Englander Institute for Precision Medicine

Publications

Found 16 results
Author Title Type [ Year(Asc)]
Filters: Author is Khurana, Ekta  [Clear All Filters]
2023
Li D, Zhan Y, Wang N, Tang F, Lee CJ, Bayshtok G, Moore AR, Wong EWP, Pachai MR, Xie Y et al..  2023.  ETV4 mediates dosage-dependent prostate tumor initiation and cooperates with p53 loss to generate prostate cancer.. Sci Adv. 9(14):eadc9446.
Xu D, Forbes ANeil, Cohen S, Palladino A, Karadimitriou T, Khurana E.  2023.  Recapitulation of patient-specific 3D chromatin conformation using machine learning.. Cell Rep Methods. 3(9):100578.
2022
Tang F, Xu D, Wang S, Wong CKhuan, Martinez-Fundichely A, Lee CJ, Cohen S, Park J, Hill CE, Eng K et al..  2022.  Chromatin profiles classify castration-resistant prostate cancers suggesting therapeutic targets.. Science. 376(6596):eabe1505.
Martinez-Fundichely A, Dixon A, Khurana E.  2022.  Modeling tissue-specific breakpoint proximity of structural variations from whole-genomes to identify cancer drivers.. Nat Commun. 13(1):5640.
2021
Baggiolini A, Callahan SJ, Montal E, Weiss JM, Trieu T, Tagore MM, Tischfield SE, Walsh RM, Suresh S, Fan Y et al..  2021.  Developmental chromatin programs determine oncogenic competence in melanoma.. Science. 373(6559):eabc1048.
Aguiar-Pulido V, Wolujewicz P, Martinez-Fundichely A, Elhaik E, Thareja G, Aleem AAbdel, Chalhoub N, Cuykendall T, Al-Zamer J, Lei Y et al..  2021.  Systems biology analysis of human genomes points to key pathways conferring spina bifida risk.. Proc Natl Acad Sci U S A. 118(51)
Carrot-Zhang J, Yao X, Devarakonda S, Deshpande A, Damrauer JS, Silva TChedraoui, Wong CK, Choi HYoung, Felau I, A Robertson G et al..  2021.  Whole-genome characterization of lung adenocarcinomas lacking the RTK/RAS/RAF pathway.. Cell Rep. 34(5):108707.
2020
Rheinbay E, Nielsen MMuhlig, Abascal F, Wala JA, Shapira O, Tiao G, Hornshøj H, Hess JM, Juul RIstrup, Lin Z et al..  2020.  Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.. Nature. 578(7793):102-111.
Trieu T, Martinez-Fundichely A, Khurana E.  2020.  DeepMILO: a deep learning approach to predict the impact of non-coding sequence variants on 3D chromatin structure.. Genome Biol. 21(1):79.
Han T, Goswami S, Hu Y, Tang F, Zafra MPaz, Murphy C, Cao Z, Poirier JT, Khurana E, Elemento O et al..  2020.  Lineage Reversion Drives WNT Independence in Intestinal Cancer.. Cancer Discov. 10(10):1590-1609.
Xu D, Gokcumen O, Khurana E.  2020.  Loss-of-function tolerance of enhancers in the human genome.. PLoS Genet. 16(4):e1008663.
Kumar S, Warrell J, Li S, McGillivray PD, Meyerson W, Salichos L, Harmanci A, Martinez-Fundichely A, W Y Chan C, Nielsen MMuhlig et al..  2020.  Passenger Mutations in More Than 2,500 Cancer Genomes: Overall Molecular Functional Impact and Consequences.. Cell. 180(5):915-927.e16.
2019
Liu EMinwei, Martinez-Fundichely A, Diaz BJay, Aronson B, Cuykendall T, MacKay M, Dhingra P, Wong EWP, Chi P, Apostolou E et al..  2019.  Identification of Cancer Drivers at CTCF Insulators in 1,962 Whole Genomes.. Cell Syst. 8(5):446-455.e8.
2017
Dhingra P, Martinez-Fundichely A, Berger A, Huang FW, Forbes ANeil, Liu EMinwei, Liu D, Sboner A, Tamayo P, Rickman DS et al..  2017.  Identification of novel prostate cancer drivers using RegNetDriver: a framework for integration of genetic and epigenetic alterations with tissue-specific regulatory network.. Genome Biol. 18(1):141.
Romanel A, Garritano S, Stringa B, Blattner M, Dalfovo D, Chakravarty D, Soong D, Cotter KA, Petris G, Dhingra P et al..  2017.  Inherited determinants of early recurrent somatic mutations in prostate cancer.. Nat Commun. 8(1):48.
Dhingra P, Fu Y, Gerstein M, Khurana E.  2017.  Using FunSeq2 for Coding and Non-Coding Variant Annotation and Prioritization.. Curr Protoc Bioinformatics. 57:15.11.1-15.11.17.