Yuzhen Ye

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 23

Top Topics

Mass Spectrometry

Pluripotent Stem Cells

Top Venues

Journal of proteome research

Bioinformatics (Oxford, England)

PLoS computational biology

This page only lists publications with an associated author ORCID identifier.

Publications

Benjamin Giovanni Iovino, Haixu Tang, Yuzhen Ye
Protein domain embeddings for fast and accurate similarity search. Genome research (2024)
Mahsa Monshizadeh, Yuzhen Ye
Incorporating metabolic activity, taxonomy and community structure to improve microbiome-based predictive models for host phenotype prediction. Gut microbes 16 (1) (2024)
Mahsa Monshizadeh, Yuzhen Ye
Incorporating metabolic activity, taxonomy and community structure to improve microbiome-based predictive models for host phenotype prediction. Gut microbes 16 (1) (2024)
Kaiyuan Liu, Chenghua Tao, Yuzhen Ye, Haixu Tang
SpecEncoder: deep metric learning for accurate peptide identification in proteomics. Bioinformatics (Oxford, England) 40 (Supplement_1) (2024)
Mahsa Monshizadeh, Yuzhen Ye
Incorporating metabolic activity, taxonomy and community structure to improve microbiome-based predictive models for host phenotype prediction. Gut microbes 16 (1) (2024)
Mahsa Monshizadeh, Yuzhen Ye
Incorporating metabolic activity, taxonomy and community structure to improve microbiome-based predictive models for host phenotype prediction. Gut microbes 16 (1) (2024)
Mahsa Monshizadeh, Yuzhen Ye
Incorporating metabolic activity, taxonomy and community structure to improve microbiome-based predictive models for host phenotype prediction. Gut microbes 16 (1) (2024)
Mahsa Monshizadeh, Yuzhen Ye
Incorporating metabolic activity, taxonomy and community structure to improve microbiome-based predictive models for host phenotype prediction. Gut microbes 16 (1) (2024)
Mahsa Monshizadeh, Yuzhen Ye
Incorporating metabolic activity, taxonomy and community structure to improve microbiome-based predictive models for host phenotype prediction. Gut microbes 16 (1) (2024)
Kaiyuan Liu, Chenghua Tao, Yuzhen Ye, Haixu Tang
SpecEncoder: deep metric learning for accurate peptide identification in proteomics. Bioinformatics (Oxford, England) 40 (Supplement_1) (2024)
Kaiyuan Liu, Chenghua Tao, Yuzhen Ye, Haixu Tang
SpecEncoder: deep metric learning for accurate peptide identification in proteomics. Bioinformatics (Oxford, England) 40 (Supplement_1) (2024)
Jamie Canderan, Moses Stamboulian, Yuzhen Ye
MetaProD: A Highly-Configurable Mass Spectrometry Analyzer for Multiplexed Proteomic and Metaproteomic Data. Journal of proteome research 22 (2) (2023)
Jamie Canderan, Moses Stamboulian, Yuzhen Ye
MetaProD: A Highly-Configurable Mass Spectrometry Analyzer for Multiplexed Proteomic and Metaproteomic Data. Journal of proteome research (2023)
Jamie Canderan, Moses Stamboulian, Yuzhen Ye
MetaProD: A Highly-Configurable Mass Spectrometry Analyzer for Multiplexed Proteomic and Metaproteomic Data. Journal of proteome research 22 (2) (2023)
Jamie Canderan, Moses Stamboulian, Yuzhen Ye
MetaProD: A Highly-Configurable Mass Spectrometry Analyzer for Multiplexed Proteomic and Metaproteomic Data. Journal of proteome research 22 (2) (2023)
Jamie Canderan, Moses Stamboulian, Yuzhen Ye
MetaProD: A Highly-Configurable Mass Spectrometry Analyzer for Multiplexed Proteomic and Metaproteomic Data. Journal of proteome research 22 (2) (2023)
Jamie Canderan, Moses Stamboulian, Yuzhen Ye
MetaProD: A Highly-Configurable Mass Spectrometry Analyzer for Multiplexed Proteomic and Metaproteomic Data. Journal of proteome research 22 (2) (2023)
Moses Stamboulian, Jamie Canderan, Yuzhen Ye
Metaproteomics as a tool for studying the protein landscape of human-gut bacterial species. PLoS computational biology 18 (3) (2022)
Fatemeh Sharifi, Yuzhen Ye
Identification and classification of reverse transcriptases in bacterial genomes and metagenomes. Nucleic acids research 50 (5) (2022)
Moses Stamboulian, Sujun Li, Yuzhen Ye
Using high-abundance proteins as guides for fast and effective peptide/protein identification from human gut metaproteomic data. Microbiome 9 (1) (2021)
Tony J Lam, Moses Stamboulian, Wontack Han, Yuzhen Ye
Model-based and phylogenetically adjusted quantification of metabolic interaction between microbial species. PLoS computational biology 16 (10) (2020)
Tony J Lam, Yuzhen Ye
Long reads reveal the diversification and dynamics of CRISPR reservoir in microbiomes. BMC genomics 20 (1) (2019)
Quan Zhang, Yuzhen Ye
Not all predicted CRISPR-Cas systems are equal: isolated cas genes and classes of CRISPR like elements. BMC bioinformatics 18 (1) (2017)