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An integrated view of the structure and function of the human 4D nucleome.
4D Nucleome Consortium; Dekker J, Oksuz BA, Zhang Y, Wang Y, Minsk MK, Kuang S, Yang L, Gibcus JH, Krietenstein N, Rando OJ, Xu J, Janssens DH, Henikoff S, Kukalev A, Willemin A, Winick-Ng W, Kempfer R, Pombo A, Yu M, Kumar P, Zhang L, Belmont AS, Sasaki T, van Schaik T, Brueckner L, Peric-Hupkes D, van Steensel B, Wang P, Chai H, Kim M, Ruan Y, Zhang R, Quinodoz SA, Bhat P, Guttman M, Zhao W, Chien S, Liu Y, Venev SV, Plewczynski D, Azcarate II, Szabó D, Thieme CJ, Szczepińska T, Chiliński M, Sengupta K, Conte M, Esposito A, Abraham A, Zhang R, Wang Y, Wen X, Wu Q, Yang Y, Liu J, Boninsegna L, Yildirim A, Zhan Y, Chiariello AM, Bianco S, Lee L, Hu M, Li Y, Barnett RJ, Cook AL, Emerson DJ, Marchal C, Zhao P, Park P, Alver BH, Schroeder A, Navelkar R, Bakker C, Ronchetti W, Ehmsen S, Veit A, Gehlenborg N, Wang T, Li D, Wang X, Nicodemi M, Ren B, Zhong S, Phillips-Cremins JE, Gilbert DM, Pollard KS, Alber F, Ma J, Noble WS, Yue F. 4D Nucleome Consortium, et al. Among authors: yang l, yang y. bioRxiv [Preprint]. 2024 Oct 27:2024.09.17.613111. doi: 10.1101/2024.09.17.613111. bioRxiv. 2024. PMID: 39484446 Free PMC article. Preprint.
Polymer physics models reveal structural folding features of single-molecule gene chromatin conformations.
Conte M, Abraham A, Esposito A, Yang L, Gibcus JH, Parsi KM, Vercellone F, Fontana A, Pierno FD, Dekker J, Nicodemi M. Conte M, et al. Among authors: yang l. bioRxiv [Preprint]. 2024 Jul 16:2024.07.16.603769. doi: 10.1101/2024.07.16.603769. bioRxiv. 2024. Update in: Int J Mol Sci. 2024 Sep 23;25(18):10215. doi: 10.3390/ijms251810215 PMID: 39071404 Free PMC article. Updated. Preprint.
Ultrastructural Details of Mammalian Chromosome Architecture.
Krietenstein N, Abraham S, Venev SV, Abdennur N, Gibcus J, Hsieh TS, Parsi KM, Yang L, Maehr R, Mirny LA, Dekker J, Rando OJ. Krietenstein N, et al. Among authors: yang l. Mol Cell. 2020 May 7;78(3):554-565.e7. doi: 10.1016/j.molcel.2020.03.003. Epub 2020 Mar 25. Mol Cell. 2020. PMID: 32213324 Free PMC article.
Systematic evaluation of chromosome conformation capture assays.
Akgol Oksuz B, Yang L, Abraham S, Venev SV, Krietenstein N, Parsi KM, Ozadam H, Oomen ME, Nand A, Mao H, Genga RMJ, Maehr R, Rando OJ, Mirny LA, Gibcus JH, Dekker J. Akgol Oksuz B, et al. Among authors: yang l. Nat Methods. 2021 Sep;18(9):1046-1055. doi: 10.1038/s41592-021-01248-7. Epub 2021 Sep 3. Nat Methods. 2021. PMID: 34480151 Free PMC article.
Cohesin-mediated loop anchors confine the locations of human replication origins.
Emerson DJ, Zhao PA, Cook AL, Barnett RJ, Klein KN, Saulebekova D, Ge C, Zhou L, Simandi Z, Minsk MK, Titus KR, Wang W, Gong W, Zhang D, Yang L, Venev SV, Gibcus JH, Yang H, Sasaki T, Kanemaki MT, Yue F, Dekker J, Chen CL, Gilbert DM, Phillips-Cremins JE. Emerson DJ, et al. Among authors: yang l, yang h. Nature. 2022 Jun;606(7915):812-819. doi: 10.1038/s41586-022-04803-0. Epub 2022 Jun 8. Nature. 2022. PMID: 35676475 Free PMC article.
Revisiting chromatin packaging in mouse sperm.
Yin Q, Yang CH, Strelkova OS, Wu J, Sun Y, Gopalan S, Yang L, Dekker J, Fazzio TG, Li XZ, Gibcus J, Rando OJ. Yin Q, et al. Among authors: yang ch, yang l. Genome Res. 2023 Dec 27;33(12):2079-2093. doi: 10.1101/gr.277845.123. Genome Res. 2023. PMID: 38129076 Free PMC article.
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