VibrioBase: A Model for Next-Generation Genome and Annotation Database Development by Siew Woh Choo, Hamed Heydari, Tze King Tan, Cheuk Chuen Siow, Ching Yew Beh, Wei Yee Wee, Naresh V. R. Mutha, Guat Jah Wong, Mia Yang Ang, Amir Hessam Yazdi

“…Other important features of this platform include our newly developed in-house tools, the pairwise genome comparison (PGC) tool, and pathogenomics profiling tool (PathoProT). The PGC tool is useful in the identification and comparative analysis of two genomes, whereas PathoProT is designed for comparative pathogenomics analysis of Vibrio strains. …”
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Development and interpretation of a pathomics-driven ensemble model for predicting the response to immunotherapy in gastric cancer by Jing Wang, Zhe Li, Wei Wang, Md Tauhidul Islam, Xiaoyan Wang, Zhen Han, Zihan Li, Guoxin Li, Yuming Jiang, Taojun Zhang, Wenjun Xiong, Zepang Sun, Lequan Yu, Zhicheng Zhang, Xianqi Yang, Shengtian Sang, Alyssa A Guo

“…Additionally, SHAP (SHapley Additive exPlanations) analysis was used to explain the model’s predicted values as the sum of the attribution values for each input feature. Pathogenomics analysis was employed to explain the molecular mechanisms underlying the model’s predictions.Results Our pathomics-driven ensemble model effectively stratified the response to ICIs in training cohort (AUC 0.985 (95% CI 0.971 to 0.999)), which was further validated in internal validation cohort (AUC 0.921 (95% CI 0.839 to 0.999)), as well as in external validation cohort 1 (AUC 0.914 (95% CI 0.837 to 0.990)), and external validation cohort 2 (0.927 (95% CI 0.802 to 0.999)). …”
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