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Journal Articles
- 2023
[j45]Xiangwen Ji
, Edwin Wang, Qinghua Cui:
Deciphering gene contributions and etiologies of somatic mutational signatures of cancer. Briefings Bioinform. 24(2) (2023)- [j44]Rui Fan, Xiangwen Ji, Jianwei Li, Qinghua Cui, Chunmei Cui:
Defining the single base importance of human mRNAs and lncRNAs. Briefings Bioinform. 24(5) (2023) - [j43]Yu Liu, Rui Fan, Jingkun Yi, Qinghua Cui, Chunmei Cui:
A fusion framework of deep learning and machine learning for predicting sgRNA cleavage efficiency. Comput. Biol. Medicine 165: 107476 (2023) - [j42]Yicong Shen, Yuanxu Gao, Jiangcheng Shi, Zhou Huang, Rongbo Dai, Yi Fu, Yuan Zhou, Wei Kong, Qinghua Cui:
MicroRNA-Disease Network Analysis Repurposes Methotrexate for the Treatment of Abdominal Aortic Aneurysm in Mice. Genom. Proteom. Bioinform. 21(5): 1030-1042 (2023) - [j41]Jianming Qi, Qinghua Cui, Le Zhang, Yiqun Sun:
Solution Structures of an Electrical Transmission Line Model with Bifurcation and Chaos in Hamiltonian Dynamics. Int. J. Bifurc. Chaos 33(9): 2350108:1-2350108:34 (2023) - 2022
- [j40]Yongbiao Xue, Yiming Bao, Zhang Zhang, Wenming Zhao, Jing-Fa Xiao, Shunmin He, Guoqing Zhang, Yixue Li, Guoping Zhao, Runsheng Chen, Jingyao Zeng, Yadong Zhang, Yunfei Shang, Jialin Mai, Shuo Shi, Mingming Lu, Congfan Bu, Zhewen Zhang, Zhenglin Du, Yinying Wang, Hongen Kang, Tianyi Xu, Lili Hao, Peilin Jia, Shuai Jiang, Qiheng Qian, Tongtong Zhu, Wenting Zong, Tong Jin, Yuansheng Zhang, Dong Zou, Qiang Du, Changrui Feng, Lina Ma, Sisi Zhang, Anke Wang, Lili Dong, Yanqing Wang, Wan Liu, Xing Yan, Yunchao Ling, Zhihua Zhou, Wang Kang, Tao Zhang, Shuai Ma, Haoteng Yan, Zunpeng Liu, Zejun Ji, Yusheng Cai, Si Wang, Moshi Song, Jie Ren, Qi Zhou, Jing Qu, Weiqi Zhang, Guanghui Liu, Xu Chen, Tingting Chen, Yanling Sun, Caixia Yu, Bixia Tang, Junwei Zhu, Shuang Zhai, Yubin Sun, Qiancheng Chen, Xiaoyu Yang, Xin Zhang, Zhengqi Sang, Yonggang Wang, Yilin Zhao, Huanxin Chen, Li Lan, Yingke Ma, Yaokai Jia, Xinchang Zheng, Meili Chen, Ming Chen, Guangyi Niu, Rong Pan, Wei Jing, Jian Sang, Chang Liu, Yujia Xiong, Mochen Zhang, Guoliang Wang, Lizhi Yi, Wei Zhao, Song Wu, Zhuang Xiong, Rujiao Li, Zheng Gong, Lin Liu, Zhao Li, Qianpeng Li, Sicheng Luo, Jiajia Wang, Yirong Shi, Honghong Zhou, Peng Zhang, Tingrui Song, Yanyan Li, Fei Yang, Mengwei Li, Zhaohua Li, Dongmei Tian, Xiaonan Liu, Cuiping Li, Xufei Teng, Shuhui Song, Yang Zhang, Ruru Chen, Rongqin Zhang, Feng Xu, Yifan Wang, Chenfen Zhou, Haizhou Wang, Andrew E. Teschendorff, Yungang He, Zhen Yang, Lun Li, Na Li, Ying Cui, Guangya Duan, Gangao Wu, Tianhao Huang, Enhui Jin, Hailong Kang, Zhonghuang Wang, Hua Chen, Mingkun Li, Wanshan Ning, Yu Xue, Yanhu Liu, Qijun Zhou, Xingyan Liu, Longlong Zhang, Bingyu Mao, Shihua Zhang, Yaping Zhang, Guodong Wang, Qianghui Zhu, Xin Li, Menghua Li, Yuanming Liu, Hong Luo, Xiaoyuan Wu, Haichun Jing, Yitong Pan, Leisheng Shi, Zhixiang Zuo, Jian Ren, Xinxin Zhang, Yun Xiao, Xia Li, Dan Liu, Chi Zhang, Zheng Zhao, Tao Jiang, Wanying Wu, Fangqing Zhao, Xianwen Meng, Di Peng, Hao Luo, Feng Gao, Shaofeng Lin, Chuijie Liu, Anyuan Guo, Hao Yuan, Tianhan Su, Yong E. Zhang, Yincong Zhou, Guoji Guo, Shanshan Fu, Xiaodan Tan, Weizhi Zhang, Mei Luo, Yubin Xie, Chenwei Wang, Xingyu Liao, Xin Gao, Jianxin Wang, Guiyan Xie, Chunhui Yuan, Feng Tian, Dechang Yang, Ge Gao, Dachao Tang, Wenyi Wu, Yujie Gou, Cheng Han, Qinghua Cui, Xiangshang Li, Chuan-Yun Li, Xiaotong Luo:
Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022. Nucleic Acids Res. 50(D1): 27-38 (2022) - 2021
- [j39]Chunmei Cui, Yuan Zhou, Qinghua Cui:
Defining the functional divergence of orthologous genes between human and mouse in the context of miRNA regulation. Briefings Bioinform. 22(6) (2021) - [j38]Rui Fan, Qinghua Cui:
Toward comprehensive functional analysis of gene lists weighted by gene essentiality scores. Bioinform. 37(23): 4399-4404 (2021) - [j37]Ruya Sun, Yuan Zhou, Qinghua Cui:
Comparative analysis of aneurysm subtypes associated genes based on protein-protein interaction network. BMC Bioinform. 22(1): 587 (2021) - [j36]Yongbiao Xue, Yiming Bao, Zhang Zhang, Wenming Zhao, Jing-Fa Xiao, Shunmin He, Guoqing Zhang, Yixue Li, Guoping Zhao, Runsheng Chen, Shuhui Song, Lina Ma, Dong Zou, Dongmei Tian, Cuiping Li, Junwei Zhu, Zheng Gong, Meili Chen, Anke Wang, Yingke Ma, Mengwei Li, Xufei Teng, Ying Cui, Guangya Duan, Mochen Zhang, Tong Jin, Chengmin Shi, Zhenglin Du, Yadong Zhang, Chuandong Liu, Rujiao Li, Jingyao Zeng, Lili Hao, Shuai Jiang, Hua Chen, Dali Han, Tao Zhang, Wang Kang, Fei Yang, Jing Qu, Weiqi Zhang, Guanghui Liu, Lin Liu, Yang Zhang, Guangyi Niu, Tongtong Zhu, Changrui Feng, Xiaonan Liu, Yuansheng Zhang, Zhao Li, Ruru Chen, Qianpeng Li, Zhongyi Hua, Chao Jiang, Ziyuan Chen, Fangshu He, Yuyang Zhao, Yan Jin, Luqi Huang, Yuan Yuan, Chenfen Zhou, Qingwei Xu, Sheng He, Wei Ye, Ruifang Cao, Pengyu Wang, Yunchao Ling, Xing Yan, Qingzhong Wang, Qiang Du, Wenting Zong, Hongen Kang, Zhuang Xiong, Wendi Huan, Sirui Zhang, Qiguang Xia, Xiaojuan Fan, Zefeng Wang, Xu Chen, Tingting Chen, Sisi Zhang, Bixia Tang, Lili Dong, Zhewen Zhang, Zhonghuang Wang, Hailong Kang, Yanqing Wang, Song Wu, Ming Chen, Chang Liu, Yujia Xiong, Xueying Shao, Yanyan Li, Honghong Zhou, Xiaomin Chen, Yu Zheng, Quan Kang, Di Hao, Lili Zhang, Huaxia Luo, Yajing Hao, Peng Zhang, Zhi Nie, Shuhuan Yu, Jian Sang, Zhaohua Li, Xiangquan Zhang, Qing Zhou, Shuang Zhai, Yaping Zhang, Guodong Wang, Qianghui Zhu, Xin Li, Menghua Li, Jun Yan, Chen Li, Zhennan Wang, Xiangfeng Wang, Yuanming Liu, Hong Luo, Xiaoyuan Wu, Hai-Chun Jing, Lianhe Zhao, Jiajia Wang, Tinrui Song, Yi Zhao, Furrukh Mehmood, Shahid Ali, Amjad Ali, Shoaib Saleem, Irfan Hussain, Amir Ali Abbasi, Zhixiang Zuo, Jian Ren, Xinxin Zhang, Yun Xiao, Xia Li, Yiran Tu, Yu Xue, Wanying Wu, Peifeng Ji, Fangqing Zhao, Xianwen Meng, Di Peng, Hao Luo, Feng Gao, Wanshan Ning, Shaofeng Lin, Teng Liu, An-Yuan Guo, Hao Yuan, Yong E. Zhang, Xiaodan Tan, Weizhi Zhang, Yubin Xie, Chenwei Wang, Chun-Jie Liu, De-Chang Yang, Feng Tian, Ge Gao, Dachao Tang, Lan Yao, Qinghua Cui, Ni A. An, Chuan-Yun Li, Xiaotong Luo:
Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021. Nucleic Acids Res. 49(Database-Issue): D18-D28 (2021) - [j35]Chunmei Cui, Chuanbo Huang, Wanlu Zhou, Xiangwen Ji, Fenghong Zhang, Liang Wang, Yuan Zhou, Qinghua Cui:
AGTR2, One Possible Novel Key Gene for the Entry of SARS-CoV-2 Into Human Cells. IEEE ACM Trans. Comput. Biol. Bioinform. 18(4): 1230-1233 (2021) - 2020
- [j34]Kaiwen Jia, Yuanxu Gao, Jiangcheng Shi, Yuan Zhou, Yong Zhou, Qinghua Cui:
Annotation and curation of the causality information in LncRNADisease. Database J. Biol. Databases Curation 2020: baz150 (2020) - [j33]Jianwei Li, Yan Huang, Qinghua Cui, Yuan Zhou:
m6Acorr: an online tool for the correction and comparison of m6A methylation profiles. BMC Bioinform. 21(1): 31 (2020) - [j32]Xiangwen Ji, Chunmei Cui, Qinghua Cui:
smORFunction: a tool for predicting functions of small open reading frames and microproteins. BMC Bioinform. 21(1): 455 (2020) - 2019
- [j31]Fei Song, Chunmei Cui, Lin Gao, Qinghua Cui:
miES: predicting the essentiality of miRNAs with machine learning and sequence features. Bioinform. 35(6): 1053-1054 (2019) - [j30]Yiran Zhou, Qinghua Cui, Yuan Zhou:
NmSEER V2.0: a prediction tool for 2′-O-methylation sites based on random forest and multi-encoding combination. BMC Bioinform. 20-S(25): 690 (2019) - [j29]Qinghua Cui, Tingting Sun, Zongyao Nie:
Combining network topology with transcriptomic data for identifying radiosensitive gene signatures. J. Comput. Methods Sci. Eng. 19(3): 565-579 (2019) - [j28]Zhou Huang, Jiangcheng Shi, Yuanxu Gao, Chunmei Cui, Shan Zhang, Jianwei Li, Yuan Zhou, Qinghua Cui:
HMDD v3.0: a database for experimentally supported human microRNA-disease associations. Nucleic Acids Res. 47(Database-Issue): D1013-D1017 (2019) - [j27]Zhenyu Bao, Zhen Yang, Zhou Huang, Yiran Zhou, Qinghua Cui, Dong Dong:
LncRNADisease 2.0: an updated database of long non-coding RNA-associated diseases. Nucleic Acids Res. 47(Database-Issue): D1034-D1037 (2019) - [j26]Zhan Tong, Qinghua Cui, Juan Wang, Yuan Zhou:
TransmiR v2.0: an updated transcription factor-microRNA regulation database. Nucleic Acids Res. 47(Database-Issue): D253-D258 (2019) - [j25]Jianwei Li, Shan Zhang, Yanping Wan, Yingshu Zhao, Jiangcheng Shi, Yuan Zhou, Qinghua Cui:
MISIM v2.0: a web server for inferring microRNA functional similarity based on microRNA-disease associations. Nucleic Acids Res. 47(Webserver-Issue): W536-W541 (2019) - 2018
- [j24]Sisi Guo, Yuan Zhou, Pan Zeng, Guoheng Xu, Guoqing Wang, Qinghua Cui:
Identification and analysis of the human sex-biased genes. Briefings Bioinform. 19(2): 188-198 (2018) - [j23]Ruya Sun, Chunmei Cui, Yuan Zhou, Qinghua Cui:
AGD: Aneurysm Gene Database. Database J. Biol. Databases Curation 2018: bay100 (2018) - [j22]Yuan Zhou, Qinghua Cui:
Comparative Analysis of Human Genes Frequently and Occasionally Regulated by m6A Modification. Genom. Proteom. Bioinform. 16(2): 127-135 (2018) - [j21]Chunmei Cui, Weili Yang, Jiangcheng Shi, Yong Zhou, Jichun Yang, Qinghua Cui, Yuan Zhou:
Identification and Analysis of Human Sex-biased MicroRNAs. Genom. Proteom. Bioinform. 16(3): 200-211 (2018) - [j20]Hao-Dong Xu, Yongbo Wang, Shaofeng Lin, Wankun Deng, Di Peng, Qinghua Cui, Yu Xue:
PTMD: A Database of Human Disease-associated Post-translational Modifications. Genom. Proteom. Bioinform. 16(4): 244-251 (2018) - [j19]Jianwei Li, Xiaofen Han, Yanping Wan, Shan Zhang, Yingshu Zhao, Rui Fan, Qinghua Cui, Yuan Zhou:
TAM 2.0: tool for MicroRNA set analysis. Nucleic Acids Res. 46(Webserver-Issue): W180-W185 (2018) - 2017
- [j18]Wei Ma, Lu Zhang, Pan Zeng, Chuanbo Huang, Jianwei Li, Bin Geng, Jichun Yang, Wei Kong, Xuezhong Zhou, Qinghua Cui:
An analysis of human microbe-disease associations. Briefings Bioinform. 18(1): 85-97 (2017) - 2015
- [j17]Jianwei Li, Wei Ma, Pan Zeng, Junyi Wang, Bin Geng, Jichun Yang, Qinghua Cui:
LncTar: a tool for predicting the RNA targets of long noncoding RNAs. Briefings Bioinform. 16(5): 806-812 (2015) - [j16]Hui Zeng, Chengxiang Qiu, Qinghua Cui:
Drug-Path: a database for drug-induced pathways. Database J. Biol. Databases Curation 2015 (2015) - [j15]Yan-Hui Li, Gaigai Zhang, Qinghua Cui:
PPUS: a web server to predict PUS-specific pseudouridine sites. Bioinform. 31(20): 3362-3364 (2015) - 2014
- [j14]Yang Li, Chengxiang Qiu, Jian Tu, Bin Geng, Jichun Yang, Tianzi Jiang, Qinghua Cui:
HMDD v2.0: a database for experimentally supported human microRNA and disease associations. Nucleic Acids Res. 42(Database-Issue): 1070-1074 (2014) - 2013
- [j13]Geng Chen, Ziyun Wang, Dongqing Wang, Chengxiang Qiu, Mingxi Liu, Xing Chen, Qipeng Zhang, Guiying Yan, Qinghua Cui:
LncRNADisease: a database for long-non-coding RNA-associated diseases. Nucleic Acids Res. 41(Database-Issue): 983-986 (2013) - 2012
- [j12]Juan Wang, Zhi-xin Li, Chengxiang Qiu, Dong Wang, Qinghua Cui:
The relationship between rational drug design and drug side effects. Briefings Bioinform. 13(3): 377-382 (2012) - [j11]Juan Wang, Jie Zhang, Kaibo Li, Wei Zhao, Qinghua Cui:
SpliceDisease database: linking RNA splicing and disease. Nucleic Acids Res. 40(Database-Issue): 1055-1059 (2012) - 2011
- [j10]Qingqing Yang, Chengxiang Qiu, Jie Yang, Qing Wu, Qinghua Cui:
miREnvironment Database: providing a bridge for microRNAs, environmental factors and phenotypes. Bioinform. 27(23): 3329-3330 (2011) - [j9]Chengxiang Qiu, Juan Wang, Qinghua Cui:
miR2Gene: pattern discovery of single gene, multiple genes, and pathways by enrichment analysis of their microRNA regulators. BMC Syst. Biol. 5(S-2): S9 (2011) - 2010
- [j8]Dong Wang, Juan Wang, Ming Lu, Fei Song, Qinghua Cui:
Inferring the human microRNA functional similarity and functional network based on microRNA-associated diseases. Bioinform. 26(13): 1644-1650 (2010) - [j7]Ming Lu, Bing Shi, Juan Wang, Qun Cao, Qinghua Cui:
TAM: A method for enrichment and depletion analysis of a microRNA category in a list of microRNAs. BMC Bioinform. 11: 419 (2010) - [j6]Chengxiang Qiu, Juan Wang, Pengying Yao, Edwin Wang, Qinghua Cui:
microRNA evolution in a human transcription factor and microRNA regulatory network. BMC Syst. Biol. 4: 90 (2010) - [j5]Juan Wang, Ming Lu, Chengxiang Qiu, Qinghua Cui:
TransmiR: a transcription factor-microRNA regulation database. Nucleic Acids Res. 38(Database-Issue): 119-122 (2010) - 2009
- [j4]Qinghua Cui, Enrico O. Purisima, Edwin Wang:
Protein evolution on a human signaling network. BMC Syst. Biol. 3: 21 (2009) - 2005
- [j3]Qinghua Cui, Bing Liu, Tianzi Jiang, Songde Ma:
Characterizing the dynamic connectivity between genes by variable parameter regression and Kalman filtering based on temporal gene expression data. Bioinform. 21(8): 1538-1541 (2005) - 2004
- [j2]Qinghua Cui, Tianzi Jiang, Bing Liu, Songde Ma:
Esub8: A novel tool to predict protein subcellular localizations in eukaryotic organisms. BMC Bioinform. 5: 66 (2004) - [j1]Bing Liu, Qinghua Cui, Tianzi Jiang, Songde Ma:
A combinational feature selection and ensemble neural network method for classification of gene expression data. BMC Bioinform. 5: 136 (2004)
Conference and Workshop Papers
- 2023
- [c2]Shihao Shao, Kaifeng Chen, Arjun Karpur, Qinghua Cui, André Araújo, Bingyi Cao:
Global Features are All You Need for Image Retrieval and Reranking. ICCV 2023: 11002-11012 - 2018
- [c1]Yiran Zhou, Qinghua Cui, Yuan Zhou:
NmSEER: A Prediction Tool for 2'-O-Methylation (Nm) Sites Based on Random Forest. ICIC (1) 2018: 893-900
Informal and Other Publications
- 2024
- [i4]Shihao Shao, Haoran Geng, Zun Wang, Qinghua Cui:
FreeCG: Free the Design Space of Clebsch-Gordan Transform for Machine Learning Force Fields. CoRR abs/2407.02263 (2024) - 2023
- [i3]Shihao Shao, Kaifeng Chen, Arjun Karpur, Qinghua Cui, André Araújo, Bingyi Cao:
Global Features are All You Need for Image Retrieval and Reranking. CoRR abs/2308.06954 (2023) - 2022
- [i2]Shihao Shao, Qinghua Cui:
1st Place Solution in Google Universal Images Embedding. CoRR abs/2210.08473 (2022) - 2021
- [i1]Shihao Shao, Yong Liu, Qinghua Cui:
A layer-stress learning framework universally augments deep neural network tasks. CoRR abs/2111.08597 (2021)
Coauthor Index
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