Analysis of tRNA Gene Sequences by Neural Network. - Jian Sun; Wen-Yuan Song; Li-Huang Zhu; Runsheng Chen (J. Comput. Biol., 1995)

Conservation analysis of small RNA genes in Escherichia coli. - Yong Zhang 006; Zhihua Zhang; Lunjiang Ling; Baochen Shi; Runsheng Chen (Bioinform., 2004)

NONCODE: an integrated knowledge database of non-coding RNAs. - Changning Liu; Baoyan Bai; Geir Skogerbø; Lun Cai; Wei Deng; Yong Zhang 006; Dongbo Bu; Yi Zhao 013; Runsheng Chen (Nucleic Acids Res., 2005)

Predicting Molecular Formulas of Fragment Ions with Isotope Patterns in Tandem Mass Spectra. - Jingfen Zhang; Wen Gao 001; Jinjin Cai; Simin He 001; Rong Zeng; Runsheng Chen (IEEE ACM Trans. Comput. Biol. Bioinform., 2005)

NMPP: a user-customized NimbleGen microarray data processing pipeline. - Xiangfeng Wang; Hang He; Lei Li; Runsheng Chen; Xing Wang Deng; Songgang Li (Bioinform., 2006)

Phylophenetic properties of metabolic pathway topologies as revealed by global analysis. - Yong Zhang 006; Shaojuan Li; Geir Skogerbø; Zhihua Zhang; Xiaopeng Zhu; Zefeng Zhang; Shiwei Sun; Hongchao Lu; Baochen Shi; Runsheng Chen (BMC Bioinform., 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)

NPInter: the noncoding RNAs and protein related biomacromolecules interaction database. - Tao Wu 002; Jie Wang; Changning Liu; Yong Zhang 006; Baochen Shi; Xiaopeng Zhu; Zhihua Zhang; Geir Skogerbø; Lan Chen; Hongchao Lu; Yi Zhao 013; Runsheng Chen (Nucleic Acids Res., 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 006; Jie Wang; Tao Wu 002; Runsheng Chen (PLoS Comput. Biol., 2006)

A Flexible Stem-Based Local Search Algorithm for Predicting RNA Secondary Structures Including Pseudoknots. - Xiang Chen; Simin He 001; Dongbo Bu; Runsheng Chen; Wen Gao 001 (BIBE, 2007)

antiCODE: a natural sense-antisense transcripts database. - Yifei Yin; Yi Zhao 013; Jie Wang; Changning Liu; Shuguang Chen; Runsheng Chen; Haitao Zhao (BMC Bioinform., 2007)

An Iterative Algorithm to Quantify Factors Influencing peptide Fragmentation during Tandem Mass Spectrometry. - Chungong Yu; Yu Lin 001; Shiwei Sun; Jinjin Cai; Jingfen Zhang; Dongbo Bu; Zhuo Zhang; Runsheng Chen (J. Bioinform. Comput. Biol., 2007)

FlexStem: improving predictions of RNA secondary structures with pseudoknots by reducing the search space. - Xiang Chen; Simin He 001; Dongbo Bu; Fa Zhang; Zhiyong Wang; Runsheng Chen; Wen Gao 001 (Bioinform., 2008)

NONCODE v2.0: decoding the non-coding. - Shunmin He; Changning Liu; Geir Skogerbø; Haitao Zhao; Jie Wang; Tao Liu 022; Baoyan Bai; Yi Zhao 013; Runsheng Chen (Nucleic Acids Res., 2008)

A binary matrix factorization algorithm for protein complex prediction. - Shikui Tu; Lei Xu 001; Runsheng Chen (BIBM Workshops, 2010)

Estimating developmental states of tumors and normal tissues using a linear time-ordered model. - Bo Zhang 009; Beibei Chen; Tao Wu 002; Zhenyu Xuan; Xiaopeng Zhu; Runsheng Chen (BMC Bioinform., 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; et al. (Nucleic Acids Res., 2011)

A non-Gaussian factor analysis approach to transcription Network Component Analysis. - Shikui Tu; Dingsheng Luo; Runsheng Chen; Lei Xu 001 (CIBCB, 2012)

Transcription Network Analysis by A Sparse Binary Factor Analysis Algorithm. - Shikui Tu; Runsheng Chen; Lei Xu 001 (J. Integr. Bioinform., 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; et al. (Nucleic Acids Res., 2012)

piRBase: a web resource assisting piRNA functional study. - Peng Zhang 047; 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)

NONCODEv4: exploring the world of long non-coding RNA genes. - Chaoyong Xie; Jiao Yuan; Hui Li 038; Ming Li; Guoguang Zhao; Dechao Bu; Weimin Zhu; Wei Wu 025; Runsheng Chen; Yi Zhao 013 (Nucleic Acids Res., 2014)

NPInter v2.0: an updated database of ncRNA interactions. - Jiao Yuan; Wei Wu 025; Chaoyong Xie; Guoguang Zhao; Yi Zhao 013; Runsheng Chen (Nucleic Acids Res., 2014)

On Bioinformatic Resources. - Runsheng Chen (Genom. Proteom. Bioinform., 2015)

A comparison study on multivariate methods for joint-SNVs association analysis. - Jin-Xiong Lv; Han-Chen Huang; Runsheng Chen; Lei Xu 001 (BIBM, 2016)

NPInter v3.0: an upgraded database of noncoding RNA-associated interactions. - Yajing Hao 001; Wei Wu 025; Hui Li 038; Jiao Yuan; Jianjun Luo 001; Yi Zhao 013; Runsheng Chen (Database J. Biol. Databases Curation, 2016)

BioCircos.js: an interactive Circos JavaScript library for biological data visualization on web applications. - Ya Cui; Xiaowei Chen; Huaxia Luo; Zhen Fan 002; Jianjun Luo 001; Shunmin He; Haiyan Yue; Peng Zhang 050; Runsheng Chen (Bioinform., 2016)

Computational identification of piRNA targets on mouse mRNAs. - Jiao Yuan; Peng Zhang 047; Ya Cui; Jiajia Wang; Geir Skogerbø; Da-Wei Huang; Runsheng Chen; Shunmin He (Bioinform., 2016)

NONCODE 2016: an informative and valuable data source of long non-coding RNAs. - Yi Zhao 013; Hui Li 038; Shuangsang Fang; Yue Kang; Wei Wu 025; Yajing Hao 001; Ziyang Li; Dechao Bu; Ninghui Sun; Michael Q. Zhang; Runsheng Chen (Nucleic Acids Res., 2016)

LncVar: a database of genetic variation associated with long non-coding genes. - Xiaowei Chen; Yajing Hao 001; Ya Cui; Zhen Fan 002; Shunmin He; Jianjun Luo 001; Runsheng Chen (Bioinform., 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 001 (Int. J. Data Min. Bioinform., 2017)

An Enviro-Geno-Pheno State Analysis Framework for Biomarker Study. - Han-Chen Huang; Xianzi Wen; Shikui Tu; Jiafu Ji; Runsheng Chen; Lei Xu 001 (IScIDE, 2018)

Dynamic-BM: multispecies Dynamic BodyMap database from temporal RNA-seq data. - Ya Cui; Xiaowei Chen; Yiwei Niu; Dongpeng Wang; Huaxia Luo; Zhen Fan 002; Dan Wang; Wei Wu 025; XueYi Teng; Shunmin He; Jianjun Luo 001; Runsheng Chen (Briefings Bioinform., 2018)

SmProt: a database of small proteins encoded by annotated coding and non-coding RNA loci. - Yajing Hao 001; Lili Zhang 007; Yiwei Niu; Tanxi Cai; Jianjun Luo 001; Shunmin He; Bao Zhang; Dejiu Zhang; Yan Qin; Fuquan Yang; Runsheng Chen (Briefings Bioinform., 2018)

NONCODEV5: a comprehensive annotation database for long non-coding RNAs. - Shuangsang Fang; LiLi Zhang 007; Jincheng Guo; Yiwei Niu; Yang Wu; Hui Li 038; Lianhe Zhao; Xiyuan Li; XueYi Teng; XianHui Sun; Liang Sun; Michael Q. Zhang; et al. (Nucleic Acids Res., 2018)

piRBase: a comprehensive database of piRNA sequences. - Jiajia Wang; Peng Zhang 047; Yiping Lu; Yanyan Li; Yu Zheng 030; Yunchao Kan; Runsheng Chen; Shunmin He (Nucleic Acids Res., 2019)

SpatialDB: a database for spatially resolved transcriptomes. - Zhen Fan 002; Runsheng Chen; Xiaowei Chen (Nucleic Acids Res., 2020)

NPInter v4.0: an integrated database of ncRNA interactions. - XueYi Teng; Xiaomin Chen; Hua Xue; Yiheng Tang; Peng Zhang 047; Quan Kang; Yajing Hao 001; Runsheng Chen; Yi Zhao 013; Shunmin He (Nucleic Acids Res., 2020)

SmProt: A Reliable Repository with Comprehensive Annotation of Small Proteins Identified from Ribosome Profiling. - Yanyan Li; Honghong Zhou; Xiaomin Chen; Yu Zheng 030; Quan Kang; Di Hao; Lili Zhang 007; Tingrui Song; Huaxia Luo; Yajing Hao 001; Runsheng Chen; Peng Zhang 047; et al. (Genom. Proteom. Bioinform., 2021)

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021. - Yongbiao Xue; Yiming Bao; Zhang Zhang 002; Wenming Zhao; Jing-Fa Xiao; Shunmin He; Guoqing Zhang 006; Yixue Li; Guoping Zhao; Runsheng Chen; Shuhui Song; Lina Ma; et al. (Nucleic Acids Res., 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 038; Liang Sun; Dong Pei; Yu Zheng 030; Jianqin Huang; et al. (Nucleic Acids Res., 2021)

Early bioinformatics research in China. - Runsheng Chen (Quant. Biol., 2021)

piRBase: integrating piRNA annotation in all aspects. - Jiajia Wang; Yirong Shi; Honghong Zhou; Peng Zhang 047; Tingrui Song; Zhiye Ying; Haopeng Yu; Yanyan Li; Yi Zhao 013; Xiaoxi Zeng; Shunmin He; Runsheng Chen (Nucleic Acids Res., 2022)

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022. - Yongbiao Xue; Yiming Bao; Zhang Zhang 002; Wenming Zhao; Jing-Fa Xiao; Shunmin He; Guoqing Zhang 006; Yixue Li; Guoping Zhao; Runsheng Chen; Jingyao Zeng; Yadong Zhang; et al. (Nucleic Acids Res., 2022)

A Historic Retrospective on the Early Bioinformatics Research in China. - Runsheng Chen (Genom. Proteom. Bioinform., 2023)

NPInter v5.0: ncRNA interaction database in a new era. - Yu Zheng 030; Huaxia Luo; XueYi Teng; Xinpei Hao; Xiaoyu Yan; Yiheng Tang; Wanyu Zhang; Yuanxin Wang; Peng Zhang 047; Yanyan Li; Yi Zhao 013; Runsheng Chen; et al. (Nucleic Acids Res., 2023)

Enzyme Repertoires and Genomic Insights into Lycium barbarum Pectin Polysaccharide Biosynthesis. - Haiyan Yue; Yiheng Tang; Aixuan Li; Lili Zhang 007; Yiwei Niu; Yiming Zhang; Hao Wang; Jianjun Luo 001; Yi Zhao 013; Shunmin He; Chang Chen; Runsheng Chen (Genom. Proteom. Bioinform., 2025)

On Relation-Specific Neurons in Large Language Models. - Yihong Liu 001; Runsheng Chen; Lea Hirlimann; Ahmad Dawar Hakimi; Mingyang Wang 003; Amir Hossein Kargaran; Sascha Rothe; François Yvon; Hinrich Schütze (CoRR, 2025)