Publications

Journal article

Segmentation Only Uses Sparse Annotations: Unified Weakly and Semi-Supervised Learning in Medical Images

Medical Image Analysis (2022)

Feng Gao*, Minhao Hu#, MinEr Zhong#, Shixiang Feng#, Xuwei Tian#, Xiaochun Meng#, Ma-yi-di-li Ni-jia-ti, Zeping Huang, Minyi Lv, Tao Song, Xiaofan Zhang*, Xiaoguang Zou*, Xiaojian Wu*

Journal article

A Transcription Factor Signature Can Identify the CMS4 Subtype and Stratify the Prognostic Risk of Colorectal Cancer

Frontiers in Oncology (2022)

Min-Er Zhong#, Ze-ping Huang#, Xin Wang#, Cai Du, Cheng-hang Li, Feng Gao*, Xiao-jian Wu*, Wei Wang*

Journal article

Multi-Size Deep Learning Based Preoperative Computed Tomography Signature for Prognosis Prediction of Colorectal Cancer

Frontiers in Genetics (2022)

Cheng-hang Li#, Cai Du#, Min-Er Zhong#, Min-yi Lv, Ze-ping Huang, Qi-qi Zhu, Chu-ling Hu, Hao-ning Qi, Xiao-jian Wu*, Feng Gao*

Journal article

The growth pattern of liver metastases on MRI predicts early recurrence in patients with colorectal cancer: a multicenter study

European Radiology (2022)

Qian Cai#, Yi-ze Mao#, Si-qi Dai#, Feng Gao#, Qian Xiao, Wan-ming Hu, Tao Qin, Qiu-xia Yang, Zhao-zhou Li, Du Cai, Min-Er Zhong, Ke-feng Ding*, Xiaojian Wu*, Rong Zhang*

Journal article

DNA Repair–Related Gene Signature in Predicting Prognosis of Colorectal Cancer Patients

Frontiers in Genetics (2022)

Min-yi Lv#, Wei Wang#, Min-Er Zhong#, Cai Du, De-jun Fan, Cheng-hang Li, Wei-Bin Kou, Ze-ping Huang, Xin Duan, Chu-ling Hu, Qi-qi Zhu, Xiao-sheng He*, Feng Gao*

Journal article

Dissecting Cellular Heterogeneity Based on Network Denoising of scRNA-seq Using Local Scaling Self-Diffusion

Frontiers in Genetics (2022)

Xin Duan#, Wei Wang, Feng Gao*, Xu-dong Lin*

Journal article

The enhanced cell cycle related to the response to adjuvant therapy in pancreatic ductal adenocarcinoma

Genomics (2022)

Yi-ze Mao#, Wei-sheng Cheng#, Qiu-xia Yang#, Li-qin Li#, Wan-ming Hu, Ze-yu Shuang, De-jun Fan, Xin-lei Jiang, Feng Gao*, Sheng-ping Li*, Wei Wang*

Journal article

Identification of an Autophagy-Related Gene Signature for the Prediction of Prognosis in Early-Stage Colorectal Cancer

Frontiers in Genetics (2021)

Xu-tao Lin#, Qiu-ning Wu#, Si Qin#, De-jun Fan, Min-yi Lv, Xi Chen, Jia-wei Cai, Ze-rong Cai, Jing-rong Weng, Yi-feng Zou, Yu-ming Rong*, Feng Gao*

Journal article

Cancer-associated fibroblasts impact the clinical outcome and treatment response in colorectal cancer via immune system modulation: a comprehensive genome-wide analysis

Molecular Medicine (2021)

Yu-feng Chen#, Zhao-liang Yu#, Min-yi Lv#, Ze-rong Cai, Yi-feng Zou, Ping Lan*, Xiao-jian Wu*, Feng Gao*

Journal article

Genome-Wide Analysis Reveals Hypoxic Microenvironment Is Associated With Immunosuppression in Poor Survival of Stage II/III Colorectal Cancer Patients

Frontiers in Medicine (2021)

Yu-feng Chen#, Zhao-liang Yu#, Min-yi Lv#, Bin Zheng, Ying-xin Tan, Jia Ke, Xuan-hui Liu, Ze-rong Cai, Yi-feng Zou, Ping Lan*, Xiao-jian Wu*, Feng Gao*

Journal article

Predicting treatment response from longitudinal images using multi-task deep learning

Nature Communications (2021)

Cheng Jin#, Heng Yu#, Jia Ke#, Peirong Ding#, Yongju Yi, Xiaofeng Jiang, Xin Duan, Jinghua Tang, Daniel T. Chang, Xiaojian Wu*, Feng Gao*, Ruijiang Li*

Journal article

A novel cell-free DNA methylation-based model improves the early detection of colorectal cancer

Molecular Oncology (2021)

Xianrui Wu#, Yunfeng Zhang#, Tuo Hu, Xiaowen He, Yifeng Zou, Qiling Deng, Jia Ke, Lei Lian, Xiaosheng He, Dezhi Zhao, Xuyu Cai, Zhiwei Chen, Xiaojian Wu, Jian‐Bing Fan*, Feng Gao*, Ping Lan*

Journal article

Identification of prognostic spatial organization features in colorectal cancer microenvironment using deep learning on histopathology images

Medicine in Omics (2021)

Lin Qi, Jia Ke, Zhaoliang Yu, Yi Cao, Yuni Lai, Yufeng Chen, Feng Gao*, Xin Wang*

Journal article

A Metabolism-Related Radiomics Signature for Predicting the Prognosis of Colorectal Cancer

Frontiers in Molecular Biosciences (2021)

Du Cai#, Xin Duan#, Wei Wang#, Ze-Ping Huang, Qi-Qi Zhu, Min-Er Zhong, Min-Yi Lv, Cheng-Hang Li, Wei-Bin Kou, Xiao-Jian Wu*, Feng Gao*

Journal article

Protein-protein interaction analysis reveals a novel cancer stem cell related target TMEM17 in colorectal cancer

Cancer Cell International (2021)

Zhao-Liang Yu#, Yu-Feng Chen#, Bin Zheng, Ze-Rong Cai, Yi-Feng Zou, Jia Ke, Ping Lan, Feng Gao*, Xiao-Jian Wu*

Conference

Identification of a stemness-related gene signature for predicting prognosis of patients with adjuvant chemotherapy in colorectal cancer

Annals of Oncology (2020)

D. Cai, Y. Che, Z. Yu, C. Li, X. Duan, J. Ke, X. Wu, F. Gao

Journal article

Immune-related gene signature in predicting prognosis of early-stage colorectal cancer patients

European Journal of Surgical Oncology (2020)

Jia Ke#, Xuan-hui Liu#, Xiao-feng Jiang, Zhen He, Jian Xiao, Bin Zheng, Yu-feng Chen, Ze-rong Cai, Xiao-bin Zheng, Yi-feng Zou, Ping Lan*, Xiao-jian Wu*, Feng Gao*

Journal article

Hippo-YAP signaling controls lineage differentiation of mouse embryonic stem cells through modulating the formation of super-enhancers

Nucleic Acids Research (2020)

Xiang Sun, Zhijun Ren, Yixian Cun, Cai Zhao, Xianglin Huang, Jiajian Zhou, Rong Hu, Xiaoxi Su, Lu Ji, Peng Li, King Lun Kingston Mak, Feng Gao, Yi Yang, He Xu, Junjun Ding, Nan Cao, Shuo Li, Wensheng Zhang, Ping Lan, Hao Sun, Jinkai Wang, Ping Yuan

Conference

Integrating diffusion components of multi-omics datasets with application to cancer molecular subtyping

Intelligent Systems for Molecular Biology (2020)

Xin Duan, Du Cai, Yufeng Chen, Qiqi Zhu, Zeping Huang, Chenghang Li, Xiaojian Wu, Feng Gao

Journal article

Roscovitine enhances All-trans retinoic acid (ATRA)-induced leukemia cell differentiation: Novel effects on signaling molecules for a putative Cdk2 inhibitor

Cellular Signalling (2020)

Asif Rashid, Xin Duan, Feng Gao, Mengsu Yang*, Andrew Yen*

Conference

Development of a novel liquid biopsy test to diagnose and locate gastrointestinal cancers

Journal of Clinical Oncology (2020)

Yuying Wang, Jianchao Zheng, Zhilong Li, Ruijingfang Jiang, Jiaxi Peng, Jianlong Sun, Guanghui Yang, Xin-Rong Yang, Ao Huang, Yupeng Wang, Yuan Jie, Xuanhui Liu, Feng Gao, Xiaojian Wu, Dansong Wang, Wenchuan Wu, Wenhui Lou, Jian Zhou, Jia Fan

Conference

Automatic and Interpretable Model for Periodontitis Diagnosis in Panoramic Radiographs

Medical Image Computing and Computer Assisted Intervention (2020)

Haoyang Li, Juexiao Zhou, Yi Zhou, Jieyu Chen, Feng Gao, Ying Xu, Xin Gao

Journal article

Development and validation of an individualized gene expression-based signature to predict overall survival in metastatic colorectal cancer

Annals of Translational Medicine (2020)

Shu-Biao Ye#, Yi-Kan Cheng#, Jian-Cong Hu#, Feng Gao*, Ping Lan*

Journal article

Immune-related gene signature for predicting the prognosis of head and neck squamous cell carcinoma

Cancer cell International (2020)

Yangyang She, Xiangbo Kong, Yaping Ge, Ping Yin, Zhiyong Liu, Jieyu Chen, Feng Gao*, Silian Fang*

Journal article

Multiomics-Based Colorectal Cancer Molecular Subtyping Using Local Scaling Network Fusion

Journal of Computational Biology (2019)

Xin Duan, Kejun Wang, Jia Ke, Ping Lan, Feng Gao*, Xiaojian Wu*

Journal article

A signature of hypoxia-related factors reveals functional dysregulation and robustly predicts clinical outcomes in stage I/II colorectal cancer patients

Cancer Cell International (2019)

Yi-Feng Zou, Yu-Ming Rong, Ying-Xin Tan, Jian Xiao, Zhao-Liang Yu, Yu-Feng Chen, Jia Ke, Cheng-Hang Li, Xi Chen, Xiao-Jian Wu, Ping Lan, Xu-Tao Lin*, Feng Gao*

Journal article

Long-Read RNA Sequencing Identifies Alternative Splice Variants in Hepatocellular Carcinoma and Tumor-Specific Isoforms

Hepatology (2019)

Hui Chen#, Feng Gao#, Mian He#, Xiao Fan Ding, Aikha M. Wong, Siu Ching Sze, Allen C. Yu, Tingting Sun, Anthony W.-H. Chan, Xin Wang*, Nathalie Wong*

Journal article

An immune-related gene pairs signature predicts overall survival in serous ovarian carcinoma

OncoTargets and Therapy (2019)

Liuyan Zhang#, Ping Zhu#, Yao Tong, Yuzhuo Wang, Haifen Ma, Xuefei Xia, Yu Zhou, Xingguo Zhang*, Feng Gao*, Peng Shu*

Journal article

DeepCC: a novel deep learning-based framework for cancer molecular subtype classification

Oncogenesis (2019)

Feng Gao, Wei Wang, Miaomiao Tan, Lina Zhu, Yuchen Zhang, Evelyn Fessler, Louis Vermeulen*, Xin Wang*

Journal article

An immune-related gene signature predicts prognosis of gastric cancer

Medicine (2019)

Bitao Jiang#, Qingsen Sun#, Yao Tong, Yuzhuo Wang, Haifen Ma, Xuefei Xia, Yu Zhou, Xingguo Zhang*, Feng Gao*, Peng Shu*

Journal article

Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen

Nature Communications (2019)

Michael P. Menden, Dennis Wang, Mike J. Mason, Bence Szalai, Krishna C. Bulusu, Yuanfang Guan, Thomas Yu, Jaewoo Kang, Minji Jeon, Russ Wolfinger, Tin Nguyen, Mikhail Zaslavskiy, { AstraZeneca-Sanger Drug Combination DREAM Consortium, including Feng Gao }, In Sock Jang, Zara Ghazoui, Mehmet Eren Ahsen, Robert Vogel, Elias Chaibub Neto, Thea Norman, Eric K. Y. Tang, Mathew J. Garnett, Giovanni Y. Di Veroli, Stephen Fawell, Gustavo Stolovitzky, Justin Guinney, Jonathan R. Dry, Julio Saez-Rodriguez

Journal article

Gene Expression Signature in Surgical Tissues and Endoscopic Biopsies Identifies High-Risk T1 Colorectal Cancers

Gastroenterology (2019)

Raju Kandimalla#, Tsuyoshi Ozawa#, Feng Gao#, Xin Wang*, Ajay Goel*, T1 Colorectal Cancer Study Group

Conference

Pathway analysis of hypoxia-related factors in early colorectal cancer patients with poor prognosis

Journal of Clinical Oncology (2019)

Yingxin Tan, Yuming Rong, Zhaoliang Yu, Feng Gao, Yufeng Chen, Xutao Lin, Yifeng Zou, Xi Chen

Conference

Immune-related gene signature in predicting prognosis of early-stage colorectal cancer patients

Journal of Clinical Oncology (2019)

Jia Ke, Xuanhui Liu, Xiaofeng Jiang, Yufeng Chen, Zerong Cai, Ping Lan, Xiaojian Wu, Feng Gao

Journal article

RNAMethyPro: a biologically conserved signature of N6-methyladenosine regulators for predicting survival at pan-cancer level

npj Precision Oncology (2019)

Raju Kandimalla#, Feng Gao#, Ying Li#, Hao Huang, Jia Ke, Xin Deng, Linjie Zhao, Shengtao Zhou, Ajay Goel*, Xin Wang*

Journal article

Genome-wide Discovery of a Novel Gene-expression Signature for the Identification of Lymph Node Metastasis in Esophageal Squamous Cell Carcinoma

Annals of Surgery (2019)

Fuminori Sonohara#, Feng Gao#, Naoki Iwata, Mitsuro Kanda, Masahiko Koike, Naoki Takahashi, Yasuhide Yamada, Yasuhiro Kodera, Xin Wang*, Ajay Goel*

Journal article

A genomewide transcriptomic approach identifies a novel gene expression signature for the detection of lymph node metastasis in patients with early stage gastric cancer

EBioMedicine (2019)

Daisuke Izumi#, Feng Gao#, Shusuke Toden, Fuminori Sonohara, Mitsuro Kanda, Takatsugu Ishimoto, Yasuhiro Kodera, Xin Wang*, Hideo Baba*, Ajay Goel*

Journal article

Retinoic acid and 6-formylindolo(3,2-b)carbazole (FICZ) combination therapy reveals putative targets for enhancing response in non-APL AML

Leukemia and Lymphoma (2018)

Rodica P. Bunaciu, Robert J. MacDonald, Holly A. Jensen, Feng Gao, Xin Wang, Lynn Johnson, Jeffrey D. Varner, Andrew Yen

Journal article

High-throughput three-dimensional chemotactic assays reveal steepness-dependent complexity in neuronal sensation to molecular gradients

Nature Communications (2018)

Zhen Xu, Peilin Fang, Bingzhe Xu, Yufeng Lu, Jinghui Xiong, Feng Gao, Xin Wang, Jun Fan, Peng Shi

Journal article

Dissecting cancer heterogeneity based on dimension reduction of transcriptomic profiles using extreme learning machines

PLoS ONE (2018)

Kejun Wang#, Xin Duan#, Feng Gao#, Wei Wang, Liangliang Liu, Xin Wang

Journal article

Genome-wide Discovery and Identification of a Novel miRNA Signature for Recurrence Prediction in Stage II and III Colorectal Cancer

Clinical Cancer Research (2018)

Raju Kandimalla#, Feng Gao#, Takatoshi Matsuyama, Toshiaki Ishikawa, Hiroyuki Uetake, Naoki Takahashi, Yasuhide Yamada, Carlos Becerra, Scott Kopetz, Xin Wang*, Ajay Goel*

Conference

A Novel Non-Invasive Circulating Mirna Signature for Detection of Esophageal Adenocarcinoma

Gastroenterology (2018)

Jinsei Miyoshi, Feng Gao, Shusuke Toden, Martha J. Shrubsole, Marco Scarpa, Timothy Whitsett, Landon Inge, Stephen J. Meltzer, Bottiglieri Teodoro, Helen G. Coleman, Lesley A. Anderson, Xin Wang, Ajay Goel

Conference

Dysregulation of m6A RNA methylation regulators in colorectal cancer: Clinical implication as prognostic biomarkers and potential therapeutic targets

Cancer Research (2018)

Raju Kandimalla, Feng Gao, Chun Ruan, Michael Hsieh, Xin Wang, Ajay Goel

Journal article

A MicroRNA Signature Associated With Metastasis of T1 Colorectal Cancers to Lymph Nodes

Gastroenterology (2018)

Tsuyoshi Ozawa#, Raju Kandimalla#, Feng Gao#, Hiroaki Nozawa, Keisuke Hata, Hiroshi Nagata, Satoshi Okada, Daisuke Izumi, Hideo Baba, James Fleshman, Xin Wang, Toshiaki Watanabe, Ajay Goel

Conference

Poor-prognosis nasopharyngeal carcinoma as defined by a molecularly distinct subgroup and prediction by a miRNA expression signature

Journal of Clinical Oncology (2017)

Lan Zhao, Feng Gao, Wei Wang, Xin Duan, Yuchen Zhang, Lina Zhu, Xin Wang

Conference

Identification, Development and Validation of a Circulating Mirna-Based Diagnostic Signature for Early Detection of Gastric Cancer

Gastroenterology (2017)

Daisuke Izumi, Shusuke Toden, Feng Gao, Jacob Turner, Mitsuro Kanda, Takatsugu Ishimoto, Yasuhiro Kodera, Xin Wang, Hideo Baba, Ajay Goel

Conference

Genome-wide discovery and identification of a novel microrna signature for recurrence prediction in colorectal cancer

Cancer Research (2017)

Raju Kandimalla, Feng Gao, Naoki Takahashi, Yasuhide Yamada, Takatoshi Matsuyama, Toshiyaki Ishikawa, Xin Wang, Ajay Goel

Conference

Genome-Wide Analysis Revealed a Robust Gene Expression Signature to Identify Lymph Node Metastasis in Submucosal Colorectal Cancer

Gastroenterology (2017)

Raju Kandimalla, Tsuyoshi Ozawa, Feng Gao, Keisuke Hata, Hiroaki Nozawa, Hiroshi Nagata, Daisuke Izumi, Hideo Baba, James W Fleshman, Xin Wang, Toshiaki Watanabe, Ajay Goel

Conference

A Novel Mirna-Based, Non-Invasive, Diagnostic Panel for Detection of Esophageal Squamous Cell Carcinoma

Gastroenterology (2017)

Jinsei Miyoshi, Shusuke Toden, Jacob Turner, Feng Gao, Raju Kandimalla, Xin Wang, Mitsuro Kanda, Hideo Baba, Yasuhiro Kodera, Ajay Goel

Conference

A Novel Mirna Signature for the Detection of Lymph Node Metastasis in Submucosal Colorectal Cancer Patients

Gastroenterology (2017)

Tsuyoshi Ozawa, Feng Gao, Hiroaki Nozawa, Keisuke Hata, Hiroshi Nagata, Daisuke Izumi, Hideo Baba, Xin Wang, Toshiaki Watanabe, Ajay Goel