Wei Shen

Postdoctoral researcher

Institute for Viral Hepatitis, The Second Affiliated Hospital of Chongqing Medical University, China

Research Interests

  • Large-scale biological sequence searching
  • Taxonomic assignment and profiling
  • Host-associated microbiomes
  • Viral (Phage) genomics
  • Reproducible tools for data science


Google Scholar | ORCID | ResearchGate | Publons

Selected Publications

  • W Shen, H Ren, TaxonKit: a practical and efficient NCBI Taxonomy toolkit. Journal of Genetics and Genomics 2021. doi:10.1016/j.jgg.2021.03.006
  • W Shen, M Shen, X Zhao, et.al., Anti-obesity effect of capsaicin in mice fed with high-fat diet is associated with an increase in population of the gut bacterium Akkermansia muciniphila. Frontiers in Microbiology 2017. doi:10.3389/fmicb.2017.00272
  • W Shen, S Le, Y Li, F Hu. SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation. PloS one 2016. doi:10.1371/journal.pone.0163962
  • W Shen, Y Li. A novel algorithm for detecting multiple covariance and clustering of biological sequences. Scientific Reports 2016. doi:10.1038/srep30425
  • W Shen, M Chen, G Wei, Y Li. MicroRNA prediction using a fixed-order Markov model based on the secondary structure pattern. PloS one 2012. doi:10.1371/journal.pone.0048236


More on Github

  • KMCP, Accurate metagenomic profiling && Fast large-scale sequence/genome searching
  • SeqKit, fast and versatile toolkit for FASTA/Q file
  • TaxonKit, practical and efficient NCBI Taxonomy toolkit
  • unikmer, toolkit for nucleic acid k-mer analysis
  • csvtk, efficient and practical CSV/TSV toolkit
  • rush, command-line tool for executing jobs in parallel
  • brename, command-line tool for safely batch renaming


  • PhD in Microbiolgy, 2017, Third Military Medical University, China
  • MSc in Bioinformatics, 2013, Third Military Medical University, China
  • BSc in Bioinformatics, 2010, Chongqing University of Posts and Telecommunications, China