Publications

Morris G, Vlachostergios PJ, Rai MP, Scherr D, Molina A, Elemento O, Mosquera JMiguel, Cheng L, Faltas BM.  2026.  19q13 amplification with AKT2 and ERCC2 gains in sarcomatoid carcinoma of the urinary bladder.. Cancer Genet. 304-305:51-57.

Waltman P, Chandra P, Eng KW, Wilkes DC, Park H, Pabon C, Delpe P, Bhinder B, Manohar J, Kane T et al..  2026.  EXaCT-2: an augmented and customizable oncology-focused whole exome sequencing platform.. NPJ Precis Oncol.

Podaza E, Capuano J, Kuo H-H, Assaad MAl, Markowitz G, M Revuelta V, Nguyen J, Irizarry A, Ravichandran H, Ackermann S et al..  2026.  Tumor immune microenvironment reconstitution in patient-derived organoids enables therapy modeling for NSCLC.. Cell Rep Methods. :101339.

Assaad MAl, Hadi K, Levine MF, Guevara D, Patel M, Tranquille M, King A, Otilano J, Semaan A, Gundem G et al..  2026.  Whole genome sequencing approach to assess homologous recombination deficiency in a pan-cancer cohort.. Commun Med (Lond). 6(1):5.

Kozan ENur, de la Mora JDelgado-, Assaad MAl, Ginter P, Gundem G, Levine MF, Gorski K, Phan A, Beg S, Sigaras A et al..  2026.  Whole genome sequencing of locally advanced and metastatic breast carcinoma unravels relevant molecular signatures and novel events.. Pathol Res Pract. 282:156469.

Nauseef JT, Chu TR, Hooper WF, Alonso A, Oku A, Geiger H, Goldstein ZR, Shah M, Sigouros M, Manohar J et al..  2025.  A complex phylogeny of lineage plasticity in metastatic castration resistant prostate cancer.. NPJ Precis Oncol. 9(1):91.

de la Mora JDelgado-, Assaad MAl, Karaaslan S, Hadi K, Halima A, Deshpande A, Manohar J, Sigouros M, Medina-Martínez JS, Lieberman MD et al..  2025.  Corrigendum to "Whole genome and transcriptome analysis of pancreatic acinar cell carcinoma elucidates mechanisms of homologous recombination deficiency and unravels novel relevant fusion events" [Pathol. - Res. Pract. 266 (2025) 155798].. Pathol Res Pract. 266:155825.

Ohara K, Assaad MAl, McNulty SN, Alnajar H, Sboner A, Wilkes DC, He F, Xiang JZhaoying, Mathew S, Elemento O et al..  2025.  Detection of rare and novel gene fusions in patients with diffuse glioma: An institutional retrospective study.. J Neuropathol Exp Neurol. 84(3):269-271.

Windon A, Assaad MAl, Hadi K, Mendelson N, Hissong E, Deshpande A, Tranquille M, Mclee J, Levine MF, Patel M et al..  2025.  Emerging molecular phenotypes and potential therapeutic targets in esophageal and gastric adenocarcinoma unearthed by whole genome and transcriptome analyses.. Pathol Res Pract. 266:155788.

Assaad MAl, Hadi K, Tu J, Levine MF, Patel M, Deshpande A, Manohar J, Sigouros M, Sboner A, Chapman-Davis E et al..  2025.  Enhancing the detection of clinically relevant biomarkers in advanced uterine and tubo-ovarian carcinomas through genome-wide analysis.. Pathol Res Pract. 266:155773.

Cheng APellan, Widman AJ, Arora A, Rusinek I, Sossin A, Rajagopalan S, Midler N, Hooper WF, Murray RM, Halmos D et al..  2025.  Error-corrected flow-based sequencing at whole-genome scale and its application to circulating cell-free DNA profiling.. Nat Methods. 22(5):973-981.

Claridge SE, Nath S, Baum A, Farias R, Cavallo J-A, Rizvi NM, De Boni L, Park E, Granados GLara, Hauesgen M et al..  2025.  Functional genomics pipeline identifies CRL4 inhibition for the treatment of ovarian cancer.. Clin Transl Med. 15(2):e70078.

Hissong E, Bhinder B, Kim J, Ohara K, Ravichandran H, Assaad MAl, Elsoukkary S, Shusterman M, Khan U, Eng KWha et al..  2025.  Integrative transcriptomic and single-cell protein characterization of colorectal carcinoma delineates distinct tumor immune microenvironments associated with overall survival.. Pathol Res Pract. 273:156150.

Rowdo FPMadorsky, Martini R, Ackermann SE, Tang CP, Tranquille M, Irizarry A, Us I, Alawa O, Moyer JE, Sigouros M et al..  2025.  Kinome-Focused CRISPR-Cas9 Screens in African Ancestry Patient-Derived Breast Cancer Organoids Identify Essential Kinases and Synergy of EGFR and FGFR1 Inhibition.. Cancer Res. 85(3):551-566.

Guevara D, Shin N, Boiko A, Valiev I, Elsaeed AG, Mosquera JMiguel, Assaad MAl, Manohar J, Sigouros M, Zaichikova A et al..  2025.  Mesonephric Adenocarcinoma in a Young Male Patient.. Anticancer Res. 45(2):619-623.

de la Mora JDelgado-, Assaad MAl, Quitian S, Levine MF, Deshpande A, Sigouros M, Manohar J, Medina-Martínez JS, Sboner A, Elemento O et al..  2025.  Novel structural variants that impact cell cycle genes are elucidated in metastatic gastrointestinal stromal tumors.. Pathol Res Pract. 266:155782.

Cheng APellan, Rusinek I, Sossin A, Widman AJ, Meiri E, Krieger G, Hirschberg O, Tov DShem, Gilad S, Jaimovich A et al..  2025.  Paired plus-minus sequencing is an ultra-high throughput and accurate method for dual strand sequencing of DNA molecules.. bioRxiv.

Guevara D, Shin N, Boiko A, Valiev I, Elsaeed AG, Mosquera JMiguel, Assaad MAl, Manohar J, Sigouros M, Zaichikova A et al..  2025.  Unusual Presentation of Advanced Urothelial Cancer in a Young Patient.. Anticancer Res. 45(2):613-618.

de la Mora JDelgado-, Assaad MAl, Karaaslan S, Hadi K, Halima A, Deshpande A, Manohar J, Sigouros M, Medina-Martínez JS, Lieberman MD et al..  2025.  Whole genome and transcriptome analysis of pancreatic acinar cell carcinoma elucidates mechanisms of homologous recombination deficiency and unravels novel relevant fusion events.. Pathol Res Pract. 266:155798.

Kalomeris T, Assaad MAl, de la Mora JDelgado-, Gundem G, Levine MF, Boyraz B, Manohar J, Sigouros M, Medina-Martínez JS, Sboner A et al..  2025.  Whole genome profiling of primary and metastatic adrenocortical carcinoma unravels significant molecular events.. Pathol Res Pract. 266:155725.

Ohara K, Rendeiro AFigueiredo, Bhinder B, Eng KWha, Ravichandran H, Nguyen D, Pisapia D, Vosoughi A, Fernandez E, Shohdy KS et al..  2024.  The evolution of metastatic upper tract urothelial carcinoma through genomic-transcriptomic and single-cell protein markers analysis.. Nat Commun. 15(1):2009.

Chatterjee SS, Linares JF, Cid-Diaz T, Duran A, Khan MImran K, Osrodek M, Brady NJ, Reina-Campos M, Marzio A, Venkadakrishnan VBalaji et al..  2024.  Increased translation driven by non-canonical EZH2 creates a synthetic vulnerability in enzalutamide-resistant prostate cancer.. Nat Commun. 15(1):9755.

Hissong E, Bhinder B, Kim J, Ohara K, Ravichandran H, Assaad MAl, Elsoukkary S, Shusterman M, Khan U, Eng KWha et al..  2024.  Integrative Transcriptomic and Single-Cell Protein Characterization of Colorectal Carcinoma Delineates Distinct Tumor Immune Microenvironments Associated with Overall Survival.. Res Sq.

Nguyen DD, Hooper WF, Liu W, Chu TR, Geiger H, Shelton JM, Shah M, Goldstein ZR, Winterkorn L, Helland A et al..  2024.  The interplay of mutagenesis and ecDNA shapes urothelial cancer evolution.. Nature. 635(8037):219-228.

Hissong E, Assaad MAl, Bal M, Reed KA, Fornelli A, Levine MF, Gundem G, Semaan A, Orr CE, Sakhadeo U et al..  2024.  NIPBL::NACC1 Fusion Hepatic Carcinoma.. Am J Surg Pathol. 48(2):183-193.