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. Anibal, J, Doctor, R, Boyer, M, Newberry, K, De Santiago, I, Awan, S et al.. Transformers for rapid detection of airway stenosis and stridor. Sci Rep. 2025;15 (1):15394. doi: 10.1038/s41598-025-99369-y. PubMed PMID:40316652 PubMed Central PMC12048665.
  2. Moothedan, E, Boyer, M, Watts, S, Abdel-Aty, Y, Ghosh, S, Rameau, A et al.. The Bridge2AI-voice application: initial feasibility study of voice data acquisition through mobile health. Front Digit Health. 2025;7 :1514971. doi: 10.3389/fdgth.2025.1514971. PubMed PMID:40302934 PubMed Central PMC12037532.
  3. Cheng, AP, Widman, AJ, Arora, A, Rusinek, I, Sossin, A, Rajagopalan, S et al.. Error-corrected flow-based sequencing at whole-genome scale and its application to circulating cell-free DNA profiling. Nat Methods. 2025;22 (5):973-981. doi: 10.1038/s41592-025-02648-9. PubMed PMID:40217113 PubMed Central PMC12077166.
  4. Bélisle-Pipon, JC, Anibal, J, Bahr, R, Bedrick, S, Coleman, O, Dorr, D et al.. Interactive Panel Summaries of the 2024 Voice AI Symposium. Front Digit Health. 2025;7 :1484521. doi: 10.3389/fdgth.2025.1484521. PubMed PMID:40212896 PubMed Central PMC11983451.
  5. Nauseef, JT, Chu, TR, Hooper, WF, Alonso, A, Oku, A, Geiger, H et al.. A complex phylogeny of lineage plasticity in metastatic castration resistant prostate cancer. NPJ Precis Oncol. 2025;9 (1):91. doi: 10.1038/s41698-025-00854-4. PubMed PMID:40155466 PubMed Central PMC11953479.
  6. Bai, Z, Osman, M, Brendel, M, Tangen, CM, Flaig, TW, Thompson, IM et al.. Predicting response to neoadjuvant chemotherapy in muscle-invasive bladder cancer via interpretable multimodal deep learning. NPJ Digit Med. 2025;8 (1):174. doi: 10.1038/s41746-025-01560-y. PubMed PMID:40121304 PubMed Central PMC11929913.
  7. Vicario, R, Fragkogianni, S, Weber, L, Lazarov, T, Hu, Y, Hayashi, SY et al.. A microglia clonal inflammatory disorder in Alzheimer's disease. Elife. 2025;13 :. doi: 10.7554/eLife.96519. PubMed PMID:40085681 PubMed Central PMC11908784.
  8. Vicario, R, Fragkogianni, S, Pokrovskii, M, Meyer, C, Lopez-Rodrigo, E, Hu, Y et al.. Role of clonal inflammatory microglia in histiocytosis-associated neurodegeneration. Neuron. 2025;113 (7):1065-1081.e13. doi: 10.1016/j.neuron.2025.02.007. PubMed PMID:40081365 .
  9. El-Deiry, WS, Bresson, C, Wunder, F, Carneiro, BA, Dizon, DS, Warner, JL et al.. Worldwide Innovative Network (WIN) Consortium in Personalized Cancer Medicine: Bringing next-generation precision oncology to patients. Oncotarget. 2025;16 :140-162. doi: 10.18632/oncotarget.28703. PubMed PMID:40073368 PubMed Central PMC11907938.
  10. Kim, J, Ravichandran, H, Yoffe, L, Bhinder, B, Finos, K, Singh, A et al.. Simultaneous immunomodulation and epithelial-to-mesenchymal transition drives lung adenocarcinoma progression. bioRxiv. 2025; :. doi: 10.1101/2025.02.19.637138. PubMed PMID:40027685 PubMed Central PMC11870609.
  11. Rubinelli, L, Manzo, OL, Sungho, J, Del Gaudio, I, Bareja, R, Marino, A et al.. Suppression of endothelial ceramide de novo biosynthesis by Nogo-B contributes to cardiometabolic diseases. Nat Commun. 2025;16 (1):1968. doi: 10.1038/s41467-025-56869-9. PubMed PMID:40000621 PubMed Central PMC11862206.
  12. Setzen, SA, Andreadis, K, Elemento, O, Rameau, A. AI-Powered Laryngoscopy: Exploring the Future With Google Gemini. Laryngoscope. 2025; :. doi: 10.1002/lary.32089. PubMed PMID:39976345 .
  13. Kim, YE, Dobko, M, Li, H, Shao, T, Periyakoil, P, Tipton, C et al.. A Deep-Learning Model for Multi-class Audio Classification of Vocal Fold Pathologies in Office Stroboscopy. Laryngoscope. 2025; :. doi: 10.1002/lary.32036. PubMed PMID:39907244 .
  14. Delgado-de la Mora, J, Al Assaad, M, Karaaslan, S, Hadi, K, Halima, A, Deshpande, A et al.. Corrigendum to "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. 266 (2025) 155798]. Pathol Res Pract. 2025;266 :155825. doi: 10.1016/j.prp.2025.155825. PubMed PMID:39893087 .
  15. Madorsky Rowdo, FP, Martini, R, Ackermann, SE, Tang, CP, Tranquille, M, Irizarry, A et al.. Kinome-Focused CRISPR-Cas9 Screens in African Ancestry Patient-Derived Breast Cancer Organoids Identify Essential Kinases and Synergy of EGFR and FGFR1 Inhibition. Cancer Res. 2025;85 (3):551-566. doi: 10.1158/0008-5472.CAN-24-0775. PubMed PMID:39891928 PubMed Central PMC11790258.
  16. Guevara, D, Shin, N, Boiko, A, Valiev, I, Elsaeed, AG, Mosquera, JM et al.. Unusual Presentation of Advanced Urothelial Cancer in a Young Patient. Anticancer Res. 2025;45 (2):613-618. doi: 10.21873/anticanres.17448. PubMed PMID:39890191 .
  17. Guevara, D, Shin, N, Boiko, A, Valiev, I, Elsaeed, AG, Mosquera, JM et al.. Mesonephric Adenocarcinoma in a Young Male Patient. Anticancer Res. 2025;45 (2):619-623. doi: 10.21873/anticanres.17449. PubMed PMID:39890190 .
  18. Phipps, W, Bhinder, B, Towlerton, A, Mooka, P, Kafeero, J, Fitzgibbon, M et al.. Exome Sequencing Reveals a Sparse Genomic Landscape in Kaposi Sarcoma. Mol Cancer Res. 2025;23 (5):438-449. doi: 10.1158/1541-7786.MCR-24-0373. PubMed PMID:39883059 PubMed Central PMC12048277.
  19. Claridge, SE, Nath, S, Baum, A, Farias, R, Cavallo, JA, Rizvi, NM et al.. Functional genomics pipeline identifies CRL4 inhibition for the treatment of ovarian cancer. Clin Transl Med. 2025;15 (2):e70078. doi: 10.1002/ctm2.70078. PubMed PMID:39856363 PubMed Central PMC11761363.
  20. 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.
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