Yuzhen Ye

Orcid: 0000-0003-3707-3185

Affiliations:
  • Indiana University, Bloomington, IN, USA


According to our database1, Yuzhen Ye authored at least 36 papers between 2003 and 2024.

Collaborative distances:
  • Dijkstra number2 of four.
  • Erdős number3 of four.

Timeline

Legend:

Book 
In proceedings 
Article 
PhD thesis 
Dataset
Other 

Links

Online presence:

On csauthors.net:

Bibliography

2024
Protein embedding based alignment.
BMC Bioinform., December, 2024

Protein Domain Embeddings for Fast and Accurate Similarity Search.
Proceedings of the Research in Computational Molecular Biology, 2024

2022
Metaproteomics as a tool for studying the protein landscape of human-gut bacterial species.
PLoS Comput. Biol., 2022

Locality-Sensitive Hashing-Based k-Mer Clustering for Identification of Differential Microbial Markers Related to Host Phenotype.
J. Comput. Biol., 2022

2020
Model-based and phylogenetically adjusted quantification of metabolic interaction between microbial species.
PLoS Comput. Biol., 2020

2019
MyDGR: a server for identification and characterization of diversity-generating retroelements.
Nucleic Acids Res., 2019

A repository of microbial marker genes related to human health and diseases for host phenotype prediction using microbiome data.
Proceedings of the Biocomputing 2019: Proceedings of the Pacific Symposium, 2019

2017
Improving de novo metatranscriptome assembly via machine learning algorithms.
Int. J. Comput. Biol. Drug Des., 2017

Not all predicted CRISPR-Cas systems are equal: isolated cas genes and classes of CRISPR like elements.
BMC Bioinform., 2017

A Concurrent Subtractive Assembly Approach for Identification of Disease Associated Sub-metagenomes.
Proceedings of the Research in Computational Molecular Biology, 2017

2016
A Graph-Centric Approach for Metagenome-Guided Peptide and Protein Identification in Metaproteomics.
PLoS Comput. Biol., 2016

Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis.
Bioinform., 2016

2014
POSA: a user-driven, interactive multiple protein structure alignment server.
Nucleic Acids Res., 2014

Gene finding in metatranscriptomic sequences.
BMC Bioinform., 2014

Identification and characterization of accessory genomes in bacterial species based on genome comparison and metagenomic recruitment.
Proceedings of the 2014 IEEE International Conference on Bioinformatics and Biomedicine, 2014

2013
Probabilistic Inference of Biochemical Reactions in Microbial Communities from Metagenomic Sequences.
PLoS Comput. Biol., 2013

2012
A <i>de Bruijn</i> Graph Approach to the Quantification of Closely-Related Genomes in a Microbial Community.
J. Comput. Biol., 2012

RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data.
Bioinform., 2012

Stitching gene fragments with a network matching algorithm improves gene assembly for metagenomics.
Bioinform., 2012

Artificial Functional Difference Between Microbial Communities Caused by Length Difference of Sequencing Reads.
Proceedings of the Biocomputing 2012: Proceedings of the Pacific Symposium, 2012

2011
A Novel Abundance-Based Algorithm for Binning Metagenomic Sequences Using <i>l</i>-tuples.
J. Comput. Biol., 2011

RAPSearch: a Fast Protein Similarity Search Tool for Short Reads.
BMC Bioinform., 2011

Comparing Bacterial Communities Inferred from 16s Rrna Gene Sequencing and Shotgun Metagenomics.
Proceedings of the Biocomputing 2011: Proceedings of the Pacific Symposium, 2011

2010
Identification and quantification of abundant species from pyrosequences of 16S rRNA by consensus alignment.
Proceedings of the 2010 IEEE International Conference on Bioinformatics and Biomedicine, 2010

2009
A Parsimony Approach to Biological Pathway Reconstruction/Inference for Genomes and Metagenomes.
PLoS Comput. Biol., 2009

Metagenomics: Facts and Artifacts, and Computational Challenges.
J. Comput. Sci. Technol., 2009

An Orfome Assembly Approach to Metagenomics Sequences Analysis.
J. Bioinform. Comput. Biol., 2009

2008
TOPS++FATCAT: Fast flexible structural alignment using constraints derived from TOPS+ Strings Model.
BMC Bioinform., 2008

2006
Flexible Structural Neighborhood - a database of protein structural similarities and alignments.
Nucleic Acids Res., 2006

Modeling and Analyzing Three-Dimensional Structures of Human Disease Proteins.
Proceedings of the Biocomputing 2006, 2006

2005
Multiple flexible structure alignment using partial order graphs.
Bioinform., 2005

Automatic detection of subsystem/pathway variants in genome analysis.
Proceedings of the Proceedings Thirteenth International Conference on Intelligent Systems for Molecular Biology 2005, 2005

2004
FATCAT: a web server for flexible structure comparison and structure similarity searching.
Nucleic Acids Res., 2004

Integrated web service for improving alignment quality based on segments comparison.
BMC Bioinform., 2004

2003
A segment alignment approach to protein comparison.
Bioinform., 2003

Flexible structure alignment by chaining aligned fragment pairs allowing twists.
Proceedings of the European Conference on Computational Biology (ECCB 2003), 2003


  Loading...