🏆 Finalist — NIH Data Sharing Index (“S-Index”) Challenge

Yuzhen Ye

First Affiliated Hospital of Guangzhou Medical University

ORCID: 0000-0003-3707-3185

Also affiliated with Indiana University Bloomington, Guangzhou Medical University

Biochemistry, Genetics and Molecular BiologyEnvironmental Science

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 1%percentile
9.6Author DataRank

Indexed papers

5in pilot corpus
datarank_citation_only_1hop_v6· scope data_onlyMethodology
Why this DataRank?

An author's DataRank is the sum of the DataRanks of all 5 indexed papers attributed to them. A prolific author with many moderate-impact papers can outrank one with a single high-impact paper.

Author scores recompute whenever paper DataRanks are refreshed, so this number lags the underlying paper scores by at most one batch run.

Read the full methodology →

Top data-sharing exemplar

The highest-impact dataset this researcher has shared, ranked by DataRank — the single contribution doing the most to lift their data-sharing standing.

A framework for human microbiome research

Nature(2012)10.1038/nature11209
Top 2%
8.4DataRank
Top 2%2766 citations

Barbara A. Methé, William Nelson, Mihai Pop, Heather H. Creasy, Michelle Giglio +236 more

Papers

Driven by 22 papers — median percentile 83. Top paper: “A framework for human microbiome research”.

A framework for human microbiome research

Nature(2012)10.1038/nature11209
Top 2%
8.4DataRank
Top 2%2766 citations

Barbara A. Methé, William Nelson, Mihai Pop, Heather H. Creasy, Michelle Giglio +236 more

Structure, function and diversity of the healthy human microbiome

Nature(2012)10.1038/nature11234
N/A
1.4DataRank · unranked
10088 citations

Curtis Huttenhower, Dirk Gevers, Rob Knight, Sahar Abubucker, Jonathan H. Badger +235 more

Using high-abundance proteins as guides for fast and effective peptide/protein identification from human gut metaproteomic data

Microbiome(2021)10.1186/s40168-021-01035-8
Top 17%
1.2DataRank
Top 17%31 citations

Sujun Li, Yuzhen Ye, Moses Stamboulian

Characterization of CRISPR RNA transcription by exploiting stranded metatranscriptomic data

RNA(2016)10.1261/rna.055988.116
N/A
0.385DataRank · unranked
12 citations

Quan Zhang, Yuzhen Ye

AN ORFOME ASSEMBLY APPROACH TO METAGENOMICS SEQUENCES ANALYSIS

Computational Systems Bioinformatics(2008)10.1142/9781848162648_0001
N/A
0.357DataRank · unranked
4 citations

Haixu Tang, Yuzhen Ye

Comparison of CRISPR–Cas Immune Systems in Healthcare-Related Pathogens

Frontiers in Microbiology(2021)10.3389/fmicb.2021.758782
N/A
0DataRank · unranked
34 citations

Tony J. Lam, Yuzhen Ye, Kate Mortensen

Using high abundance proteins as guides for fast and effective peptide/protein identification from metaproteomic data

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.05.21.109348
Top 100%
0DataRank
Top 100%0 citations

Sujun Li, Yuzhen Ye, Moses Stamboulian

Identification and Classification of Reverse Transcriptases in Bacterial Genomes and Metagenomes

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.01.26.428298
N/A
0DataRank · unranked
2 citations

Yuzhen Ye, Fatemeh Sharifi

Strain level microbial detection and quantification with applications to single cell metagenomics

Nature Communications(2022)10.1038/s41467-022-33869-7
N/A
0DataRank · unranked
14 citations

Alejandro A. Schäffer, Welles Robinson, Junyan Xu, Eytan Ruppin, A. Funda Ergun +3 more

Diversity and dynamics of the CRISPR-Cas systems associated with Bacteroides fragilis in human population

BMC Genomics(2022)10.1186/s12864-022-08770-8
N/A
0DataRank · unranked
4 citations

Kate Mortensen, Yuzhen Ye, Tony J. Lam

Revealing bacteria-phage interactions in human microbiome through the CRISPR-Cas immune systems

Frontiers in Cellular and Infection Microbiology(2022)10.3389/fcimb.2022.933516
N/A
0DataRank · unranked
3 citations

Sara Zomorodi, Kate Mortensen, Yuzhen Ye, Mahsa Monshizadeh

PepNet: A Fully Convolutional Neural Network for De novo Peptide Sequencing

Research Square(2022)10.21203/rs.3.rs-1341615/v1
N/A
0DataRank · unranked
5 citations

Yuzhen Ye, Haixu Tang, Kaiyuan Liu

Meta-analysis of Microbiome Association Networks Reveal Patterns of Dysbiosis in Diseased Microbiomes

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.01.19.476958
N/A
0DataRank · unranked
3 citations

Yuzhen Ye, Tony J. Lam

Accurate de novo peptide sequencing using fully convolutional neural networks

Nature Communications(2023)10.1038/s41467-023-43010-x
N/A
0DataRank · unranked
76 citations

Yuzhen Ye, Sujun Li, Haixu Tang, Kaiyuan Liu

Incorporating metabolic activity, taxonomy and community structure to improve microbiome-based predictive models for host phenotype prediction

Gut Microbes(2024)10.1080/19490976.2024.2302076
N/A
0DataRank · unranked
9 citations

Yuzhen Ye, Mahsa Monshizadeh

SpecEncoder: deep metric learning for accurate peptide identification in proteomics

Bioinformatics(2024)10.1093/bioinformatics/btae220
N/A
0DataRank · unranked
7 citations

Chenghua Tao, Yuzhen Ye, Haixu Tang, Kaiyuan Liu

Multitask knowledge-primed neural network for predicting missing metadata and host phenotype based on human microbiome

Bioinformatics Advances(2024)10.1093/bioadv/vbae203
N/A
0DataRank · unranked
3 citations

Yuhui Hong, Yuzhen Ye, Mahsa Monshizadeh

Protein domain embeddings for fast and accurate similarity search

Genome Research(2024)10.1101/gr.279127.124
N/A
0DataRank · unranked
11 citations

Haixu Tang, Yuzhen Ye, Benjamin Giovanni Iovino

Identification of microbial species and proteins associated with colorectal cancer by reanalyzing CPTAC proteomic datasets

Scientific Reports(2025)10.1038/s41598-025-97984-3
N/A
0DataRank · unranked
2 citations

Yuzhen Ye, Jamie Canderan

Identification and applications of disease-associated differential human and bacterial proteins with metaproteomic evidence

Health Information Science and Systems(2025)10.1007/s13755-025-00369-z
N/A
0DataRank · unranked
0 citations

Moses Stamboulian, Yuzhen Ye, Jamie Canderan

Identification and classification of reverse transcriptases in bacterial genomes and metagenomes

Nucleic Acids Research(2021)10.1093/nar/gkab1207
N/A
0DataRank · unranked
44 citations

Yuzhen Ye, Fatemeh Sharifi

A Tree of Human Gut Bacterial Species and its Applications to Metagenomics and Metaproteomics Data Analysis

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.09.24.311720
N/A
0DataRank · unranked
1 citations

Thomas G. Doak, Yuzhen Ye, Moses Stamboulian