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Bioinformatics Advances|December 30, 2024
Multitask knowledge-primed neural network for predicting missing metadata and host phenotype based on human microbiomeMahsa Monshizadeh, Yuhui Hong, Yuzhen YeGut Microbes|January 12, 2024
Incorporating metabolic activity, taxonomy and community structure to improve microbiome-based predictive models for host phenotype predictionMahsa Monshizadeh, Yuzhen YeFrontiers in Cellular and Infection Microbiology|October 17, 2022
Revealing bacteria-phage interactions in human microbiome through the CRISPR-Cas immune systemsMahsa Monshizadeh, Sara Zomorodi, Kate Mortensen, et al.Annual Review of Analytical Chemistry (Palo Alto, Calif.)|February 27, 2025
Machine Learning in Small-Molecule Mass SpectrometryYuhui Hong, Yuzhen Ye, Haixu TangNature Communications|December 12, 2025
FIDDLE: a deep learning method for chemical formulas prediction from tandem mass spectraYuhui Hong, Sujun Li, Yuzhen Ye, et al.Bioinformatics (Oxford, England)|May 30, 2023
3DMolMS: prediction of tandem mass spectra from 3D molecular conformationsYuhui Hong, Sujun Li, Christopher J Welch, et al.Proceedings. IEEE International Conference on Bioinformatics and Biomedicine|November 22, 2011
Identification and Quantification of Abundant Species from Pyrosequences of 16S rRNA by Consensus AlignmentYuzhen YeInternational Journal of Molecular Sciences|September 9, 2014
Identification of diversity-generating retroelements in human microbiomesYuzhen YeBioinformatics (Oxford, England)|August 31, 2015
Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysisYuzhen Ye, Haixu TangNucleic Acids Research|May 4, 2019
MyDGR: a server for identification and characterization of diversity-generating retroelementsFatemeh Sharifi, Yuzhen YePageof 12