Bayesian Image Recovery for Dendritic Structures Under Low Signal-to-Noise Conditions. - Geoffrey Fudenberg; Liam Paninski (IEEE Trans. Image Process., 2009)

Chromatin Loops as Allosteric Modulators of Enhancer-Promoter Interactions. - Boryana Doyle; Geoffrey Fudenberg; Maxim Imakaev; Leonid A. Mirny (PLoS Comput. Biol., 2014)

History of chromosome rearrangements reflects the spatial organization of yeast chromosomes. - Ekaterina Khrameeva; Geoffrey Fudenberg; Mikhail S. Gelfand; Leonid A. Mirny (J. Bioinform. Comput. Biol., 2016)

Cooltools: Enabling high-resolution Hi-C analysis in Python. - Nezar Abdennur; Sameer Abraham; Geoffrey Fudenberg; Ilya M. Flyamer; Aleksandra A. Galitsyna; Anton Goloborodko; Maxim Imakaev; Betul A. Oksuz; Sergey Venev; Yao Xiao (PLoS Comput. Biol., 2024)

Pairtools: From sequencing data to chromosome contacts. - Nezar Abdennur; Geoffrey Fudenberg; Ilya M. Flyamer; Aleksandra A. Galitsyna; Anton Goloborodko; Maxim Imakaev; Sergey Venev (PLoS Comput. Biol., 2024)

Bioframe: operations on genomic intervals in Pandas dataframes. - Nezar Abdennur; Geoffrey Fudenberg; Ilya M. Flyamer; Aleksandra A. Galitsyna; Anton Goloborodko; Maxim Imakaev; Sergey Venev (Bioinform., 2024)

Interpreting the CTCF-mediated sequence grammar of genome folding with AkitaV2. - Paulina N. Smaruj; Fahad Kamulegeya; David R. Kelley; Geoffrey Fudenberg (PLoS Comput. Biol., 2025)