Yuzhen Ye

Publication Activity (10 Years)

Years Active: 2003-2024
Publications (10 Years): 12

Top Topics

Machine Learning Algorithms

Protein Structure

Comparative Genomics

Top Venues

PLoS Comput. Biol.

Nucleic Acids Res.

Publications

Benjamin Giovanni Iovino, Haixu Tang, Yuzhen Ye
Protein Domain Embeddings for Fast and Accurate Similarity Search. RECOMB (2024)
Benjamin Giovanni Iovino, Yuzhen Ye
Protein embedding based alignment. BMC Bioinform. 25 (1) (2024)
Wontack Han, Haixu Tang, Yuzhen Ye
Locality-Sensitive Hashing-Based k-Mer Clustering for Identification of Differential Microbial Markers Related to Host Phenotype. J. Comput. Biol. 29 (7) (2022)
Moses Stamboulian, Jamie Canderan, Yuzhen Ye
Metaproteomics as a tool for studying the protein landscape of human-gut bacterial species. PLoS Comput. Biol. 18 (3) (2022)
Tony J. Lam, Moses Stamboulian, Wontack Han, Yuzhen Ye
Model-based and phylogenetically adjusted quantification of metabolic interaction between microbial species. PLoS Comput. Biol. 16 (10) (2020)
Wontack Han, Yuzhen Ye
A repository of microbial marker genes related to human health and diseases for host phenotype prediction using microbiome data. PSB (2019)
Fatemeh Sharifi, Yuzhen Ye
MyDGR: a server for identification and characterization of diversity-generating retroelements. Nucleic Acids Res. 47 (Webserver-Issue) (2019)
Wontack Han, Mingjie Wang, Yuzhen Ye
A Concurrent Subtractive Assembly Approach for Identification of Disease Associated Sub-metagenomes. RECOMB (2017)
Quan Zhang, Yuzhen Ye
Not all predicted CRISPR-Cas systems are equal: isolated cas genes and classes of CRISPR like elements. BMC Bioinform. 18 (1) (2017)
Hussein Mohsen, Haixu Tang, Yuzhen Ye
Improving de novo metatranscriptome assembly via machine learning algorithms. Int. J. Comput. Biol. Drug Des. 10 (2) (2017)
Haixu Tang, Sujun Li, Yuzhen Ye
A Graph-Centric Approach for Metagenome-Guided Peptide and Protein Identification in Metaproteomics. PLoS Comput. Biol. 12 (12) (2016)
Yuzhen Ye, Haixu Tang
Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis. Bioinform. 32 (7) (2016)
Yuzhen Ye, Haixu Tang
Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis. CoRR (2015)
Mingjie Wang, Haixu Tang, Yuzhen Ye
Identification and characterization of accessory genomes in bacterial species based on genome comparison and metagenomic recruitment. BIBM (2014)
Wazim Ismail, Yuzhen Ye, Haixu Tang
Gene finding in metatranscriptomic sequences. BMC Bioinform. 15 (S-9) (2014)
Zhanwen Li, Padmaja Natarajan, Yuzhen Ye, Thomas Hrabe, Adam Godzik
POSA: a user-driven, interactive multiple protein structure alignment server. Nucleic Acids Res. 42 (Webserver-Issue) (2014)
Dazhi Jiao, Yuzhen Ye, Haixu Tang
Probabilistic Inference of Biochemical Reactions in Microbial Communities from Metagenomic Sequences. PLoS Comput. Biol. 9 (3) (2013)
Yu-Wei Wu, Mina Rho, Thomas G. Doak, Yuzhen Ye
Stitching gene fragments with a network matching algorithm improves gene assembly for metagenomics. Bioinform. 28 (18) (2012)
Yongan Zhao, Haixu Tang, Yuzhen Ye
RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data. Bioinform. 28 (1) (2012)
Mingjie Wang, Yuzhen Ye, Haixu Tang
Graph Approach to the Quantification of Closely-Related Genomes in a Microbial Community. J. Comput. Biol. 19 (6) (2012)
Quan Zhang, Thomas G. Doak, Yuzhen Ye
Artificial Functional Difference Between Microbial Communities Caused by Length Difference of Sequencing Reads. Pacific Symposium on Biocomputing (2012)
Neethu Shah, Haixu Tang, Thomas G. Doak, Yuzhen Ye
Comparing Bacterial Communities Inferred from 16s Rrna Gene Sequencing and Shotgun Metagenomics. Pacific Symposium on Biocomputing (2011)
Yu-Wei Wu, Yuzhen Ye
-tuples. J. Comput. Biol. 18 (3) (2011)
Yuzhen Ye, Jeong-Hyeon Choi, Haixu Tang
RAPSearch: a Fast Protein Similarity Search Tool for Short Reads. BMC Bioinform. 12 (2011)
Yuzhen Ye
Identification and quantification of abundant species from pyrosequences of 16S rRNA by consensus alignment. BIBM (2010)
Yu-Wei Wu, Yuzhen Ye
-Tuples. RECOMB (2010)
Yuzhen Ye, Haixu Tang
An Orfome Assembly Approach to Metagenomics Sequences Analysis. J. Bioinform. Comput. Biol. 7 (3) (2009)
John C. Wooley, Yuzhen Ye
Metagenomics: Facts and Artifacts, and Computational Challenges. J. Comput. Sci. Technol. 25 (1) (2009)
Yuzhen Ye, Thomas G. Doak
A Parsimony Approach to Biological Pathway Reconstruction/Inference for Genomes and Metagenomes. PLoS Comput. Biol. 5 (8) (2009)
Mallika Veeramalai, Yuzhen Ye, Adam Godzik
TOPS++FATCAT: Fast flexible structural alignment using constraints derived from TOPS+ Strings Model. BMC Bioinform. 9 (2008)
Yuzhen Ye, Zhanwen Li, Adam Godzik
Modeling and Analyzing Three-Dimensional Structures of Human Disease Proteins. Pacific Symposium on Biocomputing (2006)
Zhanwen Li, Yuzhen Ye, Adam Godzik
Flexible Structural Neighborhood - a database of protein structural similarities and alignments. Nucleic Acids Res. 34 (Database-Issue) (2006)
Yuzhen Ye, Adam Godzik
Multiple flexible structure alignment using partial order graphs. Bioinform. 21 (10) (2005)
Yuzhen Ye, Andrei Osterman, Ross A. Overbeek, Adam Godzik
Automatic detection of subsystem/pathway variants in genome analysis. ISMB (Supplement of Bioinformatics) (2005)
Dariusz Plewczynski, Leszek Rychlewski, Yuzhen Ye, Lukasz Jaroszewski, Adam Godzik
Integrated web service for improving alignment quality based on segments comparison. BMC Bioinform. 5 (2004)
Yuzhen Ye, Adam Godzik
FATCAT: a web server for flexible structure comparison and structure similarity searching. Nucleic Acids Res. 32 (Web-Server-Issue) (2004)
Yuzhen Ye, Lukasz Jaroszewski, Weizhong Li, Adam Godzik
A segment alignment approach to protein comparison. Bioinform. 19 (6) (2003)
Yuzhen Ye, Adam Godzik
Flexible structure alignment by chaining aligned fragment pairs allowing twists. ECCB (2003)