Yuzhen Ye - RankMe

41 papers B 3C 1Misc 4Journal 30Unranked 3

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Identification and applications of disease-associated differential human and bacterial proteins with metaproteomic evidence. Health Inf. Sci. Syst. Jamie Canderan, Moses Stamboulian, Yuzhen Ye
2024	B	`conf`	Protein Domain Embeddings for Fast and Accurate Similarity Search. RECOMB Benjamin Giovanni Iovino, Haixu Tang, Yuzhen Ye
2024	J	`jnl`	Protein embedding based alignment. BMC Bioinform. Benjamin Giovanni Iovino, Yuzhen Ye
2024	J	`jnl`	SpecEncoder: deep metric learning for accurate peptide identification in proteomics. Bioinform. Kaiyuan Liu, Chenghua Tao, Yuzhen Ye, Haixu Tang
2023	J	`jnl`	3DMolMS: prediction of tandem mass spectra from 3D molecular conformations. Bioinform. Yuhui Hong, Sujun Li, Christopher J. Welch, Shane Tichy, Yuzhen Ye, Haixu Tang
2022	J	`jnl`	Locality-Sensitive Hashing-Based k-Mer Clustering for Identification of Differential Microbial Markers Related to Host Phenotype. J. Comput. Biol. Wontack Han, Haixu Tang, Yuzhen Ye
2022	J	`jnl`	Metaproteomics as a tool for studying the protein landscape of human-gut bacterial species. PLoS Comput. Biol. Moses Stamboulian, Jamie Canderan, Yuzhen Ye
2020	J	`jnl`	Model-based and phylogenetically adjusted quantification of metabolic interaction between microbial species. PLoS Comput. Biol. Tony J. Lam, Moses Stamboulian, Wontack Han, Yuzhen Ye
2019	Misc	`conf`	A repository of microbial marker genes related to human health and diseases for host phenotype prediction using microbiome data. PSB Wontack Han, Yuzhen Ye
2019	J	`jnl`	MyDGR: a server for identification and characterization of diversity-generating retroelements. Nucleic Acids Res. Fatemeh Sharifi, Yuzhen Ye
2017	B	`conf`	A Concurrent Subtractive Assembly Approach for Identification of Disease Associated Sub-metagenomes. RECOMB Wontack Han, Mingjie Wang, Yuzhen Ye
2017	J	`jnl`	Improving de novo metatranscriptome assembly via machine learning algorithms. Int. J. Comput. Biol. Drug Des. Hussein Mohsen, Haixu Tang, Yuzhen Ye
2017	J	`jnl`	Not all predicted CRISPR-Cas systems are equal: isolated cas genes and classes of CRISPR like elements. BMC Bioinform. Quan Zhang, Yuzhen Ye
2016	J	`jnl`	A Graph-Centric Approach for Metagenome-Guided Peptide and Protein Identification in Metaproteomics. PLoS Comput. Biol. Haixu Tang, Sujun Li, Yuzhen Ye
2016	J	`jnl`	Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis. Bioinform. Yuzhen Ye, Haixu Tang
2015	J	`jnl`	Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis. CoRR Yuzhen Ye, Haixu Tang
2014	J	`jnl`	Gene finding in metatranscriptomic sequences. BMC Bioinform. Wazim Ismail, Yuzhen Ye, Haixu Tang
2014	—	`conf`	Identification and characterization of accessory genomes in bacterial species based on genome comparison and metagenomic recruitment. BIBM Mingjie Wang, Haixu Tang, Yuzhen Ye
2014	J	`jnl`	POSA: a user-driven, interactive multiple protein structure alignment server. Nucleic Acids Res. Zhanwen Li, Padmaja Natarajan, Yuzhen Ye, Thomas Hrabe, Adam Godzik
2013	J	`jnl`	Probabilistic Inference of Biochemical Reactions in Microbial Communities from Metagenomic Sequences. PLoS Comput. Biol. Dazhi Jiao, Yuzhen Ye, Haixu Tang
2012	J	`jnl`	A J. Comput. Biol. Mingjie Wang, Yuzhen Ye, Haixu Tang
2012	Misc	`conf`	Artificial Functional Difference Between Microbial Communities Caused by Length Difference of Sequencing Reads. Pacific Symposium on Biocomputing Quan Zhang, Thomas G. Doak, Yuzhen Ye
2012	J	`jnl`	RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data. Bioinform. Yongan Zhao, Haixu Tang, Yuzhen Ye
2012	J	`jnl`	Stitching gene fragments with a network matching algorithm improves gene assembly for metagenomics. Bioinform. Yu-Wei Wu, Mina Rho, Thomas G. Doak, Yuzhen Ye
2011	J	`jnl`	A Novel Abundance-Based Algorithm for Binning Metagenomic Sequences Using J. Comput. Biol. Yu-Wei Wu, Yuzhen Ye
2011	Misc	`conf`	Comparing Bacterial Communities Inferred from 16s Rrna Gene Sequencing and Shotgun Metagenomics. Pacific Symposium on Biocomputing Neethu Shah, Haixu Tang, Thomas G. Doak, Yuzhen Ye
2011	J	`jnl`	RAPSearch: a Fast Protein Similarity Search Tool for Short Reads. BMC Bioinform. Yuzhen Ye, Jeong-Hyeon Choi, Haixu Tang
2010	B	`conf`	A Novel Abundance-Based Algorithm for Binning Metagenomic Sequences Using RECOMB Yu-Wei Wu, Yuzhen Ye
2010	—	`conf`	Identification and quantification of abundant species from pyrosequences of 16S rRNA by consensus alignment. BIBM Yuzhen Ye
2009	J	`jnl`	A Parsimony Approach to Biological Pathway Reconstruction/Inference for Genomes and Metagenomes. PLoS Comput. Biol. Yuzhen Ye, Thomas G. Doak
2009	J	`jnl`	An Orfome Assembly Approach to Metagenomics Sequences Analysis. J. Bioinform. Comput. Biol. Yuzhen Ye, Haixu Tang
2009	J	`jnl`	Metagenomics: Facts and Artifacts, and Computational Challenges. J. Comput. Sci. Technol. John C. Wooley, Yuzhen Ye
2008	J	`jnl`	TOPS++FATCAT: Fast flexible structural alignment using constraints derived from TOPS+ Strings Model. BMC Bioinform. Mallika Veeramalai, Yuzhen Ye, Adam Godzik
2006	J	`jnl`	Flexible Structural Neighborhood - a database of protein structural similarities and alignments. Nucleic Acids Res. Zhanwen Li, Yuzhen Ye, Adam Godzik
2006	Misc	`conf`	Modeling and Analyzing Three-Dimensional Structures of Human Disease Proteins. Pacific Symposium on Biocomputing Yuzhen Ye, Zhanwen Li, Adam Godzik
2005	—	`conf`	Automatic detection of subsystem/pathway variants in genome analysis. ISMB (Supplement of Bioinformatics) Yuzhen Ye, Andrei Osterman, Ross A. Overbeek, Adam Godzik
2005	J	`jnl`	Multiple flexible structure alignment using partial order graphs. Bioinform. Yuzhen Ye, Adam Godzik
2004	J	`jnl`	FATCAT: a web server for flexible structure comparison and structure similarity searching. Nucleic Acids Res. Yuzhen Ye, Adam Godzik
2004	J	`jnl`	Integrated web service for improving alignment quality based on segments comparison. BMC Bioinform. Dariusz Plewczynski, Leszek Rychlewski, Yuzhen Ye, Lukasz Jaroszewski, Adam Godzik
2003	J	`jnl`	A segment alignment approach to protein comparison. Bioinform. Yuzhen Ye, Lukasz Jaroszewski, Weizhong Li, Adam Godzik
2003	C	`conf`	Flexible structure alignment by chaining aligned fragment pairs allowing twists. ECCB Yuzhen Ye, Adam Godzik