Wei Shen

Associate Professor, started Dec 2022

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 | Publons

Selected Publications (* for equal contribution; for corresponding authors):

  • Wei Shen, Botond Sipos, Liuyang Zhao. (2024) SeqKit2: A Swiss army knife for sequence and alignment processing. iMeta. doi:10.1002/imt2.191 Citation Badge
  • Wei Shen, …, Peng Hu, Hong Ren. (2023) KMCP: accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping. Bioinformatics. doi:10.1093/bioinformatics/btac845 Citation Badge
  • Gang Li*, Wei Shen*, …, Yan Zhao, (2022) Essential fitness repertoire of Staphylococcus aureus during co-infection with Acinetobacter baumannii in vivo. mSystems. doi:10.1128/msystems.00338-22 Citation Badge
  • Wei Shen, Hong Ren. (2021) TaxonKit: a practical and efficient NCBI Taxonomy toolkit. Journal of Genetics and Genomics. doi:10.1016/j.jgg.2021.03.006 Citation Badge
  • Wei Shen, …, Fuquan Hu, Shuai Le. (2017) 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. doi:10.3389/fmicb.2017.00272 Citation Badge
  • Wei Shen, Shuai Le, Yan Li, Fuquan Hu. (2016) SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation. PloS one. doi:10.1371/journal.pone.0163962 Citation Badge
  • Wei Shen, Yan Li. (2016) A novel algorithm for detecting multiple covariance and clustering of biological sequences. Scientific Reports. doi:10.1038/srep30425 Citation Badge
  • Wei Shen, Ming Chen, Guo Wei, Yan Li. (2012) MicroRNA prediction using a fixed-order Markov model based on the secondary structure pattern. PloS one. doi:10.1371/journal.pone.0048236 Citation Badge


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