Publications

Reichel JB, McCormick J, Fromm JR, Elemento O, Cesarman E, Roshal M.  2017.  Flow-sorting and Exome Sequencing of the Reed-Sternberg Cells of Classical Hodgkin Lymphoma.. J Vis Exp. (124)

Reichel J, Chadburn A, Rubinstein PG, Giulino-Roth L, Tam W, Liu Y, Gaiolla R, Eng K, Brody J, Inghirami G et al..  2015.  Flow sorting and exome sequencing reveal the oncogenome of primary Hodgkin and Reed-Sternberg cells.. Blood. 125(7):1061-72.

Hess ME, Hess S, Meyer KD, Verhagen LAW, Koch L, Brönneke HS, Dietrich MO, Jordan SD, Saletore Y, Elemento O et al..  2013.  The fat mass and obesity associated gene (Fto) regulates activity of the dopaminergic midbrain circuitry.. Nat Neurosci. 16(8):1042-8.

Mason CE, Elemento O.  2012.  Faster sequencers, larger datasets, new challenges.. Genome Biol. 13(3):314.

Elemento O, Tavazoie S.  2007.  Fastcompare: a nonalignment approach for genome-scale discovery of DNA and mRNA regulatory elements using network-level conservation.. Methods Mol Biol. 395:349-66.

Elemento O, Tavazoie S.  2005.  Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach.. Genome Biol. 6(2):R18.

Velichutina I, Shaknovich R, Geng H, Johnson NA, Gascoyne RD, Melnick AM, Elemento O.  2010.  EZH2-mediated epigenetic silencing in germinal center B cells contributes to proliferation and lymphomagenesis.. Blood. 116(24):5247-55.

Bödör C, Grossmann V, Popov N, Okosun J, O'Riain C, Tan K, Marzec J, Araf S, Wang J, Lee AM et al..  2013.  EZH2 mutations are frequent and represent an early event in follicular lymphoma.. Blood. 122(18):3165-8.

Béguelin W, Popovic R, Teater M, Jiang Y, Bunting KL, Rosen M, Shen H, Yang SNing, Wang L, Ezponda T et al..  2013.  EZH2 is required for germinal center formation and somatic EZH2 mutations promote lymphoid transformation.. Cancer Cell. 23(5):677-92.

Béguelin W, Rivas MA, Fernandez MTCalvo, Teater M, Purwada A, Redmond D, Shen H, Challman MF, Elemento O, Singh A et al..  2017.  EZH2 enables germinal centre formation through epigenetic silencing of CDKN1A and an Rb-E2F1 feedback loop.. Nat Commun. 8(1):877.

Béguelin W, Teater M, Gearhart MD, Fernández MTeresa Cal, Goldstein RL, Cárdenas MG, Hatzi K, Rosen M, Shen H, Corcoran CM et al..  2016.  EZH2 and BCL6 Cooperate to Assemble CBX8-BCOR Complex to Repress Bivalent Promoters, Mediate Germinal Center Formation and Lymphomagenesis.. Cancer Cell. 30(2):197-213.

Mosquera MJ, Kim S, Bareja R, Fang Z, Cai S, Pan H, Asad M, Martin MLaura, Sigouros M, Rowdo FM et al..  2022.  Extracellular Matrix in Synthetic Hydrogel-Based Prostate Cancer Organoids Regulate Therapeutic Response to EZH2 and DRD2 Inhibitors.. Adv Mater. 34(2):e2100096.

Ma J, Redmond D, Miyaguchi A, Nam AS, Nie K, Mathew S, Elemento O, Tam W.  2019.  Exploring tumor clonal evolution in bone marrow of patients with diffuse large B-cell lymphoma by deep IGH sequencing and its potential relevance in relapse.. Blood Cancer J. 9(9):69.

Kaza S, Mohanty AS, Serpedin A, Yau J, Kim YEun, Kutler RB, Elemento O, Sulica L, Khosravi P, Rameau A.  2026.  Exploring Real-Time Tracking of Vocal Fold Polyps in Video-Stroboscopy Using Deep Learning.. Laryngoscope.

Phipps W, Bhinder B, Towlerton A, Mooka P, Kafeero J, Fitzgibbon M, Elemento O, Cesarman E.  2025.  Exome Sequencing Reveals a Sparse Genomic Landscape in Kaposi Sarcoma.. Mol Cancer Res. 23(5):438-449.

Montrose DC, Saha S, Foronda M, McNally EM, Chen J, Zhou XKathy, Ha T, Krumsiek J, Buyukozkan M, Verma A et al..  2021.  Exogenous and Endogenous Sources of Serine Contribute to Colon Cancer Metabolism, Growth, and Resistance to 5-Fluorouracil.. Cancer Res. 81(9):2275-2288.

Khani F, Hooper WF, Wang X, Chu TR, Shah M, Winterkorn L, Sigouros M, Conteduca V, Pisapia D, Wobker S et al..  2023.  Evolution of structural rearrangements in prostate cancer intracranial metastases.. NPJ Precis Oncol. 7(1):91.

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.

Romanel A, Zhang T, Elemento O, Demichelis F.  2017.  EthSEQ: ethnicity annotation from whole exome sequencing data.. Bioinformatics. 33(15):2402-2404.

Faria M, Karami S, Granados-Principal S, Dey P, Verma A, Choi DS, Elemento O, Bawa-Khalfe T, Chang JC, Strom AM et al..  2018.  The ERβ4 variant induces transformation of the normal breast mammary epithelial cell line MCF-10A; the ERβ variants ERβ2 and ERβ5 increase aggressiveness of TNBC by regulation of hypoxic signaling.. Oncotarget. 9(15):12201-12211.

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.

Sfakianos JP, Daza J, Hu Y, Anastos H, Bryant G, Bareja R, Badani KK, Galsky MD, Elemento O, Faltas BM et al..  2020.  Epithelial plasticity can generate multi-lineage phenotypes in human and murine bladder cancers.. Nat Commun. 11(1):2540.

Pan H, Jiang Y, Boi M, Tabbò F, Redmond D, Nie K, Ladetto M, Chiappella A, Cerchietti L, Shaknovich R et al..  2015.  Epigenomic evolution in diffuse large B-cell lymphomas.. Nat Commun. 6:6921.

Xylinas E, Hassler MR, Zhuang D, Krzywinski M, Erdem Z, Robinson BD, Elemento O, Clozel T, Shariat SF.  2016.  An Epigenomic Approach to Improving Response to Neoadjuvant Cisplatin Chemotherapy in Bladder Cancer.. Biomolecules. 6(3)

Lin P-C, Giannopoulou EG, Park K, Mosquera JMiguel, Sboner A, Tewari AK, Garraway LA, Beltran H, Rubin MA, Elemento O.  2013.  Epigenomic alterations in localized and advanced prostate cancer.. Neoplasia. 15(4):373-83.