Runsheng Chen

50 papers A* 1C 2Journal 44Unranked 3
YearRankTypeTitle / Venue / Authors
2025 J jnl
Enzyme Repertoires and Genomic Insights into
Genom. Proteom. Bioinform.
Haiyan Yue, Yiheng Tang, Aixuan Li, LiLi Zhang, Yiwei Niu, Yiming Zhang, Hao Wang, Jianjun Luo, Yi Zhao, Shunmin He, Chang Chen, Runsheng Chen
2025 J jnl
Modelling and solving sustainable supply chain network design based on graph autoencoder clustering algorithm.
Int. J. Prod. Res.
Yuhan Guo, Runsheng Chen, Youssef Boulaksil, Hamid Allaoui
2025 A* conf
On Relation-Specific Neurons in Large Language Models.
EMNLP
Yihong Liu, Runsheng Chen, Lea Hirlimann, Ahmad Dawar Hakimi, Mingyang Wang, Amir Hossein Kargaran, Sascha Rothe, François Yvon, Hinrich Schütze
2025 J jnl
On Relation-Specific Neurons in Large Language Models.
CoRR
Yihong Liu, Runsheng Chen, Lea Hirlimann, Ahmad Dawar Hakimi, Mingyang Wang, Amir Hossein Kargaran, Sascha Rothe, François Yvon, Hinrich Schütze
2024 J jnl
Readon: a novel algorithm to identify read-through transcripts with long-read sequencing data.
Bioinform.
Siang Chen, Hao Wang, Dongdong Zhang, Runsheng Chen, Jianjun Luo
2023 J jnl
A Historic Retrospective on the Early Bioinformatics Research in China.
Genom. Proteom. Bioinform.
Runsheng Chen
2023 J jnl
NPInter v5.0: ncRNA interaction database in a new era.
Nucleic Acids Res.
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
2022 J jnl
piRBase: integrating piRNA annotation in all aspects.
Nucleic Acids Res.
Jiajia Wang, Yirong Shi, Honghong Zhou, Peng Zhang, Tingrui Song, Zhiye Ying, Haopeng Yu, Yanyan Li, Yi Zhao, Xiaoxi Zeng, Shunmin He, Runsheng Chen
2021 J jnl
Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021.
Nucleic Acids Res.
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
2021 J jnl
Early bioinformatics research in China.
Quant. Biol.
Runsheng Chen
2021 J jnl
NONCODEV6: an updated database dedicated to long non-coding RNA annotation in both animals and plants.
Nucleic Acids Res.
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
2021 J jnl
SmProt: A Reliable Repository with Comprehensive Annotation of Small Proteins Identified from Ribosome Profiling.
Genom. Proteom. Bioinform.
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
2020 J jnl
NPInter v4.0: an integrated database of ncRNA interactions.
Nucleic Acids Res.
XueYi Teng, Xiaomin Chen, Hua Xue, Yiheng Tang, Peng Zhang, Quan Kang, Yajing Hao, Runsheng Chen, Yi Zhao, Shunmin He
2020 J jnl
SpatialDB: a database for spatially resolved transcriptomes.
Nucleic Acids Res.
Zhen Fan, Runsheng Chen, Xiaowei Chen
2019 J jnl
piRBase: a comprehensive database of piRNA sequences.
Nucleic Acids Res.
Jiajia Wang, Peng Zhang, Yiping Lu, Yanyan Li, Yu Zheng, Yunchao Kan, Runsheng Chen, Shunmin He
2018 — conf
An Enviro-Geno-Pheno State Analysis Framework for Biomarker Study.
IScIDE
Han-Chen Huang, Xianzi Wen, Shikui Tu, Jiafu Ji, Runsheng Chen, Lei Xu
2018 J jnl
Dynamic-BM: multispecies Dynamic BodyMap database from temporal RNA-seq data.
Briefings Bioinform.
Ya Cui, Xiaowei Chen, Yiwei Niu, Dongpeng Wang, Huaxia Luo, Zhen Fan, Dan Wang, Wei Wu, XueYi Teng, Shunmin He, Jianjun Luo, Runsheng Chen
2018 J jnl
NONCODEV5: a comprehensive annotation database for long non-coding RNAs.
Nucleic Acids Res.
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
2018 J jnl
SmProt: a database of small proteins encoded by annotated coding and non-coding RNA loci.
Briefings Bioinform.
Yajing Hao, LiLi Zhang, Yiwei Niu, Tanxi Cai, Jianjun Luo, Shunmin He, Bao Zhang, Dejiu Zhang, Yan Qin, Fuquan Yang, Runsheng Chen
2017 J jnl
Comparative studies on multivariate tests for joint-SNVs analysis and detection for bipolar disorder susceptibility genes.
Int. J. Data Min. Bioinform.
Jin-Xiong Lv, Han-Chen Huang, Runsheng Chen, Lei Xu
2017 J jnl
LncVar: a database of genetic variation associated with long non-coding genes.
Bioinform.
Xiaowei Chen, Yajing Hao, Ya Cui, Zhen Fan, Shunmin He, Jianjun Luo, Runsheng Chen
2016 — conf
A comparison study on multivariate methods for joint-SNVs association analysis.
BIBM
Jin-Xiong Lv, Han-Chen Huang, Runsheng Chen, Lei Xu
2016 J jnl
BioCircos.js: an interactive Circos JavaScript library for biological data visualization on web applications.
Bioinform.
Ya Cui, Xiaowei Chen, Huaxia Luo, Zhen Fan, Jianjun Luo, Shunmin He, Haiyan Yue, Peng Zhang, Runsheng Chen
2016 J jnl
Computational identification of piRNA targets on mouse mRNAs.
Bioinform.
Jiao Yuan, Peng Zhang, Ya Cui, Jiajia Wang, Geir Skogerbø, Da-Wei Huang, Runsheng Chen, Shunmin He
2016 J jnl
NONCODE 2016: an informative and valuable data source of long non-coding RNAs.
Nucleic Acids Res.
Yi Zhao, Hui Li, Shuangsang Fang, Yue Kang, Wei Wu, Yajing Hao, Ziyang Li, Dechao Bu, Ninghui Sun, Michael Q. Zhang, Runsheng Chen
2016 J jnl
NPInter v3.0: an upgraded database of noncoding RNA-associated interactions.
Database J. Biol. Databases Curation
Yajing Hao, Wei Wu, Hui Li, Jiao Yuan, Jianjun Luo, Yi Zhao, Runsheng Chen
2015 J jnl
On Bioinformatic Resources.
Genom. Proteom. Bioinform.
Runsheng Chen
2014 J jnl
NONCODEv4: exploring the world of long non-coding RNA genes.
Nucleic Acids Res.
Chaoyong Xie, Jiao Yuan, Hui Li, Ming Li, Guoguang Zhao, Dechao Bu, Weimin Zhu, Wei Wu, Runsheng Chen, Yi Zhao
2014 J jnl
NPInter v2.0: an updated database of ncRNA interactions.
Nucleic Acids Res.
Jiao Yuan, Wei Wu, Chaoyong Xie, Guoguang Zhao, Yi Zhao, Runsheng Chen
2014 J jnl
piRBase: a web resource assisting piRNA functional study.
Database J. Biol. Databases Curation
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
2012 C conf
A non-Gaussian factor analysis approach to transcription Network Component Analysis.
CIBCB
Shikui Tu, Dingsheng Luo, Runsheng Chen, Lei Xu
2012 J jnl
NONCODE v3.0: integrative annotation of long noncoding RNAs.
Nucleic Acids Res.
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
2012 J jnl
Transcription Network Analysis by A Sparse Binary Factor Analysis Algorithm.
J. Integr. Bioinform.
Shikui Tu, Runsheng Chen, Lei Xu
2011 J jnl
Estimating developmental states of tumors and normal tissues using a linear time-ordered model.
BMC Bioinform.
Bo Zhang, Beibei Chen, Tao Wu, Zhenyu Xuan, Xiaopeng Zhu, Runsheng Chen
2011 J jnl
ncFANs: a web server for functional annotation of long non-coding RNAs.
Nucleic Acids Res.
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
2010 — conf
A binary matrix factorization algorithm for protein complex prediction.
BIBM Workshops
Shikui Tu, Lei Xu, Runsheng Chen
2008 J jnl
FlexStem: improving predictions of RNA secondary structures with pseudoknots by reducing the search space.
Bioinform.
Xiang Chen, Simin He, Dongbo Bu, Fa Zhang, Zhiyong Wang, Runsheng Chen, Wen Gao
2008 J jnl
NONCODE v2.0: decoding the non-coding.
Nucleic Acids Res.
Shunmin He, Changning Liu, Geir Skogerbø, Haitao Zhao, Jie Wang, Tao Liu, Baoyan Bai, Yi Zhao, Runsheng Chen
2007 C conf
A Flexible Stem-Based Local Search Algorithm for Predicting RNA Secondary Structures Including Pseudoknots.
BIBE
Xiang Chen, Simin He, Dongbo Bu, Runsheng Chen, Wen Gao
2007 J jnl
An Iterative Algorithm to Quantify Factors Influencing peptide Fragmentation during Tandem Mass Spectrometry.
J. Bioinform. Comput. Biol.
Chungong Yu, Yu Lin, Shiwei Sun, Jinjin Cai, Jingfen Zhang, Dongbo Bu, Zhuo Zhang, Runsheng Chen
2007 J jnl
antiCODE: a natural sense-antisense transcripts database.
BMC Bioinform.
Yifei Yin, Yi Zhao, Jie Wang, Changning Liu, Shuguang Chen, Runsheng Chen, Haitao Zhao
2006 J jnl
A novel scoring schema for peptide identification by searching protein sequence databases using tandem mass spectrometry data.
BMC Bioinform.
Zhuo Zhang, Shiwei Sun, Xiaopeng Zhu, Suhua Chang, Xiaofei Liu, Chungong Yu, Dongbo Bu, Runsheng Chen
2006 J jnl
Dynamic Changes in Subgraph Preference Profiles of Crucial Transcription Factors.
PLoS Comput. Biol.
Zhihua Zhang, Changning Liu, Geir Skogerbø, Xiaopeng Zhu, Hongchao Lu, Lan Chen, Baochen Shi, Yong Zhang, Jie Wang, Tao Wu, Runsheng Chen
2006 J jnl
NMPP: a user-customized NimbleGen microarray data processing pipeline.
Bioinform.
Xiangfeng Wang, Hang He, Lei Li, Runsheng Chen, Xing Wang Deng, Songgang Li
2006 J jnl
NPInter: the noncoding RNAs and protein related biomacromolecules interaction database.
Nucleic Acids Res.
Tao Wu, Jie Wang, Changning Liu, Yong Zhang, Baochen Shi, Xiaopeng Zhu, Zhihua Zhang, Geir Skogerbø, Lan Chen, Hongchao Lu, Yi Zhao, Runsheng Chen
2006 J jnl
Phylophenetic properties of metabolic pathway topologies as revealed by global analysis.
BMC Bioinform.
Yong Zhang, Shaojuan Li, Geir Skogerbø, Zhihua Zhang, Xiaopeng Zhu, Zefeng Zhang, Shiwei Sun, Hongchao Lu, Baochen Shi, Runsheng Chen
2005 J jnl
NONCODE: an integrated knowledge database of non-coding RNAs.
Nucleic Acids Res.
Changning Liu, Baoyan Bai, Geir Skogerbø, Lun Cai, Wei Deng, Yong Zhang, Dongbo Bu, Yi Zhao, Runsheng Chen
2005 J jnl
Predicting Molecular Formulas of Fragment Ions with Isotope Patterns in Tandem Mass Spectra.
IEEE ACM Trans. Comput. Biol. Bioinform.
Jingfen Zhang, Wen Gao, Jinjin Cai, Simin He, Rong Zeng, Runsheng Chen
2004 J jnl
Conservation analysis of small RNA genes in Escherichia coli.
Bioinform.
Yong Zhang, Zhihua Zhang, Lunjiang Ling, Baochen Shi, Runsheng Chen
1995 J jnl
Analysis of tRNA Gene Sequences by Neural Network.
J. Comput. Biol.
Jian Sun, Wen-Yuan Song, Li-Huang Zhu, Runsheng Chen