Ekta Khurana, Ph.D.

Associate Professor of Physiology and Biophysics

  • Associate Professor of Computational Genomics in Computational Biomedicine
  • Co-Leader of the Genetics and Epigenetics Program, Meyer Cancer Center
  • Co-Director, Tri-Institutional PhD Program in Computational Biology and Medicine
  • WorldQuant Foundation Research Scholar

646-962-6374

1305 York Avenue, Room Y-13.06
New York, NY 10021

Lab website: http://khuranalab.med.cornell.edu/

Techniques

Research Areas

Member of:

Research Summary:

The research interests of the lab fall under the broad categories of genomics, computational biology and systems biology. We participate in multiple international genomics consortia and collaborate with scientists at Weill Cornell to develop novel approaches to understand the role of sequence variants in human disease. The decreasing costs of genome sequencing are leading to a growing repertoire of personal genomes. However, we are lagging behind in understanding the functional consequences of the millions of variants obtained from sequencing. This is also the case for somatic variants in cancer. An average cancer genome contains thousands of somatic variants – but the functional implications of these variants on cancer progression and growth are not clear. We develop integrative computational models to understand the relationship between genomic sequence variation and disease. The impact of sequence variants in non-protein-coding regions of the genome is especially less-well-understood. We have developed muliple computational approaches (for example, FunSeq and RegNetDriver) that integrate large-scale data from multiple resources to identify the DNA point mutations and rearrangements in protein-coding genes and non-coding regulatory regions leading to human disease, in particular cancer.

Recent Publications:

  1. Yost, KE, Zhao, Y, Hung, KL, Zhu, K, Xu, D, Corces, MR et al.. Three-dimensional genome landscape of primary human cancers. Nat Genet. 2025; :. doi: 10.1038/s41588-025-02188-0. PubMed PMID:40355593 .
  2. Breves, SL, Di Giammartino, DC, Nicholson, J, Cirigliano, S, Mahmood, SR, Lee, UJ et al.. Three-dimensional regulatory hubs support oncogenic programs in glioblastoma. Mol Cell. 2025;85 (7):1330-1348.e6. doi: 10.1016/j.molcel.2025.03.007. PubMed PMID:40147440 PubMed Central PMC12009607.
  3. Breves, SL, Di Giammartino, DC, Nicholson, J, Cirigliano, S, Mahmood, SR, Lee, UJ et al.. Three-dimensional regulatory hubs support oncogenic programs in glioblastoma. bioRxiv. 2024; :. doi: 10.1101/2024.12.20.629544. PubMed PMID:40034649 PubMed Central PMC11875237.
  4. Forbes, AN, Xu, D, Cohen, S, Pancholi, P, Khurana, E. Discovery of therapeutic targets in cancer using chromatin accessibility and transcriptomic data. Cell Syst. 2024;15 (9):824-837.e6. doi: 10.1016/j.cels.2024.08.004. PubMed PMID:39236711 PubMed Central PMC11415227.
  5. Sundaram, L, Kumar, A, Zatzman, M, Salcedo, A, Ravindra, N, Shams, S et al.. Single-cell chromatin accessibility reveals malignant regulatory programs in primary human cancers. Science. 2024;385 (6713):eadk9217. doi: 10.1126/science.adk9217. PubMed PMID:39236169 .
  6. Wong, EWP, Sahin, M, Yang, R, Lee, U, Zhan, YA, Misra, R et al.. TAD hierarchy restricts poised LTR activation and loss of TAD hierarchy promotes LTR co-option in cancer. bioRxiv. 2024; :. doi: 10.1101/2024.05.31.596845. PubMed PMID:38895201 PubMed Central PMC11185511.
  7. Xu, D, Forbes, AN, Cohen, S, Palladino, A, Karadimitriou, T, Khurana, E et al.. Recapitulation of patient-specific 3D chromatin conformation using machine learning. Cell Rep Methods. 2023;3 (9):100578. doi: 10.1016/j.crmeth.2023.100578. PubMed PMID:37673071 PubMed Central PMC10545938.
  8. Soni, U, Sharma, R, Sharma, M, Khurana, E, Chopra, J, Julka, D et al.. Impulsivity and Risk-Taking Behavior in School-Going Adolescents. Cureus. 2023;15 (6):e40728. doi: 10.7759/cureus.40728. PubMed PMID:37485185 PubMed Central PMC10360448.
  9. Li, D, Zhan, Y, Wang, N, Tang, F, Lee, CJ, Bayshtok, G et al.. ETV4 mediates dosage-dependent prostate tumor initiation and cooperates with p53 loss to generate prostate cancer. Sci Adv. 2023;9 (14):eadc9446. doi: 10.1126/sciadv.adc9446. PubMed PMID:37018402 PubMed Central PMC10075989.
  10. Yakneen, S, Waszak, SM, PCAWG Technical Working Group, Gertz, M, Korbel, JO, PCAWG Consortium et al.. Author Correction: Butler enables rapid cloud-based analysis of thousands of human genomes. Nat Biotechnol. 2023;41 (4):577. doi: 10.1038/s41587-022-01554-1. PubMed PMID:36944844 PubMed Central PMC10110458.
  11. Rodriguez-Martin, B, Alvarez, EG, Baez-Ortega, A, Zamora, J, Supek, F, Demeulemeester, J et al.. Author Correction: Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition. Nat Genet. 2023;55 (6):1080. doi: 10.1038/s41588-023-01319-9. PubMed PMID:36944736 PubMed Central PMC10260396.
  12. Akdemir, KC, Le, VT, Chandran, S, Li, Y, Verhaak, RG, Beroukhim, R et al.. Author Correction: Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer. Nat Genet. 2023;55 (6):1079. doi: 10.1038/s41588-023-01318-w. PubMed PMID:36944735 PubMed Central PMC10260394.
  13. Zapatka, M, Borozan, I, Brewer, DS, Iskar, M, Grundhoff, A, Alawi, M et al.. Author Correction: The landscape of viral associations in human cancers. Nat Genet. 2023;55 (6):1077. doi: 10.1038/s41588-023-01316-y. PubMed PMID:36944734 PubMed Central PMC10260395.
  14. Cortés-Ciriano, I, Lee, JJ, Xi, R, Jain, D, Jung, YL, Yang, L et al.. Author Correction: Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing. Nat Genet. 2023;55 (6):1076. doi: 10.1038/s41588-023-01315-z. PubMed PMID:36944733 PubMed Central PMC10260391.
  15. Yuan, Y, Ju, YS, Kim, Y, Li, J, Wang, Y, Yoon, CJ et al.. Author Correction: Comprehensive molecular characterization of mitochondrial genomes in human cancers. Nat Genet. 2023;55 (6):1078. doi: 10.1038/s41588-023-01317-x. PubMed PMID:36944732 PubMed Central PMC10260393.
  16. Alexandrov, LB, Kim, J, Haradhvala, NJ, Huang, MN, Tian Ng, AW, Wu, Y et al.. Author Correction: The repertoire of mutational signatures in human cancer. Nature. 2023;614 (7948):E41. doi: 10.1038/s41586-022-05600-5. PubMed PMID:36697836 PubMed Central PMC9931578.
  17. Li, Y, Roberts, ND, Wala, JA, Shapira, O, Schumacher, SE, Kumar, K et al.. Author Correction: Patterns of somatic structural variation in human cancer genomes. Nature. 2023;614 (7948):E38. doi: 10.1038/s41586-022-05597-x. PubMed PMID:36697835 PubMed Central PMC9931568.
  18. ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. Author Correction: Pan-cancer analysis of whole genomes. Nature. 2023;614 (7948):E39. doi: 10.1038/s41586-022-05598-w. PubMed PMID:36697834 PubMed Central PMC9931570.
  19. Gerstung, M, Jolly, C, Leshchiner, I, Dentro, SC, Gonzalez, S, Rosebrock, D et al.. Author Correction: The evolutionary history of 2,658 cancers. Nature. 2023;614 (7948):E42. doi: 10.1038/s41586-022-05601-4. PubMed PMID:36697833 PubMed Central PMC9931577.
  20. Rheinbay, E, Nielsen, MM, Abascal, F, Wala, JA, Shapira, O, Tiao, G et al.. Author Correction: Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature. 2023;614 (7948):E40. doi: 10.1038/s41586-022-05599-9. PubMed PMID:36697832 PubMed Central PMC9931557.
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