GLECLUBS is an algorithm for predicting cis-regulatory binding sites in prokaryotes, which was described in the following papers: 

  • Shaoqiang Zhang, MinLi Xu, Shan Li, and Zhengchang Su. Genome-wide de novo prediction of cis-regulatory binding sites in prokaryotes. Nucleic Acids Research, 2009. doi:10.1093/nar/gkp248. (pdf)
  • Zhang S, Li S, Pham PT, Su Z. Simultaneous prediction of transcription factor binding sites in a group of prokaryotic genomes. BMC Bioinformatics. 2010;11:397. PMCID: 2920276. (pdf)

TFBS PFM database search using PFV algorithm

TFBS PFM database search is web interface which demonstrate the effectiveness of our PFV algorithm for PFM searching and retrieval.

  • Xu M, Su Z. A novel alignment-free method for comparing transcription factor binding site motifs. PLoS One. 2010;5(1):e8797. (pdf)


MotifClick is a motif-finding tools

  • Shaoqiang Zhang, Shan Li, Meng Niu, Phuc Pham and Zhengchang Su. MotifClick: prediction of cis-regulatory binding sites via merging cliques. BMC Bioinformatics 2011, 12:238 (pdf)


The software and code will be released upon the publication of the the paper.

TruHMM assembles transcription unit/operons in prokaryotes using RNA-seq short reads

  • Shan Li, Xia Dong and Zhengchang Su. Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coli K12 through accurate full-length transcripts assembling. BMC Genomics. 2013 Jul 30;14:520. (pdf)


SNN-Cliq is a method for partitioning individuall cells into grooups of the same type using single-cell transcriptome data. 

  • Chen Xu and Zhengchang Su. Identification of cell types from single-cell transcriptome using a novel clustering method. Bioinformatics. 2015 Jun 15;31(12):1974-80. (pdf)


PCRMs is a database of predicted cis-regulatory modules and transcription factor binding sites in the human genome as well as in the major model plant and animanl genomes. 

  • Niu M, Tabari ES, Su Z.De novo prediction of cis-regulatory elements and modules through integrative analysis of a large number of ChIP datasets.BMC Genomics. 2014 Dec 2;15:1047. (pdf)

  • Meng Niu, Ehsan Tabari, Pengyu Ni and Zhengchang Su. Towards a map of cis-regulatory sequences in the human genome.  Nucleic Acids Research. 2018 May 4, doi: 10.1093/nar/gky338 (pdf)