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. Kandola, MS, Kulm, S, Kim, LK, Markowitz, SM, Liu, CF, Thomas, G et al.. Population-Level Prevalence of Rare Variants Associated With Atrial Fibrillation and its Impact on Patient Outcomes. JACC Clin Electrophysiol. 2023; :. doi: 10.1016/j.jacep.2022.11.022. PubMed PMID:36669898 .
  2. Mlynarczyk, C, Teater, M, Pae, J, Chin, CR, Wang, L, Arulraj, T et al.. BTG1 mutation yields supercompetitive B cells primed for malignant transformation. Science. 2023;379 (6629):eabj7412. doi: 10.1126/science.abj7412. PubMed PMID:36656933 .
  3. Johnson, JL, Yaron, TM, Huntsman, EM, Kerelsky, A, Song, J, Regev, A et al.. An atlas of substrate specificities for the human serine/threonine kinome. Nature. 2023;613 (7945):759-766. doi: 10.1038/s41586-022-05575-3. PubMed PMID:36631611 .
  4. Crowley, MJP, Bhinder, B, Markowitz, GJ, Martin, M, Verma, A, Sandoval, TA et al.. Tumor-intrinsic IRE1α signaling controls protective immunity in lung cancer. Nat Commun. 2023;14 (1):120. doi: 10.1038/s41467-022-35584-9. PubMed PMID:36624093 PubMed Central PMC9829901.
  5. Cyrta, J, Rosiene, J, Bareja, R, Kudman, S, Al Zoughbi, W, Motanagh, S et al.. Whole-genome characterization of myoepithelial carcinomas of the soft tissue. Cold Spring Harb Mol Case Stud. 2022;8 (7):. doi: 10.1101/mcs.a006227. PubMed PMID:36577525 PubMed Central PMC9808553.
  6. Barnes, J, Brendel, M, Gao, VR, Rajendran, S, Kim, J, Li, Q et al.. A non-invasive artificial intelligence approach for the prediction of human blastocyst ploidy: a retrospective model development and validation study. Lancet Digit Health. 2023;5 (1):e28-e40. doi: 10.1016/S2589-7500(22)00213-8. PubMed PMID:36543475 .
  7. Brendel, M, Su, C, Bai, Z, Zhang, H, Elemento, O, Wang, F et al.. Application of Deep Learning on Single-cell RNA Sequencing Data Analysis: A Review. Genomics Proteomics Bioinformatics. 2022; :. doi: 10.1016/j.gpb.2022.11.011. PubMed PMID:36528240 .
  8. Park, J, Kim, J, Lewy, T, Rice, CM, Elemento, O, Rendeiro, AF et al.. Spatial omics technologies at multimodal and single cell/subcellular level. Genome Biol. 2022;23 (1):256. doi: 10.1186/s13059-022-02824-6. PubMed PMID:36514162 PubMed Central PMC9746133.
  9. Rendeiro, AF, Ravichandran, H, Kim, J, Borczuk, AC, Elemento, O, Schwartz, RE et al.. Persistent alveolar type 2 dysfunction and lung structural derangement in post-acute COVID-19. medRxiv. 2022; :. doi: 10.1101/2022.11.28.22282811. PubMed PMID:36482970 PubMed Central PMC9727772.
  10. Cuppen, E, Elemento, O, Rosenquist, R, Nikic, S, IJzerman, M, Zaleski, ID et al.. Implementation of Whole-Genome and Transcriptome Sequencing Into Clinical Cancer Care. JCO Precis Oncol. 2022;6 :e2200245. doi: 10.1200/PO.22.00245. PubMed PMID:36480778 .
  11. Liu, W, Newhall, KP, Khani, F, Barlow, L, Nguyen, D, Gu, L et al.. The cytidine deaminase APOBEC3G contributes to cancer mutagenesis and clonal evolution in bladder cancer. Cancer Res. 2022; :. doi: 10.1158/0008-5472.CAN-22-2912. PubMed PMID:36480186 .
  12. Kim, J, Rustam, S, Mosquera, JM, Randell, SH, Shaykhiev, R, Rendeiro, AF et al.. Author Correction: Unsupervised discovery of tissue architecture in multiplexed imaging. Nat Methods. 2022;19 (12):1662. doi: 10.1038/s41592-022-01717-7. PubMed PMID:36414761 .
  13. Sternberg, CN, Shin, N, Chernyshov, K, Calabro, F, Cerbone, L, Procopio, G et al.. Case report: Metastatic urothelial cancer with an exceptional response to immunotherapy and comprehensive understanding of the tumor and the tumor microenvironment. Front Oncol. 2022;12 :1006017. doi: 10.3389/fonc.2022.1006017. PubMed PMID:36387205 PubMed Central PMC9661726.
  14. Kim, J, Rustam, S, Mosquera, JM, Randell, SH, Shaykhiev, R, Rendeiro, AF et al.. Unsupervised discovery of tissue architecture in multiplexed imaging. Nat Methods. 2022;19 (12):1653-1661. doi: 10.1038/s41592-022-01657-2. PubMed PMID:36316562 .
  15. Greenberg, J, Limberg, J, Verma, A, Kim, D, Chen, X, Lee, YJ et al.. Metastatic pancreatic neuroendocrine tumors feature elevated T cell infiltration. JCI Insight. 2022;7 (23):. doi: 10.1172/jci.insight.160130. PubMed PMID:36301668 PubMed Central PMC9746918.
  16. Yaron, TM, Heaton, BE, Levy, TM, Johnson, JL, Jordan, TX, Cohen, BM et al.. Host protein kinases required for SARS-CoV-2 nucleocapsid phosphorylation and viral replication. Sci Signal. 2022;15 (757):eabm0808. doi: 10.1126/scisignal.abm0808. PubMed PMID:36282911 PubMed Central PMC9830954.
  17. Jang, JY, Hwang, I, Pan, H, Yao, J, Alinari, L, Imada, E et al.. A FOXO1-dependent transcription network is a targetable vulnerability of mantle cell lymphomas. J Clin Invest. 2022;132 (24):. doi: 10.1172/JCI160767. PubMed PMID:36282572 PubMed Central PMC9753996.
  18. Charilaou, P, Mohapatra, S, Doukas, S, Kohli, M, Radadiya, D, Devani, K et al.. Predicting inpatient mortality in patients with inflammatory bowel disease: A machine learning approach. J Gastroenterol Hepatol. 2022; :. doi: 10.1111/jgh.16029. PubMed PMID:36258306 .
  19. Kulm, S, Langhans, MT, Shen, TS, Kolin, DA, Elemento, O, Rodeo, SA et al.. Genome-Wide Association Study of Adhesive Capsulitis Suggests Significant Genetic Risk Factors. J Bone Joint Surg Am. 2022;104 (21):1869-1876. doi: 10.2106/JBJS.21.01407. PubMed PMID:36223477 .
  20. Drozdz, MM, Doane, AS, Alkallas, R, Desman, G, Bareja, R, Reilly, M et al.. A nuclear cAMP microdomain suppresses tumor growth by Hippo pathway inactivation. Cell Rep. 2022;40 (13):111412. doi: 10.1016/j.celrep.2022.111412. PubMed PMID:36170819 PubMed Central PMC9549417.
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