Yuzhen Ye
Orcid: 0000-0003-3707-3185Affiliations:
- Indiana University, Bloomington, IN, USA
According to our database1,
Yuzhen Ye
authored at least 35 papers
between 2003 and 2024.
Collaborative distances:
Collaborative distances:
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Online presence:
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on linkedin.com
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on orcid.org
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on indiana.edu
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Bibliography
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
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
Bioinform., 2016
2014
Nucleic Acids Res., 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
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
J. Comput. Sci. Technol., 2009
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
Proceedings of the Biocomputing 2006, 2006
2005
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
BMC Bioinform., 2004
2003
Flexible structure alignment by chaining aligned fragment pairs allowing twists.
Proceedings of the European Conference on Computational Biology (ECCB 2003), 2003