Yuzhen Ye
Yuzhen Ye
Verified email at indiana.edu
Title
Cited by
Cited by
Year
Structure, function and diversity of the healthy human microbiome
C Huttenhower, D Gevers, R Knight, S Abubucker, JH Badger, ...
nature 486 (7402), 207, 2012
59462012
The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes
R Overbeek, T Begley, RM Butler, JV Choudhuri, HY Chuang, M Cohoon, ...
Nucleic acids research 33 (17), 5691-5702, 2005
18272005
A framework for human microbiome research
BA Methé, KE Nelson, M Pop, HH Creasy, MG Giglio, C Huttenhower, ...
nature 486 (7402), 215, 2012
14932012
The ecoresponsive genome of Daphnia pulex
JK Colbourne, ME Pfrender, D Gilbert, WK Thomas, A Tucker, TH Oakley, ...
Science 331 (6017), 555-561, 2011
10972011
Flexible structure alignment by chaining aligned fragment pairs allowing twists
Y Ye, A Godzik
Bioinformatics 19 (suppl_2), ii246-ii255, 2003
6242003
FragGeneScan: predicting genes in short and error-prone reads
M Rho, H Tang, Y Ye
Nucleic acids research 38 (20), e191-e191, 2010
5522010
The amphioxus genome illuminates vertebrate origins and cephalochordate biology
LZ Holland, R Albalat, K Azumi, È Benito-Gutiérrez, MJ Blow, ...
Genome research 18 (7), 1100-1111, 2008
4912008
A Core human microbiome as viewed through 16S rRNA sequence clusters
SM Huse, Y Ye, Y Zhou, AA Fodor
PloS one 7 (6), e34242, 2012
4672012
RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data
Y Zhao, H Tang, Y Ye
Bioinformatics 28 (1), 125-126, 2012
3212012
FATCAT: a web server for flexible structure comparison and structure similarity searching
Y Ye, A Godzik
Nucleic acids research 32 (suppl_2), W582-W585, 2004
3162004
A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes
Y Ye, TG Doak
PLoS Comput Biol 5 (8), e1000465, 2009
2132009
Metagenomics: facts and artifacts, and computational challenges
JC Wooley, Y Ye
Journal of computer science and technology 25 (1), 71-81, 2010
1682010
Comparing bacterial communities inferred from 16S rRNA gene sequencing and shotgun metagenomics
N Shah, H Tang, TG Doak, Y Ye
Biocomputing 2011, 165-176, 2011
1662011
Multiple flexible structure alignment using partial order graphs
Y Ye, A Godzik
Bioinformatics 21 (10), 2362-2369, 2005
1492005
Diverse CRISPRs Evolving in Human Microbiomes
M Rho, YW Wu, H Tang, TG Doak, Y Ye
PLoS Genetics 8 (6), e1002441, 2012
1322012
A novel abundance-based algorithm for binning metagenomic sequences using l-tuples
YW Wu, Y Ye
Journal of Computational Biology 18 (3), 523-534, 2011
1292011
Identification and quantification of abundant species from pyrosequences of 16S rRNA by consensus alignment
Y Ye
2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM …, 2010
1252010
RAPSearch: a fast protein similarity search tool for short reads
Y Ye, JH Choi, H Tang
BMC bioinformatics 12 (1), 159, 2011
1172011
The “most wanted” taxa from the human microbiome for whole genome sequencing
AA Fodor, TZ DeSantis, KM Wylie, JH Badger, Y Ye, T Hepburn, P Hu, ...
PloS one 7 (7), e41294, 2012
1102012
Comparative analysis of protein domain organization
Y Ye, A Godzik
Genome research 14 (3), 343-353, 2004
1042004
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Articles 1–20