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Selected Publications

* Corresponding Author.

16,  Epigenetic insights into GABAergic development in Dravet Syndrome iPSC and therapeutic implications.

Schuster J, Lu X, Yonglong D, Klar J, Wenz A, Dahl N*, Chen X*.  

ELife,, 2023.

* Corresponding author.

15, Cell-lineage controlled epigenetic regulation in glioblastoma stem cells determines functionally distinct subgroups and predicts patient survival. 

Lu X, Maturi P, Jarvius M, Yildirim I, Dang Y, Zhao L, Xie Y, Tan E, Xing P, Larsson R, Fryknäs M, Uhrbom L*, Chen X*.  

Nature Communications, 2022,

* Corresponding author.

14, BRD2 compartmentalizes the accessible genome. 

Xie L, Dong P, Qi Y, Hsieh T, English B, Jung S, Chen X, Marzio M, Casellas R, Chang H, Zhang B, Tjian R, Liu Z. 

Nature Genetics, 2022,

13, Epigenomic priming of immune genes implicates oligodendroglia in multiple sclerosis susceptibility.

Meijer M, Agirre E, Kabbe M, van Tuijn CA, Heskol A, Zheng C, Mendanha Falcão A, Bartosovic M, Kirby L, Calini D, Johnson MR, Corces MR, Montine TJ, Chen X, Chang HY, Malhotra D, Castelo-Branco G.

Neuron. 2022 Jan 28:S0896-6273(21)01089-8. doi: 10.1016/j.neuron.2021.12.034.

12, Focal amplifications are associated with chromothripsis events and diverse prognoses in gastric cardia adenocarcinoma.

Zhao, X., Xing P., Song X., Zhao M., Zhao L.,  Dang Y., Lei L., Xu R., Han W., Wang P., Yang M., Hu J., Zhong H., Zhou F., Han X., Meng C., Ji J.,  Chen X *., Wang L*,  

Nat Commun 12, 6489 (2021).

* Corresponding Author.

11, FACT-seq: profiling histone modifications in formalin-fixed paraffin-embedded samples with low cell numbers

Zhao, L., Xing, P., Polavarapu, V., Zhao, M., Valero-Martinez, B., Dang Y., Maturi, N., Mathot. L., Neves I., Yildirim I., Swartling. F., Sjöblom. T., Uhrbom L., Chen. X.,* , * Corresponding Author.

Nucleic Acids Research, 2021.

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

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

Genome Research, online in advance, 2021;gr.275269.121v1

9, 3D ATAC-PALM: super-resolution imaging of the accessible genome.

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

Nat Methods (2020).

8. 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.

7. 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.

6. 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.

5. 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.

4. 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.

3. 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.

2. 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.

1. 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.


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