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Topologically associating domains are stable units of replication-timing regulation.
Pope BD, Ryba T, Dileep V, Yue F, Wu W, Denas O, Vera DL, Wang Y, Hansen RS, Canfield TK, Thurman RE, Cheng Y, Gülsoy G, Dennis JH, Snyder MP, Stamatoyannopoulos JA, Taylor J, Hardison RC, Kahveci T, Ren B, Gilbert DM. Pope BD, et al. Among authors: gulsoy g. Nature. 2014 Nov 20;515(7527):402-5. doi: 10.1038/nature13986. Nature. 2014. PMID: 25409831 Free PMC article.
RINQ: Reference-based Indexing for Network Queries.
Gülsoy G, Kahveci T. Gülsoy G, et al. Bioinformatics. 2011 Jul 1;27(13):i149-58. doi: 10.1093/bioinformatics/btr203. Bioinformatics. 2011. PMID: 21685064 Free PMC article.
Profiling the long noncoding RNA interaction network in the regulatory elements of target genes by chromatin in situ reverse transcription sequencing.
Zhang S, Wang Y, Jia L, Wen X, Du Z, Wang C, Hao Y, Yu D, Zhou L, Chen N, Chen J, Chen H, Zhang H, Celik I, Gülsoy G, Luo J, Qin B, Cui X, Liu Z, Zhang S, Esteban MA, Ay F, Xu W, Chen R, Li W, Hoffman AR, Hu JF, Cui J. Zhang S, et al. Among authors: gulsoy g. Genome Res. 2019 Sep;29(9):1521-1532. doi: 10.1101/gr.244996.118. Epub 2019 Jul 17. Genome Res. 2019. PMID: 31315906 Free PMC article.
Chromatin lncRNA Platr10 controls stem cell pluripotency by coordinating an intrachromosomal regulatory network.
Du Z, Wen X, Wang Y, Jia L, Zhang S, Liu Y, Zhou L, Li H, Yang W, Wang C, Chen J, Hao Y, Salgado Figueroa D, Chen H, Li D, Chen N, Celik I, Zhu Y, Yan Z, Fu C, Liu S, Jiao B, Wang Z, Zhang H, Gülsoy G, Luo J, Qin B, Gao S, Kapranov P, Esteban MA, Zhang S, Li W, Ay F, Chen R, Hoffman AR, Cui J, Hu JF. Du Z, et al. Among authors: gulsoy g. Genome Biol. 2021 Aug 19;22(1):233. doi: 10.1186/s13059-021-02444-6. Genome Biol. 2021. PMID: 34412677 Free PMC article.
Author Correction: Chromatin lncRNA Platr10 controls stem cell pluripotency by coordinating an intrachromosomal regulatory network.
Du Z, Wen X, Wang Y, Jia L, Zhang S, Liu Y, Zhou L, Li H, Yang W, Wang C, Chen J, Hao Y, Salgado Figueroa D, Chen H, Li D, Chen N, Celik I, Zhu Y, Yan Z, Fu C, Liu S, Jiao B, Wang Z, Zhang H, Gülsoy G, Luo J, Qin B, Gao S, Kapranov P, Esteban MA, Zhang S, Li W, Ay F, Chen R, Hoffman AR, Cui J, Hu JF. Du Z, et al. Among authors: gulsoy g. Genome Biol. 2021 Sep 20;22(1):272. doi: 10.1186/s13059-021-02487-9. Genome Biol. 2021. PMID: 34544465 Free PMC article. No abstract available.