Publications

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.

Khosravi P, Kazemi E, Zhan Q, Malmsten JE, Toschi M, Zisimopoulos P, Sigaras A, Lavery S, Cooper LAD, Hickman C et al..  2019.  Deep learning enables robust assessment and selection of human blastocysts after in vitro fertilization.. NPJ Digit Med. 2:21.

Khosravi P, Lysandrou M, Eljalby M, Li Q, Kazemi E, Zisimopoulos P, Sigaras A, Brendel M, Barnes J, Ricketts C et al..  2021.  A Deep Learning Approach to Diagnostic Classification of Prostate Cancer Using Pathology-Radiology Fusion.. J Magn Reson Imaging. 54(2):462-471.

Karimzadeh M, Momen-Roknabadi A, Cavazos TB, Fang Y, Chen N-C, Multhaup M, Yen J, Ku J, Wang J, Zhao X et al..  2024.  Deep generative AI models analyzing circulating orphan non-coding RNAs enable detection of early-stage lung cancer.. Nat Commun. 15(1):10090.

Khosravi P, Kazemi E, Imielinski M, Elemento O, Hajirasouliha I.  2018.  Deep Convolutional Neural Networks Enable Discrimination of Heterogeneous Digital Pathology Images.. EBioMedicine. 27:317-328.

Assaad MAl, Shin N, Sigouros M, Manohar J, Antysheva Z, Kotlov N, Kiriy D, Nikitina A, Kleimenov M, Tsareva A et al..  2023.  Deciphering the origin and therapeutic targets of cancer of unknown primary: a case report that illustrates the power of integrative whole-exome and transcriptome sequencing analysis.. Front Oncol. 13:1274163.

Xu C, Bulusu KC, Pan H, Elemento O.  2024.  DDI-GPT: Explainable Prediction of Drug-Drug Interactions using Large Language Models enhanced with Knowledge Graphs.. bioRxiv.

Gayvert KM, Madhukar NS, Elemento O.  2016.  A Data-Driven Approach to Predicting Successes and Failures of Clinical Trials.. Cell Chem Biol. 23(10):1294-1301.

Liu W, Newhall KP, Khani F, Barlow LM, Nguyen D, Gu L, Eng K, Bhinder B, Uppal M, Récapet C et al..  2023.  The Cytidine Deaminase APOBEC3G Contributes to Cancer Mutagenesis and Clonal Evolution in Bladder Cancer.. Cancer Res. 83(4):506-520.

Noch EK, Palma L, Yim I, Bullen N, Barnett D, Walsh A, Bhinder B, Benedetti E, Krumsiek J, Gurvitch J et al..  2024.  Cysteine induces mitochondrial reductive stress in glioblastoma through hydrogen peroxide production.. Proc Natl Acad Sci U S A. 121(8):e2317343121.

Jiang Y, Ortega-Molina A, Geng H, Ying H-Y, Hatzi K, Parsa S, McNally D, Wang L, Doane AS, Agirre X et al..  2017.  CREBBP Inactivation Promotes the Development of HDAC3-Dependent Lymphomas.. Cancer Discov. 7(1):38-53.