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Nature Methods|June 13, 2017
FISH-ing for captured contacts: towards reconciling FISH and 3CGeoffrey Fudenberg, Maxim ImakaevCurrent Opinion in Genetics & Development|February 25, 2012
Higher-order chromatin structure: bridging physics and biologyGeoffrey Fudenberg, Leonid A MirnyProceedings of the National Academy of Sciences of the United States of America|August 7, 2023
HP1-driven phase separation recapitulates the thermodynamics and kinetics of heterochromatin condensate formationMaxime M C Tortora, Lucy D Brennan, Gary Karpen, et al.Science Advances|August 14, 2020
Chiral shape fluctuations and the origin of chirality in cholesteric phases of DNA origamisMaxime M C Tortora, Garima Mishra, Domen Prešern, et al.Current Opinion in Genetics & Development|January 25, 2025
Recipes and ingredients for deep learning models of 3D genome foldingPaulina N Smaruj, Yao Xiao, Geoffrey FudenbergBiorxiv : the Preprint Server for Biology|June 12, 2026
CLASH (Chromatin Loop Across-sample Score Harmonizer) quantifies the relative contributions of genetic variation, methylation, and CTCF occupancy on chromatin loop strength across individualsValmik Ranparia, , Geoffrey Fudenberg, et al.FEBS Letters|September 15, 2015
Modeling chromosomes: Beyond pretty picturesMaxim V Imakaev, Geoffrey Fudenberg, Leonid A MirnyCurrent Opinion in Genetics & Development|March 9, 2023
4D epigenomics: deciphering the coupling between genome folding and epigenomic regulation with biophysical modelingAmith Z Abdulla, Hossein Salari, Maxime M C Tortora, et al.Biorxiv : the Preprint Server for Biology|May 7, 2026
Sequence design for three-dimensional genome folding using Akita SemifreddoPaulina N Smaruj, David R Kelley, Geoffrey FudenbergPlos Computational Biology|October 24, 2014
Chromatin loops as allosteric modulators of enhancer-promoter interactionsBoryana Doyle, Geoffrey Fudenberg, Maxim Imakaev, et al.Pageof 6