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Showing 6 of 6 publications
2026
Complete Figure 1: mouse sample and sequencing workflow, transcript classes, sample correlations, PCA, transcript lengths, exon counts and isoform counts.
Figure 1图 1Wu et al. · Journal of Ovarian Research (2026)Wu 等 · Journal of Ovarian Research(2026) · Source出处 · CC BY-NC-ND 4.0
Journal of Ovarian ResearchResearch article研究论文

Full-length transcriptomic profiling reveals age-associated isoform remodeling and altered coding potential in the mouse ovary

Haiyang Wu, Xiaoyu Yin, Min Zhang, Kanghua Zhong, Yalin Liang, Yiduo Wang, Yelian Yan, Xueqi Dong, Yuxin Xu, Hao Yu, Keliang Wu, Shenli Yuan, Chuanxin Zhang

Long-read RNA sequencing profiles full-length transcripts in granulosa cells and oocytes from young and aged mice. The study identifies age-associated isoform changes, alternative polyadenylation and differences in predicted coding potential.通过长读长 RNA 测序解析年轻与衰老小鼠颗粒细胞和卵母细胞的全长转录本,识别与年龄相关的异构体变化、可变多聚腺苷酸化及预测编码潜能差异。

Co-corresponding author共同通讯作者

2026
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bioRxivPreprint · not peer reviewed预印本 · 未经同行评审

ANCHOR: haplotype-aware allelic and isoform inference from single-cell long-read RNA sequencing with de novo variant calling

Zhi-Can Fu, Chuanxin Zhang, Yelian Yan, Yuxin Xu, Xiaoyu Yin, Tietuo Tao, Peng Lu, Yalin Liang, Haiyang Wu, Wentao Cui, Runtong Hou, Xuepeng Chen, Yuwen Ke, Yanqiang Li, Zi-Jiang Chen, Tao Huang, Keliang Wu, Shenli Yuan

This preprint introduces a framework for variant discovery, haplotype assignment and allele-resolved isoform quantification in single-cell long-read RNA sequencing. Applications include parent-of-origin expression during mouse gastrulation; the work has not been peer reviewed.该预印本提出面向单细胞长读长 RNA 测序的变异发现、单倍型分配及等位基因分辨的异构体定量框架,并应用于小鼠原肠胚形成中的亲本来源表达分析;尚未经同行评议。

Co-author作者

2026
Complete Figure 1: H3K18cr genomic profiles, peak statistics and immunostaining across mouse gametes and early embryos, with all original labels and microscopy scale bars.
Figure 1图 1Yuan et al. · Advanced Science (2026)Yuan 等 · Advanced Science(2026) · Source出处 · CC BY 4.0
Advanced ScienceResearch article研究论文

The Landscape and Regulation of Histone Crotonylation in Mammalian Gametes and Early Embryos

Shenli Yuan, Yelian Yan, Yalin Liang, Kanghua Zhong, Zhican Fu, Xiaobo Wang, Chao Liu, Tao Huang, Keliang Wu

The study maps H3K18 crotonylation in mouse gametes and preimplantation embryos. It examines how remodeling of this histone mark interacts with zygotic genome activation and early development.研究绘制小鼠配子与植入前胚胎的 H3K18 巴豆酰化图谱,探索这一组蛋白修饰的重塑与合子基因组激活及早期发育之间的联系。

First-listed author第一署名作者

2024
Complete Figure 1: human embryo study design, chromatin accessibility, H3K27me3 and DNA methylation patterns, allele-related expression and imprinted-gene genome tracks.
Figure 1图 1Yuan et al. · National Science Review (2024)Yuan 等 · National Science Review(2024) · Source出处 · CC BY 4.0
National Science ReviewResearch article研究论文

Allelic reprogramming of chromatin states in human early embryos

Shenli Yuan, Lei Gao, Wenrong Tao, Jianhong Zhan, Gang Lu, Jingye Zhang, Chuanxin Zhang, Lizhi Yi, Zhenbo Liu, Zhenzhen Hou, Min Dai, Han Zhao, Zi-Jiang Chen, Jiang Liu, Keliang Wu

Parental epigenomic maps of human early embryos reveal allele-specific chromatin reprogramming. Comparisons with mouse embryos identify differences in parental epigenetic states and genomic imprinting.通过人类早期胚胎的亲本表观基因组图谱,刻画等位基因特异的染色质重编程,并比较人和小鼠在亲本表观遗传状态及基因组印记上的差异。

Co-first author共同第一作者

2023
Complete Figure 1: human parthenogenetic and androgenetic embryo design, gene-level RNA-seq heatmap and newly transcribed gene comparisons.
Figure 1图 1Yuan et al. · Cell Discovery (2023)Yuan 等 · Cell Discovery(2023) · Source出处 · CC BY 4.0
Cell DiscoveryResearch article研究论文

Human zygotic genome activation is initiated from paternal genome

Shenli Yuan, Jianhong Zhan, Jingye Zhang, Zhenbo Liu, Zhenzhen Hou, Chuanxin Zhang, Lizhi Yi, Lei Gao, Han Zhao, Zi-Jiang Chen, Jiang Liu, Keliang Wu

Using human parthenogenetic and androgenetic embryos, the study investigates parental contributions to zygotic genome activation. It identifies paternal expression of ZNF675 and LSM1 as part of the regulatory process.利用人类孤雌与孤雄胚胎研究双亲基因组对合子基因组激活的贡献,并探讨父源表达的 ZNF675 和 LSM1 在这一过程中的作用。

Co-first author共同第一作者

2022
Complete Figure 4: DMC1, ZCWPW1 and ATAC-seq genome tracks and heatmaps comparing wild-type, Zcwpw1, Prdm9 and Spo11 mutant mouse testes.
Figure 4图 4Yuan et al. · Genome Biology (2022)Yuan 等 · Genome Biology(2022) · Source出处 · CC BY 4.0
Genome BiologyResearch article研究论文

The histone modification reader ZCWPW1 promotes double-strand break repair by regulating cross-talk of histone modifications and chromatin accessibility at meiotic hotspots

Shenli Yuan, Tao Huang, Ziyou Bao, Shiyu Wang, Xinyue Wu, Jiang Liu, Hongbin Liu, Zi-Jiang Chen

The study investigates how the histone reader ZCWPW1 connects histone modifications with chromatin accessibility at meiotic recombination hotspots. The results link this regulation to homologous recombination during DNA double-strand break repair.研究探讨组蛋白修饰识别蛋白 ZCWPW1 如何联结减数分裂重组热点处的组蛋白修饰与染色质可及性,以及这一调控与 DNA 双链断裂同源重组修复的关系。

Co-first author共同第一作者

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