Publications – Xingqi Chen

Publications in DiVA

Selected publications

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. Cell-lineage controlled epigenetic regulation in glioblastoma stem cells determines functionally distinct subgroups and predicts patient survival. Nat Commun, 2022, 13:2236
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. BRD2 compartmentalizes the accessible genome. Nature Genetics, 2022, 54:481–491.
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*. Focal amplifications are associated with chromothripsis events and diverse prognoses in gastric cardia adenocarcinoma. Nat Commun 2021, 12: 6489. * Corresponding Author.
Zhao L, Xing P, Polavarapu VK, Zhao M, Valero-Martínez B, Dang Y, Maturi N, Mathot L, Neves I, Yildirim I, Swartling FJ, Sjöblom T, Uhrbom L, Chen X. FACT-seq: profiling histone modifications in formalin-fixed paraffin-embedded samples with low cell numbers. Nucleic Acids Res. 2021, 49(21):e125.
Polavarapu VK, Xing P, Zhang H, Zhao M, Mathot L, Zhao L, Rosen G, Swartling FJ, Sjöblom T, Chen X. Profiling chromatin accessibility in formalin-fixed paraffin-embedded samples. Genome Res. 2021, 32(1):150-161.
Xie L, Dong P, Chen X, Hsieh TS, Banala S, De Marzio M, English BP, Qi Y, Jung SK, Kieffer-Kwon KR, Legant WR, Hansen AS, Schulmann A, Casellas R, Zhang B, Betzig E, Lavis LD, Chang HY, Tjian R, Liu Z. 3D ATAC-PALM: super-resolution imaging of the accessible genome. Nat Methods. 2020, 17(4):430-436.
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. Circular ecDNA promotes accessible chromatin and high oncogene expression. Nature. 2019, 575(7784):699-703.
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. Activation of PDGF pathway links LMNA mutation to dilated cardiomyopathy. Nature. 2019, 572(7769):335-340.
Chen X, Litzenburger UM, Wei Y, Schep AN, LaGory EL, Choudhry H, Giaccia AJ, Greenleaf WJ, Chang HY. Joint single-cell DNA accessibility and protein epitope profiling reveals environmental regulation of epigenomic heterogeneity. Nat Commun. 2018, 9(1):4590.
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. ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing. Nature Methods. 2016, 13(12):1013-1020.