Aziz Khan

ecDNAInspector identifies high-confidence ecDNA structures from WGS data, linking them to clinical and molecular features in breast cancer.

This study shows that many premalignant colorectal polyps contain multiple genetic lineages, indicating polyclonal origins rather than single-cell expansion.

The paper reassesses pathogenicity of variants in inherited retinal diseases using population-scale genomics in the UAE, identifying clinically relevant variants and highlighting discrepancies between clinical and population-based classifications.

The paper uses spatial imaging and computational analysis to identify features in metastatic tumors that predict response to immune checkpoint inhibition in TNBC patients.

The paper uses ultra high-throughput methylation sequencing to study DNA methylation changes during colorectal cancer progression from normal tissue to adenocarcinoma.

UniBind compiles high-confidence TF-DNA interactions from ChIP-seq data across nine species, predicting 56 million TFBSs and cis-regulatory modules.

The paper develops a computational method, mCross, to model RBP binding specificity using precise crosslink site registration and validates it with ENCODE eCLIP data.

The paper identifies key genomic and epigenomic signatures of super-enhancers and their constituents through integrative analysis and computational modeling.

The paper develops a method to predict direct TF-DNA interactions from ChIP-seq data and provides a resource of these interactions and cis-regulatory modules.

The paper compares super-enhancers and stretch enhancers across ten human cell types, finding super-enhancers are more transcriptionally active and cell-type-specific.

The paper introduces a RESTful API for accessing JASPAR data, enabling programmatic retrieval in multiple formats and supporting DNA binding domain sequence analysis.

Intervene is a tool for intersecting and visualizing multiple gene or genomic region sets, offering Venn diagrams, UpSet plots, and heat maps for analysis.

dbSUPER is a database of super-enhancers in mouse and human genomes, providing integrated resources for research on transcriptional control and disease.