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)

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)

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)

CaSNP: a database for interrogating copy number alterations of cancer genome from SNP array data. - Qingyi Cao; Meng Zhou; Xujun Wang; Clifford A. Meyer; Yong Zhang 006; Zhi Chen; Cheng Li; Xiaole Shirley Liu (Nucleic Acids Res., 2011)

GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data. - Jianxing Feng; Clifford A. Meyer; Qian Wang; Jun S. Liu; Xiaole Shirley Liu; Yong Zhang 006 (Bioinform., 2012)

DiNuP: a systematic approach to identify regions of differential nucleosome positioning. - Kai Fu; Qianzi Tang; Jianxing Feng; Xiaole Shirley Liu; Yong Zhang 006 (Bioinform., 2012)

CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human. - Bo Qin; Meng Zhou; Ying Ge; Len Taing; Tao Liu 022; Qian Wang; Su Wang; Junsheng Chen; Lingling Shen; Xikun Duan; Sheng'en Hu; Wei Li 036; et al. (Bioinform., 2012)

BSeQC: quality control of bisulfite sequencing experiments. - Xueqiu Lin; Deqiang Sun; Benjamin Rodriguez; Qian Zhao; Hanfei Sun; Yong Zhang 006; Wei Li 036 (Bioinform., 2013)

CistromeFinder for ChIP-seq and DNase-seq data reuse. - Hanfei Sun; Bo Qin; Tao Liu 022; Qixuan Wang; Jing Liu; Juan Wang; Xueqiu Lin; Yulin Yang; Len Taing; Prakash K. Rao; Myles Brown; Yong Zhang 006; et al. (Bioinform., 2013)

Computational methodology for ChIP-seq analysis. - Hyunjin Shin; Tao Liu 022; Xikun Duan; Yong Zhang 006; Xiaole Shirley Liu (Quant. Biol., 2013)

CR Cistrome: a ChIP-Seq database for chromatin regulators and histone modification linkages in human and mouse. - Qixuan Wang; Jinyan Huang; Hanfei Sun; Jing Liu; Juan Wang; Qian Wang; Qian Qin; Shenglin Mei; Chengchen Zhao; Xiaoqin Yang; Xiaole Shirley Liu; Yong Zhang 006 (Nucleic Acids Res., 2014)

Dr.seq: a quality control and analysis pipeline for droplet sequencing. - Xiao Huo; Sheng'en Hu; Chengchen Zhao; Yong Zhang 006 (Bioinform., 2016)

ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline. - Qian Qin; Shenglin Mei; Qiu Wu; Hanfei Sun; Lewyn Li; Len Taing; Sujun Chen; Fugen Li; Tao Liu 022; Chongzhi Zang; Han Xu; Yiwen Chen; et al. (BMC Bioinform., 2016)

CSTEA: a webserver for the Cell State Transition Expression Atlas. - Guanghui Zhu; Hui Yang; Xiao Chen; Jun Wu; Yong Zhang 006; Xing-Ming Zhao (Nucleic Acids Res., 2017)

Design and implementation of intelligent traffic and big data mining system based on internet of things. - Weiguang Li; Juan Zhu; Yong Zhang 006; Shuyan Zhang (J. Intell. Fuzzy Syst., 2020)

CStreet: a computed Cell State trajectory inference method for time-series single-cell RNA sequencing data. - Chengchen Zhao; Wenchao Xiu; Yuwei Hua; Naiqian Zhang; Yong Zhang 006 (Bioinform., 2021)

NUCOME: A comprehensive database of nucleosome organization referenced landscapes in mammalian genomes. - Xiaolan Chen; Hui Yang; Guifen Liu; Yong Zhang 006 (BMC Bioinform., 2021)

GLEANER: a web server for GermLine cycle Expression ANalysis and Epigenetic Roadmap visualization. - Shiyang Zeng; Yuwei Hua; Yong Zhang 006; Guifen Liu; Chengchen Zhao (BMC Bioinform., 2021)

MechanoBase: a comprehensive database for the mechanics of tissues and cells. - Yanhong Xiong; Shiyu Li; Yuxuan Zhang; Qianqian Chen; Mengtan Xing; Yong Zhang 006; Qi Wang (Database J. Biol. Databases Curation, 2024)