Yuzhen Ye

发表

A Novel Abundance-Based Algorithm for Binning Metagenomic Sequences Using l-Tuples

Yu-Wei Wu, Yuzhen Ye, 2010, RECOMB.

POSA: a user-driven, interactive multiple protein structure alignment server

Padmaja Natarajan, Adam Godzik, Jim Zhanwen Li, 2014, Nucleic Acids Res..

Flexible structure alignment by chaining aligned fragment pairs allowing twists

Adam Godzik, Yuzhen Ye, A. Godzik, 2003, ECCB.

A repository of microbial marker genes related to human health and diseases for host phenotype prediction using microbiome data

Yuzhen Ye, Wontack Han, Yuzhen Ye, 2018, PSB.

Artificial Functional Difference Between Microbial Communities Caused by Length Difference of Sequencing Reads

Quan Zhang, Yuzhen Ye, Thomas G. Doak, 2011, Pacific Symposium on Biocomputing.

FATCAT: a web server for flexible structure comparison and structure similarity searching

Adam Godzik, Yuzhen Ye, A. Godzik, 2004, Nucleic Acids Res..

Flexible Structural Neighborhood—a database of protein structural similarities and alignments

Adam Godzik, Jim Zhanwen Li, Yuzhen Ye, 2005, Nucleic Acids Res..

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

Alejandro A. Schäffer, Yuzhen Ye, Kaiyuan Zhu, 2020, bioRxiv.

RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data

Yongan Zhao, Haixu Tang, Yuzhen Ye, 2011, Bioinform..

Identification and quantification of abundant species from pyrosequences of 16S rRNA by consensus alignment

Yuzhen Ye, Yuzhen Ye, 2010, 2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Integrated web service for improving alignment quality based on segments comparison

Dariusz Plewczynski, Leszek Rychlewski, Adam Godzik, 2004, BMC Bioinformatics.

A Graph-Centric Approach for Metagenome-Guided Peptide and Protein Identification in Metaproteomics

Haixu Tang, Sujun Li, Yuzhen Ye, 2016, PLoS Comput. Biol..

Dynamic Programming Algorithms for Biological Sequence and Structure Comparison

Haixu Tang, Yuzhen Ye, 2007 .

A de Bruijn Graph Approach to the Quantification of Closely-Related Genomes in a Microbial Community

Haixu Tang, Yuzhen Ye, Mingjie Wang, 2012, J. Comput. Biol..

A segment alignment approach to protein comparison

Adam Godzik, Yuzhen Ye, Lukasz Jaroszewski, 2003, Bioinform..

Combinatorial Algorithms for Strain Level Metagenomic Microbial Detection and Quantification

Yuzhen Ye, Kaiyuan Zhu, Cenk Sahinalp, 2020 .

Multiple flexible structure alignment using partial order graphs

Adam Godzik, Yuzhen Ye, A. Godzik, 2005, Bioinform..

RAPSearch: a fast protein similarity search tool for short reads

Haixu Tang, Yuzhen Ye, Jeong-Hyeon Choi, 2011, BMC Bioinformatics.

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

Yuzhen Ye, Sujun Li, Moses H. Stamboulian, 2020, bioRxiv.

Comparing Bacterial Communities Inferred from 16s Rrna Gene Sequencing and Shotgun Metagenomics

Haixu Tang, Yuzhen Ye, Thomas G. Doak, 2011, Pacific Symposium on Biocomputing.

Improving de novo metatranscriptome assembly via machine learning algorithms

Haixu Tang, Yuzhen Ye, Hussein Mohsen, 2017, Int. J. Comput. Biol. Drug Des..

Bayesian Network

Yuzhen Ye, 2010, Encyclopedia of Machine Learning.

A Concurrent Subtractive Assembly Approach for Identification of Disease Associated Sub-metagenomes

Yuzhen Ye, Mingjie Wang, Wontack Han, 2017, RECOMB.

Probabilistic Inference of Biochemical Reactions in Microbial Communities from Metagenomic Sequences

Haixu Tang, Yuzhen Ye, Dazhi Jiao, 2013, PLoS Comput. Biol..

Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis

Haixu Tang, Yuzhen Ye, Haixu Tang, 2015, Bioinform..

Stitching gene fragments with a network matching algorithm improves gene assembly for metagenomics

Yu-Wei Wu, Yuzhen Ye, Thomas G. Doak, 2012, Bioinform..

Identification and characterization of accessory genomes in bacterial species based on genome comparison and metagenomic recruitment

Haixu Tang, Yuzhen Ye, Mingjie Wang, 2014, 2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

An Orfome Assembly Approach to Metagenomics Sequences Analysis

Haixu Tang, Yuzhen Ye, Haixu Tang, 2009, J. Bioinform. Comput. Biol..

Modeling and Analyzing Three-Dimensional Structures of Human Disease Proteins

Adam Godzik, Jim Zhanwen Li, Yuzhen Ye, 2005, Pacific Symposium on Biocomputing.

Automatic detection of subsystem/pathway variants in genome analysis

Ross A. Overbeek, Adam Godzik, Andrei Osterman, 2005, ISMB.

Not all predicted CRISPR–Cas systems are equal: isolated cas genes and classes of CRISPR like elements

Quan Zhang, Yuzhen Ye, Yuzhen Ye, 2017, BMC Bioinformatics.

A Meta-proteogenomic Approach to Peptide Identification Incorporating Assembly Uncertainty and Genomic Variation*

Haixu Tang, Sujun Li, Yuzhen Ye, 2019, Molecular & Cellular Proteomics.

TOPS++FATCAT: Fast flexible structural alignment using constraints derived from TOPS+ Strings Model

Adam Godzik, Yuzhen Ye, Mallika Veeramalai, 2008, BMC Bioinformatics.

Metagenomics: Facts and Artifacts, and Computational Challenges

John C. Wooley, Yuzhen Ye, Yuzhen Ye, 2010, Journal of Computer Science and Technology.

A Novel Abundance-Based Algorithm for Binning Metagenomic Sequences Using l-Tuples

Yu-Wei Wu, Yuzhen Ye, Yuzhen Ye, 2010, RECOMB.

Gene finding in metatranscriptomic sequences

Haixu Tang, Yuzhen Ye, Wazim Ismail, 2014, BMC Bioinformatics.

A Parsimony Approach to Biological Pathway Reconstruction/Inference for Genomes and Metagenomes

Yuzhen Ye, Thomas G. Doak, Yuzhen Ye, 2009, PLoS Comput. Biol..

Expanding the catalog of cas genes with metagenomes

Yuzhen Ye, Thomas G. Doak, Yuzhen Ye, 2013, Nucleic acids research.

Novel genes dramatically alter regulatory network topology in amphioxus

Adam Godzik, Yuzhen Ye, A. Godzik, 2008, Genome Biology.

A Parsimony Approach to Biological Pathway Reconstruction/Inference for Metagenomes

Yuzhen Ye, Thomas G. Doak, Yuzhen Ye, 2011 .

Subtractive assembly for comparative metagenomics, and its application to type 2 diabetes metagenomes

Yuzhen Ye, Thomas G. Doak, Mingjie Wang, 2015, Genome Biology.

Phylogenetically Structured Differences in rRNA Gene Sequence Variation among Species of Arbuscular Mycorrhizal Fungi and Their Implications for Sequence Clustering

Yuzhen Ye, Saliya Ekanayake, James D. Bever, 2016, Applied and Environmental Microbiology.

Comparative analysis of protein domain organization.

Adam Godzik, Yuzhen Ye, A. Godzik, 2004, Genome research.

Diverse CRISPRs Evolving in Human Microbiomes

Haixu Tang, Yuzhen Ye, Thomas G. Doak, 2012, PLoS genetics.

Solution structure of Mycobacterium tuberculosis NmtR in the apo state: insights into Ni(II)-mediated allostery.

Yuzhen Ye, Kenneth M Merz, Dhruva K. Chakravorty, 2012, Biochemistry.