| Ribosomal Database Project: data and tools for high throughput rRNA analysis JR Cole, Q Wang, JA Fish, B Chai, DM McGarrell, Y Sun, CT Brown, ... Nucleic acids research 42 (D1), D633-D642, 2014 | 4337 | 2014 |
| FunGene: the functional gene pipeline and repository JA Fish, B Chai, Q Wang, Y Sun, CT Brown, JM Tiedje, JR Cole Frontiers in microbiology 4, 61153, 2013 | 591 | 2013 |
| Genome, Functional Gene Annotation, and Nuclear Transformation of the Heterokont Oleaginous Alga Nannochloropsis oceanica CCMP1779 A Vieler, G Wu, CH Tsai, B Bullard, AJ Cornish, C Harvey, IB Reca, ... PLoS genetics 8 (11), e1003064, 2012 | 425 | 2012 |
| MAKER-P: a tool kit for the rapid creation, management, and quality control of plant genome annotations MS Campbell, MY Law, C Holt, JC Stein, GD Moghe, DE Hufnagel, J Lei, ... Plant physiology 164 (2), 513-524, 2014 | 410 | 2014 |
| Ecological Patterns of nifH Genes in Four Terrestrial Climatic Zones Explored with Targeted Metagenomics Using FrameBot, a New Informatics Tool Q Wang, JF Quensen III, JA Fish, T Kwon Lee, Y Sun, JM Tiedje, JR Cole MBio 4 (5), 10.1128/mbio. 00592-13, 2013 | 288 | 2013 |
| Designing seeds for similarity search in genomic DNA J Buhler, U Keich, Y Sun Proceedings of the seventh annual international conference on Research in …, 2003 | 194 | 2003 |
| Reconstructing 16S rRNA genes in metagenomic data C Yuan, J Lei, J Cole, Y Sun Bioinformatics 31 (12), i35-i43, 2015 | 153 | 2015 |
| Designing multiple simultaneous seeds for DNA similarity search Y Sun, J Buhler Proceedings of the eighth annual international conference on Research in …, 2004 | 135 | 2004 |
| miR-PREFeR: an accurate, fast and easy-to-use plant miRNA prediction tool using small RNA-Seq data J Lei, Y Sun Bioinformatics 30 (19), 2837-2839, 2014 | 118 | 2014 |
| LncRNA-ID: Long non-coding RNA IDentification using balanced random forests R Achawanantakun, J Chen, Y Sun, Y Zhang Bioinformatics 31 (24), 3897-3905, 2015 | 105 | 2015 |
| Xander: employing a novel method for efficient gene-targeted metagenomic assembly Q Wang, JA Fish, M Gilman, Y Sun, CT Brown, JM Tiedje, JR Cole Microbiome 3, 1-13, 2015 | 96 | 2015 |
| Artificial intelligence in meta-optics MK Chen, X Liu, Y Sun, DP Tsai Chemical Reviews 122 (19), 15356-15413, 2022 | 90 | 2022 |
| FunGene: the functional gene pipeline and repository. Front Microbiol 4: 291 JA Fish, B Chai, Q Wang, Y Sun, CT Brown, JM Tiedje, JR Cole | 82 | 2013 |
| HMM-FRAME: accurate protein domain classification for metagenomic sequences containing frameshift errors Y Zhang, Y Sun BMC bioinformatics 12, 1-10, 2011 | 74 | 2011 |
| The insect-phase gRNA transcriptome in Trypanosoma brucei D Koslowsky, Y Sun, J Hindenach, T Theisen, J Lucas Nucleic acids research 42 (3), 1873-1886, 2014 | 67 | 2014 |
| Bacteriophage classification for assembled contigs using graph convolutional network J Shang, J Jiang, Y Sun Bioinformatics 37 (Supplement_1), i25-i33, 2021 | 55 | 2021 |
| Automated update, revision, and quality control of the maize genome annotations using MAKER-P improves the B73 RefGen_v3 gene models and identifies new genes MY Law, KL Childs, MS Campbell, JC Stein, AJ Olson, C Holt, N Panchy, ... Plant physiology 167 (1), 25-39, 2015 | 55 | 2015 |
| De novo haplotype reconstruction in viral quasispecies using paired-end read guided path finding J Chen, Y Zhao, Y Sun Bioinformatics 34 (17), 2927-2935, 2018 | 45 | 2018 |
| CHEER: HierarCHical taxonomic classification for viral mEtagEnomic data via deep leaRning J Shang, Y Sun Methods 189, 95-103, 2021 | 39 | 2021 |
| Choosing the best heuristic for seeded alignment of DNA sequences Y Sun, J Buhler BMC bioinformatics 7, 1-12, 2006 | 38 | 2006 |
James TiedjeUniversity Distinguished Professor Emeritus, Michigan State UniversityVerified email at msu.edu
