Publications

Vicario R, Fragkogianni S, Pokrovskii M, Mayer C, Lopez-Rodrigo E, Hu Y, Ogishi M, Alberdi A, Baako A, Ay O et al..  2024.  Mechanism of neurodegeneration mediated by clonal inflammatory microglia.. bioRxiv.

Hegewisch-Solloa E, Melsen JE, Ravichandran H, Rendeiro AF, Freud AG, Mundy-Bosse B, Melms JC, Eisman SE, Izar B, Grunstein E et al..  2023.  Mapping human natural killer cell development in pediatric tonsil by imaging mass cytometry and high-resolution microscopy.. bioRxiv.

Gilvary C, Elkhader J, Madhukar N, Henchcliffe C, Goncalves MD, Elemento O.  2020.  A machine learning and network framework to discover new indications for small molecules.. PLoS Comput Biol. 16(8):e1008098.

Chaudhry F, Kim TWan, Elemento O, Betel D.  2024.  Machine learning analysis of population-wide plasma proteins identifies hormonal biomarkers of Parkinson's Disease.. medRxiv.

Geyer JTurbiner, Subramaniyam S, Jiang Y, Elemento O, Ferry JA, de Leval L, Nakashima MO, Liu Y-C, Martin P, Mathew S et al..  2015.  Lymphoblastic transformation of follicular lymphoma: a clinicopathologic and molecular analysis of 7 patients.. Hum Pathol. 46(2):260-71.

Mendoza A, Fang V, Chen C, Serasinghe M, Verma A, Muller J, V Chaluvadi S, Dustin ML, Hla T, Elemento O et al..  2017.  Lymphatic endothelial S1P promotes mitochondrial function and survival in naive T cells.. Nature. 546(7656):158-161.

Setton J, Hadi K, Choo Z-N, Kuchin KS, Tian H, Paula ADa Cruz, Rosiene J, Selenica P, Behr J, Yao X et al..  2023.  Long-molecule scars of backup DNA repair in BRCA1- and BRCA2-deficient cancers.. Nature. 621(7977):129-137.

Rendeiro AF, Casano J, Vorkas CKyriakos, Singh H, Morales A, DeSimone RA, Ellsworth GB, Soave R, Kapadia SN, Saito K et al..  2020.  Longitudinal immune profiling of mild and severe COVID-19 reveals innate and adaptive immune dysfunction and provides an early prediction tool for clinical progression.. medRxiv.

He Y, Waltman P, Kane T, Sigouros M, Chandra P, Gorski K, Zhang C, Proietti A, Singh A, Mittal V et al..  2025.  Longitudinal Genomic Analysis of Five Cases of Recurrent Thymomas.. J Thorac Oncol.

Agirre X, Meydan C, Jiang Y, Garate L, Doane AS, Li Z, Verma A, Paiva B, Martín-Subero JI, Elemento O et al..  2019.  Long non-coding RNAs discriminate the stages and gene regulatory states of human humoral immune response.. Nat Commun. 10(1):821.

Han T, Goswami S, Hu Y, Tang F, Zafra MPaz, Murphy C, Cao Z, Poirier JT, Khurana E, Elemento O et al..  2020.  Lineage reversion drives WNT independence in intestinal cancer.. Cancer Discov.

Kaya C, Dorsaint P, Mercurio S, Campbell AM, Eng KWha, Nikiforova MN, Elemento O, Nikiforov YE, Sboner A.  2021.  Limitations of Detecting Genetic Variants from the RNA Sequencing Data in Tissue and Fine-Needle Aspiration Samples.. Thyroid. 31(4):589-595.

Marderstein AR, Davenport ER, Kulm S, Van Hout CV, Elemento O, Clark AG.  2021.  Leveraging phenotypic variability to identify genetic interactions in human phenotypes.. Am J Hum Genet. 108(1):49-67.

Legesse-Miller A, Elemento O, Pfau SJ, Forman JJ, Tavazoie S, Coller HA.  2009.  let-7 Overexpression leads to an increased fraction of cells in G2/M, direct down-regulation of Cdc34, and stabilization of Wee1 kinase in primary fibroblasts.. J Biol Chem. 284(11):6605-9.

Lieber DS, Elemento O, Tavazoie S.  2010.  Large-scale discovery and characterization of protein regulatory motifs in eukaryotes.. PLoS One. 5(12):e14444.

Vivelo C, Reilly KM, Widemann BC, Wedekind MFrances, Painter C, O'Neill AF, Mueller S, Elemento O, Gross AM, Sandler AB.  2024.  The Landscape of US and Global Rare Tumor Research Programs: A Systematic Review.. Oncologist. 29(2):106-116.

Bakht MK, Yamada Y, Ku S-Y, Venkadakrishnan VBalaji, Korsen JA, Kalidindi TM, Mizuno K, Ahn SHye, Seo J-H, Garcia MMica et al..  2023.  Landscape of prostate-specific membrane antigen heterogeneity and regulation in AR-positive and AR-negative metastatic prostate cancer.. Nat Cancer. 4(5):699-715.

Mueller FB, Yang H, Lubetzky M, Verma A, Lee JR, Dadhania DM, Xiang JZ, Salvatore SP, Seshan SV, Sharma VK et al..  2019.  Landscape of innate immune system transcriptome and acute T cell-mediated rejection of human kidney allografts.. JCI Insight. 4(13)

Linares JF, Cid-Diaz T, Duran A, Osrodek M, Martinez-Ordoñez A, Reina-Campos M, Kuo H-H, Elemento O, M Martin L, Cordes T et al..  2022.  The lactate-NAD axis activates cancer-associated fibroblasts by downregulating p62.. Cell Rep. 39(6):110792.

He Y, Kim I-K, Bian J, Polyzos A, Di Giammartino DCampigli, Zhang Y-W, Luo J, Hernandez MO, Kedei N, Cam M et al..  2022.  A Knock-In Mouse Model of Thymoma With the GTF2I L424H Mutation.. J Thorac Oncol. 17(12):1375-1386.

Elemento O.  2016.  KLF4: A new player in plasma cell development.. Cell Cycle. 15(20):2691-2.

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.

Barton BM, Son F, Verma A, Bal SKumar, Tang Q, Wang R, Umphred-Wilson K, Khan R, Trichka J, Dong H et al..  2025.  IRE1α-XBP1 safeguards hematopoietic stem and progenitor cells by restricting pro-leukemogenic gene programs.. Nat Immunol. 26(2):200-214.

Yaron-Barir TM, Joughin BA, Huntsman EM, Kerelsky A, Cizin DM, Cohen BM, Regev A, Song J, Vasan N, Lin T-Y et al..  2024.  The intrinsic substrate specificity of the human tyrosine kinome.. Nature. 629(8014):1174-1181.

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.