Ekta Khurana

cfOncoXpress: Tumor gene expression prediction from cell-free DNA whole-genome sequences

cfOncoXpress predicts tumor gene expression from cell-free DNA whole-genome sequences using fragmentation patterns and copy number aberrations, outperforming existing methods in prostate and breast cancers.

Genomic alterations in the YAP/TAZ pathway are associated with stem cell-like castration-resistant prostate cancer

The paper identifies genomic alterations in the YAP/TAZ pathway associated with stem cell-like castration-resistant prostate cancer using transcriptomic and whole-genome sequencing data.

TAD hierarchy restricts poised LTR activation and loss of TAD hierarchy promotes LTR co-option in cancer

The paper shows that TAD hierarchy restricts LTR activation, and its loss in cancer allows LTRs to act as alternative promoters, driving oncogene activation and transcriptional diversity.

BET inhibitors as a therapeutic intervention in gastrointestinal gene signature-positive castration-resistant prostate cancer.

This study identifies BET inhibitors as effective against GI transcriptome-positive CRPC by targeting HNF1A and HNF4G, improving outcomes in preclinical models.

Three-dimensional regulatory hubs support oncogenic programs in glioblastoma

This study identifies 3D regulatory hubs in glioblastoma stem cells and shows their role in oncogenic programs through computational and experimental analysis.

Discovery of novel therapeutic targets in cancer using patient-specific gene regulatory networks.

The paper identifies novel drug targets in cancer by constructing patient-specific gene regulatory networks using ATAC-seq and RNA-seq data.

Systems Biology Analysis of Human Genomes Points to Key Pathways Conferring Spina Bifida Risk

The paper uses systems biology analysis of whole-genome sequences from 298 SB case-control pairs to identify key pathways and genes associated with spina bifida risk.

Loss-of-function tolerance of enhancers in the human genome

The paper identifies LoF-tolerant enhancers in the human genome, finding they are more tissue-specific and regulate fewer genes, with predictions supported by disease enhancers and sequencing data.

A deep learning approach to predict the impact of non-coding sequence variants on 3D chromatin structure

This paper introduces DeepMILO, a deep learning model to predict how non-coding variants affect 3D chromatin loops, finding that mutations at loop boundaries are linked to upregulation of BCL2 in lymphoma.

Unique genomic features and deeply-conserved functions of long non-coding RNAs in the Cancer LncRNA Census (CLC)

The paper introduces the Cancer LncRNA Census (CLC), a curated resource of lncRNAs with causative roles in cancer, and shows their genomic and evolutionary features.

Whole genome and RNA sequencing of 1,220 cancers reveals hundreds of genes deregulated by rearrangement of cis-regulatory elements

The paper identifies hundreds of genes deregulated by SVs in cancer, showing increased expression linked to SV breakpoints and enhancer elements.

Integrative pathway enrichment analysis of multivariate omics data

ActivePathways integrates multivariate omics data to identify enriched pathways, revealing cancer driver genes and prognostic pathways in breast cancer.

Pathway and network analysis of more than 2,500 whole cancer genomes

The paper analyzes non-coding mutations across 2,583 cancer genomes to identify genes and pathways affected, finding clusters of interacting proteins and insights into cancer mechanisms.

Passenger mutations in 2500 cancer genomes: Overall molecular functional impact and consequences

The paper analyzes 2500 cancer genomes to assess the molecular functional impact of mutations, finding that some putative passenger variants may influence gene activity and contribute to cancer phenotypes.

Discovery and characterization of coding and non-coding driver mutations in more than 2,500 whole cancer genomes

The paper identifies and characterizes coding and non-coding driver mutations across 2,500 cancer genomes, revealing new candidates and questioning previous findings.

Patterns of structural variation in human cancer

The paper identifies nine structural variation signatures in cancer genomes, revealing patterns of deletions, tandem duplications, and translocations linked to replication mechanisms and oncogenic activation.

FUN-LDA: A latent Dirichlet allocation model for predicting tissue-specific functional effects of noncoding variation

FUN-LDA predicts tissue-specific functional effects of noncoding variants by integrating epigenetic data, showing higher accuracy than existing methods in eQTL and GWAS analyses.