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

Lab website: http://physiology.med.cornell.edu/faculty/elemento/lab/

Techniques

Research Areas

Member of:

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. Bahr, R, Anibal, J, Bedrick, S, Bélisle-Pipon, JC, Bensoussan, Y, Blaylock, N et al.. Workshop summaries from the 2024 voice AI symposium, presented by the Bridge2AI-voice consortium. Front Digit Health. 2024;6 :1484818. doi: 10.3389/fdgth.2024.1484818. PubMed PMID:39540145 PubMed Central PMC11557516.
  2. Schwarz, E, Benner, B, Wesolowski, R, Quiroga, D, Good, L, Sun, SH et al.. Inhibition of Bruton's tyrosine kinase with PD-1 blockade modulates T cell activation in solid tumors. JCI Insight. 2024;9 (21):. doi: 10.1172/jci.insight.169927. PubMed PMID:39513363 .
  3. Stephan, C, Al Assaad, M, Levine, MF, Deshpande, A, Sigouros, M, Manohar, J et al.. Whole genome sequencing elucidates etiological differences in MCPyV-negative Merkel cell carcinoma. Pathol Res Pract. 2024;263 :155668. doi: 10.1016/j.prp.2024.155668. PubMed PMID:39427588 .
  4. Nguyen, DD, Hooper, WF, Liu, W, Chu, TR, Geiger, H, Shelton, JM et al.. The interplay of mutagenesis and ecDNA shapes urothelial cancer evolution. Nature. 2024;635 (8037):219-228. doi: 10.1038/s41586-024-07955-3. PubMed PMID:39385020 PubMed Central PMC11541202.
  5. Glass, J, Elemento, O. The power and perils of large language models in haematology. Br J Haematol. 2024; :. doi: 10.1111/bjh.19742. PubMed PMID:39344046 .
  6. Ohara, K, Al Assaad, M, McNulty, SN, Alnajar, H, Sboner, A, Wilkes, DC et al.. Detection of rare and novel gene fusions in patients with diffuse glioma: An institutional retrospective study. J Neuropathol Exp Neurol. 2024; :. doi: 10.1093/jnen/nlae105. PubMed PMID:39340835 .
  7. Markowitz, GJ, Ban, Y, Tavarez, DA, Yoffe, L, Podaza, E, He, Y et al.. Deficiency of metabolic regulator PKM2 activates the pentose phosphate pathway and generates TCF1+ progenitor CD8+ T cells to improve immunotherapy. Nat Immunol. 2024;25 (10):1884-1899. doi: 10.1038/s41590-024-01963-1. PubMed PMID:39327500 .
  8. Rajendran, S, Brendel, M, Barnes, J, Zhan, Q, Malmsten, JE, Zisimopoulos, P et al.. Automatic ploidy prediction and quality assessment of human blastocysts using time-lapse imaging. Nat Commun. 2024;15 (1):7756. doi: 10.1038/s41467-024-51823-7. PubMed PMID:39237547 PubMed Central PMC11377764.
  9. Vicario, R, Fragkogianni, S, Pokrovskii, M, Mayer, C, Lopez-Rodrigo, E, Hu, Y et al.. Mechanism of neurodegeneration mediated by clonal inflammatory microglia. bioRxiv. 2024; :. doi: 10.1101/2024.07.30.605867. PubMed PMID:39131366 PubMed Central PMC11312538.
  10. Hissong, E, Bhinder, B, Kim, J, Ohara, K, Ravichandran, H, Assaad, MA et al.. Integrative Transcriptomic and Single-Cell Protein Characterization of Colorectal Carcinoma Delineates Distinct Tumor Immune Microenvironments Associated with Overall Survival. Res Sq. 2024; :. doi: 10.21203/rs.3.rs-4751101/v1. PubMed PMID:39108491 PubMed Central PMC11302706.
  11. Hanif, SZ, Au, CC, Torregroza, I, Jannath, SY, Fabiha, T, Bhinder, B et al.. The Orphan G Protein-Coupled Receptor GPR52 is a Novel Regulator of Breast Cancer Multicellular Organization. bioRxiv. 2024; :. doi: 10.1101/2024.07.22.604482. PubMed PMID:39091857 PubMed Central PMC11291042.
  12. Han, X, Sui, J, Nie, K, Zhao, Y, Lv, X, Xie, J et al.. Tumor evolution analysis uncovered immune-escape related mutations in relapse of diffuse large B-cell lymphoma. Leukemia. 2024;38 (10):2276-2280. doi: 10.1038/s41375-024-02349-w. PubMed PMID:39080353 .
  13. Galletti, G, Halima, A, Gjyrezi, A, Zhang, J, Zimmerman, B, Worroll, D et al.. Transferrin receptor-based circulating tumor cell enrichment provides a snapshot of the molecular landscape of solid tumors and correlates with clinical outcomes. medRxiv. 2024; :. doi: 10.1101/2024.06.16.24309003. PubMed PMID:38947080 PubMed Central PMC11213041.
  14. Bojmar, L, Zambirinis, CP, Hernandez, JM, Chakraborty, J, Shaashua, L, Kim, J et al.. Multi-parametric atlas of the pre-metastatic liver for prediction of metastatic outcome in early-stage pancreatic cancer. Nat Med. 2024;30 (8):2170-2180. doi: 10.1038/s41591-024-03075-7. PubMed PMID:38942992 PubMed Central PMC11416063.
  15. Kudman, S, Semaan, A, Assaad, MA, Gogineni, S, Martin, ML, Mathew, S et al.. Optimization of Fluorescence In Situ Hybridization Protocols in the Era of Precision Medicine. Curr Protoc. 2024;4 (6):e1093. doi: 10.1002/cpz1.1093. PubMed PMID:38923415 .
  16. Guillet, S, Lazarov, T, Jordan, N, Boisson, B, Tello, M, Craddock, B et al.. ACK1 and BRK non-receptor tyrosine kinase deficiencies are associated with familial systemic lupus and involved in efferocytosis. medRxiv. 2024; :. doi: 10.1101/2024.02.15.24302255. PubMed PMID:38883731 PubMed Central PMC11177913.
  17. Greenberg, JA, Shah, Y, Ivanov, NA, Marshall, T, Kulm, S, Williams, J et al.. Developing a predictive model for metastatic potential in pancreatic neuroendocrine tumor. J Clin Endocrinol Metab. 2024; :. doi: 10.1210/clinem/dgae380. PubMed PMID:38817124 .
  18. Yaron-Barir, TM, Joughin, BA, Huntsman, EM, Kerelsky, A, Cizin, DM, Cohen, BM et al.. The intrinsic substrate specificity of the human tyrosine kinome. Nature. 2024;629 (8014):1174-1181. doi: 10.1038/s41586-024-07407-y. PubMed PMID:38720073 PubMed Central PMC11136658.
  19. Tasci, E, Shah, Y, Jagasia, S, Zhuge, Y, Shephard, J, Johnson, MO et al.. MGMT ProFWise: Unlocking a New Application for Combined Feature Selection and the Rank-Based Weighting Method to Link MGMT Methylation Status to Serum Protein Expression in Patients with Glioblastoma. Int J Mol Sci. 2024;25 (7):. doi: 10.3390/ijms25074082. PubMed PMID:38612892 PubMed Central PMC11012706.
  20. Shah, Y, Kulm, S, Nauseef, JT, Chen, Z, Elemento, O, Kensler, KH et al.. Benchmarking multi-ancestry prostate cancer polygenic risk scores in a real-world cohort. PLoS Comput Biol. 2024;20 (4):e1011990. doi: 10.1371/journal.pcbi.1011990. PubMed PMID:38598551 PubMed Central PMC11034641.
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