Olivier Elemento, Ph.D.

Professor of Physiology and Biophysics

  • Walter B. Wriston Research Scholar
  • Professor of Computational Genomics in Computational Biomedicine and Associate Director of the Institute for Computational Biomedicine
  • Director of the Englander Institute for Precision Medicine
  • Associate Director of the Institute for Computational Biomedicine

646-962-5726

1305 York Avenue, Room Y-13.13
New York, NY 10021


Techniques

Research Areas


Research Summary:

The Elemento lab combines Big Data analytics with experimentation to develop entirely new ways to help prevent, diagnose, understand, treat and ultimately cure cancer. Our research involves routine use of ultrafast DNA sequencing, proteomics, high-performance computing, mathematical modeling, and artificial intelligence/machine learning.

More specifically, we are working on :

  • Systems biology of regulatory networks in normal and malignant cells, with a strong focus on blood cancers (lymphomas and leukemias). We use ChIP-seq, RNA-seq, computational modeling to investigate how genes are regulated in cancer cells and how gene regulation in cancer cells differs from normal cells.
  • Cancer genomics and precision medicine. Using novel computational algorithms, we seek to identify new cancer mutations and understand why and where cancer mutations occur. We work on determining whether 3D chromatin architecture predicts where mutations are most likely to occur.
  • Epigenomics of cancer. Genes coding for proteins that modify, maintain or read the epigenome (DNA methylation and histone modifications) and are among the most frequently mutated genes in cancer. We use high-throughput experimental approaches and pattern detection techniques to investigate what these genes do and the genomewide epigenomic patterns they mediate.
  • Tumor genome evolution, anticancer drug resistance. Cancer is a fundamentally evolutionary disease. Using high-throughput sequencing, we are investigating how the tumor genome (and epigenome) evolves in time and particularly upon drug treatment.
  • Early cancer detection using machine learning. We use advanced machine learning approaches (artificial intelligence techniques) to detect cancer as early as possible and help guide treatment accordingly. One of our algorithms for thyroid cancer detection, based on Support Vector Machines, was recently licensed by Prolias Technologies.
  • Development of innovative computational approaches for analysis of high-throughput experiments (metabolomics, proteomics, high-throughout sequencing, etc) performed on cancer cells. For example we have developed ChIPseeqer, a broadly used ChIPseq data analysis framework.

 

Recent Publications:

  1. Augello, MA, Liu, D, Deonarine, LD, Robinson, BD, Huang, D, Stelloo, S et al.. CHD1 Loss Alters AR Binding at Lineage-Specific Enhancers and Modulates Distinct Transcriptional Programs to Drive Prostate Tumorigenesis. Cancer Cell. 2019;35 (5):817-819. doi: 10.1016/j.ccell.2019.04.012. PubMed PMID:31085180 .
  2. Choi, S, Wang, D, Chen, X, Tang, LH, Verma, A, Chen, Z et al.. Function and clinical relevance of RHAMM isoforms in pancreatic tumor progression. Mol. Cancer. 2019;18 (1):92. doi: 10.1186/s12943-019-1018-y. PubMed PMID:31072393 PubMed Central PMC6506944.
  3. Bhardwaj, P, Ikeda, T, Zhou, XK, Wang, H, Zheng, XE, Giri, DD et al.. Supplemental estrogen and caloric restriction reduce obesity-induced periprostatic white adipose inflammation in mice. Carcinogenesis. 2019; :. doi: 10.1093/carcin/bgz088. PubMed PMID:31067318 .
  4. Roos-Weil, D, Decaudin, C, Armand, M, Della-Valle, V, Diop, MK, Ghamlouch, H et al.. A Recurrent Activating Missense Mutation in Waldenström Macroglobulinemia Affects the DNA Binding of the ETS Transcription Factor SPI1 and Enhances Proliferation. Cancer Discov. 2019; :. doi: 10.1158/2159-8290.CD-18-0873. PubMed PMID:31018969 .
  5. Lue, JK, Prabhu, SA, Liu, Y, Gonzalez, Y, Verma, A, Mundi, PS et al.. Precision Targeting with EZH2 and HDAC Inhibitors in Epigenetically Dysregulated Lymphomas. Clin. Cancer Res. 2019; :. doi: 10.1158/1078-0432.CCR-18-3989. PubMed PMID:30979734 .
  6. Augello, MA, Liu, D, Deonarine, LD, Robinson, BD, Huang, D, Stelloo, S et al.. CHD1 Loss Alters AR Binding at Lineage-Specific Enhancers and Modulates Distinct Transcriptional Programs to Drive Prostate Tumorigenesis. Cancer Cell. 2019;35 (4):603-617.e8. doi: 10.1016/j.ccell.2019.03.001. PubMed PMID:30930119 PubMed Central PMC6467783.
  7. Musselman, K, Glynn, S, Mosquera, JM, Elemento, O, Sboner, A, Beltran, H et al.. Identification of a therapeutic target using molecular sequencing for treatment of recurrent uterine serous adenocarcinoma. Gynecol Oncol Rep. 2019;28 :54-57. doi: 10.1016/j.gore.2019.01.013. PubMed PMID:30906838 PubMed Central PMC6411491.
  8. Puca, L, Gavyert, K, Sailer, V, Conteduca, V, Dardenne, E, Sigouros, M et al.. Delta-like protein 3 expression and therapeutic targeting in neuroendocrine prostate cancer. Sci Transl Med. 2019;11 (484):. doi: 10.1126/scitranslmed.aav0891. PubMed PMID:30894499 PubMed Central PMC6525633.
  9. Grive, KJ, Hu, Y, Shu, E, Grimson, A, Elemento, O, Grenier, JK et al.. Dynamic transcriptome profiles within spermatogonial and spermatocyte populations during postnatal testis maturation revealed by single-cell sequencing. PLoS Genet. 2019;15 (3):e1007810. doi: 10.1371/journal.pgen.1007810. PubMed PMID:30893341 PubMed Central PMC6443194.
  10. Karass, M, Bareja, R, Shelkey, E, Vlachostergios, PJ, Robinson, BD, Khani, F et al.. Oncogenic Addiction to ERBB2 Signaling Predicts Response to Trastuzumab in Urothelial Cancer. J Natl Compr Canc Netw. 2019;17 (3):194-200. doi: 10.6004/jnccn.2018.7264. PubMed PMID:30865916 .
  11. Vikova, V, Jourdan, M, Robert, N, Requirand, G, Boireau, S, Bruyer, A et al.. Comprehensive characterization of the mutational landscape in multiple myeloma cell lines reveals potential drivers and pathways associated with tumor progression and drug resistance. Theranostics. 2019;9 (2):540-553. doi: 10.7150/thno.28374. PubMed PMID:30809292 PubMed Central PMC6376179.
  12. Agirre, X, Meydan, C, Jiang, Y, Garate, L, Doane, AS, Li, Z et al.. Long non-coding RNAs discriminate the stages and gene regulatory states of human humoral immune response. Nat Commun. 2019;10 (1):821. doi: 10.1038/s41467-019-08679-z. PubMed PMID:30778059 PubMed Central PMC6379396.
  13. Chen, HJ, Poran, A, Unni, AM, Huang, SX, Elemento, O, Snoeck, HW et al.. Generation of pulmonary neuroendocrine cells and SCLC-like tumors from human embryonic stem cells. J. Exp. Med. 2019;216 (3):674-687. doi: 10.1084/jem.20181155. PubMed PMID:30737256 PubMed Central PMC6400536.
  14. Glynn, S, Lipkin, S, Zhang, T, Sboner, A, Elemento, O, Van Besien, K et al.. The application of precision medicine in diagnosing familial Mediterranean fever. Leuk. Lymphoma. 2019; :1-3. doi: 10.1080/10428194.2019.1571204. PubMed PMID:30698071 .
  15. Gambi, G, Di Simone, E, Basso, V, Ricci, L, Wang, R, Verma, A et al.. The Transcriptional Regulator Sin3A Contributes to the Oncogenic Potential of STAT3. Cancer Res. 2019; :. doi: 10.1158/0008-5472.CAN-18-0359. PubMed PMID:30692217 .
  16. Finnerty, BM, Moore, M, Verma, A, Aronova, A, Huang, S, Edwards, DP et al.. UCHL1 loss alters the cell-cycle in metastatic pancreatic neuroendocrine tumors. Endocr. Relat. Cancer. 2019; :. doi: 10.1530/ERC-18-0507. PubMed PMID:30689542 .
  17. Lan, Y, Pan, H, Li, C, Banks, KM, Sam, J, Ding, B et al.. TETs Regulate Proepicardial Cell Migration through Extracellular Matrix Organization during Zebrafish Cardiogenesis. Cell Rep. 2019;26 (3):720-732.e4. doi: 10.1016/j.celrep.2018.12.076. PubMed PMID:30650362 PubMed Central PMC6366638.
  18. Boehm, KM, Bhinder, B, Raja, VJ, Dephoure, N, Elemento, O. Predicting peptide presentation by major histocompatibility complex class I: an improved machine learning approach to the immunopeptidome. BMC Bioinformatics. 2019;20 (1):7. doi: 10.1186/s12859-018-2561-z. PubMed PMID:30611210 PubMed Central PMC6321722.
  19. Prabhu, VV, Madhukar, NS, Gilvary, C, Kline, CLB, Oster, S, El-Deiry, WS et al.. Dopamine Receptor D5 is a Modulator of Tumor Response to Dopamine Receptor D2 Antagonism. Clin. Cancer Res. 2019;25 (7):2305-2313. doi: 10.1158/1078-0432.CCR-18-2572. PubMed PMID:30559168 .
  20. Gayvert, K, Elemento, O. Drug-Induced Expression-Based Computational Repurposing of Small Molecules Affecting Transcription Factor Activity. Methods Mol. Biol. 2019;1903 :179-184. doi: 10.1007/978-1-4939-8955-3_10. PubMed PMID:30547442 .
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