Flexible structure alignment by chaining aligned fragment pairs allowing twists. - Yuzhen Ye; Adam Godzik (ECCB, 2003)

A segment alignment approach to protein comparison. - Yuzhen Ye; Lukasz Jaroszewski; Weizhong Li 002; Adam Godzik (Bioinform., 2003)

Integrated web service for improving alignment quality based on segments comparison. - Dariusz Plewczynski; Leszek Rychlewski; Yuzhen Ye; Lukasz Jaroszewski; Adam Godzik (BMC Bioinform., 2004)

FATCAT: a web server for flexible structure comparison and structure similarity searching. - Yuzhen Ye; Adam Godzik (Nucleic Acids Res., 2004)

Automatic detection of subsystem/pathway variants in genome analysis. - Yuzhen Ye; Andrei Osterman; Ross A. Overbeek; Adam Godzik (ISMB (Supplement of Bioinformatics), 2005)

Multiple flexible structure alignment using partial order graphs. - Yuzhen Ye; Adam Godzik (Bioinform., 2005)

Modeling and Analyzing Three-Dimensional Structures of Human Disease Proteins. - Yuzhen Ye; Zhanwen Li; Adam Godzik (Pacific Symposium on Biocomputing, 2006)

Flexible Structural Neighborhood - a database of protein structural similarities and alignments. - Zhanwen Li; Yuzhen Ye; Adam Godzik (Nucleic Acids Res., 2006)

TOPS++FATCAT: Fast flexible structural alignment using constraints derived from TOPS+ Strings Model. - Mallika Veeramalai; Yuzhen Ye; Adam Godzik (BMC Bioinform., 2008)

An Orfome Assembly Approach to Metagenomics Sequences Analysis. - Yuzhen Ye; Haixu Tang (J. Bioinform. Comput. Biol., 2009)

Metagenomics: Facts and Artifacts, and Computational Challenges. - John C. Wooley; Yuzhen Ye (J. Comput. Sci. Technol., 2009)

A Parsimony Approach to Biological Pathway Reconstruction/Inference for Genomes and Metagenomes. - Yuzhen Ye; Thomas G. Doak (PLoS Comput. Biol., 2009)

Identification and quantification of abundant species from pyrosequences of 16S rRNA by consensus alignment. - Yuzhen Ye (BIBM, 2010)

Comparing Bacterial Communities Inferred from 16s Rrna Gene Sequencing and Shotgun Metagenomics. - Neethu Shah; Haixu Tang; Thomas G. Doak; Yuzhen Ye (Pacific Symposium on Biocomputing, 2011)

RAPSearch: a Fast Protein Similarity Search Tool for Short Reads. - Yuzhen Ye; Jeong-Hyeon Choi; Haixu Tang (BMC Bioinform., 2011)

A Novel Abundance-Based Algorithm for Binning Metagenomic Sequences Using l-tuples. - Yu-Wei Wu; Yuzhen Ye (J. Comput. Biol., 2011)

Artificial Functional Difference Between Microbial Communities Caused by Length Difference of Sequencing Reads. - Quan Zhang; Thomas G. Doak; Yuzhen Ye (Pacific Symposium on Biocomputing, 2012)

Stitching gene fragments with a network matching algorithm improves gene assembly for metagenomics. - Yu-Wei Wu; Mina Rho; Thomas G. Doak; Yuzhen Ye (Bioinform., 2012)

RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data. - Yongan Zhao; Haixu Tang; Yuzhen Ye (Bioinform., 2012)

A de Bruijn Graph Approach to the Quantification of Closely-Related Genomes in a Microbial Community. - Mingjie Wang; Yuzhen Ye; Haixu Tang (J. Comput. Biol., 2012)

Probabilistic Inference of Biochemical Reactions in Microbial Communities from Metagenomic Sequences. - Dazhi Jiao; Yuzhen Ye; Haixu Tang (PLoS Comput. Biol., 2013)

Identification and characterization of accessory genomes in bacterial species based on genome comparison and metagenomic recruitment. - Mingjie Wang; Haixu Tang; Yuzhen Ye (BIBM, 2014)

Gene finding in metatranscriptomic sequences. - Wazim Ismail; Yuzhen Ye; Haixu Tang (BMC Bioinform., 2014)

POSA: a user-driven, interactive multiple protein structure alignment server. - Zhanwen Li; Padmaja Natarajan; Yuzhen Ye; Thomas Hrabe; Adam Godzik (Nucleic Acids Res., 2014)

Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis. - Yuzhen Ye; Haixu Tang (Bioinform., 2016)

A Graph-Centric Approach for Metagenome-Guided Peptide and Protein Identification in Metaproteomics. - Haixu Tang; Sujun Li; Yuzhen Ye (PLoS Comput. Biol., 2016)

A Concurrent Subtractive Assembly Approach for Identification of Disease Associated Sub-metagenomes. - Wontack Han; Mingjie Wang; Yuzhen Ye (RECOMB, 2017)

Not all predicted CRISPR-Cas systems are equal: isolated cas genes and classes of CRISPR like elements. - Quan Zhang; Yuzhen Ye (BMC Bioinform., 2017)

Improving de novo metatranscriptome assembly via machine learning algorithms. - Hussein Mohsen; Haixu Tang; Yuzhen Ye (Int. J. Comput. Biol. Drug Des., 2017)

A repository of microbial marker genes related to human health and diseases for host phenotype prediction using microbiome data. - Wontack Han; Yuzhen Ye (PSB, 2019)

MyDGR: a server for identification and characterization of diversity-generating retroelements. - Fatemeh Sharifi; Yuzhen Ye (Nucleic Acids Res., 2019)

Model-based and phylogenetically adjusted quantification of metabolic interaction between microbial species. - Tony J. Lam; Moses Stamboulian; Wontack Han; Yuzhen Ye (PLoS Comput. Biol., 2020)

Locality-Sensitive Hashing-Based k-Mer Clustering for Identification of Differential Microbial Markers Related to Host Phenotype. - Wontack Han; Haixu Tang; Yuzhen Ye (J. Comput. Biol., 2022)

Metaproteomics as a tool for studying the protein landscape of human-gut bacterial species. - Moses Stamboulian; Jamie Canderan; Yuzhen Ye (PLoS Comput. Biol., 2022)

Protein Domain Embeddings for Fast and Accurate Similarity Search. - Benjamin Giovanni Iovino; Haixu Tang; Yuzhen Ye (RECOMB, 2024)

SpecEncoder: deep metric learning for accurate peptide identification in proteomics. - Kaiyuan Liu; Chenghua Tao; Yuzhen Ye; Haixu Tang (Bioinform., 2024)

Protein embedding based alignment. - Benjamin Giovanni Iovino; Yuzhen Ye (BMC Bioinform., 2024)