Publications

Beltran H, Prandi D, Mosquera JMiguel, Benelli M, Puca L, Cyrta J, Marotz C, Giannopoulou E, Chakravarthi BVSK, Varambally S et al..  2016.  Divergent clonal evolution of castration-resistant neuroendocrine prostate cancer.. Nat Med. 22(3):298-305.

Vazirani RP, Verma A, L Sadacca A, Buckman MS, Picatoste B, Beg M, Torsitano C, Bruno JH, Patel RT, Simonyte K et al..  2016.  Disruption of Adipose Rab10-Dependent Insulin Signaling Causes Hepatic Insulin Resistance.. Diabetes. 65(6):1577-89.

da Piedade I, Tang M-HEric, Elemento O.  2009.  DISPARE: DIScriminative PAttern REfinement for Position Weight Matrices.. BMC Bioinformatics. 10:388.

Pan H, Renaud L, Chaligne R, Bloehdorn J, Tausch E, Mertens D, Fink AMaria, Fischer K, Zhang C, Betel D et al..  2021.  Discovery of candidate DNA methylation cancer driver genes.. Cancer Discov.

Allen JE, C Kline LB, Prabhu VV, Wagner J, Ishizawa J, Madhukar N, Lev A, Baumeister M, Zhou L, Lulla A et al..  2016.  Discovery and clinical introduction of first-in-class imipridone ONC201.. Oncotarget. 7(45):74380-74392.

Prasain N, Lee MRyul, Vemula S, Meador JLuke, Yoshimoto M, Ferkowicz MJ, Fett A, Gupta M, Rapp BM, Saadatzadeh MReza et al..  2014.  Differentiation of human pluripotent stem cells to cells similar to cord-blood endothelial colony-forming cells.. Nat Biotechnol. 32(11):1151-1157.

Lourenco ARita, Ban Y, Crowley MJ, Lee SB, Ramchandani D, Du W, Elemento O, George JT, Jolly MKumar, Levine H et al..  2020.  Differential Contributions of Pre- and Post-EMT Tumor Cells in Breast Cancer Metastasis.. Cancer Res. 80(2):163-169.

Cox N, Crozet L, Holtman IR, Loyher P-L, Lazarov T, White JB, Mass E, E Stanley R, Elemento O, Glass CK et al..  2021.  Diet-regulated production of PDGFcc by macrophages controls energy storage.. Science. 373(6550)

Erler P, Keutgen XM, Crowley MJ, Zetoune T, Kundel A, Kleiman D, Beninato T, Scognamiglio T, Elemento O, Zarnegar R et al..  2014.  Dicer expression and microRNA dysregulation associate with aggressive features in thyroid cancer.. Surgery. 156(6):1342-50;discussion1350.

Rennert H, Eng K, Zhang T, Tan A, Xiang J, Romanel A, Kim R, Tam W, Liu Y-C, Bhinder B et al..  2016.  Development and validation of a whole-exome sequencing test for simultaneous detection of point mutations, indels and copy-number alterations for precision cancer care.. NPJ Genom Med. 1

Elemento O.  2007.  Developing a systems-level understanding of gene expression.. Genome Biol. 8(4):304.

Greenberg JA, Shah Y, Ivanov NA, Marshall T, Kulm S, Williams J, Tran C, Scognamiglio T, Heymann JJ, Lee-Saxton YJ et al..  2024.  Developing a Predictive Model for Metastatic Potential in Pancreatic Neuroendocrine Tumor.. J Clin Endocrinol Metab. 110(1):263-274.

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.

Berchuck JE, Baca SC, McClure HM, Korthauer K, Tsai HK, Nuzzo PVitale, Kelleher KM, He M, Steinharter JA, Zacharia S et al..  2022.  Detecting Neuroendocrine Prostate Cancer Through Tissue-Informed Cell-Free DNA Methylation Analysis.. Clin Cancer Res. 28(5):928-938.

Marderstein AR, Uppal M, Verma A, Bhinder B, Tayyebi Z, Mezey J, Clark AG, Elemento O.  2020.  Demographic and genetic factors influence the abundance of infiltrating immune cells in human tissues.. Nat Commun. 11(1):2213.

Puca L, Gavyert K, Sailer V, Conteduca V, Dardenne E, Sigouros M, Isse K, Kearney M, Vosoughi A, Fernandez L et al..  2019.  Delta-like protein 3 expression and therapeutic targeting in neuroendocrine prostate cancer.. Sci Transl Med. 11(484)

Rickman KA, Lach FP, Abhyankar A, Donovan FX, Sanborn EM, Kennedy JA, Sougnez C, Gabriel SB, Elemento O, Chandrasekharappa SC et al..  2015.  Deficiency of UBE2T, the E2 Ubiquitin Ligase Necessary for FANCD2 and FANCI Ubiquitination, Causes FA-T Subtype of Fanconi Anemia.. Cell Rep. 12(1):35-41.

Markowitz GJ, Ban Y, Tavarez DA, Yoffe L, Podaza E, He Y, Martin MT, Crowley MJP, Sandoval TA, Gao D et al..  2024.  Deficiency of metabolic regulator PKM2 activates the pentose phosphate pathway and generates TCF1 progenitor CD8 T cells to improve immunotherapy.. Nat Immunol. 25(10):1884-1899.

Markowitz GJ, Ban Y, Tavarez DA, Yoffe L, Podaza E, He Y, Martin MT, Crowley MJP, Sandoval TA, Gao D et al..  2023.  Deficiency of metabolic regulator PKM2 activates the pentose phosphate pathway and generates TCF1+ progenitor CD8+ T cells to improve checkpoint blockade.. Res Sq.

Kim YE, Dobko M, Li H, Shao T, Periyakoil P, Tipton C, Colasacco C, Serpedin A, Elemento O, Sabuncu M et al..  2025.  A Deep-Learning Model for Multi-class Audio Classification of Vocal Fold Pathologies in Office Stroboscopy.. Laryngoscope. 135(7):2428-2436.

Jiang Y, Redmond D, Nie K, Eng KW, Clozel T, Martin P, Tan LHc, Melnick AM, Tam W, Elemento O.  2014.  Deep sequencing reveals clonal evolution patterns and mutation events associated with relapse in B-cell lymphomas.. Genome Biol. 15(8):432.

Page DB, Yuan J, Redmond D, Y Wen H, Durack JC, Emerson R, Solomon S, Dong Z, Wong P, Comstock C et al..  2016.  Deep Sequencing of T-cell Receptor DNA as a Biomarker of Clonally Expanded TILs in Breast Cancer after Immunotherapy.. Cancer Immunol Res. 4(10):835-844.

Courtiol P, Maussion C, Moarii M, Pronier E, Pilcer S, Sefta M, Manceron P, Toldo S, Zaslavskiy M, Le Stang N et al..  2019.  Deep learning-based classification of mesothelioma improves prediction of patient outcome.. Nat Med. 25(10):1519-1525.

Xu Z, Verma A, Naveed U, Bakhoum SF, Khosravi P, Elemento O.  2021.  Deep learning predicts chromosomal instability from histopathology images.. iScience. 24(5):102394.

Yao P, Witte D, German A, Periyakoil P, Kim YEun, Gimonet H, Sulica L, Born H, Elemento O, Barnes J et al..  2024.  A deep learning pipeline for automated classification of vocal fold polyps in flexible laryngoscopy.. Eur Arch Otorhinolaryngol. 281(4):2055-2062.