Abdennur Lab

Data Science for Genomics

We’re an interdisciplinary computational group solving challenges of multiomic data science in biology and medicine.

We have a particular interest in problems concerning the spatial and functional organization of the genome: deciphering the states of chromatin and processes that act upon it to govern cell fate.

Infrastructure

Bioinformatic data structures, standards, storage modalities and data federation to make working with massive multi-omic data sets more effective.

Methods

AI/ML approaches to explore, integrate and comprehensively understand large, heterogeneous data sets.

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Biophysical modeling to explore mechanisms in silico

Insights

Hypothesis discovery and validation through interactive visualization and integrative analysis.

People

Nezar Abdennur, PhD

Nezar received his PhD from MIT in Leonid Mirny's group, specializing in the 3D organization of the genome and its relationship to the epigenome. His work has contributed to the discovery and understanding of the biophysical processes shaping genomes and laid foundational open source software for 3C/Hi-C analysis.

Select Publications

W Schwarzer*, N Abdennur*, A Goloborodko*, et al. Two independent modes of chromatin organization revealed by cohesin removal. Nature 551:51–56 (2017). doi: 10.1038/nature24281
LA Mirny, M Imakaev, and N Abdennur. Two major mechanisms of chromosome organization. Curr Opin Cell Biol 58:142–152. (2019) doi: 10.1016/j.ceb.2019.05.001
N Abdennur* and LA Mirny. Cooler: Cooler: scalable storage for Hi-C data and other genomically labeled arrays. Bioinformatics 30(1):311–316 (2020). doi: 10.1093/bioinformatics/btz540
G Spracklin*, N Abdennur*, et al. Diverse silent chromatin states modulate genome compartmentalization and loop extrusion barriers. Nat Struct Mol Biol 30:38–51. (2023). doi: 10.1038/s41594-022-00892-7