Publications

Multiplex Imaging Analysis in Pathology: a Comprehensive Review on Analytical Approaches and Digital Toolkits
Omar M, Fanelli GN, Socciarelli F, Ullanat V, Puchala SR, Wen J, Chowdhury A, Valencia I, Scatena C, Marchionni L, Umeton R, Loda M
arXiv, 2024
Key Figure

A triple hormone receptor ER, AR, and VDR signature is a robust prognosis predictor in breast cancer
Omar M, Harrell C, Tamimi R, Marchionni L, Erdogan C, Nakshatri H, Ince TA
Breast Cancer Res, 2024
Key Figure

ChatGPT for digital pathology research
Omar M, Ullanat V, Loda M, Marchionni L, Umeton R
The Lancet Digital Health, 2024
Key Figure

Applications of Digital Pathology in Cancer: A Comprehensive Review
Omar M, Alexanderani MK, Valencia I, Loda M, Marchionni L
Ann Rev Can Biology, 2024
Key Figure

Semi-Supervised, Attention-Based Deep Learning for Predicting TMPRSS2:ERG Fusion Status in Prostate Cancer Using Whole Slide Images
Omar M, Xu Z, Rand SB, Alexanderani MK, Salles DC, Valencia I, Schaeffer EM, Robinson BD, Lotan TL, Loda M, Marchionni L
Mol Cancer Res, 2024
Key Figure

Artificial intelligence applications in histopathology
Bahadir CD, Omar M, Rosenthal J. et al.
Nat Rev Electr Eng, 2024
Key Figure

    Access the paper

Distinct mesenchymal cell states mediate prostate cancer progression
Pakula H, Omar M, Carelli R. et al.
Nat Commun, 2024
Key Figure

Notch-based gene signature for predicting the response to neoadjuvant chemotherapy in triple-negative breast cancer
Omar M, Nuzzo PV, Ravera F. et al.
J Transl Med., 2023
Key Figure

Using biological constraints to improve prediction in precision oncology
Omar M, Dinalankara W, Mulder L, Coady T, Zanettini C, Imada EL, Younes L, Geman D, Marchionni L
iScience, 2023
Key Figure

ZNF92, an unexplored transcription factor with remarkably distinct breast cancer over-expression associated with prognosis and cell-of-origin
Kamran M, Bhattacharya U, Omar M, Marchionni L, Ince TA
npj Breast Cancer, 2022
Key Figure

Donor-derived acute myeloid leukemia in solid organ transplantation
Marchionni L, Lobo FP, Kostadinov R, Serra A, Besso FG, Deaglio S, Stratta P, Berrino M, Zanettini C, Imada EL, Omar M, Gaidano G, Bruno B, Saglio G, Amoroso A
Am J Transplant., 2022
Key Figure

Building Tools for Machine Learning and Artificial Intelligence in Cancer Research: Best Practices and a Case Study with the PathML Toolkit for Computational Pathology
Rosenthal J, Carelli R, Omar M, Brundage D, Halbert E, Nyman J, Hari SN, Van Allen EM, Marchionni L, Umeton R, Loda M
Mol Cancer Res, 2022
Key Figure

A robust and interpretable gene signature for predicting the lymph node status of primary T1/T2 oral cavity squamous cell carcinoma
Ghantous Y, Omar M, Broner EC, Agrawal N, Pearson AT, Rosenberg AJ, Mishra V, Singh A, El-Naaj IA, Savage PA, Sidransky D, Marchionni L, Izumchenko E.
Int J Cancer., 2022
Key Figure

Host Blood Gene Signatures Can Detect the Progression to Severe and Cerebral Malaria
Omar M, Marchionni L, Häcker G, Badr MT
Front. Cell. Infect. Microbiol., 2021
Key Figure

covid19census: U.S. and Italy COVID-19 metrics and other epidemiological data
Zanettini C, Omar M, Dinalankara W, Imada EL, Colantuoni E, Parmigiani G, Marchionni L
Database, 2021
Key Figure

Influenza Vaccination and COVID-19 Mortality in the USA: An Ecological Study
Zanettini C, Omar M, Dinalankara W, Imada EL, Colantuoni E, Parmigiani G, Marchionni L
Vaccines, 2021
Key Figure

Comprehensive Integration of Genome-Wide Association and Gene Expression Studies Reveals Novel Gene Signatures and Potential Therapeutic Targets for Helicobacter pylori-Induced Gastric Disease
Badr MT, Omar M, Häcker G
Front. Immunol., 2021
Key Figure