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. 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; :. doi: 10.1097/PAS.0000000000001519. PubMed PMID:32604171 .
  2. 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; :. doi: 10.1038/s41591-020-0983-4. PubMed PMID:32591764 PubMed Central PMC7319223.
  3. 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 .
  4. 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 .
  5. 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; :. doi: 10.1158/2159-8290.CD-19-1262. PubMed PMID:32513774 .
  6. 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.
  7. 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.
  8. Segal, E, Zhang, F, Lin, X, King, G, Shalem, O, Shilo, S et al.. Building an international consortium for tracking coronavirus health status. Nat. Med. 2020; :. doi: 10.1038/s41591-020-0929-x. PubMed PMID:32488218 .
  9. Sfakianos, JP, Daza, J, Hu, Y, Anastos, H, Bryant, G, Bareja, R et al.. Epithelial plasticity can generate multi-lineage phenotypes in human and murine bladder cancers. Nat Commun. 2020;11 (1):2540. doi: 10.1038/s41467-020-16162-3. PubMed PMID:32439865 PubMed Central PMC7242345.
  10. Davis, M, Martini, R, Newman, L, Elemento, O, White, J, Verma, A et al.. Identification of Distinct Heterogenic Subtypes and Molecular Signatures Associated with African Ancestry in Triple Negative Breast Cancer Using Quantified Genetic Ancestry Models in Admixed Race Populations. Cancers (Basel). 2020;12 (5):. doi: 10.3390/cancers12051220. PubMed PMID:32414099 PubMed Central PMC7281131.
  11. Alsaleem, MA, Ball, G, Toss, MS, Raafat, S, Aleskandarany, M, Joseph, C et al.. A novel prognostic two-gene signature for triple negative breast cancer. Mod. Pathol. 2020; :. doi: 10.1038/s41379-020-0563-7. PubMed PMID:32404959 .
  12. Béguelin, W, Teater, M, Meydan, C, Hoehn, KB, Phillip, JM, Soshnev, AA et al.. Mutant EZH2 Induces a Pre-malignant Lymphoma Niche by Reprogramming the Immune Response. Cancer Cell. 2020;37 (5):655-673.e11. doi: 10.1016/j.ccell.2020.04.004. PubMed PMID:32396861 PubMed Central PMC7298875.
  13. Marderstein, AR, Uppal, M, Verma, A, Bhinder, B, Tayyebi, Z, Mezey, J et al.. Demographic and genetic factors influence the abundance of infiltrating immune cells in human tissues. Nat Commun. 2020;11 (1):2213. doi: 10.1038/s41467-020-16097-9. PubMed PMID:32371927 PubMed Central PMC7200670.
  14. Ginter, PS, McIntire, PJ, Kurtis, B, Mirabelli, S, Motanagh, S, Hoda, S et al.. Adenomyoepithelial tumors of the breast: molecular underpinnings of a rare entity. Mod. Pathol. 2020; :. doi: 10.1038/s41379-020-0552-x. PubMed PMID:32355271 .
  15. Liu, D, Shoag, JE, Poliak, D, Goueli, RS, Ravikumar, V, Redmond, D et al.. Integrative multiplatform molecular profiling of benign prostatic hyperplasia identifies distinct subtypes. Nat Commun. 2020;11 (1):1987. doi: 10.1038/s41467-020-15913-6. PubMed PMID:32332823 PubMed Central PMC7181734.
  16. Pine, AR, Cirigliano, SM, Nicholson, JG, Hu, Y, Linkous, A, Miyaguchi, K et al.. Tumor Microenvironment Is Critical for the Maintenance of Cellular States Found in Primary Glioblastomas. Cancer Discov. 2020;10 (7):964-979. doi: 10.1158/2159-8290.CD-20-0057. PubMed PMID:32253265 .
  17. Wagner, AH, Walsh, B, Mayfield, G, Tamborero, D, Sonkin, D, Krysiak, K et al.. A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer. Nat. Genet. 2020;52 (4):448-457. doi: 10.1038/s41588-020-0603-8. PubMed PMID:32246132 PubMed Central PMC7127986.
  18. Hwang, I, Pan, H, Yao, J, Elemento, O, Zheng, H, Paik, J et al.. CIC is a critical regulator of neuronal differentiation. JCI Insight. 2020;5 (9):. doi: 10.1172/jci.insight.135826. PubMed PMID:32229723 PubMed Central PMC7253013.
  19. Lehmann, GL, Hanke-Gogokhia, C, Hu, Y, Bareja, R, Salfati, Z, Ginsberg, M et al.. Single-cell profiling reveals an endothelium-mediated immunomodulatory pathway in the eye choroid. J. Exp. Med. 2020;217 (6):. doi: 10.1084/jem.20190730. PubMed PMID:32196081 .
  20. Bhinder, B, Elemento, O. Computational methods in tumor immunology. Meth. Enzymol. 2020;636 :209-259. doi: 10.1016/bs.mie.2020.01.001. PubMed PMID:32178820 .
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