Publication

Selected Publications (also see google scholar)

• Dong P, Zhang S, Xie L, Wang L, Lemire A, Lander A, Chang H, Liu Z. Organization of the 3D genome encodes gene co-expression programs in single cells. Under revision in Nature Genetics.

• Lange J, Rose J, Chen C, Pichugin Y, Xie L, …,  Mischel P (2022). The evolutionary dynamics of extrachromosomal DNA in human cancers. Nature Genetics. 2022 Sep 19. doi: 10.1038/s41588-022-01177-x

• Xie L, Dong P, Qi Y,…, Zhang B, Tjian R, Liu Z (2022). BRD2 Compartmentalizes the Accessible Genome. Nature Genetics. Apr;54(4):481-491.

• Hung KL*, Yost KL*, Xie L*, …, Mischel P, Liu Z, Chang H (2021). EcDNA hubs drive cooperative intermolecular oncogene expression. Nature. https://doi.org/10.1038/s41586-021-04116-8. *, co-first author

• Xie L, Liu Z (2021). Single cell Imaging of Genome Organization and Dynamics. Mol Syst. Biol. Jul;17(7):e9653. Invited review

• Grimm J,  Xie L, …, Lavis L (2021). Deuteration improves small-molecule fluorophores. JACS Au. May 24;1(5):690-696.

• Grimm JB, Tkachuk AN, Xie L, …, Lavis L. (2020) A general method to optimize and functionalize red-shifted rhodamine dyes. Nature Methods. 17(8):815-821.

• Xie L, Dong P, …, Tjian R, Liu Z (2020). 3D ATAC-PALM: super-resolution imaging of the accessible genome. Nature Methods. 17(4):430-436.

• Teves SS, An L, Bhargava-Shah A, Xie L, Darzacq X, Tjian R (2018). A stable mode of bookmarking by TBP recruits RNA Polymerase II to mitotic chromosomes. eLife.7.pii: e35621.

• Xie L, Torigoe SE, …, Tjian R (2017). A Dynamic Interplay of Enhancer Elements Regulates Klf4 expression in Naïve-pluripotency. Genes & Development. 31(17):1795-1808

• Timblin GA, Xie L, Tjian R, Schlissel MS (2017). Dual Mechanism of Rag Gene Repression by c-Myb during Pre-B Cell Proliferation. Mol Cell Biol. 37(12). pii: e00437-16.

• Teves SS, An L, Hansen AS, Xie L, Darzacq X, Tjian R (2016). A dynamic mode of mitotic bookmarking by transcription factors. Elife. 5. pii: e22280.

• Xiao J, Mai DH,Xie L* (2016).Resetting Human Naïve Pluripotency. Genet Epigenet.8:37-41. *, corresponding author.

• Knight SC, Xie L, …, Doudna JA, Tjian R (2015). Dynamics of CRISPR-Cas9 genome interrogation in living cells. Science. 350(6262):823-6.

• Xie L, Pelz C, …, Impey S (2011). KDM5B regulates embryonic stem cell self-renewal and represses cryptic intragenic transcription. EMBO J. Apr 20;30(8):1473-84.

• Xie L, Chang LN, Guan YF, Wang X (2005). C-Reactive Protein augments interleukin-8 production in human blood monocytes. J Cardiovasc Pharmacol. 46(5):690-6