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Research Team. 

Sunnybrook Research Institute.

Sunnybrook Research Institute and Sunnybrook Health Sciences Centre (SHSC) is fully affiliated with the University of Toronto.  SHSC has the largest comprehensive breast program in Canada.
Each year, approximately 13,000 patients visit the centre, and includes multidisciplinary programs in Breast Radiology, Surgical Oncology, Medical Oncology, Radiation Oncology and Anatomic Pathology . SHSC is the recent recipient of a $150 million award to fund an expansion which will be adding 100,000 ft2 of research space and also triple the space available for clinical research. It is also a recent recipient of a $130 million investment by the Canadian Federal Government to support the use of AI in medicine.



My area of clinical and research focus is high-risk breast cancer and quantitative breast imaging.  I am an assistant professor in the Department of Radiation Oncology, University of Toronto, and Associate Member of the Institute of Medical Science (University of Toronto).  My laboratory is focused on developing novel imaging biomarkers using Quantitative Digital Pathology Imaging (QDPI) to predict therapy response in breast patients. In doing so, the research aims to also develop personalized treatment regimens for patients who undergo breast chemotherapy and/or radiotherapy.
Contact the research team
radiogenomics [@]
William T. Tran, MRT(T), MSc, PhD
Principal Investigator
Radiation Therapist Clinician Scientist
Assistant Professor, University of Toronto
Dr. Sadeghi-Naini is an Assistant Professor in the Department of Electrical Engineering and Computer Science at Lassonde School of Engineering. He holds cross-appointments in the Department of Medical Biophysics at the University of Toronto as an Assistant Professor, and at Sunnybrook Research Institute and Odette Cancer Centre as a Scientist. He is also an Adjunct Professor in the School of Biomedical Engineering at Western University. The focus of his research program is to develop quantitative imaging and intelligent biomarker technologies for precision medicine and personalized therapeutics.
Ali Sadeghi-Naini, PhD, P.Eng.
Collaborating Principal Investigator
Assistant Professor, York University

Graduate Students, Fellows & Research Staff.

Andrew Lagree, MSc
Lead, Imaging Researcher
Marie Angeli Alera, BSc
Research Assistant
Shirin Saednia, MSc
PhD Student
Ethan Law
Undergraduate Student
Queen's University
Danny Jang, MSc
PhD Student
Nick Meti, MD
Medical Oncology Resident
University of Toronto
Audrey Shiner
Undergraduate Student
Western University

Lab Alumni.

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Team Publications.

1: Sannachi L, Gangeh M, Naini AS, Bhargava P, Jain A, Tran WT, Czarnota GJ.

Quantitative Ultrasound Monitoring of Breast Tumour Response to Neoadjuvant

Chemotherapy: Comparison of Results Among Clinical Scanners. Ultrasound Med Biol.

2020 Feb 25. pii: S0301-5629(20)30048-X. doi: 10.1016/j.ultrasmedbio.2020.01.022.

[Epub ahead of print] PubMed PMID: 32111456.



2: Tran WT, Ibáñez C, Pinto MP, Sanchez C, Czarnota GJ, Merino T.

Eribulin-induced radiation recall dermatitis: a case report and brief review of

the literature. Ecancermedicalscience. 2020 Jan 23;14:1006. doi:

10.3332/ecancer.2020.1006. eCollection 2020. PubMed PMID: 32104208; PubMed

Central PMCID: PMC7039694.



3: Saednia K, Tabbarah S, Lagree A, Wu T, Klein J, Garcia E, Hall M, Chow E,

Rakovitch E, Childs C, Sadeghi-Naini A, Tran WT. Quantitative Thermal Imaging

Biomarkers to Detect Acute Skin Toxicity From Breast Radiation Therapy Using

Supervised Machine Learning. Int J Radiat Oncol Biol Phys. 2020 Apr

1;106(5):1071-1083. doi: 10.1016/j.ijrobp.2019.12.032. Epub 2020 Jan 23. PubMed

PMID: 31982495.



4: Tran WT, Suraweera H, Quaioit K, Cardenas D, Leong KX, Karam I, Poon I, Jang

D, Sannachi L, Gangeh M, Tabbarah S, Lagree A, Sadeghi-Naini A, Czarnota GJ.

Predictive quantitative ultrasound radiomic markers associated with treatment

response in head and neck cancer. Future Sci OA. 2019 Nov 26;6(1):FSO433. doi:

10.2144/fsoa-2019-0048. PubMed PMID: 31915534; PubMed Central PMCID: PMC6920736.



5: Sharma D, Giles A, Hashim A, Yip J, Ji Y, Do NNA, Sebastiani J, Tran WT,

Farhat G, Oelze M, Czarnota GJ. Ultrasound microbubble potentiated enhancement of

hyperthermia-effect in tumours. PLoS One. 2019 Dec 18;14(12):e0226475. doi:

10.1371/journal.pone.0226475. eCollection 2019. PubMed PMID: 31851698; PubMed

Central PMCID: PMC6919613.



6: Tran WT, Jerzak K, Lu FI, Klein J, Tabbarah S, Lagree A, Wu T, Rosado-Mendez

I, Law E, Saednia K, Sadeghi-Naini A. Personalized Breast Cancer Treatments Using

Artificial Intelligence in Radiomics and Pathomics. J Med Imaging Radiat Sci.

2019 Dec;50(4S2):S32-S41. doi: 10.1016/j.jmir.2019.07.010. Epub 2019 Aug 22.

PubMed PMID: 31447230.



7: Sannachi L, Gangeh M, Tadayyon H, Gandhi S, Wright FC, Slodkowska E, Curpen B,

Sadeghi-Naini A, Tran W, Czarnota GJ. Breast Cancer Treatment Response Monitoring

Using Quantitative Ultrasound and Texture Analysis: Comparative Analysis of

Analytical Models. Transl Oncol. 2019 Oct;12(10):1271-1281. doi:

10.1016/j.tranon.2019.06.004. Epub 2019 Jul 17. PubMed PMID: 31325763; PubMed

Central PMCID: PMC6639683.



8: Tadayyon H, Gangeh M, Sannachi L, Trudeau M, Pritchard K, Ghandi S, Eisen A,

Look-Hong N, Holloway C, Wright F, Rakovitch E, Vesprini D, Tran WT, Curpen B,

Czarnota G. A priori prediction of breast tumour response to chemotherapy using

quantitative ultrasound imaging and artificial neural networks. Oncotarget. 2019 

Jun 11;10(39):3910-3923. doi: 10.18632/oncotarget.26996. eCollection 2019 Jun 11.

PubMed PMID: 31231468; PubMed Central PMCID: PMC6570472.



9: Fernandes J, Sannachi L, Tran WT, Koven A, Watkins E, Hadizad F, Gandhi S,

Wright F, Curpen B, El Kaffas A, Faltyn J, Sadeghi-Naini A, Czarnota G.

Monitoring Breast Cancer Response to Neoadjuvant Chemotherapy Using Ultrasound

Strain Elastography. Transl Oncol. 2019 Sep;12(9):1177-1184. doi:

10.1016/j.tranon.2019.05.004. Epub 2019 Jun 18. PubMed PMID: 31226518; PubMed

Central PMCID: PMC6586920.



10: Klein J, Tran W, Watkins E, Vesprini D, Wright FC, Look Hong NJ, Ghandi S,

Kiss A, Czarnota GJ. Locally advanced breast cancer treated with neoadjuvant

chemotherapy and adjuvant radiotherapy: a retrospective cohort analysis. BMC

Cancer. 2019 Apr 3;19(1):306. doi: 10.1186/s12885-019-5499-2. PubMed PMID:

30943923; PubMed Central PMCID: PMC6448234.



11: Tran WT, Childs C, Probst H, Farhat G, Czarnota GJ. Imaging Biomarkers for

Precision Medicine in Locally Advanced Breast Cancer. J Med Imaging Radiat Sci.

2018 Dec;49(4):342-351. doi: 10.1016/j.jmir.2017.09.006. Epub 2018 Apr 1. Review.

PubMed PMID: 30514549.



12: Nathoo D, Willis S, Tran WT. Distress Among Locally Advanced Breast Cancer

Patients from Diagnosis to Follow-Up: A Critical Review of Literature. J Med

Imaging Radiat Sci. 2018 Sep;49(3):325-336. doi: 10.1016/j.jmir.2018.04.034. Epub

2018 Jun 18. Review. PubMed PMID: 32074060.



13: Sannachi L, Gangeh M, Tadayyon H, Sadeghi-Naini A, Gandhi S, Wright FC,

Slodkowska E, Curpen B, Tran W, Czarnota GJ. Response monitoring of breast cancer

patients receiving neoadjuvant chemotherapy using quantitative ultrasound,

texture, and molecular features. PLoS One. 2018 Jan 3;13(1):e0189634. doi:

10.1371/journal.pone.0189634. eCollection 2018. PubMed PMID: 29298305; PubMed

Central PMCID: PMC5751990.



14: El Kaffas A, Gangeh MJ, Farhat G, Tran WT, Hashim A, Giles A, Czarnota GJ.

Tumour Vascular Shutdown and Cell Death Following Ultrasound-Microbubble Enhanced

Radiation Therapy. Theranostics. 2018 Jan 1;8(2):314-327. doi:

10.7150/thno.19010. eCollection 2018. PubMed PMID: 29290810; PubMed Central

PMCID: PMC5743550.



15: Kung JS, Tran WT, Poon I, Atenafu EG, Courneyea L, Higgins K, Enepekides D,

Sahgal A, Chin L, Karam I. Evaluation of the Efficacy of Rotational Corrections

for Standard-Fractionation Head and Neck Image-Guided Radiotherapy. Technol

Cancer Res Treat. 2018 Jan-Dec;18:1533033819853824. doi:

10.1177/1533033819853824. PubMed PMID: 31122178; PubMed Central PMCID:




16: Sadeghi-Naini A, Suraweera H, Tran WT, Hadizad F, Bruni G, Rastegar RF,

Curpen B, Czarnota GJ. Breast-Lesion Characterization using Textural Features of 

Quantitative Ultrasound Parametric Maps. Sci Rep. 2017 Oct 20;7(1):13638. doi:

10.1038/s41598-017-13977-x. PubMed PMID: 29057899; PubMed Central PMCID:




17: Sadeghi-Naini A, Sannachi L, Tadayyon H, Tran WT, Slodkowska E, Trudeau M,

Gandhi S, Pritchard K, Kolios MC, Czarnota GJ. Chemotherapy-Response Monitoring

of Breast Cancer Patients Using Quantitative Ultrasound-Based Intra-Tumour

Heterogeneities. Sci Rep. 2017 Sep 4;7(1):10352. doi: 10.1038/s41598-017-09678-0.

PubMed PMID: 28871171; PubMed Central PMCID: PMC5583340.



18: Tran WT, Gangeh MJ, Sannachi L, Chin L, Watkins E, Bruni SG, Rastegar RF,

Curpen B, Trudeau M, Gandhi S, Yaffe M, Slodkowska E, Childs C, Sadeghi-Naini A, 

Czarnota GJ. Predicting breast cancer response to neoadjuvant chemotherapy using 

pretreatment diffuse optical spectroscopic texture analysis. Br J Cancer. 2017

May 9;116(10):1329-1339. doi: 10.1038/bjc.2017.97. Epub 2017 Apr 18. PubMed PMID:

28419079; PubMed Central PMCID: PMC5482739.



19: Tadayyon H, Sannachi L, Gangeh MJ, Kim C, Ghandi S, Trudeau M, Pritchard K,

Tran WT, Slodkowska E, Sadeghi-Naini A, Czarnota GJ. A priori Prediction of

Neoadjuvant Chemotherapy Response and Survival in Breast Cancer Patients using

Quantitative Ultrasound. Sci Rep. 2017 Apr 12;7:45733. doi: 10.1038/srep45733.

PubMed PMID: 28401902; PubMed Central PMCID: PMC5388850.



20: Pasternak M, Doss L, Farhat G, Al-Mahrouki A, Kim CH, Kolios M, Tran WT,

Czarnota GJ. Effect of chromatin structure on quantitative ultrasound parameters.

Oncotarget. 2017 Mar 21;8(12):19631-19644. doi: 10.18632/oncotarget.14816. PubMed

PMID: 28129644; PubMed Central PMCID: PMC5386710.



21: Tran WT, Sannachi L, Papanicolau N, Tadayyon H, Al Mahrouki A, El Kaffas A,

Gorjizadeh A, Lee J, Czarnota GJ. Quantitative ultrasound imaging of therapy

response in bladder cancer in vivo. Oncoscience. 2016 Apr 18;3(3-4):122-33. doi: 

10.18632/oncoscience.302. eCollection 2016. PubMed PMID: 27226985; PubMed Central

PMCID: PMC4872650.



22: Lai P, Tarapacki C, Tran WT, El Kaffas A, Lee J, Hupple C, Iradji S, Giles A,

Al-Mahrouki A, Czarnota GJ. Breast tumor response to ultrasound mediated

excitation of microbubbles and radiation therapy in vivo. Oncoscience. 2016 Mar

24;3(3-4):98-108. doi: 10.18632/oncoscience.299. eCollection 2016. Erratum in:

Oncoscience. 2017 Jan 30;4(1-2):14. PubMed PMID: 27226983; PubMed Central PMCID: 




23: Tadayyon H, Sannachi L, Gangeh M, Sadeghi-Naini A, Tran W, Trudeau ME,

Pritchard K, Ghandi S, Verma S, Czarnota GJ. Quantitative ultrasound assessment

of breast tumor response to chemotherapy using a multi-parameter approach.

Oncotarget. 2016 Jul 19;7(29):45094-45111. doi: 10.18632/oncotarget.8862. Erratum

in: Oncotarget. 2017 May 23;8(21):35481. PubMed PMID: 27105515; PubMed Central

PMCID: PMC5216708.



24: Tran WT, Childs C, Chin L, Slodkowska E, Sannachi L, Tadayyon H, Watkins E,

Wong SL, Curpen B, El Kaffas A, Al-Mahrouki A, Sadeghi-Naini A, Czarnota GJ.

Multiparametric monitoring of chemotherapy treatment response in locally advanced

breast cancer using quantitative ultrasound and diffuse optical spectroscopy.

Oncotarget. 2016 Apr 12;7(15):19762-80. doi: 10.18632/oncotarget.7844. PubMed

PMID: 26942698; PubMed Central PMCID: PMC4991417.



25: Tadayyon H, Sannachi L, Sadeghi-Naini A, Al-Mahrouki A, Tran WT, Kolios MC,

Czarnota GJ. Quantification of Ultrasonic Scattering Properties of In Vivo Tumor 

Cell Death in Mouse Models of Breast Cancer. Transl Oncol. 2015 Dec;8(6):463-73. 

doi: 10.1016/j.tranon.2015.11.001. PubMed PMID: 26692527; PubMed Central PMCID:




26: Sadeghi-Naini A, Vorauer E, Chin L, Falou O, Tran WT, Wright FC, Gandhi S,

Yaffe MJ, Czarnota GJ. Early detection of chemotherapy-refractory patients by

monitoring textural alterations in diffuse optical spectroscopic images. Med

Phys. 2015 Nov;42(11):6130-46. doi: 10.1118/1.4931603. PubMed PMID: 26520706.



27: Merino T, Tran WT, Czarnota GJ. Re-irradiation for locally recurrent

refractory breast cancer. Oncotarget. 2015 Oct 27;6(33):35051-62. doi:

10.18632/oncotarget.6036. PubMed PMID: 26459388; PubMed Central PMCID:




28: El Kaffas A, Sadeghi-Naini A, Falou O, Tran WT, Zhou S, Hashim A, Fernandes

J, Giles A, Czarnota GJ. Assessment of tumor response to radiation and vascular

targeting therapy in mice using quantitative ultrasound spectroscopy. Med Phys.

2015 Aug;42(8):4965-73. doi: 10.1118/1.4926554. PubMed PMID: 26233222.



29: Sannachi L, Tadayyon H, Sadeghi-Naini A, Tran W, Gandhi S, Wright F, Oelze M,

Czarnota G. Non-invasive evaluation of breast cancer response to chemotherapy

using quantitative ultrasonic backscatter parameters. Med Image Anal. 2015

Feb;20(1):224-36. doi: 10.1016/ Epub 2014 Nov 25. PubMed

PMID: 25534283.



30: Al-Mahrouki AA, Iradji S, Tran WT, Czarnota GJ. Cellular characterization of 

ultrasound-stimulated microbubble radiation enhancement in a prostate cancer

xenograft model. Dis Model Mech. 2014 Mar;7(3):363-72. doi: 10.1242/dmm.012922.

Epub 2014 Jan 30. PubMed PMID: 24487407; PubMed Central PMCID: PMC3944496.



31: El Kaffas A, Al-Mahrouki A, Tran WT, Giles A, Czarnota GJ. Sunitinib effects 

on the radiation response of endothelial and breast tumor cells. Microvasc Res.

2014 Mar;92:1-9. doi: 10.1016/j.mvr.2013.10.008. Epub 2013 Nov 9. PubMed PMID:




32: Kwok SJ, El Kaffas A, Lai P, Al Mahrouki A, Lee J, Iradji S, Tran WT, Giles

A, Czarnota GJ. Ultrasound-mediated microbubble enhancement of radiation therapy 

studied using three-dimensional high-frequency power Doppler ultrasound.

Ultrasound Med Biol. 2013 Nov;39(11):1983-90. doi:

10.1016/j.ultrasmedbio.2013.03.025. Epub 2013 Aug 29. PubMed PMID: 23993051.



33: Sadeghi-Naini A, Falou O, Tadayyon H, Al-Mahrouki A, Tran W, Papanicolau N,

Kolios MC, Czarnota GJ. Conventional frequency ultrasonic biomarkers of cancer

treatment response in vivo. Transl Oncol. 2013 Jun 1;6(3):234-43. Print 2013 Jun.

Erratum in: Transl Oncol. 2013 Dec;6(6):erratum. PubMed PMID: 23761215; PubMed

Central PMCID: PMC3678128.



34: Czarnota GJ, Karshafian R, Burns PN, Wong S, Al Mahrouki A, Lee JW, Caissie

A, Tran W, Kim C, Furukawa M, Wong E, Giles A. Tumor radiation response

enhancement by acoustical stimulation of the vasculature. Proc Natl Acad Sci U S 

A. 2012 Jul 24;109(30):E2033-41. doi: 10.1073/pnas.1200053109. Epub 2012 Jul 9.

PubMed PMID: 22778441; PubMed Central PMCID: PMC3409730.



35: El Kaffas A, Tran W, Czarnota GJ. Vascular strategies for enhancing tumour

response to radiation therapy. Technol Cancer Res Treat. 2012 Oct;11(5):421-32.

Epub 2012 May 7. Review. PubMed PMID: 22568629.



36: Tran WT, Gillies C. Perspectives in Implementing Radiogenomics to

Radiotherapy. J Med Imaging Radiat Sci. 2010 Jun;41(2):79-86. doi:

10.1016/j.jmir.2010.03.005. Epub 2010 Jun 8. PubMed PMID: 31051821.



37: Tran WT. Practical Considerations in Cone Beam and Ultrasound IGRT Systems in

Prostate Localization: A Review of the Literature. J Med Imaging Radiat Sci. 2009

Mar;40(1):3-8. doi: 10.1016/j.jmir.2008.12.001. Epub 2009 Mar 9. PubMed PMID:


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