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Ye, Yuzhen
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1

Protein embedding based alignment:

Iovino, Benjamin Giovanni ; Ye, Yuzhen
BMC Bioinformatics.  25 (2024)  1 - p. , 2024
Link: https://doi.org/10.1186/..
 
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2

Incorporating metabolic activity, taxonomy and community st..:

Monshizadeh, Mahsa ; Ye, Yuzhen
Gut Microbes.  16 (2024)  1 - p. , 2024
Link: https://doi.org/10.1080/..
 
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3

Protein Domain Embeddings for Fast and Accurate Similarity ..:

, In: Lecture Notes in Computer Science; Research in Computational Molecular Biology,
Iovino, Benjamin Giovanni ; Tang, Haixu ; Ye, Yuzhen - p. 421-424 , 2024
Link: https://doi.org/10.1007/..
 
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4

SpecEncoder: deep metric learning for accurate peptide iden..:

Liu, Kaiyuan ; Tao, Chenghua ; Ye, Yuzhen.
Bioinformatics.  40 (2024)  Supplement_1 - p. i257-i265 , 2024
Link: https://doi.org/10.1093/..
 
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5

MetaProD: A Highly-Configurable Mass Spectrometry Analyzer ..:

Canderan, Jamie ; Stamboulian, Moses ; Ye, Yuzhen
Journal of Proteome Research.  22 (2023)  2 - p. 442-453 , 2023
Link: https://doi.org/10.1021/..
 
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6

Accurate de novo peptide sequencing using fully convolution..:

Liu, Kaiyuan ; Ye, Yuzhen ; Li, Sujun.
Nature Communications.  14 (2023)  1 - p. , 2023
Link: https://doi.org/10.1038/..
 
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7

Dysmenorrhea Symptoms And Gut Microbiome: A Pilot Study:

Chen, Chen ; Carpenter, Janet S. ; Shin, Andrea...
The Journal of Pain.  24 (2023)  4 - p. 1-2 , 2023
Link: https://doi.org/10.1016/..
 
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8

3DMolMS: prediction of tandem mass spectra from 3D molecula..:

Hong, Yuhui ; Li, Sujun ; Welch, Christopher J...
Bioinformatics.  39 (2023)  6 - p. , 2023
Link: https://doi.org/10.1093/..
 
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9

Diversity and dynamics of the CRISPR-Cas systems associated..:

Lam, Tony J. ; Mortensen, Kate ; Ye, Yuzhen
BMC Genomics.  23 (2022)  1 - p. , 2022
Link: https://doi.org/10.1186/..
 
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10

Revealing bacteria-phage interactions in human microbiome t..:

Monshizadeh, Mahsa ; Zomorodi, Sara ; Mortensen, Kate.
Frontiers in Cellular and Infection Microbiology.  12 (2022)  - p. , 2022
Link: https://doi.org/10.3389/..
 
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11

Meta-analysis of microbiome association networks reveal pat..:

Lam, Tony J. ; Ye, Yuzhen
Scientific Reports.  12 (2022)  1 - p. , 2022
Link: https://doi.org/10.1038/..
 
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12

Metaproteomics as a tool for studying the protein landscape..:

Stamboulian, Moses ; Canderan, Jamie ; Ye, Yuzhen.
PLOS Computational Biology.  18 (2022)  3 - p. e1009397 , 2022
Link: https://doi.org/10.1371/..
 
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13

Improvements on physical conditions of bauxite residue foll..:

Guo, Ying ; Ye, Yuzhen ; Zhu, Feng...
Journal of Environmental Sciences.  116 (2022)  - p. 198-208 , 2022
Link: https://doi.org/10.1016/..
 
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14

Strain level microbial detection and quantification with ap..:

Zhu, Kaiyuan ; Schäffer, Alejandro A. ; Robinson, Welles...
Nature Communications.  13 (2022)  1 - p. , 2022
Link: https://doi.org/10.1038/..
 
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15

Identification and classification of reverse transcriptases..:

Sharifi, Fatemeh ; Ye, Yuzhen
Nucleic Acids Research.  50 (2021)  5 - p. e29-e29 , 2021
Link: https://doi.org/10.1093/..
 
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