Ekta Khurana, Ph.D.

Associate Professor of Physiology and Biophysics

  • Associate Professor of Computational Genomics in Computational Biomedicine in the Institute for Computational Biomedicine
  • Co-leader of the Genetics and Epigenetics Program, Meyer Cancer Center
  • Associate Director, Tri-Institutional PhD Program in Computational Biology and Medicine


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


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. Martinez-Fundichely, A, Dixon, A, Khurana, E. Modeling tissue-specific breakpoint proximity of structural variations from whole-genomes to identify cancer drivers. Nat Commun. 2022;13 (1):5640. doi: 10.1038/s41467-022-32945-2. PubMed PMID:36163358 PubMed Central PMC9512825.
  2. Yan, J, Chen, Y, Patel, AJ, Warda, S, Lee, CJ, Nixon, BG et al.. Tumor-intrinsic PRC2 inactivation drives a context-dependent immune-desert microenvironment and is sensitized by immunogenic viruses. J Clin Invest. 2022;132 (17):. doi: 10.1172/JCI153437. PubMed PMID:35852856 PubMed Central PMC9433107.
  3. Tang, F, Xu, D, Wang, S, Wong, CK, Martinez-Fundichely, A, Lee, CJ et al.. Chromatin profiles classify castration-resistant prostate cancers suggesting therapeutic targets. Science. 2022;376 (6596):eabe1505. doi: 10.1126/science.abe1505. PubMed PMID:35617398 PubMed Central PMC9299269.
  4. Aguiar-Pulido, V, Wolujewicz, P, Martinez-Fundichely, A, Elhaik, E, Thareja, G, Abdel Aleem, A et al.. Systems biology analysis of human genomes points to key pathways conferring spina bifida risk. Proc Natl Acad Sci U S A. 2021;118 (51):. doi: 10.1073/pnas.2106844118. PubMed PMID:34916285 PubMed Central PMC8713748.
  5. Baggiolini, A, Callahan, SJ, Montal, E, Weiss, JM, Trieu, T, Tagore, MM et al.. Developmental chromatin programs determine oncogenic competence in melanoma. Science. 2021;373 (6559):eabc1048. doi: 10.1126/science.abc1048. PubMed PMID:34516843 PubMed Central PMC9440978.
  6. Carrot-Zhang, J, Yao, X, Devarakonda, S, Deshpande, A, Damrauer, JS, Silva, TC et al.. Whole-genome characterization of lung adenocarcinomas lacking alterations in the RTK/RAS/RAF pathway. Cell Rep. 2021;34 (8):108784. doi: 10.1016/j.celrep.2021.108784. PubMed PMID:33626341 PubMed Central PMC8608252.
  7. Carrot-Zhang, J, Yao, X, Devarakonda, S, Deshpande, A, Damrauer, JS, Silva, TC et al.. Whole-genome characterization of lung adenocarcinomas lacking the RTK/RAS/RAF pathway. Cell Rep. 2021;34 (5):108707. doi: 10.1016/j.celrep.2021.108707. PubMed PMID:33535033 PubMed Central PMC8009291.
  8. Bailey, MH, Meyerson, WU, Dursi, LJ, Wang, LB, Dong, G, Liang, WW et al.. Author Correction: Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nat Commun. 2020;11 (1):6232. doi: 10.1038/s41467-020-20128-w. PubMed PMID:33257764 PubMed Central PMC7705717.
  9. Liu, EM, Martinez-Fundichely, A, Bollapragada, R, Spiewack, M, Khurana, E. CNCDatabase: a database of non-coding cancer drivers. Nucleic Acids Res. 2021;49 (D1):D1094-D1101. doi: 10.1093/nar/gkaa915. PubMed PMID:33095860 PubMed Central PMC7778916.
  10. Bailey, MH, Meyerson, WU, Dursi, LJ, Wang, LB, Dong, G, Liang, WW et al.. Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nat Commun. 2020;11 (1):4748. doi: 10.1038/s41467-020-18151-y. PubMed PMID:32958763 PubMed Central PMC7505971.
  11. Li, CH, Prokopec, SD, Sun, RX, Yousif, F, Schmitz, N, PCAWG Tumour Subtypes and Clinical Translation et al.. Sex differences in oncogenic mutational processes. Nat Commun. 2020;11 (1):4330. doi: 10.1038/s41467-020-17359-2. PubMed PMID:32859912 PubMed Central PMC7455744.
  12. Han, T, Goswami, S, Hu, Y, Tang, F, Zafra, MP, Murphy, C et al.. Lineage Reversion Drives WNT Independence in Intestinal Cancer. Cancer Discov. 2020;10 (10):1590-1609. doi: 10.1158/2159-8290.CD-19-1536. PubMed PMID:32546576 PubMed Central PMC7541594.
  13. Xu, D, Gokcumen, O, Khurana, E. Loss-of-function tolerance of enhancers in the human genome. PLoS Genet. 2020;16 (4):e1008663. doi: 10.1371/journal.pgen.1008663. PubMed PMID:32243438 PubMed Central PMC7159235.
  14. Trieu, T, Martinez-Fundichely, A, Khurana, E. DeepMILO: a deep learning approach to predict the impact of non-coding sequence variants on 3D chromatin structure. Genome Biol. 2020;21 (1):79. doi: 10.1186/s13059-020-01987-4. PubMed PMID:32216817 PubMed Central PMC7098089.
  15. Kumar, S, Warrell, J, Li, S, McGillivray, PD, Meyerson, W, Salichos, L et al.. Passenger Mutations in More Than 2,500 Cancer Genomes: Overall Molecular Functional Impact and Consequences. Cell. 2020;180 (5):915-927.e16. doi: 10.1016/j.cell.2020.01.032. PubMed PMID:32084333 PubMed Central PMC7210002.
  16. PCAWG Transcriptome Core Group, Calabrese, C, Davidson, NR, Demircioğlu, D, Fonseca, NA, He, Y et al.. Genomic basis for RNA alterations in cancer. Nature. 2020;578 (7793):129-136. doi: 10.1038/s41586-020-1970-0. PubMed PMID:32025019 PubMed Central PMC7054216.
  17. Rheinbay, E, Nielsen, MM, Abascal, F, Wala, JA, Shapira, O, Tiao, G et al.. Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature. 2020;578 (7793):102-111. doi: 10.1038/s41586-020-1965-x. PubMed PMID:32025015 PubMed Central PMC7054214.
  18. Li, Y, Roberts, ND, Wala, JA, Shapira, O, Schumacher, SE, Kumar, K et al.. Patterns of somatic structural variation in human cancer genomes. Nature. 2020;578 (7793):112-121. doi: 10.1038/s41586-019-1913-9. PubMed PMID:32025012 PubMed Central PMC7025897.
  19. ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. Pan-cancer analysis of whole genomes. Nature. 2020;578 (7793):82-93. doi: 10.1038/s41586-020-1969-6. PubMed PMID:32025007 PubMed Central PMC7025898.
  20. Carlevaro-Fita, J, Lanzós, A, Feuerbach, L, Hong, C, Mas-Ponte, D, Pedersen, JS et al.. Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis. Commun Biol. 2020;3 (1):56. doi: 10.1038/s42003-019-0741-7. PubMed PMID:32024996 PubMed Central PMC7002399.
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