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Cross-species cell-type assignment from single-cell RNA-seq data by a heterogeneous graph neural network
Author: Liu, Xingyan; Shen, Qunlun; Zhang, Shihua
Journal: GENOME RESEARCH. 2023; Vol. 33, Issue 1, pp. 96-111. DOI: 10.1101/gr.276868.122
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Characterization of network hierarchy reflects cell state specificity in genome organization
Author: Wang, Jingyao; Xue, Yue; He, Yueying; Quan, Hui; Zhang, Jun; Gao, Yi Qin
Journal: GENOME RESEARCH. 2023; Vol. 33, Issue 2, pp. 247-260. DOI: 10.1101/gr.277206.122
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Regulation of endogenous retrovirus-derived regulatory elements by GATA2/3 and MSX2 in human trophoblast stem cells
Author: Du, Cui; Jiang, Jing; Li, Yuzhuo; Yu, Miao; Jin, Jian; Chen, Shuai; Fan, Hairui; Macfarlan, Todd S.; Cao, Bin; Sun, Ming-an
Journal: GENOME RESEARCH. 2023; Vol. 33, Issue 2, pp. 197-207. DOI: 10.1101/gr.277150.122
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SWATH-MS-based proteogenomic analysis reveals the involvement of alternative splicing in poplar upon lead stress
Author: Zhu, Fu-Yuan; Chen, Xin; Song, Yu-Chen; Lam, Lydia Pui Ying; Tobimatsu, Yuki; Gao, Bei; Chen, Mo-Xian; Cao, Fu-Liang
Journal: GENOME RESEARCH. 2023; Vol. 33, Issue 3, pp. 371-385. DOI: 10.1101/gr.277473.122
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Tn5 tagments and transposes oligos to single-stranded DNA for strand-specific RNA sequencing
Author: Zhang, Yanjun; Tang, Yin; Sun, Zhongxing; Jia, Junqi; Fang, Yuan; Wan, Xinyi; Fang, Dong
Journal: GENOME RESEARCH. 2023; Vol. 33, Issue 3, pp. 412-426. DOI: 10.1101/gr.277213.122
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Simultaneous profiling of host expression and microbial abundance by spatial metatranscriptome sequencing
Author: Lyu, Lin; Li, Xue; Feng, Ru; Zhou, Xin; Guha, Tuhin K.; Yu, Xiaofei; Chen, Guo Qiang; Yao, Yufeng; Su, Bing; Zou, Duowu; Snyder, Michael P.; Chen, Lei
Journal: GENOME RESEARCH. 2023; Vol. 33, Issue 3, pp. 401-411. DOI: 10.1101/gr.277178.122
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Defining the separation landscape of topological domains for decoding consensus domain organization of the 3D genome
Author: Dang, Dachang; Zhang, Shao-Wu; Duan, Ran; Zhang, Shihua
Journal: GENOME RESEARCH. 2023; Vol. 33, Issue 3, pp. 386-400. DOI: 10.1101/gr.277187.122
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Widespread roles of enhancer-like transposable elements in cell identity and long-range genomic interactions.
Author: Cao Y#1, Chen G#1, Wu G#1, Zhang X#1, McDermott J1, Chen X1, Xu C1, Jiang Q1, Chen Z1, Zeng Y1,2, Ai D1, Huang Y1, Han JJ1.
Journal: Genome Res. 2019 Jan;29(1):40-52. doi: 10.1101/gr.235747.118. Epub 2018 Nov 19.
