Genome Taxonomy Database (English Wikipedia)

Analysis of information sources in references of the Wikipedia article "Genome Taxonomy Database" in English language version.

refsWebsite

Global rank English rank

12nih.gov

4^th place

10doi.org

2^nd place

3semanticscholar.org

11^th place

8^th place

3ecogenomic.org

low place

2biorxiv.org

5,061^st place

5,698^th place

1worldcat.org

5^th place

1researchgate.net

120^th place

125^th place

1bergeys.org

low place

1uea.ac.uk

low place

6,989^th place

bergeys.org

"Incorporation of Phylogenomics into BMSAB". Bergey's Manual Trust.

biorxiv.org

Parks, DH; Chuvochina, M; Waite, DW; Rinke, C; Skarshewski, A; Chaumeil, PA; Hugenholtz, P (November 2018). "A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life" (PDF). Nature Biotechnology. 36 (10): 996–1004. bioRxiv 10.1101/256800. doi:10.1038/nbt.4229. PMID 30148503. S2CID 52093100.
Rinke, Christian; Chuvochina, Maria; Mussig, Aaron J.; Chaumeil, Pierre-Alain; Davín, Adrián A.; Waite, David W.; Whitman, William B.; Parks, Donovan H.; Hugenholtz, Philip (21 June 2021). "A standardized archaeal taxonomy for the Genome Taxonomy Database" (PDF). Nature Microbiology. 6 (7): 946–959. doi:10.1038/s41564-021-00918-8. ISSN 2058-5276. PMID 34155373. S2CID 235595884.

doi.org

Parks, DH; Chuvochina, M; Waite, DW; Rinke, C; Skarshewski, A; Chaumeil, PA; Hugenholtz, P (November 2018). "A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life" (PDF). Nature Biotechnology. 36 (10): 996–1004. bioRxiv 10.1101/256800. doi:10.1038/nbt.4229. PMID 30148503. S2CID 52093100.
Rinke, Christian; Chuvochina, Maria; Mussig, Aaron J.; Chaumeil, Pierre-Alain; Davín, Adrián A.; Waite, David W.; Whitman, William B.; Parks, Donovan H.; Hugenholtz, Philip (21 June 2021). "A standardized archaeal taxonomy for the Genome Taxonomy Database" (PDF). Nature Microbiology. 6 (7): 946–959. doi:10.1038/s41564-021-00918-8. ISSN 2058-5276. PMID 34155373. S2CID 235595884.
Parks, DH; Chuvochina, M; Chaumeil, PA; Rinke, C; Mussig, AJ; Hugenholtz, P (September 2020). "A complete domain-to-species taxonomy for Bacteria and Archaea". Nature Biotechnology. 38 (9): 1079–1086. bioRxiv 10.1101/771964. doi:10.1038/s41587-020-0501-8. PMID 32341564. S2CID 216560589.
Chaumeil, PA; Mussig, AJ; Hugenholtz, P; Parks, DH (15 November 2019). "GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database". Bioinformatics. 36 (6): 1925–1927. doi:10.1093/bioinformatics/btz848. PMC 7703759. PMID 31730192.
Almeida, Alexandre; Nayfach, Stephen; Boland, Miguel; Strozzi, Francesco; Beracochea, Martin; Shi, Zhou Jason; Pollard, Katherine S.; Sakharova, Ekaterina; Parks, Donovan H.; Hugenholtz, Philip; Segata, Nicola; Kyrpides, Nikos C.; Finn, Robert D. (20 July 2020). "A unified catalog of 204,938 reference genomes from the human gut microbiome". Nature Biotechnology. 39 (1): 105–114. doi:10.1038/s41587-020-0603-3. PMC 7801254. PMID 32690973.
Nayfach, Stephen; et al. (9 November 2020). "A genomic catalog of Earth's microbiomes". Nature Biotechnology. 39 (4): 499–509. doi:10.1038/s41587-020-0718-6. PMC 8041624. PMID 33169036.
Gupta, Radhey S.; Patel, Sudip; Saini, Navneet; Chen, Shu (1 November 2020). "Robust demarcation of 17 distinct Bacillus species clades, proposed as novel Bacillaceae genera, by phylogenomics and comparative genomic analyses: description of Robertmurraya kyonggiensis sp. nov. and proposal for an emended genus Bacillus limiting it only to the members of the Subtilis and Cereus clades of species". International Journal of Systematic and Evolutionary Microbiology. 70 (11): 5753–5798. doi:10.1099/ijsem.0.004475.
Pallen, MJ; Rodriguez-R, LM; Alikhan, NF (September 2022). "Naming the unnamed: over 65,000 Candidatus names for unnamed Archaea and Bacteria in the Genome Taxonomy Database" (PDF). International Journal of Systematic and Evolutionary Microbiology. 72 (9). doi:10.1099/ijsem.0.005482. PMID 36125864.
Chuvochina, M; Mussig, AJ; Chaumeil, PA; Skarshewski, A; Rinke, C; Parks, DH; Hugenholtz, P (17 January 2023). "Proposal of names for 329 higher rank taxa defined in the Genome Taxonomy Database under two prokaryotic codes". FEMS microbiology letters. 370. doi:10.1093/femsle/fnad071. PMC 10408702. PMID 37480240.
Oren, Aharon; Göker, Markus (1 February 2024). "Validation List no. 215. Valid publication of new names and new combinations effectively published outside the IJSEM". International Journal of Systematic and Evolutionary Microbiology. 74 (1). doi:10.1099/ijsem.0.006173.

ecogenomic.org

data.gtdb.ecogenomic.org

"METHODS.txt (GTDB release 220)". data.gtdb.ecogenomic.org. 2024.
"220.0/FILE_DESCRIPTIONS.txt".

gtdb.ecogenomic.org

For information on each update, see relevant change logs. For notable, paper-worthy changes, see "Cite GTDB" section on the About page.

nih.gov

pubmed.ncbi.nlm.nih.gov

Parks, DH; Chuvochina, M; Waite, DW; Rinke, C; Skarshewski, A; Chaumeil, PA; Hugenholtz, P (November 2018). "A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life" (PDF). Nature Biotechnology. 36 (10): 996–1004. bioRxiv 10.1101/256800. doi:10.1038/nbt.4229. PMID 30148503. S2CID 52093100.
Rinke, Christian; Chuvochina, Maria; Mussig, Aaron J.; Chaumeil, Pierre-Alain; Davín, Adrián A.; Waite, David W.; Whitman, William B.; Parks, Donovan H.; Hugenholtz, Philip (21 June 2021). "A standardized archaeal taxonomy for the Genome Taxonomy Database" (PDF). Nature Microbiology. 6 (7): 946–959. doi:10.1038/s41564-021-00918-8. ISSN 2058-5276. PMID 34155373. S2CID 235595884.
Parks, DH; Chuvochina, M; Chaumeil, PA; Rinke, C; Mussig, AJ; Hugenholtz, P (September 2020). "A complete domain-to-species taxonomy for Bacteria and Archaea". Nature Biotechnology. 38 (9): 1079–1086. bioRxiv 10.1101/771964. doi:10.1038/s41587-020-0501-8. PMID 32341564. S2CID 216560589.
Chaumeil, PA; Mussig, AJ; Hugenholtz, P; Parks, DH (15 November 2019). "GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database". Bioinformatics. 36 (6): 1925–1927. doi:10.1093/bioinformatics/btz848. PMC 7703759. PMID 31730192.
Almeida, Alexandre; Nayfach, Stephen; Boland, Miguel; Strozzi, Francesco; Beracochea, Martin; Shi, Zhou Jason; Pollard, Katherine S.; Sakharova, Ekaterina; Parks, Donovan H.; Hugenholtz, Philip; Segata, Nicola; Kyrpides, Nikos C.; Finn, Robert D. (20 July 2020). "A unified catalog of 204,938 reference genomes from the human gut microbiome". Nature Biotechnology. 39 (1): 105–114. doi:10.1038/s41587-020-0603-3. PMC 7801254. PMID 32690973.
Nayfach, Stephen; et al. (9 November 2020). "A genomic catalog of Earth's microbiomes". Nature Biotechnology. 39 (4): 499–509. doi:10.1038/s41587-020-0718-6. PMC 8041624. PMID 33169036.
Pallen, MJ; Rodriguez-R, LM; Alikhan, NF (September 2022). "Naming the unnamed: over 65,000 Candidatus names for unnamed Archaea and Bacteria in the Genome Taxonomy Database" (PDF). International Journal of Systematic and Evolutionary Microbiology. 72 (9). doi:10.1099/ijsem.0.005482. PMID 36125864.
Chuvochina, M; Mussig, AJ; Chaumeil, PA; Skarshewski, A; Rinke, C; Parks, DH; Hugenholtz, P (17 January 2023). "Proposal of names for 329 higher rank taxa defined in the Genome Taxonomy Database under two prokaryotic codes". FEMS microbiology letters. 370. doi:10.1093/femsle/fnad071. PMC 10408702. PMID 37480240.

ncbi.nlm.nih.gov

Chaumeil, PA; Mussig, AJ; Hugenholtz, P; Parks, DH (15 November 2019). "GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database". Bioinformatics. 36 (6): 1925–1927. doi:10.1093/bioinformatics/btz848. PMC 7703759. PMID 31730192.
Almeida, Alexandre; Nayfach, Stephen; Boland, Miguel; Strozzi, Francesco; Beracochea, Martin; Shi, Zhou Jason; Pollard, Katherine S.; Sakharova, Ekaterina; Parks, Donovan H.; Hugenholtz, Philip; Segata, Nicola; Kyrpides, Nikos C.; Finn, Robert D. (20 July 2020). "A unified catalog of 204,938 reference genomes from the human gut microbiome". Nature Biotechnology. 39 (1): 105–114. doi:10.1038/s41587-020-0603-3. PMC 7801254. PMID 32690973.
Nayfach, Stephen; et al. (9 November 2020). "A genomic catalog of Earth's microbiomes". Nature Biotechnology. 39 (4): 499–509. doi:10.1038/s41587-020-0718-6. PMC 8041624. PMID 33169036.
Chuvochina, M; Mussig, AJ; Chaumeil, PA; Skarshewski, A; Rinke, C; Parks, DH; Hugenholtz, P (17 January 2023). "Proposal of names for 329 higher rank taxa defined in the Genome Taxonomy Database under two prokaryotic codes". FEMS microbiology letters. 370. doi:10.1093/femsle/fnad071. PMC 10408702. PMID 37480240.

researchgate.net

Parks, DH; Chuvochina, M; Chaumeil, PA; Rinke, C; Mussig, AJ; Hugenholtz, P (September 2020). "A complete domain-to-species taxonomy for Bacteria and Archaea". Nature Biotechnology. 38 (9): 1079–1086. bioRxiv 10.1101/771964. doi:10.1038/s41587-020-0501-8. PMID 32341564. S2CID 216560589.

semanticscholar.org

api.semanticscholar.org

Parks, DH; Chuvochina, M; Waite, DW; Rinke, C; Skarshewski, A; Chaumeil, PA; Hugenholtz, P (November 2018). "A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life" (PDF). Nature Biotechnology. 36 (10): 996–1004. bioRxiv 10.1101/256800. doi:10.1038/nbt.4229. PMID 30148503. S2CID 52093100.
Rinke, Christian; Chuvochina, Maria; Mussig, Aaron J.; Chaumeil, Pierre-Alain; Davín, Adrián A.; Waite, David W.; Whitman, William B.; Parks, Donovan H.; Hugenholtz, Philip (21 June 2021). "A standardized archaeal taxonomy for the Genome Taxonomy Database" (PDF). Nature Microbiology. 6 (7): 946–959. doi:10.1038/s41564-021-00918-8. ISSN 2058-5276. PMID 34155373. S2CID 235595884.
Parks, DH; Chuvochina, M; Chaumeil, PA; Rinke, C; Mussig, AJ; Hugenholtz, P (September 2020). "A complete domain-to-species taxonomy for Bacteria and Archaea". Nature Biotechnology. 38 (9): 1079–1086. bioRxiv 10.1101/771964. doi:10.1038/s41587-020-0501-8. PMID 32341564. S2CID 216560589.

uea.ac.uk

ueaeprints.uea.ac.uk

Pallen, MJ; Rodriguez-R, LM; Alikhan, NF (September 2022). "Naming the unnamed: over 65,000 Candidatus names for unnamed Archaea and Bacteria in the Genome Taxonomy Database" (PDF). International Journal of Systematic and Evolutionary Microbiology. 72 (9). doi:10.1099/ijsem.0.005482. PMID 36125864.

worldcat.org

search.worldcat.org

Rinke, Christian; Chuvochina, Maria; Mussig, Aaron J.; Chaumeil, Pierre-Alain; Davín, Adrián A.; Waite, David W.; Whitman, William B.; Parks, Donovan H.; Hugenholtz, Philip (21 June 2021). "A standardized archaeal taxonomy for the Genome Taxonomy Database" (PDF). Nature Microbiology. 6 (7): 946–959. doi:10.1038/s41564-021-00918-8. ISSN 2058-5276. PMID 34155373. S2CID 235595884.