Selected Research Publications

GEPIA3: Enhanced drug sensitivity and interaction network analysis for cancer research

Yu-Jian Kang, Lingjie Pan, Yiyu Liu, Zhengqin Rong, Jiaxi Liu, Fenglin Liu

Nucleic Acids Research · 2025 · 53(W1) · W283-W290

A pan-cancer platform for gene-expression, drug-sensitivity, interaction-network, regulatory-network, and RNA-alteration analyses.

GEPIA2021: integrating multiple deconvolution-based analysis into GEPIA

Chenwei Li, Zefang Tang, Wenjie Zhang, Zhaochen Ye, Fenglin Liu

Nucleic Acids Research · 2021 · 49(W1) · W242-W246

A standalone GEPIA extension for deconvolution-based cell-type proportion, correlation, differential-expression, and survival analyses of TCGA and GTEx data.

The GEPIA2021 server has shown intermittent availability; the publication links remain accessible.

Genomic basis for RNA alterations in cancer

PCAWG Transcriptome Core Group, Claudia Calabrese, Natalie R. Davidson, Deniz Demircioğlu, Nuno A. Fonseca, Yao He, André Kahles, Kjong-Van Lehmann, Fenglin Liu, Yuichi Shiraishi, Cameron M. Soulette, Lara Urban, et al., PCAWG Transcriptome Working Group, PCAWG Consortium

Nature · 2020 · 578(7793) · 129-136

A PCAWG study connecting recurrent RNA alterations—including expression, splicing, promoter use, and gene fusions—to genomic changes across cancer types.

The author list shown here is abbreviated; use the official record for the complete consortium author list.

Systematic comparative analysis of single-nucleotide variant detection methods from single-cell RNA sequencing data

Fenglin Liu, Yuanyuan Zhang, Lei Zhang, Ziyi Li, Qiao Fang, Ranran Gao, Zemin Zhang

Genome Biology · 2019 · 20(1) · 242

A systematic benchmark of SNV detection from single-cell RNA sequencing, evaluating performance across sequencing depth, gene expression, allele frequency, and genomic context.

AnnoLnc: a web server for systematically annotating novel human lncRNAs

Mei Hou, Xing Tang, Feng Tian, Fangyuan Shi, Fenglin Liu, Ge Gao

BMC Genomics · 2016 · 17(1) · 931

The original AnnoLnc web server integrated multidimensional annotations for novel human lncRNAs; its current successor resource is AnnoLnc2.

Fenglin Liu contributed to the original AnnoLnc pilot build and is listed in the previous AnnoLnc development team, not the AnnoLnc2 development team.