Nezar Abdennur
I am an Assistant Professor in the Department of Genomics and Computational Biology and the Department of Systems Biology at UMass Chan Medical School.
I lead a computational research group (https://abdenlab.org) with a dual mandate. My group's biological research focuses on the 3D organization of the genome (3C/Hi-C technologies), its relationship to the epigenome, and the resulting manifold influences on cellular fate, differentiation, aging, and disease. My group's open-source interests are in supporting foundational infrastructure to improve AI and data science for genomics and multi-omics, especially in the scientific Python ecosystem.
Session
Genomic workflows remain tightly coupled to specialized file formats, forcing researchers to build brittle pipelines of format-specific CLI tools. We present projects that help shift this emphasis away from file parsing and towards declarative querying. Oxbow is a library that projects common genomic formats into Apache Arrow, enabling zero-copy integration with data frame libraries and analytics engines. GIQL (Genomic Interval Query Language) is an extended SQL dialect supporting genomic interval operations and semantics that transpiles to standard SQL, making genomic queries composable, readable, and backend-agnostic. Together, this architecture also facilitates the integration of genomic data into data warehouse and lakehouse platforms as well as agentic MCP workflows.