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q-bio.GN2026
ECLIPSE: A Composable Pipeline for Predicting ecDNA Formation, Evolution, and Therapeutic Vulnerabilities in Cancer
Bryan Cheng, Jasper Zhang
Extrachromosomal DNA (ecDNA) represents one of the most pressing challenges in cancer biology: circular DNA structures that amplify oncogenes, evade targeted therapies, and drive t…
q-bio.GN2026
The Mechanistic Invariance Test: Genomic Language Models Fail to Learn Positional Regulatory Logic
Bryan Cheng, Jasper Zhang
Genomic language models (gLMs) have transformed computational biology, achieving state-of-the-art performance across genomic tasks. Yet a fundamental question threatens the foundat…