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
- …
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
- 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
- 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
- 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
- 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
- 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
- Wei Shen, Yan Li†.
(2016) A novel algorithm for detecting multiple covariance and clustering of biological sequences.
Scientific Reports.
doi:10.1038/srep30425
- 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
Softwares
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
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