Jens Luebeck

This paper introduces ecEvol, a method to infer ecDNA emergence time and other parameters from bulk whole-genome sequencing data, finding that ecDNA typically emerges early and is associated with poorer survival.

This study examines ecDNA in lung cancer, finding it in 18.9% of patients and associating it with worse survival and genomic instability.

This study compares ecDNA prevalence, conservation, and clonal dynamics in PDX models and primary tumors of childhood cancers, finding high sequence conservation and selective growth advantage of ecDNA-positive clones.

Cycle-Extractor accurately reconstructs ecDNA structures from both short- and long-read sequencing data, outperforming existing methods in speed and completeness.

This study identifies subtype-specific mutational mechanisms and links them to host metabolic factors in endometrial cancer using genomic and transcriptomic data from 440 tumors.

scAmp detects and analyzes ecDNA at single-cell resolution, showing its impact on chromatin accessibility in cancer cells.

The paper introduces ec3D, a method to reconstruct 3D structures of ecDNA from Hi-C data, revealing spherical configurations and unique long-range interactions in cancer.

The paper identifies enhancer-like elements on ecDNA in colorectal cancer that are derived from transposable elements and are functionally active in cancer cell fitness.

This study investigates the spatial-temporal evolution of extrachromosomal DNA (ecDNA) in glioblastoma, showing that EGFR ecDNA drives tumor evolution and identifies a potential therapeutic window for early intervention.

The paper shows that ecDNA-borne PVT1 fusions stabilize oncogenic mRNAs by interacting with SRSF1, enhancing RNA stability and supporting MYC dependency in cancer.

This paper identifies how PVT1 rearrangements in MYC+ cancers generate oncogenic peptides that synergistically activate MYC, AKT, and RAS-MAPK pathways, enhancing tumor aggressiveness.

This paper identifies transcription-replication conflict as a vulnerability in ecDNA-containing cancers and demonstrates that CHK1 inhibition selectively kills these tumors.

AmpliconSuite identifies focal amplifications in cancer genomes, showing ecDNA has higher copy numbers and stronger oncogene enrichment compared to other amplification types.

CoRAL improves ecDNA structure reconstruction using long-read sequencing, outperforming short-read methods in simulations and cell-line datasets.

The paper investigates the development and evolution of extrachromosomal DNA (ecDNA) in Barrett's esophagus patients progressing to esophageal adenocarcinoma, finding ecDNA is strongly associated with cancer progression and enriched for oncogenes and immunomodulatory genes.

AmpliconReconstructor integrates optical mapping and NGS to resolve focal amplifications in cancer, revealing complex structures and origins of ecDNA and other rearrangements.

AmpliconArchitect reconstructs focal amplifications in cancer genomes, revealing novel insights into extrachromosomal mechanisms and oncoviral pathogenesis.