Abdullah Kahraman

A web database and REST API of 124,687 AlphaFold 3 structures for human splice isoforms, annotated against canonical proteins for domains, decay, modifications, neoantigens and drug pockets.

This study uses single-cell long-read sequencing to analyze transcriptomes of ccRCC organoids, identifying novel transcripts and highlighting cell-specific alternative splicing events.

scROSHI identifies cell types without training data by using pre-existing gene sets and hierarchical relationships, outperforming methods in low-data and high-diversity scenarios.

CanIsoNet is a database that integrates isoform expression data with interaction networks and ClinVar annotations to predict the pathogenic impact of isoform switching events in diseases.

SCIM matches single-cell measurements across technologies by learning a technology-invariant latent space and applying bipartite matching, achieving high accuracy in real-world datasets.

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.

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

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.

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