Publications

Journal articles

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

Preprints