Publications

A comprehensive toolkit for analyzing cell-free DNA genomic sequencing data in liquid biopsy

Junpeng Zhou^, Keyao Zhu^, Xiaoqian Huang, Jinqi Yuan, Yumei Li#

iScience · 2026

PMID: 42111187

Systematic evaluation of methylation-based cell type deconvolution methods for plasma cell-free DNA

Tongyue Sun^, Jinqi Yuan^, Yacheng Zhu, Jingqi Li, Shen Yang, Junpeng Zhou, Xinzhou Ge, Susu Qu, Wei Li#, Jingyi Jessica Li#, Yumei Li#

Genome Biology · 2024

PMID:39702273

Response to 'Neglecting normalization impact in semi-synthetic RNA-seq data simulation generates artificial false positives' and 'Winsorization greatly reduces false positives by popular differential expression methods when analyzing human population samples

Xinzhou Ge^, Yumei Li^, Wei Li#, Jingyi Jessica Li#

Genome Biology · 2024

Multimodal Epigenetic Sequencing Analysis (MESA) of Cell-free DNA for Non-invasive Colorectal Cancer Detection

Yumei Li^, Jianfeng Xu^, Chaorong Chen^, Zhenhai Lu, Desen Wan, Diange Li, Jason S. Li, Allison J. Sorg, Curt C. Roberts, Shivani Mahajan, Maxime A. Gallant, Itai Pinkoviezky, Ya Cui, David J. Taggart#, Wei Li#

Genome Medicine · 2024

Exaggerated false positives by popular differential expression methods when analyzing human population samples

Yumei Li^, Xinzhou Ge^, Fanglue Peng, Wei Li#, Jingyi Jessica Li#

Genome Biology · 2022

PMID: 35292087

NSD2 dimethylation at H3K36 promotes lung adenocarcinoma pathogenesis

Deepanwita Sengupta^, Liyong Zeng^, Yumei Li^, Simone Hausmann, Debopam Ghosh, Gang Yuan, Thuyen N Nguyen, Ruitu Lyu, Marcello Caporicci, Ana Morales Benitez, Garry L Coles, Vladlena Kharchenko, Iwona Czaban, Dulat Azhibek, Wolfgang Fischle, Mariusz Jaremko, Ignacio I Wistuba, Julien Sage, Łukasz Jaremko, Wei Li#, Pawel K Mazur#, Or Gozani#

Molecular Cell · 2021

PMID: 34555356

Polyadenylation- related isoform switching in human evolution revealed by full-length transcript structure

Yumei Li^, Qing Sunny Shen^, Qi Peng^, Wanqiu Ding, Jie Zhang, Xiaoming Zhong, Ni A An, Mingjun Ji, Wei-Zhen Zhou, Chuan-Yun Li#

Briefings in Bioinformatics · 2021

PMID: 33973996

Replication-independent histone turnover underlines the epigenetic homeostasis in adult heart

Yumei Li^, Shanshan Ai^, Xianhong Yu^, Chen Li, Xin Li, Yanzhu Yue, Yusheng Wei, Chuan-Yun Li#, Aibin He#

Circulation Research · 2019

PMID: 31104571

Human exonization through differential nucleosome occupancy

Yumei Li^, Chen Li^, Shuxian Li, Qi Peng, Ni A. An, Aibin He#, Chuan-Yun Li#

PNAS · 2018

PMID: 30104384