Publications

Galletti G, Halima A, Gjyrezi A, Zhang J, Zimmerman B, Worroll D, Kallergi G, Barreja R, Ocean A, Saxena A et al..  2024.  Transferrin receptor-based circulating tumor cell enrichment provides a snapshot of the molecular landscape of solid tumors and correlates with clinical outcomes.. medRxiv.

Han X, Sui J, Nie K, Zhao Y, Lv X, Xie J, Tan L, Au-Yeung RKH, Ma J, Inghirami G et al..  2024.  Tumor evolution analysis uncovered immune-escape related mutations in relapse of diffuse large B-cell lymphoma.. Leukemia. 38(10):2276-2280.

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.

Pine AR, Cirigliano SM, Nicholson JG, Hu Y, Linkous A, Miyaguchi K, Edwards L, Singhania R, Schwartz TH, Ramakrishna R et al..  2020.  Tumor Microenvironment Is Critical for the Maintenance of Cellular States Found in Primary Glioblastomas.. Cancer Discov. 10(7):964-979.

Newman LA, Chen Y, Martini R, Demaria S, Formenti S, Elemento O, Davis MB.  2024.  Tumor-Associated Lymphocytes and Breast Cancer Survival in Black and White Women.. JAMA Surg. 159(6):712-714.

Alnajar H, Ravichandran H, Rendeiro AFigueiredo, Ohara K, Zoughbi WAl, Manohar J, Greco N, Sigouros M, Fox J, Muth E et al..  2022.  Tumor-immune microenvironment revealed by Imaging Mass Cytometry in a metastatic sarcomatoid urothelial carcinoma with a prolonged response to pembrolizumab.. Cold Spring Harb Mol Case Stud. 8(3)

Schad SE, Chow A, Mangarin L, Pan H, Zhang J, Ceglia N, Caushi JX, Malandro N, Zappasodi R, Gigoux M et al..  2022.  Tumor-induced double positive T cells display distinct lineage commitment mechanisms and functions.. J Exp Med. 219(6)

Yu H, Sfakianos JP, Wang L, Hu Y, Daza J, Galsky MD, Sandhu HS, Elemento O, Faltas BM, Farkas AM et al..  2022.  Tumor-Infiltrating Myeloid Cells Confer De Novo Resistance to PD-L1 Blockade through EMT-Stromal and Tgfβ-Dependent Mechanisms.. Mol Cancer Ther. 21(11):1729-1741.

Crowley MJP, Bhinder B, Markowitz GJ, Martin M, Verma A, Sandoval TA, Chae C-S, Yomtoubian S, Hu Y, Chopra S et al..  2023.  Tumor-intrinsic IRE1α signaling controls protective immunity in lung cancer.. Nat Commun. 14(1):120.

Honigsberg R, Cruz T, Yoffe L, Tang MStephanie, Dicle O, Markowitz G, Michael M, Singh A, Altorki NK, Elemento O et al..  2025.  Tumor-specific draining lymph node CD8 T cells orchestrate an anti-tumor response to neoadjuvant PD-1 immune checkpoint blockade.. bioRxiv.

Finnerty BM, Moore MD, Verma A, Aronova A, Huang S, Edwards DP, Chen Z, Seandel M, Scognamiglio T, Du Y-CNancy et al..  2019.  UCHL1 loss alters the cell-cycle in metastatic pancreatic neuroendocrine tumors.. Endocr Relat Cancer. 26(4):411-423.

Rustam S, Hu Y, Mahjour SBabak, Rendeiro AF, Ravichandran H, Urso A, D'Ovidio F, Martinez FJ, Altorki NK, Richmond B et al..  2023.  A Unique Cellular Organization of Human Distal Airways and Its Disarray in Chronic Obstructive Pulmonary Disease.. Am J Respir Crit Care Med. 207(9):1171-1182.

Chu C-S, Hellmuth JC, Singh R, Ying H-Y, Skrabanek L, Teater MR, Doane AS, Elemento O, Melnick AM, Roeder RG.  2020.  Unique Immune Cell Coactivators Specify Locus Control Region Function and Cell Stage.. Mol Cell. 80(5):845-861.e10.

Elemento O, Slonim N, Tavazoie S.  2007.  A universal framework for regulatory element discovery across all genomes and data types.. Mol Cell. 28(2):337-50.

Nath S, Claridge S, Granados GLara, Assaad MAl, Park E, Cavallo J-A, Nuwere U, Ackon MEsi, De Boni L, Baker S et al..  2025.  Unlocking the therapeutic potential of rigosertib as a selective therapy for ovarian cancer.. Cell Rep Med. 6(7):102218.

De Renzis S, Elemento O, Tavazoie S, Wieschaus EF.  2007.  Unmasking activation of the zygotic genome using chromosomal deletions in the Drosophila embryo.. PLoS Biol. 5(5):e117.

Kim J, Rustam S, Mosquera JMiguel, Randell SH, Shaykhiev R, Rendeiro AF, Elemento O.  2022.  Unsupervised discovery of tissue architecture in multiplexed imaging.. Nat Methods. 19(12):1653-1661.

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.

Robinson BD, Vlachostergios PJ, Bhinder B, Liu W, Li K, Moss TJ, Bareja R, Park K, Tavassoli P, Cyrta J et al..  2019.  Upper tract urothelial carcinoma has a luminal-papillary T-cell depleted contexture and activated FGFR3 signaling.. Nat Commun. 10(1):2977.

Dooley BJ, Verma A, Ding R, Yang H, Muthukumar T, Lubetzky M, Shankaranarayanan D, Elemento O, Suthanthiran M.  2020.  Urinary Cell Transcriptome Profiling and Identification of ITM2A, SLAMF6, and IKZF3 as Biomarkers of Acute Rejection in Human Kidney Allografts.. Transplant Direct. 6(8):e588.

Verma A, Muthukumar T, Yang H, Lubetzky M, Cassidy MF, Lee JR, Dadhania DM, Snopkowski C, Shankaranarayanan D, Salvatore SP et al..  2020.  Urinary cell transcriptomics and acute rejection in human kidney allografts.. JCI Insight. 5(4)

Elemento O, Khozin S, Sternberg CN.  2025.  The use of artificial intelligence for cancer therapeutic decision-making.. NEJM AI. 2(5)

Giannopoulou EG, Elemento O, Ivashkiv LB.  2015.  Use of RNA sequencing to evaluate rheumatic disease patients.. Arthritis Res Ther. 17:167.

Wickersham M, Bartelo N, Kulm S, Liu Y, Zhang Y, Elemento O.  2023.  USING MACHINE LEARNING METHODS TO ASSESS THE RISK OF ALCOHOL MISUSE IN OLDER ADULTS.. Res Sq.

Wacker SA, Houghtaling BR, Elemento O, Kapoor TM.  2012.  Using transcriptome sequencing to identify mechanisms of drug action and resistance.. Nat Chem Biol. 8(3):235-7.