Publications

2025

Nature, 2025.
*Quinodoz SA, *Jiang L, Abu-Alfa AA, Comi TJ, Zhao H, Yu Q, Wiesner LW, Botello JF, Donlic A, Soehalim E, Bhat P, Zorbas C, Wacheul L, Košmrlj A, †Lafontaine DLJ, †Klinge S, †Brangwynne CP. Mapping and engineering RNA-driven architecture of the multiphase nucleolus. Nature. 2025;644:557-566.
*Contributed equally to this work, †Corresponding authors
Biorxiv, 2025.
Becker LA, Quinodoz SA, Comi TJ, Kimchi O, Knowles DA, Brangwynne CP. Genome-wide mapping of mesoscale neuronal RNA organization and condensation. bioRxiv. 2025;doi:10.1101/2025.04.19.649570

bioRxiv, 2024.
4D Nucleome Consortium, Dekker J, et al., […] Quinodoz SA […]. An integrated view of the structure and function of the human 4D nucleome. bioRxiv. 2024;doi:10.1101/2024.09.17.613111
eLife, 2024.
Chang YC, Quinodoz SA, Brangwynne CP. Live imaging of Alu elements reveals non-uniform euchromatin dynamics coupled to transcription. eLife. 2024;13:RP97537.
Nature, 2024.
Bhat P, Chow A, Emert B, Ettlin O, Quinodoz SA, Strehle M, Takei Y, Burr A, Goronzy IN, Chen AW, Huang W, Ferrer JLM, Soehalim E, Goh ST, Chari T, Sullivan DK, Blanco MR, Guttman M. Genome organization around nuclear speckles drives mRNA splicing efficiency. Nature. 2024;629(8014):1165-1173.

Molecular Cell, 2023.
Riback JA*, Eeftens JM*, Lee DSW*, Quinodoz SA, Donlic A, Orlovsky N, Wiesner L, Beckers L, Becker LA, Strom AR, Rana U, Tolbert M, Purse BW, Kliener R, Kriwacki R, Brangwynne CP. Viscoelasticity and advective flow of RNA underlies nucleolar form and function. Mol Cell. 2023;83(17):3095-3107.

Cell Reports, 2022.
*Goronzy I, *†Quinodoz SA, Jachowicz JW, Ollikainen N, Bhat P, †Guttman M. Simultaneous mapping of 3D structure and nascent RNAs argues against nuclear compartments that preclude transcription. Cell Rep. 2022;41(9):111730.
*Contributed equally to this work, order listed alphabetically
†Co-corresponding author
The Nucleus, 2nd Ed, 2022.
Quinodoz SA, Guttman M. Essential roles for RNA in shaping nuclear organization. In Pombo A, Hetzer MW, Misteli T (eds). The Nucleus. 2nd Ed. Cold Spring Harbor Laboratory Press. 2022.
Nature Protocols, 2022.
Quinodoz SA, Bhat P, Chovanec P, Jachowicz JW, Ollikainen N, Detmar E, Soehalim E, Guttman M. SPRITE: A genome-wide method for mapping higher-order 3D interactions in the nucleus using combinatorial split-and-pool barcoding. Nat Protoc. 2022;17(1):36-75.
Nature Methods, 2022.
Boninsegna S, Yildirim A, Polles G, Zhan Y, Quinodoz SA, Finn EH, Guttman M, Zhou XJ, Alber F. Integrative genome modeling platform reveals essentiality of rare contact events in 3D genome organizations. Nat Methods. 2022;19(8):938-949.
Nature Biotechnology, 2022.
Arrastia MV*, Jachowicz JW*, Ollikainen N, Curtis MS, Lai C, Quinodoz SA, Selck DA, Ismagilov RF, Guttman M. Single-cell measurement of higher-order 3D genome organization with scSPRITE. Nat Biotechnol. 2022;40(1):64-73.

Cell, 2021.
Quinodoz SA, Jachowicz JW, Bhat P, Ollikainen N, Banerjee AK, Goronzy IN, Blanco MR, Chovanec P, Chow A, Markaki Y, Thai J, Plath K, Guttman M. RNA promotes the formation of spatial compartments in the nucleus. Cell. 2021;184(23):5775-5790.

Molecular Cell.
Vangala P, Murphy R, Quinodoz SA, Gellatly K, McDonel P, Guttman M, Garber M. High-resolution mapping of multiway enhancer-promoter interactions regulating pathogen detection. Mol Cell. 2020;80(2):359-373.

Cell, 2018.
Quinodoz SA, Ollikainen N, Tabak B, Palla A, Schmidt JM, Detmar E, Lai M, Shishkin A, Bhat P, Takei Y, Trinh V, Aznauryan E, Russell P, Cheng C, Jovanovic M, Chow A, Cai L, McDonel P, Garber M, Guttman M. Higher-order inter-chromosomal hubs shape 3D genome organization in the nucleus. Cell. 2018;174(3):744-757.

Trends in Cell Biology, 2014.
Quinodoz S, Guttman M. Long noncoding RNAs: an emerging link between gene regulation and nuclear organization. Trends Cell Biol. 2014;24(11):651-663.