| Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences MGI Langille, J Zaneveld, JG Caporaso, D McDonald, D Knights, ... Nature biotechnology 31 (9), 814-821, 2013 | 8902 | 2013 |
| STAMP: statistical analysis of taxonomic and functional profiles DH Parks, GW Tyson, P Hugenholtz, RG Beiko Bioinformatics 30 (21), 3123-3124, 2014 | 3694 | 2014 |
| CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database BP Alcock, AR Raphenya, TTY Lau, KK Tsang, M Bouchard, ... Nucleic acids research 48 (D1), D517-D525, 2020 | 2875 | 2020 |
| Identifying biologically relevant differences between metagenomic communities DH Parks, RG Beiko Bioinformatics 26 (6), 715-721, 2010 | 974 | 2010 |
| A phylogenomic view of ecological specialization in the Lachnospiraceae, a family of digestive tract-associated bacteria CJ Meehan, RG Beiko Genome biology and evolution 6 (3), 703-713, 2014 | 750 | 2014 |
| CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database BP Alcock, W Huynh, R Chalil, KW Smith, AR Raphenya, MA Wlodarski, ... Nucleic acids research 51 (D1), D690-D699, 2023 | 628 | 2023 |
| Highways of gene sharing in prokaryotes RG Beiko, TJ Harlow, MA Ragan Proceedings of the National Academy of Sciences 102 (40), 14332-14337, 2005 | 586 | 2005 |
| 16S rRNA gene analysis with QIIME2 M Hall, RG Beiko Microbiome analysis: methods and protocols, 113-129, 2018 | 460 | 2018 |
| Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs BA Curtis, G Tanifuji, F Burki, A Gruber, M Irimia, S Maruyama, MC Arias, ... Nature 492 (7427), 59-65, 2012 | 434 | 2012 |
| Microbial shifts in the aging mouse gut MGI Langille, CJ Meehan, JE Koenig, AS Dhanani, RA Rose, SE Howlett, ... Microbiome 2, 1-12, 2014 | 427 | 2014 |
| Genome and low-iron response of an oceanic diatom adapted to chronic iron limitation M Lommer, M Specht, AS Roy, L Kraemer, R Andreson, MA Gutowska, ... Genome biology 13, 1-21, 2012 | 290 | 2012 |
| Prokaryotic evolution and the tree of life are two different things E Bapteste, MA O'Malley, RG Beiko, M Ereshefsky, JP Gogarten, ... Biology direct 4, 1-20, 2009 | 279 | 2009 |
| Interactions in the microbiome: communities of organisms and communities of genes E Boon, CJ Meehan, C Whidden, DHJ Wong, MGI Langille, RG Beiko FEMS microbiology reviews 38 (1), 90-118, 2014 | 244 | 2014 |
| Predicting the functional potential of the microbiome from marker genes using PICRUSt GM Douglas, RG Beiko, MGI Langille Microbiome analysis: Methods and protocols, 169-177, 2018 | 222 | 2018 |
| Inter-personal diversity and temporal dynamics of dental, tongue, and salivary microbiota in the healthy oral cavity MW Hall, N Singh, KF Ng, DK Lam, MB Goldberg, HC Tenenbaum, ... NPJ biofilms and microbiomes 3 (1), 2, 2017 | 200 | 2017 |
| Phylogenetic identification of lateral genetic transfer events RG Beiko, N Hamilton BMC evolutionary biology 6, 1-17, 2006 | 193 | 2006 |
| Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores GDP Clarke, RG Beiko, MA Ragan, RL Charlebois Journal of bacteriology 184 (8), 2072-2080, 2002 | 170 | 2002 |
| SNVPhyl: a single nucleotide variant phylogenomics pipeline for microbial genomic epidemiology A Petkau, P Mabon, C Sieffert, NC Knox, J Cabral, M Iskander, M Iskander, ... Microbial genomics 3 (6), e000116, 2017 | 157 | 2017 |
| GenGIS: A geospatial information system for genomic data DH Parks, M Porter, S Churcher, S Wang, C Blouin, J Whalley, S Brooks, ... Genome research 19 (10), 1896-1904, 2009 | 156 | 2009 |
| Comparative metagenomics of three Dehalococcoides-containing enrichment cultures: the role of the non-dechlorinating community LA Hug, RG Beiko, AR Rowe, RE Richardson, EA Edwards BMC genomics 13, 1-19, 2012 | 145 | 2012 |
