Publications

Group highlights

(For a full list of publications and patents see below or go to Google Scholar, ReseachGate ID)

Deciphering clonal dynamics and metastatic routines in a rare patient of synchronous triple-primary tumors and multiple metastases with MPTevol

We developed a practical computational framework for comprehensively exploring the MPT from multiregion sequencing (MRS) experiments.To verify the utility of MPTevol, we performed whole-exome MRS for 33 samples of a rare patient with triple-primary tumors and three metastatic sites and systematically investigated clonal dynamics and metastatic routines.

Qingjian Chen, Qi-Nian Wu, Yu-Ming Rong, Shixiang Wang, Zhixiang Zuo, Long Bai, Bei Zhang, Shuqiang Yuan*, Qi Zhao*

Briefings in Bioinformatics, bbac175, 2022

Comprehensive profiling of 1015 patients’ exomes reveals genomic-clinical associations in colorectal cancer

We perform ultradeep whole-exome sequencing on 1015 patients with CRC as part of the ChangKang Project. we find that mitochondrial DNA copy number is an independent factor for predicting the survival outcome of CRCs. Overall, our results provide CRC-related molecular features for clinical practice and a valuable resource for translational research.

Qi Zhao, Feng Wang*, Yan-Xing Chen, Shifu Chen, Yi-Chen Yao, Zhao-Lei Zeng, Teng-Jia Jiang, Ying-Nan Wang, Chen-Yi Wu, Ying Jing, You-Sheng Huang, Jing Zhang, Zi-Xian Wang, Ming-Ming He, Heng-Ying Pu, Zong-Jiong Mai, Qi-Nian Wu, Renwen Long, Xiaoni Zhang, Tanxiao Huang, Mingyan Xu, Miao-Zheng Qiu, Hui-Yan Luo, Yu-Hong Li, Dong-Shen Zhang, Wei-Hua Jia, Gong Chen, Pei-Rong Ding, Li-Ren Li, Zheng-Hai Lu, Zhi-Zhong Pan & Rui-Hua Xu *

Nat Commun 13, 2342 (2022).

MesKit: a tool kit for dissecting cancer evolution of multi-region tumor biopsies through somatic alterations

We present MesKit, an R/Bioconductor package that can assist in characterizing genetic ITH and tracing the evolutionary history of tumors based on somatic alterations detected by MRS.

Mengni Liu, Jianyu Chen, Xin Wang, Chengwei Wang, Xiaolong Zhang, Yubin Xie, Zhixiang Zuo, Jian Ren, Qi Zhao*

GigaScience, 10(5), 2021, giab036

MYC-activated lncRNA MNX1-AS1 promotes the progression of colorectal cancer by stabilizing YB1

In this work, through transcriptomic profiling analysis of 21 paired tumor and normal samples, we identified a novel colorectal cancer–related lncRNA, MNX1-AS1.

Qi-Nian Wu, Xiao-Jing Luo, Jia Liu, Yun-Xin Lu, Yun Wang, Jingjing Qi, Ze-Xian Liu, Qi-Tao Huang, Ze-Kun Liu, Jia-Bin Lu, Ying Jin, Heng-Ying Pu, Pei-Shan Hu, Jia-Bo Zheng, Zhao-Lei Zeng, Huai-Qiang Ju, Dan Xie, Qi Zhao*, Ruihua Xu*

Cancer Research, 2021, 81(10):2636-2650

Novel Genetic and Epigenetic Biomarkers of Prognostic and Predictive Significance in Stage II/III Colorectal Cancer

In this work, we reviewed current Genetic and Epigenetic Biomarkers of Prognostic and Predictive Significance in Stage II/III Colorectal Cancer”

Luo, Xiao-Jing, Qi Zhao, Jia Liu, Jia-Bo Zheng, Miao-Zhen Qiu, Huai-Qiang Ju, and Rui-Hua Xu*.

Molecular Therapy, 2021 Feb 3;29(2):587-596.

Systematic analysis of the transcriptome in small-cell carcinoma of the esophagus reveals its immune microenvironment

In this study, transcriptomic aberrance and immune microenvironment of small‐cell carcinoma of the esophagus (SCCE) was comprehensively characterized with transcriptome and immunohistochemistry analysis. Assessment of immune checkpoint blockade (ICB) treatment biomarkers provides a rationale for use of ICB treatment in patients with SCCE.

Qi Zhao, Yan-Xing Chen, Qi-Nian Wu, Chao Zhang, Min Liu Ying-Nan Wang, Yan-Fen Feng, Jia-Jia Hu, Jian-Hua Fu, Hong Yang, Jing-Jing Qi, Zi-Xian Wang, Yun-Xin Lu, Hui Sheng, Ze-Xian Liu, Zhi-Xiang Zuo, Jian Zheng, Jing-Ping Yun, Jin-Xin Bei, Wei-Hua Jia, Dong-Xin Lin, Rui-hua Xu, Feng Wang*.

Clinical & Translational Immunology, 2020 Oct 5;9(10):e1173

 

Selected publications

(See also Google Scholar; † for equal contribution; * for corresponding authors)

2022

[29]. Deciphering clonal dynamics and metastatic routines in a rare patient of synchronous triple-primary tumors and multiple metastases with MPTevol
Qingjian Chen, Qi-Nian Wu, Yu-Ming Rong, Shixiang Wang, Zhixiang Zuo, Long Bai, Bei Zhang, Shuqiang Yuan*, Qi Zhao*
Briefings in Bioinformatics, bbac175, 2022

[28]. Comprehensive profiling of 1015 patients’ exomes reveals genomic-clinical associations in colorectal cancer
Qi Zhao, Feng Wang*, Yan-Xing Chen, Shifu Chen, Yi-Chen Yao, Zhao-Lei Zeng, Teng-Jia Jiang, Ying-Nan Wang, Chen-Yi Wu, Ying Jing, You-Sheng Huang, Jing Zhang, Zi-Xian Wang, Ming-Ming He, Heng-Ying Pu, Zong-Jiong Mai, Qi-Nian Wu, Renwen Long, Xiaoni Zhang, Tanxiao Huang, Mingyan Xu, Miao-Zheng Qiu, Hui-Yan Luo, Yu-Hong Li, Dong-Shen Zhang, Wei-Hua Jia, Gong Chen, Pei-Rong Ding, Li-Ren Li, Zheng-Hai Lu, Zhi-Zhong Pan & Rui-Hua Xu *
Nat Commun 13, 2342 (2022).

[27]. [Review]Raman Spectroscopy: A Novel Technology for Gastric Cancer Diagnosis
Kunxiang Liu, Qi Zhao, Bei Li*, and Xia Zhao*
Front. Bioeng. Biotechnol (2022).

[26]. Driver mutations in ADGRL3 are involved in the evolution of ependymoma
Jing Wang*, Shao-yan Xi, Qi Zhao, Yun-fei Xia, Qun-ying Yang, Hai-ping Cai, Fang Wang, Yi-ying Zhao, Huan-jing Hu, Zhi-hui Yu, Fu-rong Chen, Peng-Fei Xu, Ri-zhen Xu, Jian Wang, Ji Zhang, Chao Ke, Xiang-heng Zhang, Fu-hua Lin, Cheng-cheng Guo, Yan-chun Lv, Cong Li, Hai-tao Xie, Qian Cui, Hong-mei Wu, Yan-hui Liu, Zhi Li, Hong-kai Su, Jing Zeng, Fu Han, Zhao-jie Li, Ke Sai* & Zhong-ping Chen*
Lab Invest (2022).

2021

[25]. POLE/POLD1 mutation in non-exonuclease domain matters for predicting efficacy of immune-checkpoint-inhibitor therapy
Yan-Xing Chen, Zi-Xian Wang, Shu-Qiang Yuan, Teng-Jia Jiang, You-Sheng Huang, Rui-Hua Xu, Feng Wang*, Qi Zhao*
Clin Transl Med. 2021 Sep;11(9):e524.

[24]. MesKit: a tool kit for dissecting cancer evolution of multi-region tumor biopsies through somatic alterations
Mengni Liu, Jianyu Chen, Xin Wang, Chengwei Wang, Xiaolong Zhang, Yubin Xie, Zhixiang Zuo, Jian Ren, Qi Zhao*
GigaScience, 10(5), 2021, giab036

[23]. MYC-activated lncRNA MNX1-AS1 promotes the progression of colorectal cancer by stabilizing YB1
Qi-Nian Wu, Xiao-Jing Luo, Jia Liu, Yun-Xin Lu, Yun Wang, Jingjing Qi, Ze-Xian Liu, Qi-Tao Huang, Ze-Kun Liu, Jia-Bin Lu, Ying Jin, Heng-Ying Pu, Pei-Shan Hu, Jia-Bo Zheng, Zhao-Lei Zeng, Huai-Qiang Ju, Dan Xie, Qi Zhao*, Ruihua Xu*
Cancer Research, 2021, 81(10):2636-2650

[22]. Novel Genetic and Epigenetic Biomarkers of Prognostic and Predictive Significance in Stage II/III Colorectal Cancer
Luo, Xiao-Jing, Qi Zhao, Jia Liu, Jia-Bo Zheng, Miao-Zhen Qiu, Huai-Qiang Ju, and Rui-Hua Xu*.
Molecular Therapy, 2021 Feb 3;29(2):587-596.

[21]. Image-driven classification of functioning and nonfunctioning pituitary adenoma by deep convolutional neural networks
Hongyu Li, Qi Zhao, Yihua Zhang, Ke Sai, Lunshan Xu, Yonggao Mou, Yubin Xie, Jian Ren*, Xiaobing Jiang*.
Computational and Structural Biotechnology Journal, 2021 May 14;19:3077-3086.

2020

[20]. Evaluation of POLE / POLD1 Variants as Potential Biomarkers for Immune Checkpoint Inhibitor Treatment Outcomes—Reply
Feng Wang , Qi Zhao, Rui-Hua Xu
JAMA oncology, 2020 Mar 5.

[19]. Systematic analysis of the aberrances and functional implications of ferroptosis in cancer.
Zekun Liu, Qi Zhao, Zhi-Xiang Zuo, Shu-Qiang Yuan, Kai Yu, Qingfeng Zhang, Xiaolong Zhang, Hui Sheng, Huai-Qiang Ju, Han Cheng, Feng Wang, Rui-Hua Xu, Ze-Xian Liu
iScience, 2020 Jul 24;23(7):101302.

[18]. p.P476S mutation of RBPJL inhibits the efficacy of anti-PD-1 therapy in esophageal squamous cell carcinoma by blunting T-cell responses.
Lei Miao, Xiao-Li Wei, Qi Zhao, JingJing Qi, Chao Ren, Qi-Nian Wu, Da-Liang Wei, Jia Liu, Feng-Hua Wang, Rui-Hua Xu
Clinical & Translational Immunology, 2020 Sep 16;9(9):e1172

[17]. Systematic analysis of the transcriptome in small-cell carcinoma of the esophagus reveals its immune microenvironment
Qi Zhao, Yan-Xing Chen, Qi-Nian Wu, Chao Zhang, Min Liu Ying-Nan Wang, Yan-Fen Feng, Jia-Jia Hu, Jian-Hua Fu, Hong Yang, Jing-Jing Qi, Zi-Xian Wang, Yun-Xin Lu, Hui Sheng, Ze-Xian Liu, Zhi-Xiang Zuo, Jian Zheng, Jing-Ping Yun, Jin-Xin Bei, Wei-Hua Jia, Dong-Xin Lin, Rui-hua Xu, Feng Wang*.
Clinical & Translational Immunology, 2020 Oct 5;9(10):e1173

[16]. autoRPA: A web server for constructing cancer staging models by recursive partitioning analysis
Xie, Yubin, Xiaotong Luo, Huiqin Li, Qingxian Xu, Zhihao He, Qi Zhao*, Zhixiang Zuo*, and Jian Ren*
Computational and Structural Biotechnology Journal, 2020 Nov 10;18:3361-3367. 

[15]. Germline mutational profile of Chinese patients under 70 years old with colorectal cancer.
Teng-Jia Jiang, Fang Wang, Ying-Nan Wang, Jia-Jia Hu, Pei-Rong Ding, Jun-Zhong Lin, Zhi-Zhong Pan, Gong Chen, Jian-Yong Shao, Rui-hua Xu, Qi Zhao*, Feng Wang*.
Cancer Communications, 2020 Nov;40(11):620-632

[14]. MUC4, MUC16 and TTN genes mutation correlated with prognosis, and predicted tumor mutation burden and immunotherapy efficacy in gastric cancer and pan-cancer.
Yue Yang, Jieyun Zhang, Yanxing Chen, Rui-Hua Xu, Zhao Qi*, Weijian Guo*.
Clinical and Translational Medicine, 2020 Aug; 10(4):e155

[13]. Targeting the STING pathway in tumor-associated macrophages regulates innate immune sensing of gastric cancer cells
Miao Lei, Jingjing Qi, Qi Zhao, Qi-Nian Wu, Da-Liang Wei, Xiao-Li Wei, Jia Liu, Jun Chen, Zhaolei Zeng, Huaiqiang Ju, Huiyan Luo, Rui-hua Xu
Theranostics, 2020 Jan 1;10(2):498-515

[12]. BBCancer: an expression atlas of blood-based biomarkers in the early diagnosis of cancers
Zuo, Zhixiang, Huanjing Hu, Qingxian Xu, Xiaotong Luo, Di Peng, Kaiyu Zhu, Qi Zhao, Yubin Xie, Jian Ren*
Nucleic Acids Research, 2020 Jan 8;48(D1):D789-D796

[11]. Circulating tumor DNA methylation profiles enable early diagnosis, prognosis prediction, and screening for colorectal cancer
Huiyan Luo, Qi Zhao, Wei Wei, Lianghong Zheng, Shaohua Yi, Gen Li, Wenqiu Wang, Hui Sheng, Hengying Pu, Haiyu Mo, Zhixiang Zuo, Zexian Liu, Chaofeng Li, Chuanbo Xie, Zhaolei Zeng, Weimin Li, Xiaoke Hao, Yuying Liu, Sumei Cao, Wanli Liu, Sarah Gibson, Kang Zhang, Guoliang Xu, Rui-hua Xu*
Science Translational Medicine, 2020 Jan 1;12(524):eaax7533

2019

[10]. Tumor mutational and indel burden: a systematic pan-cancer evaluation as prognostic biomarkers
Hao-Xiang Wu , Zi-Xian Wang , Qi Zhao , Dong-Liang Chen , Ming-Ming He , Lu-Ping Yang , Ying-Nan Wang , Ying Jin , Chao Ren , Hui-Yan Luo , Zhi-Qiang Wang , Feng Wang
Annals of Translational Medicine, 2019 Nov;7(22):640

[9]. Dysregulation, functional implications, and prognostic ability of the circadian clock across cancers
Zekun Liu, Kai Yu, Jian Zheng, Huan Lin, Qi Zhao, Xiaolong Zhang, Weiyi Feng, Liyu Wang, Jianjun Xu, Dawei Xie, Zhi‐Xiang Zuo, Ze‐Xian Liu, Qichang Zheng
Cancer Medicine, 2019 Apr;8(4):1710-1720.

[8]. CrossICC: Iterative consensus clustering of cross-platform gene expression data without adjusting batch effect.
Qi Zhao, Yu Sun, Zekun Liu, Hongwan Zhang, Xingyang Li, Kaiyu Zhu, Ze-Xian Liu, Jian Ren, Zhixiang Zuo*.
Briefings in Bioinformatics, 2020 Sep 25;21(5):1818-1824

[7]. A circRNA signature predicts postoperative recurrence in stage II/III colon cancer
Huai-Qiang Ju, Qi Zhao, Feng Wang, Ping Lan, Zi-Xian Wang, Zhixiang Zuo, Qi-Nian Wu, Xin-Juan Fan, Hai-Yu Mo, Li Chen, Ting Li, Chao Ren, Xiang-Bo Wan, Gong Chen, Yu-Hong Li, Wei-Hua Jia, Rui-Hua Xu
EMBO Molecular Medicine, 2019 Oct;11(10):e10168

[6]. Evaluation of POLE and POLD1 Mutations as Biomarkers for Immunotherapy Outcomes Across Multiple Cancer Types
Feng Wang, Qi Zhao, Ying-Nan Wang, Ying Jin, Ming-Ming He, Zexian Liu, Rui-Hua Xu*
JAMA oncology, 2019 Aug 15;5(10):1504–6

2018

[5]. LncPipe: A Nextflow-based pipeline for identification and analysis of long non-coding RNAs from RNA-Seq data
Qi Zhao, Yu Sun, Dawei Wang, Hongwan Zhang, Kai Yu, Jian Zheng, Zhixiang Zuo
Journal of Genetics and Genomics, 2018 Jul 20;45(7):399-401

[4]. qPhos: a database of protein phosphorylation dynamics in humans
Kai Yu, Qingfeng Zhang, Zekun Liu, Qi Zhao, Xiaolong Zhang, Yan Wang, Zi-Xian Wang, Ying Jin, Xiaoxing Li, Ze-Xian Liu, Rui-Hua Xu
Nucleic Acids Research, 10/2018;47(Databaseissue)

[3]. The genomic landscape of small cell carcinoma of the esophagus
Feng Wang, Dong-Bing Liu, Qi Zhao, Gang Chen, Xin-Ming Liu, Ying-Nan Wang, Hong Su, Yan-Ru Qin, Yi-Fu He, Qing-Feng Zou, Yan-Hui Liu, You-En Lin, Ze-Xian Liu, Jin-Xin Bei, Rui-Hua Xu
Cell Research, 2018 Jul;28(7):771-774.

2017

[2]. VirusMap: A visualization database for the influenza A virus
Yubin Xie, Xiaotong Luo, Zhihao He, Yueyuan Zheng, Zhixiang Zuo, Qi Zhao*, Yanyan Miao*, Jian Ren*
Journal of Genetics and Genomics, 2017 May 20;44(5):281-284.

2016

2015

2014

[1]. GPS-SUMO: A tool for the prediction of sumoylation sites and SUMO-interaction motifs
Qi Zhao, Yubin Xie, Yueyuan Zheng, Shuai Jiang, Wenzhong Liu, Weiping Mu, Zexian Liu, Yong Zhao, Yu Xue, Jian Ren
Nucleic Acids Research,  2014 Jul;42(Web Server issue):W325-30