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. Jacobsen, JOB, Baudis, M, Baynam, GS, Beckmann, JS, Beltran, S, Buske, OJ et al.. The GA4GH Phenopacket schema defines a computable representation of clinical data. Nat Biotechnol. 2022;40 (6):817-820. doi: 10.1038/s41587-022-01357-4. PubMed PMID:35705716 .
  2. Hu, Y, Bloy, N, Elemento, O, Buqué, A. Nicotinamide drives T cell activation in the mammary tumor microenvironment. J Transl Med. 2022;20 (1):251. doi: 10.1186/s12967-022-03454-z. PubMed PMID:35659314 .
  3. Brendel, M, Getseva, V, Assaad, MA, Sigouros, M, Sigaras, A, Kane, T et al.. Weakly-supervised tumor purity prediction from frozen H&E stained slides. EBioMedicine. 2022;80 :104067. doi: 10.1016/j.ebiom.2022.104067. PubMed PMID:35644123 .
  4. Doane, AS, Elemento, O. Alterations in transcriptional networks in cancer: the role of noncoding somatic driver mutations. Curr Opin Genet Dev. 2022;75 :101919. doi: 10.1016/j.gde.2022.101919. PubMed PMID:35609422 .
  5. Schad, SE, Chow, A, Mangarin, L, Pan, H, Zhang, J, Ceglia, N et al.. Tumor-induced double positive T cells display distinct lineage commitment mechanisms and functions. J Exp Med. 2022;219 (6):. doi: 10.1084/jem.20212169. PubMed PMID:35604411 .
  6. Linares, JF, Cid-Diaz, T, Duran, A, Osrodek, M, Martinez-Ordoñez, A, Reina-Campos, M et al.. The lactate-NAD+ axis activates cancer-associated fibroblasts by downregulating p62. Cell Rep. 2022;39 (6):110792. doi: 10.1016/j.celrep.2022.110792. PubMed PMID:35545049 .
  7. Jaiswal, A, Verma, A, Dannenfelser, R, Melssen, M, Tirosh, I, Izar, B et al.. An activation to memory differentiation trajectory of tumor-infiltrating lymphocytes informs metastatic melanoma outcomes. Cancer Cell. 2022;40 (5):524-544.e5. doi: 10.1016/j.ccell.2022.04.005. PubMed PMID:35537413 PubMed Central PMC9122099.
  8. Raman, R, Villefranc, JA, Ullmann, TM, Thiesmeyer, J, Anelli, V, Yao, J et al.. Inhibition of FGF receptor blocks adaptive resistance to RET inhibition in CCDC6-RET-rearranged thyroid cancer. J Exp Med. 2022;219 (6):. doi: 10.1084/jem.20210390. PubMed PMID:35510953 PubMed Central PMC9082625.
  9. Alnajar, H, Ravichandran, H, Figueiredo Rendeiro, A, Ohara, K, Al Zoughbi, W, Manohar, J et al.. Tumor-immune microenvironment revealed by Imaging Mass Cytometry in a metastatic sarcomatoid urothelial carcinoma with a prolonged response to pembrolizumab. Cold Spring Harb Mol Case Stud. 2022;8 (3):. doi: 10.1101/mcs.a006151. PubMed PMID:35483877 PubMed Central PMC9059779.
  10. Rajappa, P, Eng, KW, Bareja, R, Bander, ED, Yuan, M, Dua, A et al.. Utility of multimodality molecular profiling for pediatric patients with central nervous system tumors. Neurooncol Adv. ;4 (1):vdac031. doi: 10.1093/noajnl/vdac031. PubMed PMID:35475276 PubMed Central PMC9034114.
  11. Argueta, LB, Lacko, LA, Bram, Y, Tada, T, Carrau, L, Rendeiro, AF et al.. Inflammatory responses in the placenta upon SARS-CoV-2 infection late in pregnancy. iScience. 2022;25 (5):104223. doi: 10.1016/j.isci.2022.104223. PubMed PMID:35434541 PubMed Central PMC8996470.
  12. Yao, P, Witte, D, Gimonet, H, German, A, Andreadis, K, Cheng, M et al.. Automatic classification of informative laryngoscopic images using deep learning. Laryngoscope Investig Otolaryngol. 2022;7 (2):460-466. doi: 10.1002/lio2.754. PubMed PMID:35434326 PubMed Central PMC9008155.
  13. Ertl, IE, Lemberger, U, Ilijazi, D, Hassler, MR, Bruchbacher, A, Brettner, R et al.. Molecular and Pharmacological Bladder Cancer Therapy Screening: Discovery of Clofarabine as a Highly Active Compound. Eur Urol. 2022; :. doi: 10.1016/j.eururo.2022.03.009. PubMed PMID:35393162 .
  14. Altorki, NK, Borczuk, AC, Harrison, S, Groner, LK, Bhinder, B, Mittal, V et al.. Global evolution of the tumor microenvironment associated with progression from preinvasive invasive to invasive human lung adenocarcinoma. Cell Rep. 2022;39 (1):110639. doi: 10.1016/j.celrep.2022.110639. PubMed PMID:35385730 PubMed Central PMC9033258.
  15. Kotani, D, Nakamura, Y, Fujisawa, T, Bando, H, Sakamoto, N, Johns, AL et al.. ICGC-ARGO precision medicine: targeted therapy according to longitudinal assessment of tumour heterogeneity in colorectal cancer. Lancet Oncol. 2022;23 (4):463-464. doi: 10.1016/S1470-2045(22)00142-5. PubMed PMID:35358454 .
  16. Kulm, S, Kofman, L, Mezey, J, Elemento, O. Simple Linear Cancer Risk Prediction Models With Novel Features Outperform Complex Approaches. JCO Clin Cancer Inform. 2022;6 :e2100166. doi: 10.1200/CCI.21.00166. PubMed PMID:35239414 PubMed Central PMC8920463.
  17. Park, J, Foox, J, Hether, T, Danko, DC, Warren, S, Kim, Y et al.. System-wide transcriptome damage and tissue identity loss in COVID-19 patients. Cell Rep Med. 2022;3 (2):100522. doi: 10.1016/j.xcrm.2022.100522. PubMed PMID:35233546 PubMed Central PMC8784611.
  18. van der Mijn, JC, Eng, KW, Chandra, P, Fernandez, E, Ramazanoglu, S, Sigaras, A et al.. The genomic landscape of metastatic clear cell renal cell carcinoma after systemic therapy. Mol Oncol. 2022;16 (12):2384-2395. doi: 10.1002/1878-0261.13204. PubMed PMID:35231161 .
  19. Ullmann, TM, Thiesmeyer, JW, Lee, YJ, Beg, S, Mosquera, JM, Elemento, O et al.. RET Fusion-Positive Papillary Thyroid Cancers are Associated with a More Aggressive Phenotype. Ann Surg Oncol. 2022; :. doi: 10.1245/s10434-022-11418-2. PubMed PMID:35230579 .
  20. DiNapoli, SE, Martinez-McFaline, R, Shen, H, Doane, AS, Perez, AR, Verma, A et al.. Histone 3 Methyltransferases Alter Melanoma Initiation and Progression Through Discrete Mechanisms. Front Cell Dev Biol. 2022;10 :814216. doi: 10.3389/fcell.2022.814216. PubMed PMID:35223844 PubMed Central PMC8866878.
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