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. Fontugne, J, Cai, PY, Alnajar, H, Bhinder, B, Park, K, Ye, H et al.. Collision tumors revealed by prospectively assessing subtype-defining molecular alterations in 904 individual prostate cancer foci. JCI Insight. 2022; :. doi: 10.1172/jci.insight.155309. PubMed PMID:35050902 .
  2. Shohdy, KS, Villamar, DM, Cao, Y, Trieu, J, Price, KS, Nagy, R et al.. Serial ctDNA analysis predicts clinical progression in patients with advanced urothelial carcinoma. Br J Cancer. 2022; :. doi: 10.1038/s41416-021-01648-8. PubMed PMID:35046520 .
  3. Milella, M, Luchini, C, Lawlor, RT, Johns, AL, Casolino, R, Yoshino, T et al.. ICGC-ARGO precision medicine: familial matters in pancreatic cancer. Lancet Oncol. 2022;23 (1):25-26. doi: 10.1016/S1470-2045(21)00703-8. PubMed PMID:34973218 .
  4. Tang, CP, Clark, O, Ferrarone, JR, Campos, C, Lalani, AS, Chodera, JD et al.. GCN2 kinase activation by ATP-competitive kinase inhibitors. Nat Chem Biol. 2021; :. doi: 10.1038/s41589-021-00947-8. PubMed PMID:34949839 .
  5. Aguiar-Pulido, V, Wolujewicz, P, Martinez-Fundichely, A, Elhaik, E, Thareja, G, Abdel Aleem, A et al.. Systems biology analysis of human genomes points to key pathways conferring spina bifida risk. Proc Natl Acad Sci U S A. 2021;118 (51):. doi: 10.1073/pnas.2106844118. PubMed PMID:34916285 PubMed Central PMC8713748.
  6. Berchuck, JE, Baca, SC, McClure, HM, Korthauer, K, Tsai, HK, Nuzzo, PV et al.. Detecting Neuroendocrine Prostate Cancer Through Tissue-Informed Cell-Free DNA Methylation Analysis. Clin Cancer Res. 2021; :. doi: 10.1158/1078-0432.CCR-21-3762. PubMed PMID:34907080 .
  7. Shah, Y, Verma, A, Marderstein, AR, White, J, Bhinder, B, Garcia Medina, JS et al.. Pan-cancer analysis reveals molecular patterns associated with age. Cell Rep. 2021;37 (10):110100. doi: 10.1016/j.celrep.2021.110100. PubMed PMID:34879281 .
  8. Lan, Y, Banks, KM, Pan, H, Verma, N, Dixon, GR, Zhou, T et al.. Stage-specific regulation of DNA methylation by TET enzymes during human cardiac differentiation. Cell Rep. 2021;37 (10):110095. doi: 10.1016/j.celrep.2021.110095. PubMed PMID:34879277 .
  9. Kolin, DA, Kulm, S, Elemento, O. Publisher Correction: Prediction of primary venous thromboembolism based on clinical and genetic factors within the U.K. Biobank. Sci Rep. 2021;11 (1):23364. doi: 10.1038/s41598-021-02115-3. PubMed PMID:34845243 PubMed Central PMC8630148.
  10. Ciani, Y, Fedrizzi, T, Prandi, D, Lorenzin, F, Locallo, A, Gasperini, P et al.. Allele-specific genomic data elucidate the role of somatic gain and copy-number neutral loss of heterozygosity in cancer. Cell Syst. 2021; :. doi: 10.1016/j.cels.2021.10.001. PubMed PMID:34731645 .
  11. Kolin, DA, Kulm, S, Elemento, O. Prediction of primary venous thromboembolism based on clinical and genetic factors within the U.K. Biobank. Sci Rep. 2021;11 (1):21340. doi: 10.1038/s41598-021-00796-4. PubMed PMID:34725413 PubMed Central PMC8560817.
  12. Alaterre, E, Vikova, V, Kassambara, A, Bruyer, A, Robert, N, Requirand, G et al.. RNA-Sequencing-Based Transcriptomic Score with Prognostic and Theranostic Values in Multiple Myeloma. J Pers Med. 2021;11 (10):. doi: 10.3390/jpm11100988. PubMed PMID:34683129 PubMed Central PMC8541503.
  13. Mosquera, MJ, Kim, S, Bareja, R, Fang, Z, Cai, S, Pan, H et al.. Extracellular Matrix in Synthetic Hydrogel-Based Prostate Cancer Organoids Regulate Therapeutic Response to EZH2 and DRD2 Inhibitors. Adv Mater. 2022;34 (2):e2100096. doi: 10.1002/adma.202100096. PubMed PMID:34676924 .
  14. Allen, JE, Kline, CLB, Prabhu, VV, Wagner, J, Ishizawa, J, Madhukar, N et al.. Correction: Discovery and clinical introduction of first-in-class imipridone ONC201. Oncotarget. 2021;12 (21):2231. doi: 10.18632/oncotarget.28012. PubMed PMID:34676056 PubMed Central PMC8522842.
  15. Thakkar, PV, Kita, K, Castillo, UD, Galletti, G, Madhukar, N, Navarro, EV et al.. CLIP-170S is a microtubule +TIP variant that confers resistance to taxanes by impairing drug-target engagement. Dev Cell. 2021;56 (23):3264-3275.e7. doi: 10.1016/j.devcel.2021.09.023. PubMed PMID:34672971 PubMed Central PMC8665049.
  16. Melms, JC, Biermann, J, Huang, H, Wang, Y, Nair, A, Tagore, S et al.. Author Correction: A molecular single-cell lung atlas of lethal COVID-19. Nature. 2021;598 (7882):E2. doi: 10.1038/s41586-021-03921-5. PubMed PMID:34625743 PubMed Central PMC8498978.
  17. Rivas, MA, Durmaz, C, Kloetgen, A, Chin, CR, Chen, Z, Bhinder, B et al.. Cohesin Core Complex Gene Dosage Contributes to Germinal Center Derived Lymphoma Phenotypes and Outcomes. Front Immunol. 2021;12 :688493. doi: 10.3389/fimmu.2021.688493. PubMed PMID:34621263 PubMed Central PMC8490713.
  18. McNally, DR, Elemento, O, Melnick, A. Dissecting bulk transcriptomes of diffuse large B cell lymphoma. Cancer Cell. 2021;39 (10):1305-1307. doi: 10.1016/j.ccell.2021.09.006. PubMed PMID:34597590 .
  19. Doane, AS, Chu, CS, Di Giammartino, DC, Rivas, MA, Hellmuth, JC, Jiang, Y et al.. OCT2 pre-positioning facilitates cell fate transition and chromatin architecture changes in humoral immunity. Nat Immunol. 2021;22 (10):1327-1340. doi: 10.1038/s41590-021-01025-w. PubMed PMID:34556886 .
  20. Elemento, O, Leslie, C, Lundin, J, Tourassi, G. Artificial intelligence in cancer research, diagnosis and therapy. Nat Rev Cancer. 2021;21 (12):747-752. doi: 10.1038/s41568-021-00399-1. PubMed PMID:34535775 .
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