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. Melms, JC, Biermann, J, Huang, H, Wang, Y, Nair, A, Tagore, S et al.. Author Correction: A molecular single-cell lung atlas of lethal COVID-19. Nature. 2021; :. doi: 10.1038/s41586-021-03921-5. PubMed PMID:34625743 PubMed Central PMC8498978.
  2. Rivas, MA, Durmaz, C, Kloetgen, A, Chin, CR, Chen, Z, Bhinder, B et al.. Cohesin Core Complex Gene Dosage Contributes to Germinal Center Derived Lymphoma Phenotypes and Outcomes. Front Immunol. 2021;12 :688493. doi: 10.3389/fimmu.2021.688493. PubMed PMID:34621263 PubMed Central PMC8490713.
  3. McNally, DR, Elemento, O, Melnick, A. Dissecting bulk transcriptomes of diffuse large B cell lymphoma. Cancer Cell. 2021;39 (10):1305-1307. doi: 10.1016/j.ccell.2021.09.006. PubMed PMID:34597590 .
  4. Doane, AS, Chu, CS, Di Giammartino, DC, Rivas, MA, Hellmuth, JC, Jiang, Y et al.. OCT2 pre-positioning facilitates cell fate transition and chromatin architecture changes in humoral immunity. Nat Immunol. 2021;22 (10):1327-1340. doi: 10.1038/s41590-021-01025-w. PubMed PMID:34556886 .
  5. Elemento, O, Leslie, C, Lundin, J, Tourassi, G. Artificial intelligence in cancer research, diagnosis and therapy. Nat Rev Cancer. 2021; :. doi: 10.1038/s41568-021-00399-1. PubMed PMID:34535775 .
  6. Nilsson-Payant, BE, Uhl, S, Grimont, A, Doane, AS, Cohen, P, Patel, RS et al.. The NF-κB transcriptional footprint is essential for SARS-CoV-2 replication. J Virol. 2021; :JVI0125721. doi: 10.1128/JVI.01257-21. PubMed PMID:34523966 .
  7. Bloehdorn, J, Braun, A, Taylor-Weiner, A, Jebaraj, BMC, Robrecht, S, Krzykalla, J et al.. Multi-platform profiling characterizes molecular subgroups and resistance networks in chronic lymphocytic leukemia. Nat Commun. 2021;12 (1):5395. doi: 10.1038/s41467-021-25403-y. PubMed PMID:34518531 PubMed Central PMC8438057.
  8. Grbesa, I, Augello, MA, Liu, D, McNally, DR, Gaffney, CD, Huang, D et al.. Reshaping of the androgen-driven chromatin landscape in normal prostate cells by early cancer drivers and effect on therapeutic sensitivity. Cell Rep. 2021;36 (10):109625. doi: 10.1016/j.celrep.2021.109625. PubMed PMID:34496233 PubMed Central PMC8477443.
  9. Weissler, EH, Naumann, T, Andersson, T, Ranganath, R, Elemento, O, Luo, Y et al.. Correction to: The role of machine learning in clinical research: transforming the future of evidence generation. Trials. 2021;22 (1):593. doi: 10.1186/s13063-021-05571-4. PubMed PMID:34488840 PubMed Central PMC8419891.
  10. Matrai, CE, Ohara, K, Eng, KW, Glynn, SM, Chandra, P, Chatterjee-Paer, S et al.. Molecular Evaluation of Low-grade Low-stage Endometrial Cancer With and Without Recurrence. Int J Gynecol Pathol. 2021; :. doi: 10.1097/PGP.0000000000000798. PubMed PMID:34483300 .
  11. Weissler, EH, Naumann, T, Andersson, T, Ranganath, R, Elemento, O, Luo, Y et al.. The role of machine learning in clinical research: transforming the future of evidence generation. Trials. 2021;22 (1):537. doi: 10.1186/s13063-021-05489-x. PubMed PMID:34399832 PubMed Central PMC8365941.
  12. Shohdy, KS, Bareja, R, Sigouros, M, Wilkes, DC, Dorsaint, P, Manohar, J et al.. Functional comparison of exome capture-based methods for transcriptomic profiling of formalin-fixed paraffin-embedded tumors. NPJ Genom Med. 2021;6 (1):66. doi: 10.1038/s41525-021-00231-7. PubMed PMID:34385467 PubMed Central PMC8360986.
  13. Marderstein, AR, Kulm, S, Peng, C, Tamimi, R, Clark, AG, Elemento, O et al.. A polygenic-score-based approach for identification of gene-drug interactions stratifying breast cancer risk. Am J Hum Genet. 2021;108 (9):1752-1764. doi: 10.1016/j.ajhg.2021.07.008. PubMed PMID:34363748 PubMed Central PMC8456164.
  14. Cho, BA, Iyengar, NM, Zhou, XK, Morrow, M, Giri, DD, Verma, A et al.. Blood Biomarkers Reflect the Effects of Obesity and Inflammation on the Human Breast Transcriptome. Carcinogenesis. 2021; :. doi: 10.1093/carcin/bgab066. PubMed PMID:34314488 .
  15. Al Zoughbi, W, Fox, J, Beg, S, Papp, E, Hissong, E, Ohara, K et al.. Validation of a Circulating Tumor DNA-Based Next-Generation Sequencing Assay in a Cohort of Patients with Solid tumors: A Proposed Solution for Decentralized Plasma Testing. Oncologist. 2021; :. doi: 10.1002/onco.13905. PubMed PMID:34286887 .
  16. Jobanputra, V, Wrzeszczynski, KO, Buttner, R, Caldas, C, Cuppen, E, Grimmond, S et al.. Clinical interpretation of whole-genome and whole-transcriptome sequencing for precision oncology. Semin Cancer Biol. 2021; :. doi: 10.1016/j.semcancer.2021.07.003. PubMed PMID:34256129 .
  17. Cox, N, Crozet, L, Holtman, IR, Loyher, PL, Lazarov, T, White, JB et al.. Diet-regulated production of PDGFcc by macrophages controls energy storage. Science. 2021;373 (6550):. doi: 10.1126/science.abe9383. PubMed PMID:34210853 .
  18. Croker, JA, Patel, R, Campbell, KS, Barton-Baxter, M, Wallet, S, Firestein, GS et al.. Building biorepositories in the midst of a pandemic. J Clin Transl Sci. 2021;5 (1):e92. doi: 10.1017/cts.2021.6. PubMed PMID:34192049 PubMed Central PMC8134891.
  19. Rosenquist, R, Cuppen, E, Buettner, R, Caldas, C, Dreau, H, Elemento, O et al.. Clinical utility of whole-genome sequencing in precision oncology. Semin Cancer Biol. 2021; :. doi: 10.1016/j.semcancer.2021.06.018. PubMed PMID:34175442 .
  20. Napoli, S, Cascione, L, Rinaldi, A, Spriano, F, Guidetti, F, Zhang, F et al.. Characterization of GECPAR, a noncoding RNA that regulates the transcriptional program of diffuse large B cell lymphoma. Haematologica. 2021; :. doi: 10.3324/haematol.2020.267096. PubMed PMID:34162177 .
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