Publications

Click for a full list of publications

Selected papers and preprints from the lab:

TCF-1 promotes chromatin interactions across topologically associating domains in T cell progenitors.
Wang W, Chandra A, Goldman N, Yoon S, Ferrari EK, Nguyen SC, Joyce EF, Vahedi G. Nat Immunol. 2022 Jul. PMID: 35726060.

Preprint: NIPBL and WAPL balance cohesin activity to regulate chromatin folding and gene expression.
Luppino JM, Field A, Nguyen SC, Park DS, Shah PP, Lan Y, Yunker R, Jain R, Adelman K, Joyce EF. biorxiv. 2022

Preprint: High-throughput Oligopaint screen identifies druggable regulators of genome folding.
Park DS, Nguyen SC, Isenhart R, Shah PP, Kim W, Barnett RJ, Chandra A, Luppino JM, Harke J, Wai M, Yang R, Lan Y, Yoon S, Yunker R, Vahedi G, Phillips-Cremins JE, Jain R, Joyce EF. biorxiv. 2022

BRD4 orchestrates genome folding to promote neural crest differentiation.
Linares-Saldana R, Kim W, Bolar NA, Zhang H, Koch-Bojalad BA, Yoon S, Shah PP, Karnay A, Park DS, Luppino JM, Nguyen SC, Padmanabhan A, Smith CL, Poleshko A, Wang Q, Li L, Srivastava D, Vahedi G, Eom GH, Blobel GA, Joyce EF, Jain R. Nature Genetics. 2021 Oct 5. PMID: 34611363.

p53 mediates target gene association with nuclear speckles for amplified RNA expression.
Alexander KA, Coté A, Nguyen SC, Zhang L, Gholamalamdari O, Agudelo-Garcia P, Lin-Shiao E, Tanim KMA, Lim J, Biddle N, Dunagin MC, Good CR, Mendoza MR, Little SC, Belmont A, Joyce EF, Raj A, Berger SL. Molecular Cell. 2021 Apr 15. PMID: 33823140.

Large-Scale Topological Changes Restrain Malignant Progression in Colorectal Cancer.
Johnstone SE, Reyes A, Qi Y, Adriaens C, Hegazi E, Pelka K, Chen JH, Zou LS, Drier Y, Hecht V, Shoresh N, Selig MK, Lareau CA, Iyer S, Nguyen SC, Joyce EF, Hacohen N, Irizarry RA, Zhang B, Aryee MJ, Bernstein BE. Cell. 2020 Aug 18. PMID: 32841603.

Cohesin promotes stochastic domain intermingling to ensure proper regulation of boundary-proximal genes.
Luppino JM, Park DS, Nguyen SC, Lan Y, Xu Z, Yunker R, Joyce EF. Nature Genetics. 2020. Jun 22. PMID: 32572210.
Associated News & Views: TADs without borders. Farabella I, Marti-Renom MA. Nat Genet. 2020 Aug. PMID: 32747821

Single cell analysis pushes the boundaries of TAD formation and function.
Luppino JM and Joyce EF. Curr Opin Genet Dev.. 2020. Apr 14. PMID: 32302920.

Core components of the nuclear pore bind distinct states of chromatin and contribute to polycomb repression.
Gozalo A, Duke A, Lan Y, Pascual-Garcia P, Talamas JA, Nguyen SC, Shah PP, Jain R, Joyce EF, Capelson M. Mol Cell. 2019. Nov 20. PMID: 31784359.

Chromosome territory formation attenuates the translocation potential of cells.
Rosin LF, Crocker O, Isenhart RL, Nguyen SC, Xu Z, Joyce EF. Elife. 2019. Nov. PMID: 31682226.

H3K9me2 orchestrates inheritance of spatial positioning of peripheral heterochromatin through mitosis.
Poleshko A, Smith CL, Nguyen SC, Sivaramakrishnan P, Wong KG, Murray JI, Lakadamyali M, Joyce EF, Jain R, Epstein JA. Elife. 2019. Oct. PMID: 31573510.

Programmable Chromosome Painting with Oligopaints.
Nguyen SC and Joyce EF. Methods in Molecular Biology. 2019. Aug. PMID: 31407284

ARID1A spatially partitions interphase chromosomes.
Wu S, Fatkhutdinov N, Rosin L, Luppino JM, Iwasaki O, Tanizawa H, Tang HY, Kossenkov AV, Gardini A, Noma KI, Speicher DW, Joyce EF, Zhang R. Science Advances. 2019. May. PMID: 31131328.

Recurrent losses and rapid evolution of the condensin II complex in insects.
King TD, Leonard CJ, Cooper JC, Nguyen SC, Joyce EF, Phadnis N. Molecular Biology and Evolution. 2019. July. PMID: 31270536

Condensin II drives large-scale folding and spatial partitioning of interphase chromosomes in Drosophila nuclei.
Rosin LF, Nguyen SC, Joyce EF. PLoS Genetics. 2018. July. PMID: 30001329.

Toward High-Throughput and Multiplexed Imaging of Genome Organization.
Joyce EF. Assay and Drug Development Technologies. 2017 Jan. PMID: 28092459.