Institute for Viral Hepatitis, The Second Affiliated Hospital of Chongqing Medical University, China
- 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
- W Shen†, H Ren†,
TaxonKit: a practical and efficient NCBI Taxonomy toolkit.
Journal of Genetics and Genomics 2021.
- 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.
- W Shen, S Le, Y Li, F Hu.
SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation.
PloS one 2016.
- W Shen, Y Li.
A novel algorithm for detecting multiple covariance and clustering of biological sequences.
Scientific Reports 2016.
- 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.
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