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

Foundational 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

Principal Investigator

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.

Vedat Yilmaz

Project Manager

Vedat is a former experimentalist with a deep passion for genomic data science. He has played a pivotal role in the safety of first-in-class medicines for rare diseases. As project manager, Vedat provides essential resources and supports our team and our collaborators across the research project lifecycle.

Garrett Ng, MD

Research Software Engineer

Garrett is a medical doctor turned software engineer specializing in building software systems for processing and analyzing biological data. His goal is to revolutionize healthcare by leveraging his expertise to unlock deeper insights from multiomic data.

Select Publications

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
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
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
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

Opportunities

Trainees, get in touch!

We are looking for motivated computational biologists to join our team.

Developers, contributors

Get involved in our communities (see below).