Publications

1, Profiling chromatin accessibility in formalin-fixed paraffin-embedded samples

Genome Research, In press.  online now, 2021

Polavarapu, V., Xing, P., Zhang, H., Zhao, M., Mathot. L., Zhao. L., Rosen. G., Swartling. F., Sjöblom. T., Chen. X.,*

https://genome.cshlp.org/content/early/2021/07/14/gr.275269.121.abstract?cited-by=yes&legid=genome;gr.275269.121v1

2, Extrachromosomal DNA is associated with chromothripsis events and diverse prognoses in gastric cardia adenocarcinoma

Xue-Ke Zhao, Pengwei Xing, Xin Song, Miao Zhao, Linxuan Zhao, Yonglong Dang, Ling-Ling Lei, Rui-Hua Xu, Wen-Li Han, Pan-Pan Wang, Miao-Miao Yang, Jing-Feng Hu, Kan Zhong, Fu-You Zhou, Xue-Na Han, Chao-Long Meng, Jia-Jia Ji,  Xingqi Chen*, Li-Dong Wang*

https://www.biorxiv.org/content/10.1101/2021.07.02.450861v1

3, Conserved cell-lineage controlled epigenetic regulation in human and mouse glioblastoma stem cells determines functionally distinct subgroups

Xi Lu, Naga Prathyusha Maturi, Malin Jarvius, Linxuan Zhao, Yuan Xie, E-Jean Tan, Pengwei Xing, Marten Fryknas, Lene Uhrbom, Xingqi Chen*

bioRxiv, doi: https://doi.org/10.1101/2021.02.22.431953 

4, 3D ATAC-PALM: super-resolution imaging of the accessible genome.

Xie, L., Dong, P., Chen, X. et al.

Nat Methods (2020). https://doi.org/10.1038/s41592-020-0775-2

5. Circular ecDNA promotes accessible chromatin and high oncogene expression.

Wu S, Turner KM, Nguyen N, Raviram R, Erb M, Santini J, Luebeck J, Rajkumar U, Diao Y, Li B, Zhang W, Jameson N, Corces MR, Granja JM, Chen X, Coruh C, Abnousi A, Houston J, Ye Z, Hu R, Yu M, Kim H, Law JA, Verhaak RGW, Hu M, Furnari FB, Chang HY, Ren B, Bafna V, Mischel PS.

Nature. 2019, 575(7784):699-703.

6. Activation of PDGF pathway links LMNA mutation to dilated cardiomyopathy.

Lee J, Termglinchan V, Diecke S, Itzhaki I, Lam CK, Garg P, Lau E, Greenhaw M, Seeger T, Wu H, Zhang JZ, Chen X, Gil IP, Ameen M, Sallam K, Rhee JW, Churko JM, Chaudhary R, Chour T, Wang PJ, Snyder MP, Chang HY, Karakikes I, Wu JC. Nature. 2019, 572(7769):335-340.

7. Joint single-cell DNA accessibility and protein epitope profiling reveals environmental regulation of epigenomic heterogeneity.

Chen X, Litzenburger UM, Wei Y, Schep AN, LaGory EL, Choudhry H, Giaccia AJ, Greenleaf WJ, Chang HY.

Nat Commun. 2018, 9(1):4590.

8. Sensing self and nonself circular RNAs.

Chen YG, Kim MV, Chen X, Batista PJ, Aoyama S, Wilusz JE, Iwasaki A, Chang HY.

Mol Cell. 2017, 67(2):228-238.e5.
 

9. ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing.

Chen X, Shen Y, Draper W, Buenrostrol J D, Litzenburger U, Cho S W, Satpathy A, Carter A C, Ghosh R P, East-Seletsky A, Doudna J A, Greenleaf W J, Liphardt J T, Chang H Y.

Nature Methods. 2016, 13(12):1013-1020.
 

10. PARP1- and CTCF-mediated interactions between active and repressed chromatin at the lamina promote oscillating transcription.

Zhao H, Sifakis E, Sumida N, Millán-Ariño L, Scholz B, Svensson P, Chen X, Ronnegren A, Lima C, Varnoosfaderani F, Shi C, Loseva O, Yammine S, Israelsson M, Rathje l, Németi B, Fredlund E, Helleday T, Imreh M, Göndör A.

Mol Cell. 2015, 59(6):984-97.
 

11. The visualization of large organized chromatin domains enriched in the H3K9me2 mark within a single chromosome in a single cell.

Chen X, Yammine S, Shi C, Tark-Dame M, Göndör A, Ohlsson R. Epigenetics. 2014, 9(11):1439-45.
 

12. Chromatin in situ proximity (ChrISP): single-cell analysis of chromatin proximities at a high resolution.

Chen X, Shi C, Yammine S, Göndör A, Rönnlund D, Fernandez-Woodbridge A, Sumida N, Widengren J, Ohlsson R. Biotechniques. 2014, 56(3):117-8, 120-4.