Publications

This study found racial differences of mutational signatures to be associated with differences in diverse genetic backgrounds and environmental factors, which might help guide the personalized treatment of HCC patients.

Baifeng Zhang*, Xinyuan Guan#

Hepatoma Research

Single-cell RNA sequencing to 66,627 cells from 14 patients, integrated with clonotype identification on T and B cells.

Lanqi Gong, Dora Lai-Wan Kwong, Wei Dai, Pingan Wu, Shanshan Li, Qian Yan, Yu Zhang, Baifeng Zhang*, Xiaona Fang, Li Liu, Min Luo, Beilei Liu, Larry Ka-Yue Chow, Qingyun Chen, Jinlin Huang, Victor Ho-Fun Lee, Ka-On Lam, Anthony Wing-Ip Lo, Zhiwei Chen, Yan Wang, Anne Wing-Mui Lee & Xinyuan Guan#

Nature Communications 12, 1540 (2021)

A companion data analysis platform named SplitFusion, to detect gene fusion based on split alignments, such as reads crossing fusion breakpoints, with the ability to accurately infer in-frame or out-of-frame of fusion partners of a given fusion candidate. SplitFusion also outputs example breakpoint-supporting sequences in FASTA format, allowing for further investigations. SplitFusion can economically and effectively distinguish true oncogenic fusions from environment noise, amplification or sequencing errors, especially for low quality input of clinical samples.

Baifeng Zhang</a>, Zhengbo Song, Chloe Yufan Bao, Chunwei Xu, Wenxian Wang, Hoi Yee Chu, Chenyu Lu, Hongxiang Wang, Siyu Bao, Zhenyu Gong, Hoi Yee Keung, Maggie Chow, Yiping Zhang, Wah Cheuk, Mengsu Yang, William Cho#, Juxiang Chen#, Zongli Zheng#</em>

Research Square

The detection of differentially methylated regions (DMRs) and DMRs annotation, the correlation analysis between DMRs and gene expression/splice site/transcript factor site, to study the effect of epigenetic modifications in ovarian cancer tumorigenesis.

Fangfang Song, Lian Li, Baifang Zhang*, Hong Zheng, Meng Yang, Xiangchun Li, Jing Tian, Qinghua Wang, Wei Zhang, Kexin Chen#

Gynecologic Oncology

The personalized analysis of the project including the detection of somatic structure variants, false positive results filter, SV cluster chain identification, result interpretation, and pan-cancer integrated analysis of TCGA database.

Yi Huang, Changxi Wang, Jiayin Wang, Baifeng Zhang, Jiajia Cai, Dan Shen, Xin Yi, Zhiming Cai, and Song Wu#

Under review on Clinical Cancer Research

The clonal evolution structure and immunogenicity analysis of 489 clear cell renal carcinomas patients from Japanese/Chinese/TCGA cohorts, including mutational signature analysis, intra-tumor heterogeneity and cancer evolution history analysis, tumor specific neo-antigen analysis, survival analysis.

Yi Huang, Jiayin Wang, Peilin Jia, Xiangchun Li, Guangsheng Pei , Changxi Wang, Xiaodong Fang, Zhongming Zhao, Zhiming Cai, Xin Yi, Song Wu, Baifeng Zhang*#

Nature Communications 10, 1245 (2019)

We have uncovered several new SMGs in ESCC and defined an alcohol consumption related mutational signature. TENM3 mutations and the TP53 hotspot mutation p.R213* are independent prognosticators for poor survival in ESCC.

X.C. Li, M.Y. Wang, M. Yang, H.J. Dai, B.F. Zhang, W. Wang, X.L. Chu, X. Wang, H. Zheng, R.F. Niu, W. Zhang, K.X. Chen#

Annals of Oncology 29, 4 (2018)

We designed a set of LAMP primers to target the sequence of the mcyG gene, which is responsible for the first step in the biosynthesis of Adda (3-amino-9-methoxy-2, 6, 8-trim ethyl-10-phenyldeca-4, 6-dienoic acid), an important part of microcystin.

ZHANG Baifeng, ZHU Peng#, YAN Xiaojun, DANG Chenyang, LV Yating ,WU Jinghua

Acta Ecologica Sinica 35, 9 (2015)

We designed a new loop-mediated isothermal amplification (LAMP) assay based on microcystin biosynthesis genes, which allowed the workers, through routine monitoring of potential toxin status in the freshwater, to have enough time to implement a series of control strategies for avoiding human exposure to cyanobacterial hepatotoxins at dangerous levels.

Peng Zhu*, Bai-Feng Zhang*, Jing-Hua Wu, Chen-Yang Dang, Ya-Ting Lv, Jian-Zhong Fan, Xiao-Jun Yan#

Harmful Algae 37, 8–16 (2014)