Runsheng Chen

According to our database, Runsheng Chen authored at least 46 papers between 1995 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2023

NPInter v5.0: ncRNA interaction database in a new era.

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

Nucleic Acids Res., January, 2023

A Historic Retrospective on the Early Bioinformatics Research in China.

Runsheng Chen

Genom. Proteom. Bioinform., 2023

2022

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022.

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

Nucleic Acids Res., 2022

piRBase: integrating piRNA annotation in all aspects.

Jiajia Wang, Yirong Shi, Honghong Zhou, Peng Zhang, Tingrui Song, Zhiye Ying, Haopeng Yu, Yanyan Li, Yi Zhao, Xiaoxi Zeng, Shunmin He, Runsheng Chen

Nucleic Acids Res., 2022

2021

Early bioinformatics research in China.

Runsheng Chen

Quant. Biol., September, 2021

NONCODEV6: an updated database dedicated to long non-coding RNA annotation in both animals and plants.

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

Nucleic Acids Res., 2021

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021.

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

Nucleic Acids Res., 2021

SmProt: A Reliable Repository with Comprehensive Annotation of Small Proteins Identified from Ribosome Profiling.

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

Genom. Proteom. Bioinform., 2021

2020

NPInter v4.0: an integrated database of ncRNA interactions.

XueYi Teng, Xiaomin Chen, Hua Xue, Yiheng Tang, Peng Zhang, Quan Kang, Yajing Hao, Runsheng Chen, Yi Zhao, Shunmin He

Nucleic Acids Res., 2020

SpatialDB: a database for spatially resolved transcriptomes.

Zhen Fan, Runsheng Chen, Xiaowei Chen

Nucleic Acids Res., 2020

2019

piRBase: a comprehensive database of piRNA sequences.

Jiajia Wang, Peng Zhang, Yiping Lu, Yanyan Li, Yu Zheng, Yunchao Kan, Runsheng Chen, Shunmin He

Nucleic Acids Res., 2019

2018

NONCODEV5: a comprehensive annotation database for long non-coding RNAs.

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

Nucleic Acids Res., 2018

SmProt: a database of small proteins encoded by annotated coding and non-coding RNA loci.

Yajing Hao, Lili Zhang, Yiwei Niu, Tanxi Cai, Jianjun Luo, Shunmin He, Bao Zhang, Dejiu Zhang, Yan Qin, Fuquan Yang, Runsheng Chen

Briefings Bioinform., 2018

Dynamic-BM: multispecies Dynamic BodyMap database from temporal RNA-seq data.

Ya Cui, Xiaowei Chen, Yiwei Niu, Dongpeng Wang, Huaxia Luo, Zhen Fan, Dan Wang, Wei Wu, XueYi Teng, Shunmin He, Jianjun Luo, Runsheng Chen

Briefings Bioinform., 2018

An Enviro-Geno-Pheno State Analysis Framework for Biomarker Study.

Han-Chen Huang, Xianzi Wen, Shikui Tu, Jiafu Ji, Runsheng Chen, Lei Xu

Proceedings of the Intelligence Science and Big Data Engineering, 2018

2017

Comparative studies on multivariate tests for joint-SNVs analysis and detection for bipolar disorder susceptibility genes.

Jin-Xiong Lv, Han-Chen Huang, Runsheng Chen, Lei Xu

Int. J. Data Min. Bioinform., 2017

LncVar: a database of genetic variation associated with long non-coding genes.

Xiaowei Chen, Yajing Hao, Ya Cui, Zhen Fan, Shunmin He, Jianjun Luo, Runsheng Chen

Bioinform., 2017

2016

NONCODE 2016: an informative and valuable data source of long non-coding RNAs.

Yi Zhao, Hui Li, Shuangsang Fang, Yue Kang, Wei Wu, Yajing Hao, Ziyang Li, Dechao Bu, Ninghui Sun, Michael Q. Zhang, Runsheng Chen

Nucleic Acids Res., 2016

Computational identification of piRNA targets on mouse mRNAs.

Jiao Yuan, Peng Zhang, Ya Cui, Jiajia Wang, Geir Skogerbø, Da-Wei Huang, Runsheng Chen, Shunmin He

Bioinform., 2016

BioCircos.js: an interactive Circos JavaScript library for biological data visualization on web applications.

Ya Cui, Xiaowei Chen, Huaxia Luo, Zhen Fan, Jianjun Luo, Shunmin He, Haiyan Yue, Peng Zhang, Runsheng Chen

Bioinform., 2016

NPInter v3.0: an upgraded database of noncoding RNA-associated interactions.

Yajing Hao, Wei Wu, Hui Li, Jiao Yuan, Jianjun Luo, Yi Zhao, Runsheng Chen

Database J. Biol. Databases Curation, 2016

A comparison study on multivariate methods for joint-SNVs association analysis.

Jin-Xiong Lv, Han-Chen Huang, Runsheng Chen, Lei Xu

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016

2015

On Bioinformatic Resources.

Runsheng Chen

Genom. Proteom. Bioinform., 2015

2014

NPInter v2.0: an updated database of ncRNA interactions.

Jiao Yuan, Wei Wu, Chaoyong Xie, Guoguang Zhao, Yi Zhao, Runsheng Chen

Nucleic Acids Res., 2014

NONCODEv4: exploring the world of long non-coding RNA genes.

Chaoyong Xie, Jiao Yuan, Hui Li, Ming Li, Guoguang Zhao, Dechao Bu, Weimin Zhu, Wei Wu, Runsheng Chen, Yi Zhao

Nucleic Acids Res., 2014

piRBase: a web resource assisting piRNA functional study.

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

Database J. Biol. Databases Curation, 2014

2012

NONCODE v3.0: integrative annotation of long noncoding RNAs.

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

Nucleic Acids Res., 2012

Transcription Network Analysis by A Sparse Binary Factor Analysis Algorithm.

Shikui Tu, Runsheng Chen, Lei Xu

J. Integr. Bioinform., 2012

A non-Gaussian factor analysis approach to transcription Network Component Analysis.

Shikui Tu, Dingsheng Luo, Runsheng Chen, Lei Xu

Proceedings of the 2012 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, 2012

2011

ncFANs: a web server for functional annotation of long non-coding RNAs.

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

Nucleic Acids Res., 2011

Estimating developmental states of tumors and normal tissues using a linear time-ordered model.

Bo Zhang, Beibei Chen, Tao Wu, Zhenyu Xuan, Xiaopeng Zhu, Runsheng Chen

BMC Bioinform., 2011

2010

A binary matrix factorization algorithm for protein complex prediction.

Shikui Tu, Lei Xu, Runsheng Chen

Proceedings of the 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2010

2008

NONCODE v2.0: decoding the non-coding.

Shunmin He, Changning Liu, Geir Skogerbø, Haitao Zhao, Jie Wang, Tao Liu, Baoyan Bai, Yi Zhao, Runsheng Chen

Nucleic Acids Res., 2008

FlexStem: improving predictions of RNA secondary structures with pseudoknots by reducing the search space.

Xiang Chen, Simin He, Dongbo Bu, Fa Zhang, Zhiyong Wang, Runsheng Chen, Wen Gao

Bioinform., 2008

2007

An Iterative Algorithm to Quantify Factors Influencing peptide Fragmentation during Tandem Mass Spectrometry.

Chungong Yu, Yu Lin, Shiwei Sun, Jinjin Cai, Jingfen Zhang, Dongbo Bu, Zhuo Zhang, Runsheng Chen

J. Bioinform. Comput. Biol., 2007

antiCODE: a natural sense-antisense transcripts database.

Yifei Yin, Yi Zhao, Jie Wang, Changning Liu, Shuguang Chen, Runsheng Chen, Haitao Zhao

BMC Bioinform., 2007

A Flexible Stem-Based Local Search Algorithm for Predicting RNA Secondary Structures Including Pseudoknots.

Xiang Chen, Simin He, Dongbo Bu, Runsheng Chen, Wen Gao

Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, 2007

2006

Dynamic Changes in Subgraph Preference Profiles of Crucial Transcription Factors.

Zhihua Zhang, Changning Liu, Geir Skogerbø, Xiaopeng Zhu, Hongchao Lu, Lan Chen, Baochen Shi, Yong Zhang, Jie Wang, Tao Wu, Runsheng Chen

PLoS Comput. Biol., 2006

NPInter: the noncoding RNAs and protein related biomacromolecules interaction database.

Tao Wu, Jie Wang, Changning Liu, Yong Zhang, Baochen Shi, Xiaopeng Zhu, Zhihua Zhang, Geir Skogerbø, Lan Chen, Hongchao Lu, Yi Zhao, Runsheng Chen

Nucleic Acids Res., 2006

A novel scoring schema for peptide identification by searching protein sequence databases using tandem mass spectrometry data.

Zhuo Zhang, Shiwei Sun, Xiaopeng Zhu, Suhua Chang, Xiaofei Liu, Chungong Yu, Dongbo Bu, Runsheng Chen

BMC Bioinform., 2006

Phylophenetic properties of metabolic pathway topologies as revealed by global analysis.

Yong Zhang, Shaojuan Li, Geir Skogerbø, Zhihua Zhang, Xiaopeng Zhu, Zefeng Zhang, Shiwei Sun, Hongchao Lu, Baochen Shi, Runsheng Chen

BMC Bioinform., 2006

NMPP: a user-customized NimbleGen microarray data processing pipeline.

Xiangfeng Wang, Hang He, Lei Li, Runsheng Chen, Xing Wang Deng, Songgang Li

Bioinform., 2006

2005

Predicting Molecular Formulas of Fragment Ions with Isotope Patterns in Tandem Mass Spectra.

Jingfen Zhang, Wen Gao, Jinjin Cai, Simin He, Rong Zeng, Runsheng Chen

IEEE ACM Trans. Comput. Biol. Bioinform., 2005

NONCODE: an integrated knowledge database of non-coding RNAs.

Changning Liu, Baoyan Bai, Geir Skogerbø, Lun Cai, Wei Deng, Yong Zhang, Dongbo Bu, Yi Zhao, Runsheng Chen

Nucleic Acids Res., 2005

2004

Conservation analysis of small RNA genes in Escherichia coli.

Yong Zhang, Zhihua Zhang, Lunjiang Ling, Baochen Shi, Runsheng Chen

Bioinform., 2004

1995

Analysis of tRNA Gene Sequences by Neural Network.

Jian Sun, Wen-Yuan Song, Li-Huang Zhu, Runsheng Chen

J. Comput. Biol., 1995