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


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. Kaya, C, Dorsaint, P, Mercurio, S, Campbell, AM, Wha Eng, K, Nikiforova, MN et al.. Limitations of Detecting Genetic Variants from the RNA-Seq Data in Tissue and FNA Samples. Thyroid. 2020; :. doi: 10.1089/thy.2020.0307. PubMed PMID:32948110 .
  2. Buqué, A, Bloy, N, Perez-Lanzón, M, Iribarren, K, Humeau, J, Pol, JG et al.. Publisher Correction: Immunoprophylactic and immunotherapeutic control of hormone receptor-positive breast cancer. Nat Commun. 2020;11 (1):4787. doi: 10.1038/s41467-020-18719-8. PubMed PMID:32943636 .
  3. Rendeiro, AF, Casano, J, Vorkas, CK, Singh, H, Morales, A, DeSimone, RA et al.. 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. 2020; :. doi: 10.1101/2020.09.08.20189092. PubMed PMID:32935114 PubMed Central PMC7491529.
  4. Palikuqi, B, Nguyen, DT, Li, G, Schreiner, R, Pellegata, AF, Liu, Y et al.. Adaptable haemodynamic endothelial cells for organogenesis and tumorigenesis. Nature. 2020;585 (7825):426-432. doi: 10.1038/s41586-020-2712-z. PubMed PMID:32908310 .
  5. Elemento, O. The future of precision medicine: towards a more predictive personalized medicine. Emerg Top Life Sci. 2020;4 (2):175-177. doi: 10.1042/ETLS20190197. PubMed PMID:32856697 .
  6. Nie, K, Redmond, D, Eng, KW, Zhang, T, Cheng, S, Mathew, S et al.. Mutation landscape, clonal evolution pattern, and potential pathogenic pathways in B-lymphoblastic transformation of follicular lymphoma. Leukemia. 2020; :. doi: 10.1038/s41375-020-01014-2. PubMed PMID:32788647 .
  7. Dooley, BJ, Verma, A, Ding, R, Yang, H, Muthukumar, T, Lubetzky, M et al.. Urinary Cell Transcriptome Profiling and Identification of ITM2A, SLAMF6, and IKZF3 as Biomarkers of Acute Rejection in Human Kidney Allografts. Transplant Direct. 2020;6 (8):e588. doi: 10.1097/TXD.0000000000001035. PubMed PMID:32766436 PubMed Central PMC7377920.
  8. Gilvary, C, Elkhader, J, Madhukar, N, Henchcliffe, C, Goncalves, MD, Elemento, O et al.. A machine learning and network framework to discover new indications for small molecules. PLoS Comput. Biol. 2020;16 (8):e1008098. doi: 10.1371/journal.pcbi.1008098. PubMed PMID:32764756 PubMed Central PMC7437923.
  9. Ricker, E, Verma, A, Marullo, R, Gupta, S, Ye, C, Pannellini, T et al.. Selective dysregulation of ROCK2 activity promotes aberrant transcriptional networks in ABC diffuse large B-cell lymphoma. Sci Rep. 2020;10 (1):13094. doi: 10.1038/s41598-020-69884-1. PubMed PMID:32753663 PubMed Central PMC7403583.
  10. Buqué, A, Bloy, N, Perez-Lanzón, M, Iribarren, K, Humeau, J, Pol, JG et al.. Immunoprophylactic and immunotherapeutic control of hormone receptor-positive breast cancer. Nat Commun. 2020;11 (1):3819. doi: 10.1038/s41467-020-17644-0. PubMed PMID:32732875 PubMed Central PMC7393498.
  11. Shah, MA, Enzinger, P, Ko, AH, Ocean, AJ, Philip, PA, Thakkar, PV et al.. Multicenter Phase II Study of Cabazitaxel in Advanced Gastroesophageal Cancer: Association of HER2 Expression and M2-Like Tumor-Associated Macrophages with Patient Outcome. Clin. Cancer Res. 2020;26 (18):4756-4766. doi: 10.1158/1078-0432.CCR-19-3920. PubMed PMID:32641434 .
  12. De Micheli, AJ, Spector, JA, Elemento, O, Cosgrove, BD. A reference single-cell transcriptomic atlas of human skeletal muscle tissue reveals bifurcated muscle stem cell populations. Skelet Muscle. 2020;10 (1):19. doi: 10.1186/s13395-020-00236-3. PubMed PMID:32624006 PubMed Central PMC7336639.
  13. Venturutti, L, Teater, M, Zhai, A, Chadburn, A, Babiker, L, Kim, D et al.. TBL1XR1 Mutations Drive Extranodal Lymphoma by Inducing a Pro-tumorigenic Memory Fate. Cell. 2020;182 (2):297-316.e27. doi: 10.1016/j.cell.2020.05.049. PubMed PMID:32619424 PubMed Central PMC7384961.
  14. Matrai, C, Motanagh, S, Mirabelli, S, Ma, L, He, B, Chapman-Davis, E et al.. Molecular Profiles of Mixed Endometrial Carcinoma. Am. J. Surg. Pathol. 2020;44 (8):1104-1111. doi: 10.1097/PAS.0000000000001519. PubMed PMID:32604171 .
  15. Segal, E, Zhang, F, Lin, X, King, G, Shalem, O, Shilo, S et al.. Publisher Correction: Building an international consortium for tracking coronavirus health status. Nat. Med. 2020;26 (8):1309. doi: 10.1038/s41591-020-0983-4. PubMed PMID:32591764 PubMed Central PMC7319223.
  16. Auguste, A, Blanc-Durand, F, Deloger, M, Le Formal, A, Bareja, R, Wilkes, DC et al.. Small Cell Carcinoma of the Ovary, Hypercalcemic Type (SCCOHT) beyond SMARCA4 Mutations: A Comprehensive Genomic Analysis. Cells. 2020;9 (6):. doi: 10.3390/cells9061496. PubMed PMID:32575483 PubMed Central PMC7349095.
  17. Han, T, Goswami, S, Hu, Y, Tang, F, Zafra, MP, Murphy, C et al.. Lineage Reversion Drives WNT Independence in Intestinal Cancer. Cancer Discov. 2020; :. doi: 10.1158/2159-8290.CD-19-1536. PubMed PMID:32546576 .
  18. Liu, H, Paddock, MN, Wang, H, Murphy, CJ, Geck, RC, Navarro, AJ et al.. The INPP4B Tumor Suppressor Modulates EGFR Trafficking and Promotes Triple-Negative Breast Cancer. Cancer Discov. 2020;10 (8):1226-1239. doi: 10.1158/2159-8290.CD-19-1262. PubMed PMID:32513774 PubMed Central PMC7415683.
  19. Kolin, DA, Kulm, S, Elemento, O. Clinical and Genetic Characteristics of Covid-19 Patients from UK Biobank. medRxiv. 2020; :. doi: 10.1101/2020.05.05.20075507. PubMed PMID:32511589 PubMed Central PMC7276016.
  20. Pisapia, DJ, Ohara, K, Bareja, R, Wilkes, DC, Hissong, E, Croyle, JA et al.. Fusions involving BCOR and CREBBP are rare events in infiltrating glioma. Acta Neuropathol Commun. 2020;8 (1):80. doi: 10.1186/s40478-020-00951-4. PubMed PMID:32493417 PubMed Central PMC7271411.
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