Subgenomic mRNA Position Exploration with RNA-seq. This tool is designed to identify TRS-B sites in coronavirus genomes.

Paper: Yang, Yiyan; Yan, Wei; Hall, A Brantley; Jiang, Xiaofang (2021). Characterizing transcriptional regulatory sequences in coronaviruses and their role in recombination. Molecular Biology and Evolution, 38(4), 1241-1248.

Evolink is a phylogenetic approach for rapid identification of genotype-phenotype associations in large-scale microbial multi-species data. 

Paper: Yang, Yiyan; Jiang, Xiaofang (2023). Evolink: A Phylogenetic Approach for Rapid Identification of Genotype-Phenotype Associations in Large-scale Microbial Multispecies Data. Bioinformatics, 39(5), btad215.

SpikeHunter utilizes a deep learning approach to identify phage tailspike proteins, which is a significant kind of phage binding proteins targeting host receptors.

Paper: Yang, Yiyan; Dufault-Thompson, Keith; Yan, Wei; Cai, Tian; Xie, Lei; Jiang, Xiaofang (2023). Deciphering Phage-Host Specificity Based on the Association of Phage Depolymerases and Bacterial Surface Glycan with Deep Learning. bioRxiv, 2023-06.

A python script to measure the dissimilarity distance between SARS-CoV-2 metagenome samples. 

Paper: Salgado Fontenele, Rafaela; Yang, Yiyan; Driver, Erin M; Magge, Arjun; Kraberger, Simona; Custer, Joy M; Dufault-Thompson, Keith; Cox, Erin; Newell, Melanie Engstrom; Varsani, Arvind; et al. (2023). Wastewater surveillance uncovers regional diversity and dynamics of SARS-CoV-2 variants across nine states in the USA. Science of The Total Environment, 877, 162862.

CE-BLAST is a tool to rapidly compare antigenic similarity for protein antigens using structural data.

Paper: Qiu, Tianyi*; Yang, Yiyan*; Qiu, Jingxuan; Huang, Yang; Xu, Tianlei; Xiao, Han; Wu, Dingfeng; Zhang, Qingchen; Zhou, Chen; Zhang, Xiaoyan (2018). CE-BLAST makes it possible to compute antigenic similarity for newly emerging pathogens. Nature Communications, 9(1), 1772.