Publications

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

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)

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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)

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)

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.

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.

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.

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.

Shah Y, Yang H, Mueller FB, Li C, Rahim SEGul, Varma E, Salinas T, Dadhania DM, Salvatore SP, Seshan SV et al..  2024.  Transcriptomic signatures of chronic active antibody-mediated rejection deciphered by RNA sequencing of human kidney allografts.. Kidney Int. 105(2):347-363.

Verma A, Jiang Y, Du W, Fairchild L, Melnick A, Elemento O.  2015.  Transcriptome sequencing reveals thousands of novel long non-coding RNAs in B cell lymphoma.. Genome Med. 7:110.

Roshal M, Kong IY, Dinalankara W, Reichel JB, Teater M, Binder B, Zairis S, Brody JD, Park SI, Kovach AE et al..  2025.  Transcriptome sequencing of Hodgkin lymphoma Hodgkin and Reed-Sternberg cells reveals escape from NK cell recognition and an unfolded protein response.. bioRxiv.

Choi H, Sheng J, Gao D, Li F, Durrans A, Ryu S, Lee SB, Narula N, Rafii S, Elemento O et al..  2015.  Transcriptome analysis of individual stromal cell populations identifies stroma-tumor crosstalk in mouse lung cancer model.. Cell Rep. 10(7):1187-201.