Software

MotifClick

MotifClick is a motif-finding tool

  • 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)

SNN-Cliq

SNN-Cliq is a method for partitioning individuall cells into groups 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

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 animanl and plant 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)
  • Ni P, Su Z. Accurate prediction of cis-regulatory modules reveals a prevalent regulatory genome of humans.  NAR Genom Bioinform. 2021 Jun 17;3(2):lqab052. doi: 10.1093/nargab/lqab052
  • Ni P, Moe J, Su Z.  Accurate prediction of functional states of cis-regulatory modules reveals common epigenetic rules in humans and mice. BMC Biol. 2022 Oct 5;20(1):221. doi: 10.1186/s12915-022-01426-9.PMID: 36199141. 
  • Ni P, Su Z. PCRMS: a database of predicted cis-regulatory modules and constituent transcription factor binding sites in genomes. Database (Oxford). 2022 Apr 22;2022. doi: 10.1093/database/baac024. 

ProSampler

ProSampler is an ultra-fast motif finding program in a large transcription factor ChIP-seq dataset

  • Li Y, Ni P, Zhang S, Li G, Su Z. ProSampler: an ultra-fast and accurate motif finder in large ChIP-seq datasets for combinatory motif discovery. Bioinformatics. 2019 May 9. pii: btz290. doi: 10.1093/bioinformatics/btz290. Google Scholar citations: 8.

Genome Assembling and Annotation Piple line 

A pipeline for assembling and annotating vertebrate genomes using Illumina short reads, PacBio or Nanopore long reads and HiC data

  • Siwen Wu, Kun Wang, Sisi Yuan, Tengfei Dou, Zhengchang Su, Changrong Ge, Junjing Jia. De novo assembly of four indigenous chicken genomes reveal loss of function as a major driving force in chicken domestication and evolution. https://assets.researchsquare.com/files/rs-2019326/v1/8c0f16b2-39ca-46e7-a1ba-f12d154d1bad.pdf?c=1662734768