BE, Ferbeyre G. Cytokine. 2016 Jun;82:70-9.
     
  22. Dataset of STAT5A status in breast cancer. Mukhopadhyay UK, Cass J, Raptis L, Craig AW, Bourdeau V, Varma S, Gupta SS, Elliott BE, Ferbeyre G. Data Brief. 2016 Mar 4;7:490-2.