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. Nazha, A, Elemento, O, McWeeney, SK, Miles, M, Haferlach, T. How I read an article that uses machine learning methods. Blood Adv. 2023; :. doi: 10.1182/bloodadvances.2023010140. PubMed PMID:37276509 .
  2. Sloan, SL, Brown, F, Long, ME, Weigel, C, Koirala, S, Chung, JH et al.. PRMT5 supports multiple oncogenic pathways in mantle cell lymphoma. Blood. 2023; :. doi: 10.1182/blood.2022019419. PubMed PMID:37267517 .
  3. Bhinder, B, Ferguson, A, Sigouros, M, Uppal, M, Elsaeed, AG, Bareja, R et al.. The Immunogenomic Landscape of Neuroendocrine Prostate Cancer. Clin Cancer Res. 2023; :. doi: 10.1158/1078-0432.CCR-22-3743. PubMed PMID:37223924 .
  4. Kulm, S, Kaidi, AC, Kolin, D, Langhans, MT, Bostrom, MP, Elemento, O et al.. Genetic Risk Factors for End-Stage Hip Osteoarthritis Treated with Total Hip Arthroplasty: A Genome-Wide Association Study. J Arthroplasty. 2023; :. doi: 10.1016/j.arth.2023.05.006. PubMed PMID:37179025 .
  5. Scarpa, JR, Elemento, O. Multi-omic molecular profiling and network biology for precision anaesthesiology: a narrative review. Br J Anaesth. 2023; :. doi: 10.1016/j.bja.2023.03.006. PubMed PMID:37055274 .
  6. You, J, Reilly, MD, Eljalby, M, Bareja, R, Yusupova, M, Vyas, NS et al.. Soluble adenylyl cyclase contributes to imiquimod-mediated inflammation and is a potential therapeutic target in psoriasis. Exp Dermatol. 2023; :. doi: 10.1111/exd.14811. PubMed PMID:37039485 .
  7. Bakht, MK, Yamada, Y, Ku, SY, Venkadakrishnan, VB, Korsen, JA, Kalidindi, TM et al.. Landscape of prostate-specific membrane antigen heterogeneity and regulation in AR-positive and AR-negative metastatic prostate cancer. Nat Cancer. 2023;4 (5):699-715. doi: 10.1038/s43018-023-00539-6. PubMed PMID:37038004 .
  8. Huang, SH, Sartorello, G, Shen, PT, Xu, C, Elemento, O, Shvets, G et al.. Metasurface-enhanced infrared spectroscopy in multiwell format for real-time assaying of live cells. Lab Chip. 2023;23 (9):2228-2240. doi: 10.1039/d3lc00017f. PubMed PMID:37010356 PubMed Central PMC10159923.
  9. Shah, SB, Carlson, CR, Lai, K, Zhong, Z, Marsico, G, Lee, KM et al.. Combinatorial treatment rescues tumour-microenvironment-mediated attenuation of MALT1 inhibitors in B-cell lymphomas. Nat Mater. 2023;22 (4):511-523. doi: 10.1038/s41563-023-01495-3. PubMed PMID:36928381 PubMed Central PMC10069918.
  10. Bovonratwet, P, Kulm, S, Kolin, DA, Song, J, Morse, KW, Cunningham, ME et al.. Identification of Novel Genetic Markers for the Risk of Spinal Pathologies: A Genome-Wide Association Study of 2 Biobanks. J Bone Joint Surg Am. 2023; :. doi: 10.2106/JBJS.22.00872. PubMed PMID:36927824 .
  11. Ladewig, MS, Jacobsen, JOB, Wagner, AH, Danis, D, El Kassaby, B, Gargano, M et al.. GA4GH Phenopackets: A Practical Introduction. Adv Genet (Hoboken). 2023;4 (1):2200016. doi: 10.1002/ggn2.202200016. PubMed PMID:36910590 PubMed Central PMC10000265.
  12. Rajendran, S, Hu, Y, Canella, A, Peterson, C, Gross, A, Cam, M et al.. Single-cell RNA sequencing reveals immunosuppressive myeloid cell diversity during malignant progression in a murine model of glioma. Cell Rep. 2023;42 (3):112197. doi: 10.1016/j.celrep.2023.112197. PubMed PMID:36871221 .
  13. Wood, WA, Dilip, D, Derkach, A, Grover, NS, Elemento, O, Levine, R et al.. Wearable sensor-based performance status assessment in cancer: A pilot multicenter study from the Alliance for Clinical Trials in Oncology (A19_Pilot2). PLOS Digit Health. 2023;2 (1):e0000178. doi: 10.1371/journal.pdig.0000178. PubMed PMID:36812616 PubMed Central PMC9931326.
  14. Bhardwaj, P, Iyengar, NM, Zahid, H, Carter, KM, Byun, DJ, Choi, MH et al.. Obesity promotes breast epithelium DNA damage in women carrying a germline mutation in BRCA1 or BRCA2. Sci Transl Med. 2023;15 (684):eade1857. doi: 10.1126/scitranslmed.ade1857. PubMed PMID:36812344 .
  15. Liu, S, Benito-Martin, A, Pelissier Vatter, FA, Hanif, SZ, Liu, C, Bhardwaj, P et al.. Breast adipose tissue-derived extracellular vesicles from women with obesity stimulate mitochondrial-induced dysregulated tumor cell metabolism. bioRxiv. 2023; :. doi: 10.1101/2023.02.08.527715. PubMed PMID:36798307 PubMed Central PMC9934680.
  16. Rustam, S, Hu, Y, Mahjour, SB, Rendeiro, AF, Ravichandran, H, Urso, A et al.. A Unique Cellular Organization of Human Distal Airways and Its Disarray in Chronic Obstructive Pulmonary Disease. Am J Respir Crit Care Med. 2023;207 (9):1171-1182. doi: 10.1164/rccm.202207-1384OC. PubMed PMID:36796082 PubMed Central PMC10161760.
  17. Ruan, J, Moskowitz, A, Mehta-Shah, N, Sokol, L, Chen, Z, Kotlov, N et al.. Multicenter phase 2 study of oral azacitidine (CC-486) plus CHOP as initial treatment for PTCL. Blood. 2023;141 (18):2194-2205. doi: 10.1182/blood.2022018254. PubMed PMID:36796016 .
  18. Maura, F, Ziccheddu, B, Xiang, JZ, Bhinder, B, Rosiene, J, Abascal, F et al.. Molecular Evolution of Classic Hodgkin Lymphoma Revealed Through Whole-Genome Sequencing of Hodgkin and Reed Sternberg Cells. Blood Cancer Discov. 2023;4 (3):208-227. doi: 10.1158/2643-3230.BCD-22-0128. PubMed PMID:36723991 PubMed Central PMC10150291.
  19. 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 .
  20. 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 .
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