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- affiliation: Chinese Academy of Sciences, Institute of Biophysics, Key Laboratory of RNA Biology, Beijing, China
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Journal Articles
- 2023
[j40]Yu Zheng, Huaxia Luo
, XueYi Teng, Xinpei Hao, Xiaoyu Yan, Yiheng Tang, Wanyu Zhang, Yuanxin Wang, Peng Zhang, Yanyan Li, Yi Zhao, Runsheng Chen, Shunmin He:
NPInter v5.0: ncRNA interaction database in a new era. Nucleic Acids Res. 51(D1): 232-239 (2023)- 2022
- [j39]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) - [j38]Jiajia Wang, Yirong Shi, Honghong Zhou, Peng Zhang, Tingrui Song, Zhiye Ying, Haopeng Yu, Yanyan Li, Yi Zhao, Xiaoxi Zeng, Shunmin He, Runsheng Chen:
piRBase: integrating piRNA annotation in all aspects. Nucleic Acids Res. 50(D1): 265-272 (2022) - 2021
- [j37]Yanyan Li, Honghong Zhou, Xiaomin Chen, Yu Zheng, Quan Kang, Di Hao, Lili Zhang, Tingrui Song, Huaxia Luo, Yajing Hao, Runsheng Chen, Peng Zhang, Shunmin He:
SmProt: A Reliable Repository with Comprehensive Annotation of Small Proteins Identified from Ribosome Profiling. Genom. Proteom. Bioinform. 19(4): 602-610 (2021) - [j36]Lianhe Zhao, Jiajia Wang, Yanyan Li, Tingrui Song, Yang Wu, Shuangsang Fang, Dechao Bu, Hui Li, Liang Sun, Dong Pei, Yu Zheng, Jianqin Huang, Mingqing Xu, Runsheng Chen, Yi Zhao, Shunmin He:
NONCODEV6: an updated database dedicated to long non-coding RNA annotation in both animals and plants. Nucleic Acids Res. 49(Database-Issue): D165-D171 (2021) - [j35]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) - [j34]Runsheng Chen:
Early bioinformatics research in China. Quant. Biol. 9(3): 242-250 (2021) - 2020
- [j33]XueYi Teng, Xiaomin Chen, Hua Xue, Yiheng Tang, Peng Zhang, Quan Kang, Yajing Hao, Runsheng Chen, Yi Zhao, Shunmin He:
NPInter v4.0: an integrated database of ncRNA interactions. Nucleic Acids Res. 48(Database-Issue): D160-D165 (2020) - [j32]Zhen Fan, Runsheng Chen, Xiaowei Chen:
SpatialDB: a database for spatially resolved transcriptomes. Nucleic Acids Res. 48(Database-Issue): D233-D237 (2020) - 2019
- [j31]Jiajia Wang, Peng Zhang, Yiping Lu, Yanyan Li, Yu Zheng, Yunchao Kan, Runsheng Chen, Shunmin He:
piRBase: a comprehensive database of piRNA sequences. Nucleic Acids Res. 47(Database-Issue): D175-D180 (2019) - 2018
- [j30]Yajing Hao, Lili Zhang, Yiwei Niu, Tanxi Cai, Jianjun Luo, Shunmin He, Bao Zhang, Dejiu Zhang, Yan Qin, Fuquan Yang, Runsheng Chen:
SmProt: a database of small proteins encoded by annotated coding and non-coding RNA loci. Briefings Bioinform. 19(4): 636-643 (2018) - [j29]Ya Cui, Xiaowei Chen, Yiwei Niu, Dongpeng Wang, Huaxia Luo, Zhen Fan, Dan Wang, Wei Wu, XueYi Teng, Shunmin He, Jianjun Luo, Runsheng Chen:
Dynamic-BM: multispecies Dynamic BodyMap database from temporal RNA-seq data. Briefings Bioinform. 19(6): 1302-1309 (2018) - [j28]Shuangsang Fang, LiLi Zhang, Jincheng Guo, Yiwei Niu, Yang Wu, Hui Li, Lianhe Zhao, Xiyuan Li, XueYi Teng, XianHui Sun, Liang Sun, Michael Q. Zhang, Runsheng Chen, Yi Zhao:
NONCODEV5: a comprehensive annotation database for long non-coding RNAs. Nucleic Acids Res. 46(Database-Issue): D308-D314 (2018) - 2017
- [j27]Xiaowei Chen, Yajing Hao, Ya Cui, Zhen Fan, Shunmin He, Jianjun Luo, Runsheng Chen:
LncVar: a database of genetic variation associated with long non-coding genes. Bioinform. 33(1): 112-118 (2017) - [j26]Jin-Xiong Lv, Han-Chen Huang, Runsheng Chen, Lei Xu:
Comparative studies on multivariate tests for joint-SNVs analysis and detection for bipolar disorder susceptibility genes. Int. J. Data Min. Bioinform. 17(4): 341-358 (2017) - 2016
- [j25]Yajing Hao, Wei Wu, Hui Li, Jiao Yuan, Jianjun Luo, Yi Zhao, Runsheng Chen:
NPInter v3.0: an upgraded database of noncoding RNA-associated interactions. Database J. Biol. Databases Curation 2016 (2016) - [j24]Jiao Yuan, Peng Zhang, Ya Cui, Jiajia Wang, Geir Skogerbø, Da-Wei Huang, Runsheng Chen, Shunmin He:
Computational identification of piRNA targets on mouse mRNAs. Bioinform. 32(8): 1170-1177 (2016) - [j23]Ya Cui, Xiaowei Chen, Huaxia Luo, Zhen Fan, Jianjun Luo, Shunmin He, Haiyan Yue, Peng Zhang, Runsheng Chen:
BioCircos.js: an interactive Circos JavaScript library for biological data visualization on web applications. Bioinform. 32(11): 1740-1742 (2016) - [j22]Yi Zhao, Hui Li, Shuangsang Fang, Yue Kang, Wei Wu, Yajing Hao, Ziyang Li, Dechao Bu, Ninghui Sun, Michael Q. Zhang, Runsheng Chen:
NONCODE 2016: an informative and valuable data source of long non-coding RNAs. Nucleic Acids Res. 44(Database-Issue): 203-208 (2016) - 2015
- [j21]Runsheng Chen:
On Bioinformatic Resources. Genom. Proteom. Bioinform. 13(1): 1-3 (2015) - 2014
- [j20]Peng Zhang, Xiaohui Si, Geir Skogerbø, Jiajia Wang, Dongya Cui, Yongxing Li, Xubin Sun, Li Liu, Baofa Sun, Runsheng Chen, Shunmin He, Da-Wei Huang:
piRBase: a web resource assisting piRNA functional study. Database J. Biol. Databases Curation 2014 (2014) - [j19]Chaoyong Xie, Jiao Yuan, Hui Li, Ming Li, Guoguang Zhao, Dechao Bu, Weimin Zhu, Wei Wu, Runsheng Chen, Yi Zhao:
NONCODEv4: exploring the world of long non-coding RNA genes. Nucleic Acids Res. 42(Database-Issue): 98-103 (2014) - [j18]Jiao Yuan, Wei Wu, Chaoyong Xie, Guoguang Zhao, Yi Zhao, Runsheng Chen:
NPInter v2.0: an updated database of ncRNA interactions. Nucleic Acids Res. 42(Database-Issue): 104-108 (2014) - 2012
- [j17]Shikui Tu, Runsheng Chen, Lei Xu:
Transcription Network Analysis by A Sparse Binary Factor Analysis Algorithm. J. Integr. Bioinform. 9(2) (2012) - [j16]Dechao Bu, Kuntao Yu, Silong Sun, Chaoyong Xie, Geir Skogerbø, Ruoyu Miao, Hui Xiao, Qi Liao, Haitao Luo, Guoguang Zhao, Haitao Zhao, Zhiyong Liu, Changning Liu, Runsheng Chen, Yi Zhao:
NONCODE v3.0: integrative annotation of long noncoding RNAs. Nucleic Acids Res. 40(Database-Issue): 210-215 (2012) - 2011
- [j15]Bo Zhang, Beibei Chen, Tao Wu, Zhenyu Xuan, Xiaopeng Zhu, Runsheng Chen:
Estimating developmental states of tumors and normal tissues using a linear time-ordered model. BMC Bioinform. 12: 53 (2011) - [j14]Qi Liao, Hui Xiao, Dechao Bu, Chaoyong Xie, Ruoyu Miao, Haitao Luo, Guoguang Zhao, Kuntao Yu, Haitao Zhao, Geir Skogerbø, Runsheng Chen, Zhongdao Wu, Changning Liu, Yi Zhao:
ncFANs: a web server for functional annotation of long non-coding RNAs. Nucleic Acids Res. 39(Web-Server-Issue): 118-124 (2011) - 2008
- [j13]Xiang Chen, Simin He, Dongbo Bu, Fa Zhang, Zhiyong Wang, Runsheng Chen, Wen Gao:
FlexStem: improving predictions of RNA secondary structures with pseudoknots by reducing the search space. Bioinform. 24(18): 1994-2001 (2008) - [j12]Shunmin He, Changning Liu, Geir Skogerbø, Haitao Zhao, Jie Wang, Tao Liu, Baoyan Bai, Yi Zhao, Runsheng Chen:
NONCODE v2.0: decoding the non-coding. Nucleic Acids Res. 36(Database-Issue): 170-172 (2008) - 2007
- [j11]Yifei Yin, Yi Zhao, Jie Wang, Changning Liu, Shuguang Chen, Runsheng Chen, Haitao Zhao:
antiCODE: a natural sense-antisense transcripts database. BMC Bioinform. 8 (2007) - [j10]Chungong Yu, Yu Lin, Shiwei Sun, Jinjin Cai, Jingfen Zhang, Dongbo Bu, Zhuo Zhang, Runsheng Chen:
An Iterative Algorithm to Quantify Factors Influencing peptide Fragmentation during Tandem Mass Spectrometry. J. Bioinform. Comput. Biol. 5(2a): 297-311 (2007) - 2006
- [j9]Xiangfeng Wang, Hang He, Lei Li, Runsheng Chen, Xing Wang Deng, Songgang Li:
NMPP: a user-customized NimbleGen microarray data processing pipeline. Bioinform. 22(23): 2955-2957 (2006) - [j8]Zhuo Zhang, Shiwei Sun, Xiaopeng Zhu, Suhua Chang, Xiaofei Liu, Chungong Yu, Dongbo Bu, Runsheng Chen:
A novel scoring schema for peptide identification by searching protein sequence databases using tandem mass spectrometry data. BMC Bioinform. 7: 222 (2006) - [j7]Yong Zhang, Shaojuan Li, Geir Skogerbø, Zhihua Zhang, Xiaopeng Zhu, Zefeng Zhang, Shiwei Sun, Hongchao Lu, Baochen Shi, Runsheng Chen:
Phylophenetic properties of metabolic pathway topologies as revealed by global analysis. BMC Bioinform. 7: 252 (2006) - [j6]Tao Wu, Jie Wang, Changning Liu, Yong Zhang, Baochen Shi, Xiaopeng Zhu, Zhihua Zhang, Geir Skogerbø, Lan Chen, Hongchao Lu, Yi Zhao, Runsheng Chen:
NPInter: the noncoding RNAs and protein related biomacromolecules interaction database. Nucleic Acids Res. 34(Database-Issue): 150-152 (2006) - [j5]Zhihua Zhang, Changning Liu, Geir Skogerbø, Xiaopeng Zhu, Hongchao Lu, Lan Chen, Baochen Shi, Yong Zhang, Jie Wang, Tao Wu, Runsheng Chen:
Dynamic Changes in Subgraph Preference Profiles of Crucial Transcription Factors. PLoS Comput. Biol. 2(5) (2006) - 2005
- [j4]Changning Liu, Baoyan Bai, Geir Skogerbø, Lun Cai, Wei Deng, Yong Zhang, Dongbo Bu, Yi Zhao, Runsheng Chen:
NONCODE: an integrated knowledge database of non-coding RNAs. Nucleic Acids Res. 33(Database-Issue): 112-115 (2005) - [j3]Jingfen Zhang, Wen Gao, Jinjin Cai, Simin He, Rong Zeng, Runsheng Chen:
Predicting Molecular Formulas of Fragment Ions with Isotope Patterns in Tandem Mass Spectra. IEEE ACM Trans. Comput. Biol. Bioinform. 2(3): 217-230 (2005) - 2004
- [j2]Yong Zhang, Zhihua Zhang, Lunjiang Ling, Baochen Shi, Runsheng Chen:
Conservation analysis of small RNA genes in Escherichia coli. Bioinform. 20(5): 599-603 (2004) - 1995
- [j1]Jian Sun, Wen-Yuan Song, Li-Huang Zhu, Runsheng Chen:
Analysis of tRNA Gene Sequences by Neural Network. J. Comput. Biol. 2(3): 409-416 (1995)
Conference and Workshop Papers
- 2018
- [c5]Han-Chen Huang, Xianzi Wen, Shikui Tu, Jiafu Ji, Runsheng Chen, Lei Xu:
An Enviro-Geno-Pheno State Analysis Framework for Biomarker Study. IScIDE 2018: 663-671 - 2016
- [c4]Jin-Xiong Lv, Han-Chen Huang, Runsheng Chen, Lei Xu:
A comparison study on multivariate methods for joint-SNVs association analysis. BIBM 2016: 1771-1776 - 2012
- [c3]Shikui Tu, Dingsheng Luo, Runsheng Chen, Lei Xu:
A non-Gaussian factor analysis approach to transcription Network Component Analysis. CIBCB 2012: 404-411 - 2010
- [c2]Shikui Tu, Lei Xu, Runsheng Chen:
A binary matrix factorization algorithm for protein complex prediction. BIBM Workshops 2010: 113-118 - 2007
- [c1]Xiang Chen, Simin He, Dongbo Bu, Runsheng Chen, Wen Gao:
A Flexible Stem-Based Local Search Algorithm for Predicting RNA Secondary Structures Including Pseudoknots. BIBE 2007: 411-417
Coauthor Index
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