Wei Shen

Associate Professor in Bioinformatics, started Dec 2022

Lab site: https://mbio.info

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

Research Interests

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

Publications

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

Softwares

More on Github

Bioinformatics

  • LexicMap, efficient sequence alignment against millions of prokaryotic genomes
  • 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
  • perfect-bioinformatic-tools, suggestions for improving the usability of bioinformatic (command-line) tools

Utilities

  • csvtk, efficient and practical CSV/TSV toolkit
  • rush, command-line tool for executing jobs in parallel
  • brename, command-line tool for safely batch renaming

Education

  • 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

Professional experience

  • Visiting scholar: Oct 2023 - Sep 2024, EMBL-EBI, UK. Hosted by Zamin Iqbal, Sequence alignment against millions of prokaryotic genomes.
  • Postdoc: Dec 2020 - Nov 2022, Chongqing Medical University. Supervised by Hong Ren. Metagenomic profiling and pathogen detection.

Honours and awards

  • EMBL Sabbatical Visitor Fellowship (2024)
  • Theory@EMBL Fellowship (2023)
  • Chinese Scholarship Council fellowship (2023)

Grants

  • China Postdoctoral Science Foundation (2021, 2021M700640)
  • National Natural Science Foundation of China (2020, 32000474)

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