default search action
Google
Google Scholar
Semantic Scholar
Internet Archive Scholar
CiteSeerX
ORCIDYuzhen Ye
Person information
- affiliation: Indiana University, Bloomington, IN, USA
Refine list
refinements active!
zoomed in on ?? of ?? records
view refined list in
export refined list as
2020 – today
- 2024
[j26]Benjamin Giovanni Iovino
, Yuzhen Ye:
Protein embedding based alignment. BMC Bioinform. 25(1): 85 (2024)- [c11]Benjamin Giovanni Iovino, Haixu Tang, Yuzhen Ye:
Protein Domain Embeddings for Fast and Accurate Similarity Search. RECOMB 2024: 421-424 - 2022
- [j25]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): 738-751 (2022) - [j24]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) - 2020
- [j23]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)
2010 – 2019
- 2019
- [j22]Fatemeh Sharifi, Yuzhen Ye:
MyDGR: a server for identification and characterization of diversity-generating retroelements. Nucleic Acids Res. 47(Webserver-Issue): W289-W294 (2019) - [c10]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: 236-247 - 2017
- [j21]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): 92:1-92:12 (2017) - [j20]Hussein Mohsen, Haixu Tang, Yuzhen Ye:
Improving de novo metatranscriptome assembly via machine learning algorithms. Int. J. Comput. Biol. Drug Des. 10(2): 91-107 (2017) - [c9]Wontack Han, Mingjie Wang, Yuzhen Ye:
A Concurrent Subtractive Assembly Approach for Identification of Disease Associated Sub-metagenomes. RECOMB 2017: 18-33 - 2016
- [j19]Yuzhen Ye, Haixu Tang:
Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis. Bioinform. 32(7): 1001-1008 (2016) - [j18]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) - 2015
- [i1]Yuzhen Ye, Haixu Tang:
Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis. CoRR abs/1504.01304 (2015) - 2014
- [j17]Wazim Ismail, Yuzhen Ye, Haixu Tang:
Gene finding in metatranscriptomic sequences. BMC Bioinform. 15(S-9): S8 (2014) - [j16]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): 240-245 (2014) - [c8]Mingjie Wang, Haixu Tang, Yuzhen Ye:
Identification and characterization of accessory genomes in bacterial species based on genome comparison and metagenomic recruitment. BIBM 2014: 17-24 - 2013
- [j15]Dazhi Jiao, Yuzhen Ye, Haixu Tang:
Probabilistic Inference of Biochemical Reactions in Microbial Communities from Metagenomic Sequences. PLoS Comput. Biol. 9(3) (2013) - 2012
- [j14]Yongan Zhao, Haixu Tang, Yuzhen Ye:
RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data. Bioinform. 28(1): 125-126 (2012) - [j13]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): 363-369 (2012) - [j12]Mingjie Wang, Yuzhen Ye, Haixu Tang:
A de Bruijn Graph Approach to the Quantification of Closely-Related Genomes in a Microbial Community. J. Comput. Biol. 19(6): 814-825 (2012) - [c7]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: 259-270 - 2011
- [j11]Yuzhen Ye, Jeong-Hyeon Choi, Haixu Tang:
RAPSearch: a Fast Protein Similarity Search Tool for Short Reads. BMC Bioinform. 12: 159 (2011) - [j10]Yu-Wei Wu, Yuzhen Ye:
A Novel Abundance-Based Algorithm for Binning Metagenomic Sequences Using l-tuples. J. Comput. Biol. 18(3): 523-534 (2011) - [c6]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: 165-176 - 2010
- [c5]Yuzhen Ye:
Identification and quantification of abundant species from pyrosequences of 16S rRNA by consensus alignment. BIBM 2010: 153-157 - [c4]Yu-Wei Wu, Yuzhen Ye:
A Novel Abundance-Based Algorithm for Binning Metagenomic Sequences Using l-Tuples. RECOMB 2010: 535-549
2000 – 2009
- 2009
- [j9]Yuzhen Ye, Haixu Tang:
An Orfome Assembly Approach to Metagenomics Sequences Analysis. J. Bioinform. Comput. Biol. 7(3): 455-471 (2009) - [j8]John C. Wooley, Yuzhen Ye:
Metagenomics: Facts and Artifacts, and Computational Challenges. J. Comput. Sci. Technol. 25(1): 71-81 (2009) - [j7]Yuzhen Ye, Thomas G. Doak:
A Parsimony Approach to Biological Pathway Reconstruction/Inference for Genomes and Metagenomes. PLoS Comput. Biol. 5(8) (2009) - 2008
- [j6]Mallika Veeramalai, Yuzhen Ye, Adam Godzik:
TOPS++FATCAT: Fast flexible structural alignment using constraints derived from TOPS+ Strings Model. BMC Bioinform. 9 (2008) - 2006
- [j5]Zhanwen Li, Yuzhen Ye, Adam Godzik:
Flexible Structural Neighborhood - a database of protein structural similarities and alignments. Nucleic Acids Res. 34(Database-Issue): 277-280 (2006) - [c3]Yuzhen Ye, Zhanwen Li, Adam Godzik:
Modeling and Analyzing Three-Dimensional Structures of Human Disease Proteins. Pacific Symposium on Biocomputing 2006: 439-450 - 2005
- [j4]Yuzhen Ye, Adam Godzik:
Multiple flexible structure alignment using partial order graphs. Bioinform. 21(10): 2362-2369 (2005) - [c2]Yuzhen Ye, Andrei Osterman, Ross A. Overbeek, Adam Godzik:
Automatic detection of subsystem/pathway variants in genome analysis. ISMB (Supplement of Bioinformatics) 2005: 478-486 - 2004
- [j3]Dariusz Plewczynski, Leszek Rychlewski, Yuzhen Ye, Lukasz Jaroszewski, Adam Godzik:
Integrated web service for improving alignment quality based on segments comparison. BMC Bioinform. 5: 98 (2004) - [j2]Yuzhen Ye, Adam Godzik:
FATCAT: a web server for flexible structure comparison and structure similarity searching. Nucleic Acids Res. 32(Web-Server-Issue): 582-585 (2004) - 2003
- [j1]Yuzhen Ye, Lukasz Jaroszewski, Weizhong Li, Adam Godzik:
A segment alignment approach to protein comparison. Bioinform. 19(6): 742-749 (2003) - [c1]Yuzhen Ye, Adam Godzik:
Flexible structure alignment by chaining aligned fragment pairs allowing twists. ECCB 2003: 246-255
Coauthor Index
manage site settings
To protect your privacy, all features that rely on external API calls from your browser are turned off by default. You need to opt-in for them to become active. All settings here will be stored as cookies with your web browser. For more information see our F.A.Q.
Unpaywalled article links
Add open access links from 
to the list of external document links (if available).
Privacy notice: By enabling the option above, your browser will contact the API of unpaywall.org to load hyperlinks to open access articles. Although we do not have any reason to believe that your call will be tracked, we do not have any control over how the remote server uses your data. So please proceed with care and consider checking the Unpaywall privacy policy.
Archived links via Wayback Machine
For web page which are no longer available, try to retrieve content from the 
of the Internet Archive (if available).
Privacy notice: By enabling the option above, your browser will contact the API of archive.org to check for archived content of web pages that are no longer available. Although we do not have any reason to believe that your call will be tracked, we do not have any control over how the remote server uses your data. So please proceed with care and consider checking the Internet Archive privacy policy.
Reference lists
Add a list of references from 
, 
, and 
to record detail pages.
load references from crossref.org and opencitations.net
Privacy notice: By enabling the option above, your browser will contact the APIs of crossref.org, opencitations.net, and semanticscholar.org to load article reference information. Although we do not have any reason to believe that your call will be tracked, we do not have any control over how the remote server uses your data. So please proceed with care and consider checking the Crossref privacy policy and the OpenCitations privacy policy, as well as the AI2 Privacy Policy covering Semantic Scholar.
Citation data
Add a list of citing articles from and to record detail pages.
load citations from opencitations.net
Privacy notice: By enabling the option above, your browser will contact the API of opencitations.net and semanticscholar.org to load citation information. Although we do not have any reason to believe that your call will be tracked, we do not have any control over how the remote server uses your data. So please proceed with care and consider checking the OpenCitations privacy policy as well as the AI2 Privacy Policy covering Semantic Scholar.
OpenAlex data
Load additional information about publications from 
.
Privacy notice: By enabling the option above, your browser will contact the API of openalex.org to load additional information. Although we do not have any reason to believe that your call will be tracked, we do not have any control over how the remote server uses your data. So please proceed with care and consider checking the information given by OpenAlex.
last updated on 2024-10-07 22:11 CEST by the dblp team
all metadata released as open data under CC0 1.0 license
see also: Terms of Use | Privacy Policy | Imprint
dblp was originally created in 1993 at:
since 2018, dblp has been operated and maintained by:
the dblp computer science bibliography is funded and supported by:
