Journal articles

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

• Wei Shen^†, John A Lees and Zamin Iqbal^†. (2025) Efficient sequence alignment against millions of prokaryotic genomes with LexicMap. Nature Biotechnology. doi:10.1038/s41587-025-02812-8
  • Research Briefing: New algorithm enables fast ‘gold-standard’ search of the world’s largest microbial DNA archives
• 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