2023

• Wu T*, Chen J, Diao K, Wang G, Wang J, Yao H, Liu XS. Neodb: a comprehensive neoantigen database and discovery platform for cancer immunotherapy. Database (Oxford). Jun 2023

• Ning, Wei*; Wu, Tao; Wu, Chenxu; Wang, Shixiang; Tao, Ziyu; Wang, Guangshuai; Zhao, Xiangyu; Diao, Kaixuan; Wang, Jinyu; Chen, Jing; Chen, Fuxiang; Liu, Xue-Song^#.Accurate prediction of pan-cancer types using machine learning with minimal number of DNA methylation sites.JOURNAL OF MOLECULAR CELL BIOLOGY. Apr 2023

• Wang, Guangshuai*; Wu, Tao; Ning, Wei; Diao, Kaixuan; Sun, Xiaoqin; Wang, Jinyu; Wu, Chenxu; Chen, Jing; Xu, Dongliang; Liu, Xue-Song^#.TLimmuno2: predicting MHC class II antigen immunogenicity through transfer learning.BRIEFINGS IN BIOINFORMATICS. Mar 2023.

• Tao, Ziyu*; Wang, Shixiang*; Wu, Chenxu*; Wu, Tao; Zhao, Xiangyu; Ning, Wei; Wang, Guangshuai; Wang, Jinyu; Chen, Jing; Diao, Kaixuan; Chen, Fuxiang; Liu, Xue-Song^#.The repertoire of copy number alteration signatures in human cancer.BRIEFINGS IN BIOINFORMATICS. 01 Feb 2023.

• Wu, Tao*; Diao, Kaixuan; Liu, Xue-Song^#.Quantification of Neoantigen-Mediated Immunoediting in Cancer Evolution-Reply.CANCER RESEARCH. Mar 2023. 83(6):973.

• Diao, Kaixuan*; Chen, Jing*; Wu, Tao; Wang, Xuan; Wang, Guangshuai; Sun, Xiaoqin; Zhao, Xiangyu; Wu, Chenxu; Wang, Jinyu; Yao, Huizi; Gerarduzzi, Casimiro; Liu, Xue-Song^#.Seq2Neo: A Comprehensive Pipeline for Cancer Neoantigen Immunogenicity Prediction.INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES. Oct 2022. 23(19).

• Zhao, Xiangyu*; Chen, Yuxing; Sun, Xiaoqin; He, Zaoke; Wu, Tao; Wu, Chenxu; Chen, Jing; Wang, Jinyu; Diao, Kaixuan; Liu, Xue-Song^#.Oncogenic EFNA4 Amplification Promotes Lung Adenocarcinoma Lymph Node Metastasis.CANCERS. Sep 2022. 14(17).

2022

• Jianfeng Li^#*; Benben Miao*; Shixiang Wang*; Wei Dong*; Houshi Xu*; Chenchen Si*; Wei Wang; Songqi Duan; Jiacheng Lou; Zhiwei Bao; Hailuan Zeng; Zengzeng Yang; Wenyan Cheng; Fei Zhao; Jianming Zeng; Xue-Song Liu^#; Renxie Wu^#; Yang Shen^#; Zhu Chen^#; Saijuan Chen^#; Mingjie Wang^#.Hiplot: a comprehensive and easy-to-use web service for boosting publication-ready biomedical data visualization.BRIEFINGS IN BIOINFORMATICS. Jul 2022.

• Wu, Tao*; Wang, Guangshuai; Wang, Xuan; Wang, Shixiang; Zhao, Xiangyu; Wu, Chenxu; Ning, Wei; Tao, Ziyu; Chen, Fuxiang; Liu, Xue-Song^#.Quantification of neoantigen-mediated immunoediting in cancer evolution.CANCER RESEARCH. 15 Jun 2022. 82(12).

• Wu, Tao*; Wu, Chenxu*; Zhao, Xiangyu; Wang, Guangshuai; Ning, Wei; Tao, Ziyu; Chen, Fuxiang; Liu, Xue-Song^#.Extrachromosomal DNA formation enables tumor immune escape potentially through regulating antigen presentation gene expression.SCIENTIFIC REPORTS. Mar 2022.

2021

• He, Zaoke*; Sun, Xiaoqin; Wang, Shixiang; Bai, Dongsheng; Zhao, Xiangyu; Han, Ying; Hao, Piliang; Liu, Xue-Song^#.Ggct (g-glutamyl cyclotransferase) plays an important role in erythrocyte antioxidant defense and red blood cell survival.BRITISH JOURNAL OF HAEMATOLOGY. Oct 2021. 195(2):267-275.

• Wang, Shixiang*; Xiong, Yi; Zhao, Longfei; Gu, Kai; Li, Yin; Zhao, Fei; Li, Jianfeng; Wang, Mingjie; Wang, Haitao; Tao, Ziyu; Wu, Tao; Zheng, Yichao; Li, Xuejun^#; Liu, Xue-Song^#.UCSCXenaShiny: An R/CRAN Package for Interactive Analysis of UCSC Xena Data.BIOINFORMATICS. Jul 2021. 38(2).

• Wang, Shixiang*; Li, Huimin; Song, Minfang; Tao, Ziyu; Wu, Tao; He, Zaoke; Zhao, Xiangyu; Wu, Kai; Liu, Xue-Song^#.Copy number signature analysis tool and its application in prostate cancer reveals distinct mutational processes and clinical outcomes.PLOS GENETICS. May 2021.

• He, Zaoke*; Wu, Tao; Wang, Shixiang; Zhang, Jing; Sun, Xiaoqin; Tao, Ziyu; Zhao, Xiangyu; Li, Huimin; Wu, Kai; Liu, Xue-Song^#.Pan-cancer noncoding genomic analysis identifies functional CDC20 promoter mutation hotspots.ISCIENCE. Mar 2021.

• Wang, Shixiang*; Tao, Ziyu; Wu, Tao; Liu, Xue-Song^#.Sigflow: an automated and comprehensive pipeline for cancer genome mutational signature analysis.BIOINFORMATICS. 01 Jun 2021.

2019

• Wang, Shixiang*; He, Zaoke; Wang, Xuan; Li, Huimin; Liu, Xue-Song^#.Antigen presentation and tumor immunogenicity in cancer immunotherapy response prediction.ELIFE. 26 Nov 2019. 8.

• Wang, Shixiang*; Zhang, Jing; He, Zaoke; Wu, Kai; Liu, Xue-Song^#.The predictive power of tumor mutational burden in lung cancer immunotherapy response is influenced by patients’ sex.INTERNATIONAL JOURNAL OF CANCER. 15 Nov 2019. 145(10):2840-2849.

• He, Zaoke*; Wang, Shixiang; Shao, Yuanyuan; Zhang, Jing; Wu, Xiaolin; Chen, Yuxing; Hu, Junhao; Zhang, Feng; Liu, Xue-Song^#.Ras Downstream Effector GGCT Alleviates Oncogenic Stress.ISCIENCE. 27 Sep 2019. 19:256-266.

• Wang, Shixiang*; Cowley, Li An*; Liu, Xue-Song^#.Sex Differences in Cancer Immunotherapy Efficacy, Biomarkers, and Therapeutic Strategy.MOLECULES. Sep 2019. 24(18).

• Shixiang Wang*; Xuesong Liu^#.The UCSCXenaTools R package: a toolkit for accessing genomics data from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq.JOURNAL OF OPEN SOURCE SOFTWARE. 05 Aug 2019. 4(40).

• Wang, Shixiang*; He, Zaoke; Wang, Xuan; Li, Huimin; Wu, Tao; Sun, Xiaoqin; Wu, Kai; Liu, Xue-Song^#.Can tumor mutational burden determine the most effective treatment for lung cancer patients?.LUNG CANCER MANAGEMENT. Dec 2019. 8(4).

2018

• Wang, Shixiang*; Jia, Mingming*; He, Zaoke; Liu, Xue-Song^#.APOBEC3B and APOBEC mutational signature as potential predictive markers for immunotherapy response in non-small cell lung cancer.ONCOGENE. 19 Jul 2018. 37(29):3924-3936.