Khurana, Ekta

Publications

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selected publications

Recapitulation of patient-specific 3D chromatin conformation using machine learning. Cell reports methods. 2023 Academic Article GET IT
Impulsivity and Risk-Taking Behavior in School-Going Adolescents. Cureus. 2023 Academic Article GET IT
ETV4 mediates dosage-dependent prostate tumor initiation and cooperates with p53 loss to generate prostate cancer. Science advances. 2023 Academic Article GET IT
Modeling tissue-specific breakpoint proximity of structural variations from whole-genomes to identify cancer drivers. Nature communications. 2022 Academic Article GET IT
Tumor-intrinsic PRC2 inactivation drives a context-dependent immune-desert microenvironment and is sensitized by immunogenic viruses. The Journal of clinical investigation. 2022 Academic Article GET IT
Chromatin profiles classify castration-resistant prostate cancers suggesting therapeutic targets. Science (New York, N.Y.). 2022 Academic Article GET IT
Systems biology analysis of human genomes points to key pathways conferring spina bifida risk. Proceedings of the National Academy of Sciences of the United States of America. 2021 Academic Article GET IT
Developmental chromatin programs determine oncogenic competence in melanoma. Science (New York, N.Y.). 2021 Academic Article GET IT
Times cited: 1
Whole-genome characterization of lung adenocarcinomas lacking the RTK/RAS/RAF pathway. Cell reports. 2021 Academic Article GET IT
CNCDatabase: a database of non-coding cancer drivers. Nucleic acids research. 2021 Academic Article GET IT
Times cited: 8
Lineage Reversion Drives WNT Independence in Intestinal Cancer. Cancer discovery. 2020 Academic Article GET IT
Times cited: 42
Loss-of-function tolerance of enhancers in the human genome. PLoS genetics. 2020 Academic Article GET IT
Times cited: 7
DeepMILO: a deep learning approach to predict the impact of non-coding sequence variants on 3D chromatin structure. Genome biology. 2020 Academic Article GET IT
Times cited: 28
Passenger Mutations in More Than 2,500 Cancer Genomes: Overall Molecular Functional Impact and Consequences. Cell. 2020 Academic Article GET IT
Times cited: 74
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature. 2020 Academic Article GET IT
Times cited: 333
Genomic basis for RNA alterations in cancer. Nature. 2020 Academic Article GET IT
Times cited: 235
Pan-cancer analysis of whole genomes. Nature. 2020 Academic Article GET IT
Times cited: 1533
Pathway and network analysis of more than 2500 whole cancer genomes. Nature communications. 2020 Academic Article GET IT
Times cited: 62
Patterns of somatic structural variation in human cancer genomes. Nature. 2020 Academic Article GET IT
Times cited: 408
Identification of Cancer Drivers at CTCF Insulators in 1,962 Whole Genomes. Cell systems. 2019 Academic Article GET IT
Times cited: 47
FUN-LDA: A Latent Dirichlet Allocation Model for Predicting Tissue-Specific Functional Effects of Noncoding Variation: Methods and Applications. American journal of human genetics. 2018 Academic Article GET IT
Times cited: 58
Comprehensive Characterization of Cancer Driver Genes and Mutations. Cell. 2018 Academic Article GET IT
Times cited: 1204
MYBL1 rearrangements and MYB amplification in breast adenoid cystic carcinomas lacking the MYB-NFIB fusion gene. The Journal of pathology. 2017 Academic Article GET IT
Times cited: 71
Identification of novel prostate cancer drivers using RegNetDriver: a framework for integration of genetic and epigenetic alterations with tissue-specific regulatory network. Genome biology. 2017 Academic Article GET IT
Times cited: 24
Health beliefs regarding pediatric cerebral palsy among caregivers in Botswana: A qualitative study. Child: care, health and development. 2017 Academic Article GET IT
Times cited: 9
Inherited determinants of early recurrent somatic mutations in prostate cancer. Nature communications. 2017 Academic Article GET IT
Times cited: 24
Recurrent noncoding regulatory mutations in pancreatic ductal adenocarcinoma. Nature genetics. 2017 Academic Article GET IT
Times cited: 46
Using FunSeq2 for Coding and Non-Coding Variant Annotation and Prioritization. Current protocols in bioinformatics. 2017 Academic Article GET IT
Times cited: 1
Role of non-coding sequence variants in cancer. Nature reviews. Genetics. 2016 Information Resource GET IT
Times cited: 250
The Molecular Taxonomy of Primary Prostate Cancer. Cell. 2015 Academic Article GET IT
Times cited: 2119
LARVA: an integrative framework for large-scale analysis of recurrent variants in noncoding annotations. Nucleic acids research. 2015 Academic Article GET IT
Times cited: 54
Cellular superspreaders: an epidemiological perspective on HIV infection inside the body. PLoS pathogens. 2014 Academic Article GET IT
Times cited: 18
FunSeq2: a framework for prioritizing noncoding regulatory variants in cancer. Genome biology. 2014 Academic Article GET IT
Times cited: 231
Integrative annotation of variants from 1092 humans: application to cancer genomics. Science (New York, N.Y.). 2013 Academic Article GET IT
Times cited: 285
Interpretation of genomic variants using a unified biological network approach. PLoS computational biology. 2013 Academic Article GET IT
Times cited: 129
An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Academic Article GET IT
Times cited: 12176
Architecture of the human regulatory network derived from ENCODE data. Nature. 2012 Academic Article GET IT
Times cited: 1121
VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment. Bioinformatics (Oxford, England). 2012 Academic Article GET IT
Times cited: 54
A systematic survey of loss-of-function variants in human protein-coding genes. Science (New York, N.Y.). 2012 Academic Article GET IT
Times cited: 914
A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS biology. 2011 Academic Article GET IT
Times cited: 902
Mapping copy number variation by population-scale genome sequencing. Nature. 2011 Academic Article GET IT
Times cited: 854
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (New York, N.Y.). 2010 Academic Article GET IT
Times cited: 751
Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data. Genome research. 2010 Academic Article GET IT
Times cited: 56
Segmental duplications in the human genome reveal details of pseudogene formation. Nucleic acids research. 2010 Academic Article GET IT
Times cited: 24
Using semantic web rules to reason on an ontology of pseudogenes. Bioinformatics (Oxford, England). 2010 Academic Article GET IT
Times cited: 19
Computational study of drug binding to the membrane-bound tetrameric M2 peptide bundle from influenza A virus. Biochimica et biophysica acta. 2010 Academic Article GET IT
Times cited: 36
Comprehensive analysis of the pseudogenes of glycolytic enzymes in vertebrates: the anomalously high number of GAPDH pseudogenes highlights a recent burst of retrotrans-positional activity. BMC genomics. 2009 Academic Article GET IT
Times cited: 43
Computational analysis of membrane proteins: the largest class of drug targets. Drug discovery today. 2009 Information Resource GET IT
Times cited: 193
Artificial transmembrane oncoproteins smaller than the bovine papillomavirus E5 protein redefine sequence requirements for activation of the platelet-derived growth factor beta receptor. Journal of virology. 2009 Academic Article GET IT
Times cited: 20
Molecular dynamics calculations suggest a conduction mechanism for the M2 proton channel from influenza A virus. Proceedings of the National Academy of Sciences of the United States of America. 2009 Academic Article GET IT
Times cited: 105
Pseudofam: the pseudogene families database. Nucleic acids research. 2008 Academic Article GET IT
Times cited: 34
Probing peptide nanotube self-assembly at a liquid-liquid interface with coarse-grained molecular dynamics. Nano letters. 2008 Academic Article GET IT
Times cited: 34
Gemini surfactants at the air/water interface: a fully atomistic molecular dynamics study. The journal of physical chemistry. B. 2006 Academic Article GET IT
Self-assembling cyclic peptides: molecular dynamics studies of dimers in polar and nonpolar solvents. The journal of physical chemistry. B. 2006 Academic Article GET IT

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Research

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Co-investigator Network

Funding awarded

Computational and experimental methods for scalable identification of oncogenic non-coding regions awarded by National Cancer Institute Principal Investigator 2024 - 2029
Clinical identification and targeting of non-neuroendocrine lineage plasticity in castration-resistant prostate cancer awarded by United States Department of Defense Principal Investigator 2023 - 2026
Computational Methods for Identifying Non-Coding Cancer Drivers awarded by National Cancer Institute Principal Investigator 2018 - 2024

(PQ1) Adaptive immune and microbial mechanisms regulating Lynch syndrome penetrance awarded by National Cancer Institute Co-Investigator 2018 - 2024
Elucidating the Role of MALAT1 Somatic Driver Mutations in Colorectal Cancer awarded by National Cancer Institute Co-Investigator 2018 - 2024

The joint WCM-NYGC Center for Functional and Clinical Interpretation of Tumor Profiles awarded by National Cancer Institute Co-Principal Investigator 2021 - 2026

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Background

education and training

Ph.D., University of Pennsylvania 2008
M.Sc., Indian Institute of Technology (India) 2002
B.Sc., University of Delhi (India) 2000

Contact

full name

Ekta Khurana

primary email

ekk2003@med.cornell.edu

VIVO Weill Cornell Medical College

Ekta Khurana Associate Professor of Physiology and Biophysics

Publications

selected publications

Research

Funding awarded

Background

education and training

Contact

full name

primary email

Phone

Publications

selected publications

Research

Funding awarded

Background

education and training

Contact

full name

primary email