| Structure, function and diversity of the healthy human microbiome nature 486 (7402), 207-214, 2012 | 10221 | 2012 |
| A framework for human microbiome research nature 486 (7402), 215-221, 2012 | 2410 | 2012 |
| 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 | 2297 | 2005 |
| The ecoresponsive genome of Daphnia pulex JK Colbourne, ME Pfrender, D Gilbert, WK Thomas, A Tucker, TH Oakley, ... Science 331 (6017), 555-561, 2011 | 1401 | 2011 |
| FragGeneScan: predicting genes in short and error-prone reads M Rho, H Tang, Y Ye Nucleic acids research 38 (20), e191-e191, 2010 | 840 | 2010 |
| Flexible structure alignment by chaining aligned fragment pairs allowing twists Y Ye, A Godzik Bioinformatics 19 (suppl_2), ii246-ii255, 2003 | 734 | 2003 |
| 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 | 661 | 2012 |
| 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 | 564 | 2008 |
| A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes Y Ye, TG Doak PLoS computational biology 5 (8), e1000465, 2009 | 544 | 2009 |
| 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 | 451 | 2012 |
| 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 | 410 | 2004 |
| 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 | 251 | 2011 |
| Metagenomics: facts and artifacts, and computational challenges JC Wooley, Y Ye Journal of computer science and technology 25 (1), 71-81, 2010 | 251 | 2010 |
| Diverse CRISPRs Evolving in Human Microbiomes M Rho, YW Wu, H Tang, TG Doak, Y Ye PLoS Genetics 8 (6), e1002441, 2012 | 230 | 2012 |
| 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 | 184 | 2011 |
| Multiple flexible structure alignment using partial order graphs Y Ye, A Godzik Bioinformatics 21 (10), 2362-2369, 2005 | 169 | 2005 |
| RAPSearch: a fast protein similarity search tool for short reads Y Ye, JH Choi, H Tang BMC bioinformatics 12, 1-10, 2011 | 164 | 2011 |
| Not all predicted CRISPR–Cas systems are equal: isolated cas genes and classes of CRISPR like elements Q Zhang, Y Ye BMC bioinformatics 18, 1-12, 2017 | 162 | 2017 |
| 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 | 151 | 2010 |
| 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, ... Public Library of Science 7 (7), e41294, 2012 | 141 | 2012 |
