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Stepwise activities of mSWI/SNF family chromatin remodeling complexes direct T cell activation and exhaustion.
Battistello E, Hixon KA, Comstock DE, Collings CK, Chen X, Rodriguez Hernaez J, Lee S, Cervantes KS, Hinkley MM, Ntatsoulis K, Cesarano A, Hockemeyer K, Haining WN, Witkowski MT, Qi J, Tsirigos A, Perna F, Aifantis I, Kadoch C. Battistello E, et al. Among authors: rodriguez hernaez j. Mol Cell. 2023 Apr 20;83(8):1216-1236.e12. doi: 10.1016/j.molcel.2023.02.026. Epub 2023 Mar 20. Mol Cell. 2023. PMID: 36944333 Free PMC article.
RNA Interactions Are Essential for CTCF-Mediated Genome Organization.
Saldaña-Meyer R, Rodriguez-Hernaez J, Escobar T, Nishana M, Jácome-López K, Nora EP, Bruneau BG, Tsirigos A, Furlan-Magaril M, Skok J, Reinberg D. Saldaña-Meyer R, et al. Among authors: rodriguez hernaez j. Mol Cell. 2019 Nov 7;76(3):412-422.e5. doi: 10.1016/j.molcel.2019.08.015. Epub 2019 Sep 12. Mol Cell. 2019. PMID: 31522988 Free PMC article.
Cell-type-specific prediction of 3D chromatin organization enables high-throughput in silico genetic screening.
Tan J, Shenker-Tauris N, Rodriguez-Hernaez J, Wang E, Sakellaropoulos T, Boccalatte F, Thandapani P, Skok J, Aifantis I, Fenyö D, Xia B, Tsirigos A. Tan J, et al. Among authors: rodriguez hernaez j. Nat Biotechnol. 2023 Aug;41(8):1140-1150. doi: 10.1038/s41587-022-01612-8. Epub 2023 Jan 9. Nat Biotechnol. 2023. PMID: 36624151 Free PMC article.
3D Enhancer-promoter networks provide predictive features for gene expression and coregulation in early embryonic lineages.
Murphy D, Salataj E, Di Giammartino DC, Rodriguez-Hernaez J, Kloetgen A, Garg V, Char E, Uyehara CM, Ee LS, Lee U, Stadtfeld M, Hadjantonakis AK, Tsirigos A, Polyzos A, Apostolou E. Murphy D, et al. Among authors: rodriguez hernaez j. Nat Struct Mol Biol. 2024 Jan;31(1):125-140. doi: 10.1038/s41594-023-01130-4. Epub 2023 Dec 5. Nat Struct Mol Biol. 2024. PMID: 38053013
Systematic mapping and modeling of 3D enhancer-promoter interactions in early mouse embryonic lineages reveal regulatory principles that determine the levels and cell-type specificity of gene expression.
Murphy D, Salataj E, Di Giammartino DC, Rodriguez-Hernaez J, Kloetgen A, Garg V, Char E, Uyehara CM, Ee LS, Lee U, Stadtfeld M, Hadjantonakis AK, Tsirigos A, Polyzos A, Apostolou E. Murphy D, et al. Among authors: rodriguez hernaez j. bioRxiv [Preprint]. 2023 Jul 19:2023.07.19.549714. doi: 10.1101/2023.07.19.549714. bioRxiv. 2023. PMID: 37577543 Free PMC article. Preprint.
The first complete genomic structure of Butyrivibrio fibrisolvens and its chromid.
Rodríguez Hernáez J, Cerón Cucchi ME, Cravero S, Martinez MC, Gonzalez S, Puebla A, Dopazo J, Farber M, Paniego N, Rivarola M. Rodríguez Hernáez J, et al. Microb Genom. 2018 Oct;4(10):e000216. doi: 10.1099/mgen.0.000216. Epub 2018 Sep 14. Microb Genom. 2018. PMID: 30216146 Free PMC article.