Fudenberg, Geoffrey

Formation of chromosomal domains by loop extrusion

Fudenberg, G., Imakaev, M., Lu, C., Goloborodko, A., Abdennur, N., & Mirny, L. A. (2016) · Cell Reports

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 2,003

Iterative correction of Hi-C data reveals hallmarks of chromosome organization

Imakaev, M., Fudenberg, G., McCord, R. P., Naumova, N., Goloborodko, A., Lajoie, B. R., Dekker, J., & Mirny, L. A. (2012) · Nature Methods

Genomics and Chromatin DynamicsGenomic variations and chromosomal abnormalities

Cited by 1,423

Two independent modes of chromatin organization revealed by cohesin removal

Schwarzer, W., Abdennur, N., Goloborodko, A., Pekowska, A., Fudenberg, G., Loe-Mie, Y., Fonseca, N. A., Huber, W., Haering, C. H., Mirny, L., et al. (2017) · Nature

Genomics and Chromatin DynamicsNuclear Structure and Function

Cited by 1,196

Organization of the mitotic chromosome

Naumova, N., Imakaev, M., Fudenberg, G., Zhan, Y., Lajoie, B. R., Mirny, L. A., & Dekker, J. (2013) · Science

Genomics and Chromatin DynamicsChromosomal and Genetic Variations

Cited by 976

Heterochromatin drives compartmentalization of inverted and conventional nuclei

Falk, M., Feodorova, Y., Naumova, N., Imakaev, M., Lajoie, B. R., Leonhardt, H., Joffe, B., Dekker, J., Fudenberg, G., Solovei, I., et al. (2019) · Nature

Genomics and Chromatin DynamicsNuclear Structure and Function

Cited by 646

Cooltools: Enabling high-resolution Hi-C analysis in Python

Open2C, Abdennur, N., Abraham, S., Fudenberg, G., Flyamer, I. M., Galitsyna, A. A., Goloborodko, A., Imakaev, M., Oksuz, B. A., Venev, S. V., et al. (2024) · PLOS Computational Biology

Genomics and Chromatin DynamicsGenomics and Phylogenetic Studies

Cited by 313

Micro-C XL: assaying chromosome conformation from the nucleosome to the entire genome

Hsieh, T.-H. S., Fudenberg, G., Goloborodko, A., & Rando, O. J. (2016) · Nature Methods

Genomics and Chromatin DynamicsChromosomal and Genetic Variations

Cited by 216

FISH-ing for captured contacts: towards reconciling FISH and 3C

Fudenberg, G., & Imakaev, M. (2017) · Nature Methods

Genomics and Chromatin DynamicsChromosomal and Genetic Variations

Cited by 141

Chromatin loops as allosteric modulators of enhancer-promoter interactions

Doyle, B., Fudenberg, G., Imakaev, M., & Mirny, L. A. (2014) · PLoS Computational Biology

Genomics and Chromatin DynamicsDiffusion and Search Dynamics

Cited by 114

Synergy between regulatory elements can render cohesin dispensable for distal enhancer function

Hansen, K. L., Adachi, A. S., Braccioli, L., Kadvani, S., Boileau, R. M., Martinovic, M., Pokorny, B., Shah, R., Anderson, E. C., Zhang, K., et al. (2026) · Science

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 29

Dosage sensitivity of the loop extrusion rate confers tunability to genome folding while creating vulnerability to genetic disruption

Shah, R., Tortora, M. M. C., Louafi, N., Rahmaninejad, H., Hansen, K. L., Anderson, E. C., Wen, D., Giorgetti, L., Fudenberg, G., & Nora, E. P. (2025) · bioRxiv (Cold Spring Harbor Laboratory)

Genomics and Chromatin DynamicsNuclear Structure and Function

Cited by 15

Dynamic barriers modulate cohesin positioning and genome folding at fixed occupancy

Rahmaninejad, H., Xiao, Y., Tortora, M. M. C., & Fudenberg, G. (2025) · Genome Research

Genomics and Chromatin DynamicsProtein Structure and Dynamics

Cited by 8