54(top 5%)
PR articles
40.4K(top 0.1%)
PR citations
38(top 2%)
PR h-index
42(top 1%)
h-index
68
documents
55.0K
doc citations
3.0K
citing journals
100
times ranked

Publications

58 peer-reviewed articles • 48,098 peer-reviewed citations • Sorted by year • Download PDF (PDF by citations)
Sort: Year | Citations
#ArticleIFCitationsLinks
1GenomeFISH: genome-based fluorescence in situ hybridization for strain-level visualization of microbial communities
ISME Journal, 2025, 19,
9.111Citations (PDF)
2AnnoView enables large-scale analysis, comparison, and visualization of microbial gene neighborhoods
Briefings in Bioinformatics, 2024, 25,
6.619Citations (PDF)
3Putative genome contamination has minimal impact on the GTDB taxonomy
Microbial Genomics, 2024, 10,
2.05Citations (PDF)
4Greengenes2 unifies microbial data in a single reference tree
Nature Biotechnology, 2023, 42, 715-718
29.8567Citations (PDF)
5CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning
Nature Methods, 2023, 20, 1203-1212
24.61,321Citations (PDF)
6Proposal of names for 329 higher rank taxa defined in the Genome Taxonomy Database under two prokaryotic codes
FEMS Microbiology Letters, 2023, 370,
1.977Citations (PDF)
7GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy
Nucleic Acids Research, 2022, 50, D785-D794
15.52,325Citations (PDF)
8Chemotaxis shapes the microscale organization of the ocean’s microbiome
Nature, 2022, 605, 132-138
37.9133Citations (PDF)
9Chemotaxis may assist marine heterotrophic bacterial diazotrophs to find microzones suitable for N2 fixation in the pelagic ocean
ISME Journal, 2022, 16, 2525-2534
9.126Citations (PDF)
10SeqCode: a nomenclatural code for prokaryotes described from sequence data
Nature Microbiology, 2022, ,
16.0126Citations (PDF)
11GTDB-Tk v2: memory friendly classification with the genome taxonomy database
Bioinformatics, 2022, 38, 5315-5316
4.71,866Citations (PDF)
12Evidence for non‐methanogenic metabolisms in globally distributed archaeal clades basal to the Methanomassiliicoccales
Environmental Microbiology, 2021, 23, 340-357
3.729Citations (PDF)
13Evaluation of the Microba Community Profiler for Taxonomic Profiling of Metagenomic Datasets From the Human Gut Microbiome
Frontiers in Microbiology, 2021, 12,
3.947Citations (PDF)
14Prokaryotic taxonomy and nomenclature in the age of big sequence data
ISME Journal, 2021, 15, 1879-1892
9.1183Citations (PDF)
15Critical evaluation of faecal microbiome preservation using metagenomic analysis
ISME Communications, 2021, 1,
5.436Citations (PDF)
16A standardized archaeal taxonomy for the Genome Taxonomy Database
Nature Microbiology, 2021, 6, 946-959
16.0444Citations (PDF)
17Diverse sediment microbiota shape methane emission temperature sensitivity in Arctic lakes
Nature Communications, 2021, 12,
13.739Citations (PDF)
18Successional dynamics and alternative stable states in a saline activated sludge microbial community over 9 years
Microbiome, 2021, 9,
11.578Citations (PDF)
19GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database
Bioinformatics, 2020, 36, 1925-1927
4.74,857Citations (PDF)
20Roadmap for naming uncultivated Archaea and Bacteria
Nature Microbiology, 2020, 5, 987-994
16.0136Citations (PDF)
21Lateral Gene Transfer Drives Metabolic Flexibility in the Anaerobic Methane-Oxidizing Archaeal Family Methanoperedenaceae
MBio, 2020, 11,
4.478Citations (PDF)
22A complete domain-to-species taxonomy for Bacteria and Archaea
Nature Biotechnology, 2020, 38, 1079-1086
29.81,418Citations (PDF)
23A unified catalog of 204,938 reference genomes from the human gut microbiome
Nature Biotechnology, 2020, 39, 105-114
29.81,298Citations (PDF)
24Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities
International Journal of Systematic and Evolutionary Microbiology, 2020, 70, 5972-6016
1.7918Citations (PDF)
25The importance of designating type material for uncultured taxa
Systematic and Applied Microbiology, 2019, 42, 15-21
3.5163Citations (PDF)
26An evolving view of methane metabolism in the Archaea
Nature Reviews Microbiology, 2019, 17, 219-232
83.4560Citations (PDF)
27Evaluation of a concatenated protein phylogeny for classification of tailed double-stranded DNA viruses belonging to the order Caudovirales
Nature Microbiology, 2019, 4, 1306-1315
16.0107Citations (PDF)
28AnnoTree: visualization and exploration of a functionally annotated microbial tree of life
Nucleic Acids Research, 2019, 47, 4442-4448
15.5320Citations (PDF)
29Culture- and metagenomics-enabled analyses of the Methanosphaera genus reveals their monophyletic origin and differentiation according to genome size
ISME Journal, 2018, 12, 2942-2953
9.137Citations (PDF)
30A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life
Nature Biotechnology, 2018, 36, 996-1004
29.83,608Citations (PDF)
31A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.)
ISME Journal, 2018, 13, 663-675
9.1199Citations (PDF)
32Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life
Nature Microbiology, 2017, 2, 1533-1542
16.01,903Citations (PDF)
33Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.)
Frontiers in Microbiology, 2017, 8,
3.9477Citations (PDF)
34A Phylogenomic Analysis of the Bacterial Phylum Fibrobacteres
Frontiers in Microbiology, 2016, 6,
3.9144Citations (PDF)
35Genome-Centric Analysis of Microbial Populations Enriched by Hydraulic Fracture Fluid Additives in a Coal Bed Methane Production Well
Frontiers in Microbiology, 2016, 7,
3.976Citations (PDF)
36A catalogue of 136 microbial draft genomes from Red Sea metagenomes
Scientific Data, 2016, 3,
5.753Citations (PDF)
37Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota
Nature Microbiology, 2016, 1,
16.0545Citations (PDF)
38Genome-Based Microbial Taxonomy Coming of Age
Cold Spring Harbor Perspectives in Biology, 2016, 8, a018085
7.280Citations (PDF)
39Comparative Genomics of Candidate Phylum TM6 Suggests That Parasitism Is Widespread and Ancestral in This Lineage
Molecular Biology and Evolution, 2016, 33, 915-927
4.7123Citations (PDF)
40CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
Genome Research, 2015, 25, 1043-1055
4.612,437Citations (PDF)
41A molecular survey of Australian and North American termite genera indicates that vertical inheritance is the primary force shaping termite gut microbiomes
Microbiome, 2015, 3,
11.5122Citations (PDF)
42An Expanded Genomic Representation of the Phylum Cyanobacteria
Genome Biology and Evolution, 2014, 6, 1031-1045
2.4361Citations (PDF)
43STAMP: statistical analysis of taxonomic and functional profiles
Bioinformatics, 2014, 30, 3123-3124
4.74,387Citations (PDF)
44GenGIS 2: Geospatial Analysis of Traditional and Genetic Biodiversity, with New Gradient Algorithms and an Extensible Plugin Framework
PLoS ONE, 2013, 8, e69885
2.3128Citations (PDF)
45Measuring Community Similarity with Phylogenetic Networks
Molecular Biology and Evolution, 2012, 29, 3947-3958
4.725Citations (PDF)
46Rapid identification of high-confidence taxonomic assignments for metagenomic data
Nucleic Acids Research, 2012, 40, e111-e111
15.563Citations (PDF)
47Measures of phylogenetic differentiation provide robust and complementary insights into microbial communities
ISME Journal, 2012, 7, 173-183
9.146Citations (PDF)
48Classifying short genomic fragments from novel lineages using composition and homology
BMC Bioinformatics, 2011, 12,
3.064Citations (PDF)
49Identifying biologically relevant differences between metagenomic communities
Bioinformatics, 2010, 26, 715-721
4.7990Citations (PDF)
50GenGIS: A geospatial information system for genomic data
Genome Research, 2009, 19, 1896-1904
4.6125Citations (PDF)
51Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
Applied and Environmental Microbiology, 2009, 75, 7537-7541
3.621,086Citations (PDF)
52Is local colour normalization good enough for local appearance-based classification?
Machine Vision and Applications, 2009, 21, 789-796
1.50Citations (PDF)
53Tracking the evolution and geographic spread of Influenza A
PLOS Currents, 2009, 1, RRN1014
1.610Citations (PDF)
54SeqMonitor: Influenza Analysis Pipeline and Visualization
PLOS Currents, 2009, 1, RRN1040
1.63Citations (PDF)
55GroopM: an automated tool for the recovery of population genomes from related metagenomes
PeerJ, 0, 2, e603
0.0287Citations (PDF)
56First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking
PeerJ, 0, 3, e740
0.0157Citations (PDF)
57Back from the dead; the curious tale of the predatory cyanobacterium Vampirovibrio chlorellavorus
PeerJ, 0, 3, e968
0.0129Citations (PDF)
58GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes
Nucleic Acids Research, 0, 54, D743-D754
15.552Citations (PDF)