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Cold Spring Harbor Perspectives in Biology|August 17, 2021
Essential Roles for RNA in Shaping Nuclear OrganizationSofia A Quinodoz, Mitchell GuttmanMolecular Cell|September 29, 2020
High-Resolution Mapping of Multiway Enhancer-Promoter Interactions Regulating Pathogen DetectionPranitha Vangala, Rachel Murphy, Sofia A Quinodoz, et al.Cell Reports|November 30, 2022
Simultaneous mapping of 3D structure and nascent RNAs argues against nuclear compartments that preclude transcriptionIsabel N Goronzy, Sofia A Quinodoz, Joanna W Jachowicz, et al.Nature Protocols|January 11, 2022
SPRITE: a genome-wide method for mapping higher-order 3D interactions in the nucleus using combinatorial split-and-pool barcodingSofia A Quinodoz, Prashant Bhat, Peter Chovanec, et al.Biorxiv : the Preprint Server for Biology|January 30, 2023
3D genome organization around nuclear speckles drives mRNA splicing efficiencyPrashant Bhat, Amy Chow, Benjamin Emert, et al.Nature Methods|July 11, 2022
Integrative genome modeling platform reveals essentiality of rare contact events in 3D genome organizationsLorenzo Boninsegna, Asli Yildirim, Guido Polles, et al.Nature Biotechnology|August 24, 2021
Single-cell measurement of higher-order 3D genome organization with scSPRITEMary V Arrastia, Joanna W Jachowicz, Noah Ollikainen, et al.Cell|June 4, 2026
Deep learning of functional perturbations from condensate morphologyAnita Donlic, Troy J Comi, Sofia A Quinodoz, et al.Cell|November 5, 2021
RNA promotes the formation of spatial compartments in the nucleusSofia A Quinodoz, Joanna W Jachowicz, Prashant Bhat, et al.Biorxiv : the Preprint Server for Biology|May 4, 2026
Ribosome biogenesis bottlenecks reveal vulnerabilities in cancerLifei Jiang, Qiwei Yu, Sofia A Quinodoz, et al.Pageof 2