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Chromatin conformation, gene transcription, and nucleosome remodeling as an emergent system.
Almassalha LM, Carignano M, Liwag EP, Li WS, Gong R, Acosta N, Dunton CL, Gonzalez PC, Carter LM, Kakkaramadam R, Kröger M, MacQuarrie KL, Frederick J, Ye IC, Su P, Kuo T, Medina KI, Pritchard JA, Skol A, Nap R, Kanemaki M, Dravid V, Szleifer I, Backman V. Almassalha LM, et al. Sci Adv. 2025 Jan 10;11(2):eadq6652. doi: 10.1126/sciadv.adq6652. Epub 2025 Jan 10. Sci Adv. 2025. PMID: 39792661
Leveraging chromatin packing domains to target chemoevasion in vivo.
Frederick J, Virk RKA, Ye IC, Almassalha LM, Wodarcyk GM, VanDerway D, Gonzalez PC, Nap RJ, Agrawal V, Anthony NM, Carinato J, Li WS, Dunton CL, Medina KI, Kakkaramadam R, Jain S, Shahabi S, Ameer G, Szleifer IG, Backman V. Frederick J, et al. Among authors: almassalha lm. bioRxiv [Preprint]. 2024 Nov 15:2024.11.14.623612. doi: 10.1101/2024.11.14.623612. bioRxiv. 2024. PMID: 39605341 Free PMC article. Preprint.
Formamide denaturation of double-stranded DNA for fluorescence in situ hybridization (FISH) distorts nanoscale chromatin structure.
Shim AR, Frederick J, Pujadas EM, Kuo T, Ye IC, Pritchard JA, Dunton CL, Gonzalez PC, Acosta N, Jain S, Anthony NM, Almassalha LM, Szleifer I, Backman V. Shim AR, et al. Among authors: almassalha lm. PLoS One. 2024 May 28;19(5):e0301000. doi: 10.1371/journal.pone.0301000. eCollection 2024. PLoS One. 2024. PMID: 38805476 Free PMC article.
Nuclear blebs are associated with destabilized chromatin packing domains.
Pujadas Liwag EM, Acosta N, Almassalha LM, Su YP, Gong R, Kanemaki MT, Stephens AD, Backman V. Pujadas Liwag EM, et al. Among authors: almassalha lm. bioRxiv [Preprint]. 2024 Mar 29:2024.03.28.587095. doi: 10.1101/2024.03.28.587095. bioRxiv. 2024. PMID: 38585954 Free PMC article. Preprint.
Depletion of lamins B1 and B2 promotes chromatin mobility and induces differential gene expression by a mesoscale-motion-dependent mechanism.
Pujadas Liwag EM, Wei X, Acosta N, Carter LM, Yang J, Almassalha LM, Jain S, Daneshkhah A, Rao SSP, Seker-Polat F, MacQuarrie KL, Ibarra J, Agrawal V, Aiden EL, Kanemaki MT, Backman V, Adli M. Pujadas Liwag EM, et al. Among authors: almassalha lm. Genome Biol. 2024 Mar 22;25(1):77. doi: 10.1186/s13059-024-03212-y. Genome Biol. 2024. PMID: 38519987 Free PMC article.
Nanoscale chromatin imaging and analysis platform bridges 4D chromatin organization with molecular function.
Li Y, Eshein A, Virk RKA, Eid A, Wu W, Frederick J, VanDerway D, Gladstein S, Huang K, Shim AR, Anthony NM, Bauer GM, Zhou X, Agrawal V, Pujadas EM, Jain S, Esteve G, Chandler JE, Nguyen TQ, Bleher R, de Pablo JJ, Szleifer I, Dravid VP, Almassalha LM, Backman V. Li Y, et al. Among authors: almassalha lm. Sci Adv. 2021 Jan 1;7(1):eabe4310. doi: 10.1126/sciadv.abe4310. Print 2021 Jan. Sci Adv. 2021. PMID: 33523864 Free PMC article.
Physical and data structure of 3D genome.
Huang K, Li Y, Shim AR, Virk RKA, Agrawal V, Eshein A, Nap RJ, Almassalha LM, Backman V, Szleifer I. Huang K, et al. Among authors: almassalha lm. Sci Adv. 2020 Jan 10;6(2):eaay4055. doi: 10.1126/sciadv.aay4055. eCollection 2020 Jan. Sci Adv. 2020. PMID: 31950084 Free PMC article.
30 results