Basu D, Sannigrahi MK, Raghav L, Rajagopalan P, Brody R, Jalaly J, Gallant JN Evidence of a role for oropharyngeal cancer cells with low HPV gene expression in treatment failure , Journal of Clinical Oncology (ASCO): 2025

Hieromnimon HM, Trzcinska A, Wen F, Howard FM, Dolezal JM, Dyer E, Kochanny S, Schulte J, Wang C, Chen H, Chin J, …, Jalaly JB, et al Interpretable HPV detection in head and neck cancer using foundation models and synthetic digital pathology , Cancer Research: 2025

Sannigrahi MK, Raghav L, Rich DJ, Schrank TP, Califano JA, Lukens JN, Sun L, Morgan IM, Cohen RB, Lin A, Liu X…, Jalaly JB, et al Tumor-intrinsic and immune-related features associated with treatment failure in human papillomavirus-related oropharyngeal cancer , JNCI: Journal of the National Cancer Institute: 2025

Hieromnimon HM, Trzcinska A, Wen FT, Howard FM, Dolezal JM, Dyer E, Kochanny S, Schulte JJ, Wang C, Chen H, Chin J, Blair E, Agrawal N, Rosenberg A, Vokes E, Katipally R, Juloori A, Izumchenko E, Lingen MW, Cipriani N, Jalaly JB, Basu D, Riesenfeld SJ, Pearson AT Analysis of AI foundation model features decodes the histopathologic landscape of HPV-positive head and neck squamous cell carcinomas , Oral Oncology, 163: 2025

Jalaly JB MMP11 as a Prognostic Indicator for Inverted Papilloma Histologic Grade and Recurrence , The Laryngoscope: 2025

Rossi ED, Agarwal S, Erkilic S, Hang JF, Jalaly JB, Khanafshar E, Ladenheim A, Baloch Z Psammoma bodies in thyroid: are they always indicative of malignancy? A multi-institutional study , Virchows Archiv, 485: 2024

Sannigrahi, Malay K., ..., Jalaly JB, et al Association of oropharyngeal cancer recurrence with tumor-intrinsic and immune-mediated sequelae of reduced genomic instability. , bioRxiv: 2024

Resta IT, Jalaly JB Mucosal neuroma , Pathology Outlines : 2024

Tong CCL, Lin X, Seckar T, Koptyra M, Kohanski MA, Cohen NA, Kennedy DW, Adappa ND, Papagiannopoulos P, Kuan EC, Baranov E, Jalaly JB, Feldman MD, Storm PB, Resnick AC, Palmer JN, Wei Z, Robertson ES. A Metagenomic Analysis of the Virome of Inverted Papilloma and Squamous Cell Carcinoma. , Int Forum Allergy Rhinol, 13(11): 2023,2055-2062

Jalaly JB, Baloch ZW. Salivary Gland Neoplasms in Small Biopsies and Fine Needle Aspirations. , Semin Diagn Pathol, 40(5): 2023,340-348