| # | Title | Journal | Year | Citations |
|---|
| 1 | Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB | Applied and Environmental Microbiology | 2006 | 9,859 |
| 2 | The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata | Nucleic Acids Research | 2010 | 6,188 |
| 3 | Phytozome: a comparative platform for green plant genomics | Nucleic Acids Research | 2012 | 4,204 |
| 4 | Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data | Nature Methods | 2013 | 4,029 |
| 5 | The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray) | Science | 2006 | 3,945 |
| 6 | Genome sequence of the palaeopolyploid soybean | Nature | 2010 | 3,854 |
| 7 | The Sorghum bicolor genome and the diversification of grasses | Nature | 2009 | 2,642 |
| 8 | Genome-Based Taxonomic Classification of the Phylum Actinobacteria | Frontiers in Microbiology | 2018 | 2,599 |
| 9 | Defining the core Arabidopsis thaliana root microbiome | Nature | 2012 | 2,475 |
| 10 | Insights into the phylogeny and coding potential of microbial dark matter | Nature | 2013 | 2,239 |
| 11 | Community structure and metabolism through reconstruction of microbial genomes from the environment | Nature | 2004 | 2,045 |
| 12 | MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | PeerJ | 2019 | 1,704 |
| 13 | Phased diploid genome assembly with single-molecule real-time sequencing | Nature Methods | 2016 | 1,658 |
| 14 | Diversity and heritability of the maize rhizosphere microbiome under field conditions | Proceedings of the National Academy of Sciences of the United States of America | 2013 | 1,594 |
| 15 | Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria | Frontiers in Microbiology | 2020 | 1,537 |
| 16 | The Phaeodactylum genome reveals the evolutionary history of diatom genomes | Nature | 2008 | 1,458 |
| 17 | Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes | Frontiers in Microbiology | 2019 | 1,281 |
| 18 | Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products | Journal of Computational Biology | 2013 | 1,235 |
| 19 | Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite | Nature | 2007 | 1,181 |
| 20 | Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates | Environmental Microbiology | 2010 | 1,138 |
| 21 | Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen | Science | 2011 | 1,135 |
| 22 | Genomic variation in 3,010 diverse accessions of Asian cultivated rice | Nature | 2018 | 1,091 |
| 23 | Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation | Nature | 2003 | 1,086 |
| 24 | Next-generation transcriptome assembly | Nature Reviews Genetics | 2011 | 1,073 |
| 25 | The minimum information about a genome sequence (MIGS) specification | Nature Biotechnology | 2008 | 1,069 |
| 26 | Genomics of cellulosic biofuels | Nature | 2008 | 954 |
| 27 | Hybrid error correction and de novo assembly of single-molecule sequencing reads | Nature Biotechnology | 2012 | 946 |
| 28 | A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea | Nature | 2009 | 924 |
| 29 | Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy | Nature Microbiology | 2018 | 906 |
| 30 | The genome of Tetranychus urticae reveals herbivorous pest adaptations | Nature | 2011 | 897 |
| 31 | BBMerge – Accurate paired shotgun read merging via overlap | PLoS ONE | 2017 | 897 |
| 32 | CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription | Cell | 2015 | 881 |
| 33 | Uncovering Earth’s virome | Nature | 2016 | 880 |
| 34 | Insights into Secondary Metabolism from a Global Analysis of Prokaryotic Biosynthetic Gene Clusters | Cell | 2014 | 801 |
| 35 | IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes | Nucleic Acids Research | 2019 | 799 |
| 36 | Programmed DNA destruction by miniature CRISPR-Cas14 enzymes | Science | 2018 | 757 |
| 37 | CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats | BMC Bioinformatics | 2007 | 754 |
| 38 | The genome sequence of Bifidobacterium longum subsp. infantis reveals adaptations for milk utilization within the infant microbiome | Proceedings of the National Academy of Sciences of the United States of America | 2008 | 748 |
| 39 | The BioMart community portal: an innovative alternative to large, centralized data repositories | Nucleic Acids Research | 2015 | 682 |
| 40 | Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris | Nature Biotechnology | 2004 | 675 |
| 41 | Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species | New Phytologist | 2016 | 663 |
| 42 | Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software | Nature Methods | 2017 | 635 |
| 43 | Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities | Nature Biotechnology | 2006 | 634 |
| 44 | The genome of a motile marine Synechococcus | Nature | 2003 | 611 |
| 45 | Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications | Nature Biotechnology | 2011 | 608 |
| 46 | Toward an Online Repository of Standard Operating Procedures (SOPs) for (Meta)genomic Annotation | OMICS A Journal of Integrative Biology | 2008 | 598 |
| 47 | Insights into bilaterian evolution from three spiralian genomes | Nature | 2013 | 564 |
| 48 | Legumes Symbioses: Absence of Nod Genes in Photosynthetic Bradyrhizobia | Science | 2007 | 557 |
| 49 | Pathways of Carbon Assimilation and Ammonia Oxidation Suggested by Environmental Genomic Analyses of Marine Crenarchaeota | PLoS Biology | 2006 | 554 |
| 50 | Genomic Analysis of Organismal Complexity in the Multicellular Green Alga Volvox carteri | Science | 2010 | 536 |
