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Paircounting.
Nguyen HQ, Lee SD, Wu CT. Nguyen HQ, et al. Trends Genet. 2019 Nov;35(11):787-790. doi: 10.1016/j.tig.2019.07.010. Epub 2019 Sep 12. Trends Genet. 2019. PMID: 31521404 Free PMC article.
Transcription-mediated supercoiling regulates genome folding and loop formation.
Neguembor MV, Martin L, Castells-García Á, Gómez-García PA, Vicario C, Carnevali D, AlHaj Abed J, Granados A, Sebastian-Perez R, Sottile F, Solon J, Wu CT, Lakadamyali M, Cosma MP. Neguembor MV, et al. Mol Cell. 2021 Aug 5;81(15):3065-3081.e12. doi: 10.1016/j.molcel.2021.06.009. Epub 2021 Jul 22. Mol Cell. 2021. PMID: 34297911 Free PMC article.
MiOS, an integrated imaging and computational strategy to model gene folding with nucleosome resolution.
Neguembor MV, Arcon JP, Buitrago D, Lema R, Walther J, Garate X, Martin L, Romero P, AlHaj Abed J, Gut M, Blanc J, Lakadamyali M, Wu CT, Brun Heath I, Orozco M, Dans PD, Cosma MP. Neguembor MV, et al. Nat Struct Mol Biol. 2022 Oct;29(10):1011-1023. doi: 10.1038/s41594-022-00839-y. Epub 2022 Oct 11. Nat Struct Mol Biol. 2022. PMID: 36220894 Free PMC article.
Islands of retroelements are major components of Drosophila centromeres.
Chang CH, Chavan A, Palladino J, Wei X, Martins NMC, Santinello B, Chen CC, Erceg J, Beliveau BJ, Wu CT, Larracuente AM, Mellone BG. Chang CH, et al. PLoS Biol. 2019 May 14;17(5):e3000241. doi: 10.1371/journal.pbio.3000241. eCollection 2019 May. PLoS Biol. 2019. PMID: 31086362 Free PMC article.
Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling.
Nir G, Farabella I, Pérez Estrada C, Ebeling CG, Beliveau BJ, Sasaki HM, Lee SD, Nguyen SC, McCole RB, Chattoraj S, Erceg J, AlHaj Abed J, Martins NMC, Nguyen HQ, Hannan MA, Russell S, Durand NC, Rao SSP, Kishi JY, Soler-Vila P, Di Pierro M, Onuchic JN, Callahan SP, Schreiner JM, Stuckey JA, Yin P, Aiden EL, Marti-Renom MA, Wu CT. Nir G, et al. PLoS Genet. 2018 Dec 26;14(12):e1007872. doi: 10.1371/journal.pgen.1007872. eCollection 2018 Dec. PLoS Genet. 2018. PMID: 30586358 Free PMC article.
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