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


Techniques

Research Areas


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. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. PCAWG Transcriptome Core Group, Calabrese, C, Davidson, NR, Demircioğlu, D, Fonseca, NA, He, Y et al.. Author Correction: Genomic basis for RNA alterations in cancer. Nature. 2023;614 (7948):E37. doi: 10.1038/s41586-022-05596-y. PubMed PMID:36697831 PubMed Central PMC9931574.
  16. Carlevaro-Fita, J, Lanzós, A, Feuerbach, L, Hong, C, Mas-Ponte, D, Pedersen, JS et al.. Author Correction: Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis. Commun Biol. 2022;5 (1):1347. doi: 10.1038/s42003-022-03769-z. PubMed PMID:36482178 PubMed Central PMC9732278.
  17. Rubanova, Y, Shi, R, Harrigan, CF, Li, R, Wintersinger, J, Sahin, N et al.. Author Correction: Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig. Nat Commun. 2022;13 (1):7567. doi: 10.1038/s41467-022-32336-7. PubMed PMID:36482170 PubMed Central PMC9731941.
  18. Sieverling, L, Hong, C, Koser, SD, Ginsbach, P, Kleinheinz, K, Hutter, B et al.. Author Correction: Genomic footprints of activated telomere maintenance mechanisms in cancer. Nat Commun. 2022;13 (1):7574. doi: 10.1038/s41467-022-32328-7. PubMed PMID:36481818 PubMed Central PMC9731961.
  19. Shuai, S, PCAWG Drivers and Functional Interpretation Working Group, Gallinger, S, Stein, LD, PCAWG Consortium. Author Correction: Combined burden and functional impact tests for cancer driver discovery using DriverPower. Nat Commun. 2022;13 (1):7571. doi: 10.1038/s41467-022-32343-8. PubMed PMID:36481739 PubMed Central PMC9732291.
  20. Cmero, M, Yuan, K, Ong, CS, Schröder, J, PCAWG Evolution and Heterogeneity Working Group, Corcoran, NM et al.. Author Correction: Inferring structural variant cancer cell fraction. Nat Commun. 2022;13 (1):7568. doi: 10.1038/s41467-022-32338-5. PubMed PMID:36481724 PubMed Central PMC9732297.
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