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

Yuzhen Ye Indiana University, Bloomington, IN, USA http://www.indiana.edu/~mcbdept/graduate/ye.shtml https://scholar.google.com/citations?user=fH_ea0kAAAAJ https://www.linkedin.com/in/yuzhen-ye-06a56015 https://orcid.org/0000-0003-3707-3185 https://www.wikidata.org/entity/Q89214476 https://www.researchgate.net/profile/Yuzhen_Ye

Jamie Canderan Moses Stamboulian Yuzhen Ye Identification and applications of disease-associated differential human and bacterial proteins with metaproteomic evidence. 54 2025 December 13 Health Inf. Sci. Syst. 1 https://doi.org/10.1007/s13755-025-00369-z db/journals/hisas/hisas13.html#CanderanSY25 streams/journals/hisas

Kaiyuan Liu Chenghua Tao Yuzhen Ye Haixu Tang SpecEncoder: deep metric learning for accurate peptide identification in proteomics. i257-i265 2024 40 Bioinform. Supplement_1 https://doi.org/10.1093/bioinformatics/btae220 db/journals/bioinformatics/bioinformatics40.html#LiuTYT24

Benjamin Giovanni Iovino Yuzhen Ye Protein embedding based alignment. 85 2024 December 25 BMC Bioinform. 1 https://doi.org/10.1186/s12859-024-05699-5 db/journals/bmcbi/bmcbi25.html#IovinoY24

Benjamin Giovanni Iovino Haixu Tang Yuzhen Ye Protein Domain Embeddings for Fast and Accurate Similarity Search. 421-424 2024 RECOMB https://doi.org/10.1007/978-1-0716-3989-4_44 conf/recomb/2024 db/conf/recomb/recomb2024.html#IovinoTY24

Yuhui Hong Sujun Li Christopher J. Welch Shane Tichy Yuzhen Ye Haixu Tang 3DMolMS: prediction of tandem mass spectra from 3D molecular conformations. 2023 39 Bioinform. 6 https://doi.org/10.1093/bioinformatics/btad354 db/journals/bioinformatics/bioinformatics39.html#HongLWTYT23

Wontack Han Haixu Tang Yuzhen Ye Locality-Sensitive Hashing-Based k-Mer Clustering for Identification of Differential Microbial Markers Related to Host Phenotype. 738-751 2022 29 J. Comput. Biol. 7 https://doi.org/10.1089/cmb.2021.0640 https://www.wikidata.org/entity/Q113823470 db/journals/jcb/jcb29.html#HanTY22

Moses Stamboulian Jamie Canderan Yuzhen Ye Metaproteomics as a tool for studying the protein landscape of human-gut bacterial species. 2022 18 PLoS Comput. Biol. 3 https://doi.org/10.1371/journal.pcbi.1009397 https://www.wikidata.org/entity/Q112280069 db/journals/ploscb/ploscb18.html#StamboulianCY22

Tony J. Lam Moses Stamboulian Wontack Han Yuzhen Ye Model-based and phylogenetically adjusted quantification of metabolic interaction between microbial species. 2020 16 PLoS Comput. Biol. 10 https://doi.org/10.1371/journal.pcbi.1007951 https://www.wikidata.org/entity/Q101126441 db/journals/ploscb/ploscb16.html#LamSHY20

Fatemeh Sharifi Yuzhen Ye MyDGR: a server for identification and characterization of diversity-generating retroelements. W289-W294 2019 47 Nucleic Acids Res. Webserver-Issue https://doi.org/10.1093/nar/gkz329 https://www.wikidata.org/entity/Q91719572 db/journals/nar/nar47.html#SharifiY19

Wontack Han Yuzhen Ye A repository of microbial marker genes related to human health and diseases for host phenotype prediction using microbiome data. 236-247 2019 PSB http://psb.stanford.edu/psb-online/proceedings/psb19/han.pdf conf/psb/2019 db/conf/psb/psb2019.html#HanY19

Quan Zhang Yuzhen Ye Not all predicted CRISPR-Cas systems are equal: isolated cas genes and classes of CRISPR like elements. 92:1-92:12 2017 18 BMC Bioinform. 1 https://doi.org/10.1186/s12859-017-1512-4 https://www.wikidata.org/entity/Q36271931 db/journals/bmcbi/bmcbi18.html#ZhangY17

Hussein Mohsen Haixu Tang Yuzhen Ye Improving de novo metatranscriptome assembly via machine learning algorithms. 91-107 2017 10 Int. J. Comput. Biol. Drug Des. 2 https://doi.org/10.1504/IJCBDD.2017.10004575 db/journals/ijcbdd/ijcbdd10.html#MohsenTY17

Wontack Han Mingjie Wang Yuzhen Ye A Concurrent Subtractive Assembly Approach for Identification of Disease Associated Sub-metagenomes. 18-33 2017 RECOMB https://doi.org/10.1007/978-3-319-56970-3_2 https://www.wikidata.org/entity/Q89408691 conf/recomb/2017 db/conf/recomb/recomb2017.html#HanWY17

Yuzhen Ye Haixu Tang Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis. 1001-1008 2016 32 Bioinform. 7 https://doi.org/10.1093/bioinformatics/btv510 https://www.wikidata.org/entity/Q28828749 db/journals/bioinformatics/bioinformatics32.html#YeT16

Haixu Tang Sujun Li Yuzhen Ye A Graph-Centric Approach for Metagenome-Guided Peptide and Protein Identification in Metaproteomics. 2016 12 PLoS Comput. Biol. 12 https://doi.org/10.1371/journal.pcbi.1005224 https://www.wikidata.org/entity/Q28554789 db/journals/ploscb/ploscb12.html#TangLY16

Yuzhen Ye Haixu Tang Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis. 2015 abs/1504.01304 CoRR http://arxiv.org/abs/1504.01304 db/journals/corr/corr1504.html#YeT15

Wazim Ismail Yuzhen Ye Haixu Tang Gene finding in metatranscriptomic sequences. S8 2014 15 BMC Bioinform. S-9 https://doi.org/10.1186/1471-2105-15-S9-S8 https://www.wikidata.org/entity/Q34211294 db/journals/bmcbi/bmcbi15S.html#IsmailYT14

Zhanwen Li Padmaja Natarajan Yuzhen Ye Thomas Hrabe Adam Godzik POSA: a user-driven, interactive multiple protein structure alignment server. 240-245 2014 42 Nucleic Acids Res. Webserver-Issue https://doi.org/10.1093/nar/gku394 https://www.wikidata.org/entity/Q30362677 db/journals/nar/nar42.html#LiNYHG14

Mingjie Wang Haixu Tang Yuzhen Ye Identification and characterization of accessory genomes in bacterial species based on genome comparison and metagenomic recruitment. 17-24 2014 BIBM https://doi.org/10.1109/BIBM.2014.6999121 https://doi.ieeecomputersociety.org/10.1109/BIBM.2014.6999121 conf/bibm/2014 db/conf/bibm/bibm2014.html#WangTY14

Dazhi Jiao Yuzhen Ye Haixu Tang Probabilistic Inference of Biochemical Reactions in Microbial Communities from Metagenomic Sequences. 2013 9 PLoS Comput. Biol. 3 https://doi.org/10.1371/journal.pcbi.1002981 https://www.wikidata.org/entity/Q28488586 db/journals/ploscb/ploscb9.html#JiaoYT13

Yongan Zhao Haixu Tang Yuzhen Ye RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data. 125-126 2012 28 Bioinform. 1 https://doi.org/10.1093/bioinformatics/btr595 https://www.wikidata.org/entity/Q34062055 db/journals/bioinformatics/bioinformatics28.html#ZhaoTY12

Yu-Wei Wu Mina Rho Thomas G. Doak Yuzhen Ye Stitching gene fragments with a network matching algorithm improves gene assembly for metagenomics. 363-369 2012 28 Bioinform. 18 https://doi.org/10.1093/bioinformatics/bts388 https://www.wikidata.org/entity/Q42324042 db/journals/bioinformatics/bioinformatics28.html#WuRDY12

Mingjie Wang Yuzhen Ye Haixu Tang A de Bruijn Graph Approach to the Quantification of Closely-Related Genomes in a Microbial Community. 814-825 2012 19 J. Comput. Biol. 6 https://doi.org/10.1089/cmb.2012.0058 https://www.wikidata.org/entity/Q34303971 db/journals/jcb/jcb19.html#WangYT12

Quan Zhang Thomas G. Doak Yuzhen Ye Artificial Functional Difference Between Microbial Communities Caused by Length Difference of Sequencing Reads. 259-270 2012 Pacific Symposium on Biocomputing http://psb.stanford.edu/psb-online/proceedings/psb12/zhang-q.pdf conf/psb/2012 db/conf/psb/psb2012.html#ZhangDY12

Yuzhen Ye Jeong-Hyeon Choi Haixu Tang RAPSearch: a Fast Protein Similarity Search Tool for Short Reads. 159 2011 12 BMC Bioinform. https://doi.org/10.1186/1471-2105-12-159 https://www.wikidata.org/entity/Q33901400 db/journals/bmcbi/bmcbi12.html#YeCT11

Yu-Wei Wu Yuzhen Ye A Novel Abundance-Based Algorithm for Binning Metagenomic Sequences Using l-tuples. 523-534 2011 18 J. Comput. Biol. 3 https://doi.org/10.1089/cmb.2010.0245 https://www.wikidata.org/entity/Q42132014 db/journals/jcb/jcb18.html#WuY11

Neethu Shah Haixu Tang Thomas G. Doak Yuzhen Ye Comparing Bacterial Communities Inferred from 16s Rrna Gene Sequencing and Shotgun Metagenomics. 165-176 2011 Pacific Symposium on Biocomputing http://psb.stanford.edu/psb-online/proceedings/psb11/shah.pdf conf/psb/2011 db/conf/psb/psb2011.html#ShahTDY11 Yuzhen Ye Identification and quantification of abundant species from pyrosequences of 16S rRNA by consensus alignment. 153-157 2010 BIBM https://doi.org/10.1109/BIBM.2010.5706555 https://doi.ieeecomputersociety.org/10.1109/BIBM.2010.5706555 https://www.wikidata.org/entity/Q35553075 conf/bibm/2010 db/conf/bibm/bibm2010.html#Ye10 Yu-Wei Wu Yuzhen Ye A Novel Abundance-Based Algorithm for Binning Metagenomic Sequences Using l-Tuples. 535-549 2010 RECOMB https://doi.org/10.1007/978-3-642-12683-3_35 https://www.wikidata.org/entity/Q62806990 conf/recomb/2010 db/conf/recomb/recomb2010.html#WuY10

Yuzhen Ye Haixu Tang An Orfome Assembly Approach to Metagenomics Sequences Analysis. 455-471 2009 7 J. Bioinform. Comput. Biol. 3 https://doi.org/10.1142/S0219720009004151 https://www.wikidata.org/entity/Q39323567 db/journals/jbcb/jbcb7.html#YeT09

John C. Wooley Yuzhen Ye Metagenomics: Facts and Artifacts, and Computational Challenges. 71-81 2009 25 J. Comput. Sci. Technol. 1 https://doi.org/10.1007/s11390-010-9306-4 https://www.wikidata.org/entity/Q34002492 db/journals/jcst/jcst25.html#WooleyY09

Yuzhen Ye Thomas G. Doak A Parsimony Approach to Biological Pathway Reconstruction/Inference for Genomes and Metagenomes. 2009 5 PLoS Comput. Biol. 8 https://doi.org/10.1371/journal.pcbi.1000465 https://www.wikidata.org/entity/Q28475856 db/journals/ploscb/ploscb5.html#YeD09

Mallika Veeramalai Yuzhen Ye Adam Godzik TOPS++FATCAT: Fast flexible structural alignment using constraints derived from TOPS+ Strings Model. 2008 9 BMC Bioinform. https://doi.org/10.1186/1471-2105-9-358 https://www.wikidata.org/entity/Q30371736 db/journals/bmcbi/bmcbi9.html#VeeramalaiYG08

Zhanwen Li Yuzhen Ye Adam Godzik Flexible Structural Neighborhood - a database of protein structural similarities and alignments. 277-280 2006 34 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkj124 https://www.wikidata.org/entity/Q25256632 db/journals/nar/nar34.html#LiYG06

Yuzhen Ye Zhanwen Li Adam Godzik Modeling and Analyzing Three-Dimensional Structures of Human Disease Proteins. 439-450 2006 conf/psb/2006 Pacific Symposium on Biocomputing http://psb.stanford.edu/psb-online/proceedings/psb06/ye.pdf db/conf/psb/psb2006.html#YeLG06

Yuzhen Ye Adam Godzik Multiple flexible structure alignment using partial order graphs. 2362-2369 2005 21 Bioinform. 10 https://doi.org/10.1093/bioinformatics/bti353 https://www.wikidata.org/entity/Q30350312 db/journals/bioinformatics/bioinformatics21.html#YeG05

Yuzhen Ye Andrei Osterman Ross A. Overbeek Adam Godzik Automatic detection of subsystem/pathway variants in genome analysis. 478-486 2005 conf/ismb/2005 ISMB (Supplement of Bioinformatics) https://doi.org/10.1093/bioinformatics/bti1052 https://www.wikidata.org/entity/Q48484662 db/conf/ismb/ismb2005.html#YeOOG05

Dariusz Plewczynski Leszek Rychlewski Yuzhen Ye Lukasz Jaroszewski Adam Godzik Integrated web service for improving alignment quality based on segments comparison. 98 2004 5 BMC Bioinform. https://doi.org/10.1186/1471-2105-5-98 https://www.wikidata.org/entity/Q24795664 db/journals/bmcbi/bmcbi5.html#PlewczynskiRYJG04

Yuzhen Ye Adam Godzik FATCAT: a web server for flexible structure comparison and structure similarity searching. 582-585 2004 32 Nucleic Acids Res. Web-Server-Issue db/journals/nar/nar32.html#YeG04 https://doi.org/10.1093/nar/gkh430 https://www.wikidata.org/entity/Q24562059

Yuzhen Ye Lukasz Jaroszewski Weizhong Li 0002 Adam Godzik A segment alignment approach to protein comparison. 742-749 2003 19 Bioinform. 6 db/journals/bioinformatics/bioinformatics19.html#YeJLG03 https://doi.org/10.1093/bioinformatics/btg073 https://www.wikidata.org/entity/Q30332730

Yuzhen Ye Adam Godzik Flexible structure alignment by chaining aligned fragment pairs allowing twists. 246-255 2003 conf/eccb/2003 ECCB db/conf/eccb/eccb2003.html#YeG03 https://doi.org/10.1093/bioinformatics/btg1086 Jamie Canderan Jeong-Hyeon Choi Thomas G. Doak Adam Godzik Wontack Han Yuhui Hong Thomas Hrabe Benjamin Giovanni Iovino Wazim Ismail Lukasz Jaroszewski Dazhi Jiao Tony J. Lam Jim Zhanwen LiZhanwen Li Sujun Li Weizhong Li 0002 Kaiyuan Liu Hussein Mohsen Padmaja Natarajan Andrei Osterman Ross A. Overbeek Dariusz Plewczynski Mina Rho Leszek Rychlewski Neethu Shah Fatemeh Sharifi Moses Stamboulian Haixu Tang Chenghua Tao Shane Tichy Mallika Veeramalai Mingjie Wang Christopher J. Welch John C. Wooley Yu-Wei Wu Quan Zhang Yongan Zhao