Thomas G. Paulson

This paper introduces a 3D microdissection method combining CNC milling and light-sheet microscopy to study tumor evolution in complex 3D structures.

This study evaluates the impact of a 3D pathology workflow on DNA, RNA, and protein integrity, showing minimal effect on amplifiability and transcriptomic profiles.

The paper models microbial community assembly dynamics in Barrett's esophagus and esophageal adenocarcinoma, finding neutral dynamics in normal tissue and BE but not EAC, with H. pylori showing non-neutral behavior in BE non-cancer outcomes.

The paper introduces OM2BFB, an algorithm detecting BFB amplifications using OGMs, showing high precision and recall, and finds BFB events are common in certain cancers but not linked to intratumoral heterogeneity or rapid genome change.

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.

The paper identifies three novel complex structural variation patterns in cancer genomes using genome graph analysis across 2,833 tumor WGS.