iATMEcell: identification of abnormal tumor microenvironment cells to predict the clinical outcomes in cancer based on cell–cell crosstalk network, Yuqi Sheng, Jiashuo Wu, Xiangmei Li, Jiayue Qiu, Ji Li, Qinyu Ge, Liang Cheng, Junwei Han, 2023
Anovel pathway mutation perturbation score predicts the clinical outcomes of immunotherapy, Li, Xiangmei; He, Yalan; Wu, Jiashuo; Qiu, Jiayue; Ji Li; Wang, Qian; Jiang, Ying; Junwei Han, 2022
CNA2Subpathway: identification of dysregulated subpathway driven by copy number alterations in cancer, Sheng, Yuqi; Jiang, Ying; Yang, Yang; Li, Xiangmei; Qiu, Jiayue; Wu, Jiashuo; Cheng, Liang; Han, Junwei, 2021
psSubpathway: a software package for flexible identification of phenotype-specific subpathways in cancer progression, Han, Junwei; Han, Xudong; Kong, Qingfei; Cheng, Liang, 2020
SubtypeDrug: a software package for prioritization of candidate cancer subtype-specific drugs, Han, Xudong; Kong, Qingfei; Liu, Chonghui; Cheng, Liang; Han, Junwei, 2021
DRviaSPCN: a software package for drug repurposing in cancer via a subpathway crosstalk network, Wu, Jiashuo; Li, Xiangmei; Wang, Qian; Han, Junwei, 2022
DrugSim2DR: systematic prediction of drug functional similarities in the context of specific disease for drug repurposing, Jiashuo Wu, Ji Li, Yalan He, Junling Huang, Xilong Zhao, Bingyue Pan, Yahui Wang, Liang Cheng, Junwei Han, 2023
DTSEA: A network-based drug target set enrichment analysis method for drug repurposing against COVID-19, Yinchun Su, Jiashuo Wu, Xiangmei Li, Ji Li, Xilong Zhao, Bingyue Pan, Junling Huang, Qingfei Kong, Junwei Han, 2023
PathwayTMB: A pathway-based tumor mutational burden analysis method for predicting the clinical outcome of cancer immunotherapy, Xiangmei Li, Yalan He, Ying Jiang, Bingyue Pan, Jiashuo Wu, Xilong Zhao, Junling Huang, Qian Wang, Liang Cheng, Junwei Han, 2023
Identification of comutation in signaling pathways to predict the clinical outcomes of immunotherapy, Qiu, Jiayue; Li, Xiangmei; He, Yalan; Wang, Qian; Li, Ji; Wu, Jiashuo; Jiang, Ying; Han, Junwei, 2022
Prioritization of candidate cancer drugs based on a drug functional similarity network constructed by integrating pathway activities and drug activities, Di, Jieyi; Zheng, Baotong; Kong, Qingfei; Jiang, Ying; Liu, Siyao; Yang, Yang; Han, Xudong; Sheng, Yuqi; Zhang, Yunpeng; Cheng, Liang; Han, Junwei, 2019
A pathway-based mutation signature to predict the clinical outcomes and response to CTLA-4 inhibitors in melanoma, Qian Wang, Xiangmei Li, Jiayue Qiu, Yalan He, Jiashuo Wu, Ji Li, Wei Liu, Junwei Han, 2023
PCLassoLog: A protein complex-based, group Lasso-logistic model for cancer classification and risk protein complex discovery, Wang, Wei; Yuan, Haiyan; Han, Junwei; Liu, Wei, 2022
Tumor Microenvironment Characterization in Breast Cancer Identifies Prognostic Pathway Signatures, Li, Ji; Qiu, Jiayue; Han, Junwei; Li, Xiangmei; Jiang, Ying, 2022
Analysis of Tumor Microenvironment Heterogeneity among Breast Cancer Subtypes to Identify Subtype-Specific Signatures, Li, Ji; Wu, Jiashuo; Han, Junwei, 2022
Development and Validation of a Three-Gene Prognostic Signature Based on Tumor Microenvironment for Gastric Cancer, Wang, Qian; Li, Xiangmei; Wang, Yahui; Qiu Jiayue; Wu, Jiashuo; He, Yalan Li, Ji; Kong, Qingfei; Han, Junwei; Jiang, Ying, 2022
Inference of patient-specific subpathway activities reveals a functional signature associated with the prognosis of patients with breast cancer, Han, Junwei; Liu, Siyao; Jiang, Ying; Xu, Chaohan; Zheng, Baotong; Jiang, Minghao; Yang, Haixiu; Su, Fei; Li, Chunquan; Zhang, Yunpeng, 2018
Integrative Pathway Analysis of Genes and Metabolites Reveals Metabolism Abnormal Subpathway Regions and Modules in Esophageal Squamous Cell Carcinoma, Li, Chunquan; Wang, Qiuyu; Ma, Jiquan; Shi, Shengshu; Chen, Xin; Yang, Haixiu; Han, Junwei, 2017
Identification of Cancer Dysfunctional Subpathways by Integrating DNA Methylation, Copy Number Variation, and Gene-Expression Data, Liu Siyao; Zheng Baotong; Sheng Yuqi; Kong Qingfei; Jiang Ying; Yang Yang; Han Xudong; Cheng Liang; Zhang Yunpeng; Han Junwei, 2019
Identification of Somatic Mutation-Driven Immune Cells by Integrating Genomic and Transcriptome Data, Jiang, Ying; Zheng, Baotong; Yang, Yang; Li, Xiangmei; Han, Junwei, 2021
Identifying disease related sub-pathways for analysis of genome-wide association studies, Li, Chunquan; Han, Junwei; Shang, Desi; Li, Jing; Wang, Yan; Wang, YingYing; Zhang, Yunpeng; Yao, Qianlan; Zhang, Chunlong; Li, Kongning; Li, Xia, 2012
Subpathway-GM: identification of metabolic subpathways via joint power of interesting genes and metabolites and their topologies within pathways, Li, Chunquan; Han, Junwei; Yao, Qianlan; Zou, Chendan; Xu, Yanjun; Zhang, Chunlong; Shang, Desi; Zhou, Lingyun; Zou, Chaoxia; Sun, Zeguo; Li, Jing; Zhang, Yunpeng; Yang, Haixiu; Gao, Xu; Li, Xia, 2013
LncRNAs2Pathways: Identifying the pathways influenced by a set of lncRNAs of interest based on a global network propagation method, Han, Junwei; Liu, Siyao; Sun, Zeguo; Zhang, Yunpeng; Zhang, Fan; Zhang, Chunlong; Shang, Desi; Yang, Haixiu; Su, Fei; Xu, Yanjun; Li, Chunquan; Ren, Huan; Li, Xia, 2017
A novel dysregulated pathway-identification analysis based on global influence of within-pathway effects and crosstalk between pathways, Han, Junwei; Li, Chunquan; Yang, Haixiu; Xu, Yanjun; Zhang, Chunlong; Ma, Jiquan; Shi, Xinrui; Liu, Wei; Shang, Desi; Yao, Qianlan; Zhang, Yunpeng; Su, Fei; Feng, Li; Li, Xia, 2015
ESEA: Discovering the Dysregulated Pathways based on Edge Set Enrichment Analysis, Han, Junwei; Shi, Xinrui; Zhang, Yunpeng; Xu, Yanjun; Jiang, Ying; Zhang, Chunlong; Feng, Li; Yang, Haixiu; Shang, Desi; Sun, Zeguo; Su, Fei; Li, Chunquan; Li, Xia, 2015
