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. Yoffe, L, Bhinder, B, Kang, SW, Zhang, H, Singh, A, Ravichandran, H et al.. Acquisition of discrete immune suppressive barriers contributes to the initiation and progression of preinvasive to invasive human lung cancer. bioRxiv. 2025; :. doi: 10.1101/2024.12.31.630523. PubMed PMID:39803458 PubMed Central PMC11722343.
  2. Barton, BM, Son, F, Verma, A, Bal, SK, Tang, Q, Wang, R et al.. IRE1α-XBP1 safeguards hematopoietic stem and progenitor cells by restricting pro-leukemogenic gene programs. Nat Immunol. 2025; :. doi: 10.1038/s41590-024-02063-w. PubMed PMID:39789376 .
  3. Chaudhry, F, Kim, TW, Elemento, O, Betel, D. Machine learning analysis of population-wide plasma proteins identifies hormonal biomarkers of Parkinson's Disease. medRxiv. 2024; :. doi: 10.1101/2024.12.21.24313256. PubMed PMID:39763525 PubMed Central PMC11703317.
  4. Anibal, J, Gunkel, J, Awan, S, Huth, H, Nguyen, H, Le, T et al.. The doctor will polygraph you now. Npj Health Syst. 2024;1 (1):1. doi: 10.1038/s44401-024-00001-4. PubMed PMID:39759269 PubMed Central PMC11698301.
  5. Delgado-de la Mora, J, Al Assaad, M, Karaaslan, S, Hadi, K, Halima, A, Deshpande, A et al.. Whole genome and transcriptome analysis of pancreatic acinar cell carcinoma elucidates mechanisms of homologous recombination deficiency and unravels novel relevant fusion events. Pathol Res Pract. 2024;266 :155798. doi: 10.1016/j.prp.2024.155798. PubMed PMID:39731868 .
  6. Xu, C, Bulusu, KC, Pan, H, Elemento, O. DDI-GPT: Explainable Prediction of Drug-Drug Interactions using Large Language Models enhanced with Knowledge Graphs. bioRxiv. 2024; :. doi: 10.1101/2024.12.06.627266. PubMed PMID:39713430 PubMed Central PMC11661079.
  7. Windon, A, Al Assaad, M, Hadi, K, Mendelson, N, Hissong, E, Deshpande, A et al.. Emerging molecular phenotypes and potential therapeutic targets in esophageal and gastric adenocarcinoma unearthed by whole genome and transcriptome analyses. Pathol Res Pract. 2024;266 :155788. doi: 10.1016/j.prp.2024.155788. PubMed PMID:39708521 .
  8. Delgado-de la Mora, J, Al Assaad, M, Quitian, S, Levine, MF, Deshpande, A, Sigouros, M et al.. Novel structural variants that impact cell cycle genes are elucidated in metastatic gastrointestinal stromal tumors. Pathol Res Pract. 2024;266 :155782. doi: 10.1016/j.prp.2024.155782. PubMed PMID:39708519 .
  9. Patel, R, Price, N, Bahr, R, Bedrick, S, Bensoussan, Y, Bélisle-Pipon, JC et al.. Summary of Keynote Speeches from the 2024 Voice AI Symposium, presented by the Bridge2AI-Voice Consortium. Front Digit Health. 2024;6 :1484503. doi: 10.3389/fdgth.2024.1484503. PubMed PMID:39691415 PubMed Central PMC11649621.
  10. Al Assaad, M, Hadi, K, Tu, J, Levine, MF, Patel, M, Deshpande, A et al.. Enhancing the detection of clinically relevant biomarkers in advanced uterine and tubo-ovarian carcinomas through genome-wide analysis. Pathol Res Pract. 2024;266 :155773. doi: 10.1016/j.prp.2024.155773. PubMed PMID:39673888 .
  11. Wolujewicz, P, Aguiar-Pulido, V, Thareja, G, Suhre, K, Elemento, O, Finnell, RH et al.. Integrative computational analyses implicate regulatory genomic elements contributing to spina bifida. Genet Med Open. 2024;2 :101894. doi: 10.1016/j.gimo.2024.101894. PubMed PMID:39669613 PubMed Central PMC11613821.
  12. Buqué, A, Bloy, N, Petroni, G, Jiménez-Cortegana, C, Sato, A, Iribarren, C et al.. Impact of radiotherapy dose, fractionation and immunotherapeutic partner in a mouse model of HR+ mammary carcinogenesis. J Natl Cancer Inst. 2024; :. doi: 10.1093/jnci/djae329. PubMed PMID:39661487 .
  13. Kalomeris, T, Assaad, MA, la Mora, JD, Gundem, G, Levine, MF, Boyraz, B et al.. Whole genome profiling of primary and metastatic adrenocortical carcinoma unravels significant molecular events. Pathol Res Pract. 2024;266 :155725. doi: 10.1016/j.prp.2024.155725. PubMed PMID:39626581 .
  14. Xu, C, Us, I, Cohen-Setton, J, Milo, M, Sidders, B, Fitzgibbon, J et al.. PAIRWISE: Deep Learning-based Prediction of Effective Personalized Drug Combinations in Cancer. bioRxiv. 2024; :. doi: 10.1101/2024.11.04.621884. PubMed PMID:39574568 PubMed Central PMC11580853.
  15. Karimzadeh, M, Momen-Roknabadi, A, Cavazos, TB, Fang, Y, Chen, NC, Multhaup, M et al.. Deep generative AI models analyzing circulating orphan non-coding RNAs enable detection of early-stage lung cancer. Nat Commun. 2024;15 (1):10090. doi: 10.1038/s41467-024-53851-9. PubMed PMID:39572521 PubMed Central PMC11582319.
  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. Elife. 2024;13 :. doi: 10.7554/eLife.96085. PubMed PMID:39570652 PubMed Central PMC11581429.
  17. Chatterjee, SS, Linares, JF, Cid-Diaz, T, Duran, A, Khan, MIK, Osrodek, M et al.. Increased translation driven by non-canonical EZH2 creates a synthetic vulnerability in enzalutamide-resistant prostate cancer. Nat Commun. 2024;15 (1):9755. doi: 10.1038/s41467-024-53874-2. PubMed PMID:39567499 PubMed Central PMC11579030.
  18. Lukose, G, Al Assaad, M, Driskill, JH, Levine, MF, Gundem, G, Semaan, A et al.. Whole genome profiling of rare pediatric thoracic tumors elucidates a YAP1::LEUTX fusion in an unclassified biphasic embryonal neoplasm. Pathol Res Pract. 2024;264 :155726. doi: 10.1016/j.prp.2024.155726. PubMed PMID:39566337 .
  19. 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.
  20. 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 PubMed Central PMC11601564.
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