Microbial phylogenetics (English Wikipedia)

Analysis of information sources in references of the Wikipedia article "Microbial phylogenetics" in English language version.

refsWebsite

Global rank English rank

36nih.gov

4^th place

24doi.org

2^nd place

9worldcat.org

5^th place

7semanticscholar.org

11^th place

8^th place

6harvard.edu

18^th place

17^th place

1archives-ouvertes.fr

1,031^st place

879^th place

1escholarship.org

1,523^rd place

976^th place

1nature.com

234^th place

397^th place

1uchicago.edu

230^th place

214^th place

archives-ouvertes.fr

hal.archives-ouvertes.fr

Delusc, F.; Brinkmann, H.; Philippe, H. (2005). "Phylogenomics and the reconstruction of the tree of life" (PDF). Nature Reviews Genetics. 6 (5): 361–375. doi:10.1038/nrg1603. PMID 15861208. S2CID 16379422.

doi.org

Sapp, J. (2007). "The structure of microbial evolutionary theory". Stud. Hist. Phil. Biol. & Biomed. Sci. 38 (4): 780–795. doi:10.1016/j.shpsc.2007.09.011. PMID 18053933.
Dietrich, M. (1998). "Paradox and persuasion: Negotiating the place of molecular evolution within evolutionary biology". Journal of the History of Biology. 31 (1): 85–111. doi:10.1023/A:1004257523100. PMID 11619919. S2CID 29935487.
Dietrich, M. (1994). "The origins of the neutral theory of molecular evolution". Journal of the History of Biology. 27 (1): 21–59. doi:10.1007/BF01058626. PMID 11639258. S2CID 367102.
Woese, C.R.; Fox, G.E. (1977). "Phylogenetic structure of the procaryote domain: The primary kingdoms". Proceedings of the National Academy of Sciences. 75 (11): 5088–5090. Bibcode:1977PNAS...74.5088W. doi:10.1073/pnas.74.11.5088. PMC 432104. PMID 270744.
Sanger, F.; Nicklen, S.; Coulson, A.R. (1977). "DNA sequencing with chain-terminating inhibitors". Proceedings of the National Academy of Sciences. 74 (12): 5463–5467. Bibcode:1977PNAS...74.5463S. doi:10.1073/pnas.74.12.5463. PMC 431765. PMID 271968.
Maxam, A.M. (1977). "A new method for sequencing DNA". Proceedings of the National Academy of Sciences. 74 (2): 560–564. Bibcode:1977PNAS...74..560M. doi:10.1073/pnas.74.2.560. PMC 392330. PMID 265521.
Mullis, K.F.; et al. (1986). "Specific enzymatic amplification of DNA in vitro: The polymerase chain reaction". Cold Spring Harbor Symposia on Quantitative Biology. 51: 263–273. doi:10.1101/SQB.1986.051.01.032. PMID 3472723. S2CID 26180176.
Woese, C.R.; et al. (1990). "Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya". Proceedings of the National Academy of Sciences. 87 (12): 4576–4579. Bibcode:1990PNAS...87.4576W. doi:10.1073/pnas.87.12.4576. PMC 54159. PMID 2112744.
Pace, N (1997). "A molecular view of microbial diversity and the biosphere". Science. 276 (5313): 734–740. doi:10.1126/science.276.5313.734. PMID 9115194.
Whitman, W. B; et al. (1998). "Procaryotes: The unseen majority". Proceedings of the National Academy of Sciences. 95 (12): 6578–6583. Bibcode:1998PNAS...95.6578W. doi:10.1073/pnas.95.12.6578. PMC 33863. PMID 9618454.
Delusc, F.; Brinkmann, H.; Philippe, H. (2005). "Phylogenomics and the reconstruction of the tree of life" (PDF). Nature Reviews Genetics. 6 (5): 361–375. doi:10.1038/nrg1603. PMID 15861208. S2CID 16379422.
Doolittle, W.F. (1999). "Phylogenetic classification and the universal tree". Science. 284 (5423): 2124–2128. doi:10.1126/science.284.5423.2124. PMID 10381871.
Andam, Cheryl P.; Williams, David; Gogarten, J. Peter (2010-06-08). "Biased gene transfer mimics patterns created through shared ancestry". Proceedings of the National Academy of Sciences. 107 (23): 10679–10684. doi:10.1073/pnas.1001418107. ISSN 0027-8424. PMC 2890805. PMID 20495090.
Ochman, H.; Lawrence, J.G.; Groisman, E.A. (2000). "Lateral gene transfer and the nature of bacterial innovation". Nature. 405 (6784): 299–304. Bibcode:2000Natur.405..299O. doi:10.1038/35012500. PMID 10830951. S2CID 85739173.
Eisen, J. (2000). "Horizontal gene transfer among microbial genomes: new insights from complete genome analysis". Current Opinion in Genetics & Development. 10 (6): 606–611. doi:10.1016/S0959-437X(00)00143-X. PMID 11088009.
Kunin, V.; Goldovsky, L.; Darzentas, N.; Ouzounis, C. A. (2005). "The net of life: Reconstructing the microbial phylogenetic network". Genome Research. 15 (7): 954–959. doi:10.1101/gr.3666505. PMC 1172039. PMID 15965028.
Washburne, Alex D.; Morton, James T.; Sanders, Jon; McDonald, Daniel; Zhu, Qiyun; Oliverio, Angela M.; Knight, Rob (2018-05-24). "Methods for phylogenetic analysis of microbiome data". Nature Microbiology. 3 (6): 652–661. doi:10.1038/s41564-018-0156-0. ISSN 2058-5276. PMID 29795540. S2CID 43962376.
Wu, Martin; Eisen, Jonathan A (2008). "A simple, fast, and accurate method of phylogenomic inference". Genome Biology. 9 (10): R151. doi:10.1186/gb-2008-9-10-r151. ISSN 1465-6906. PMC 2760878. PMID 18851752.
Hillis, David M.; Dixon, Michael T. (1991). "Ribosomal DNA: Molecular Evolution and Phylogenetic Inference". The Quarterly Review of Biology. 66 (4): 411–453. doi:10.1086/417338. ISSN 0033-5770. PMID 1784710. S2CID 32027097.
Bradley, Patrick H.; Nayfach, Stephen; Pollard, Katherine S. (2018-08-09). "Phylogeny-corrected identification of microbial gene families relevant to human gut colonization". PLOS Computational Biology. 14 (8): e1006242. doi:10.1371/journal.pcbi.1006242. ISSN 1553-7358. PMC 6084841. PMID 30091981.
Langille, Morgan G I; Zaneveld, Jesse; Caporaso, J Gregory; McDonald, Daniel; Knights, Dan; Reyes, Joshua A; Clemente, Jose C; Burkepile, Deron E; Vega Thurber, Rebecca L; Knight, Rob; Beiko, Robert G; Huttenhower, Curtis (2013). "Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences". Nature Biotechnology. 31 (9): 814–821. doi:10.1038/nbt.2676. ISSN 1087-0156. PMC 3819121. PMID 23975157.
Silverman, Justin D; Washburne, Alex D; Mukherjee, Sayan; David, Lawrence A (2017-02-15). "A phylogenetic transform enhances analysis of compositional microbiota data". eLife. 6. doi:10.7554/eLife.21887. ISSN 2050-084X. PMC 5328592. PMID 28198697.
Washburne, Alex D.; Silverman, Justin D.; Leff, Jonathan W.; Bennett, Dominic J.; Darcy, John L.; Mukherjee, Sayan; Fierer, Noah; David, Lawrence A. (2017-02-09). "Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets". PeerJ. 5: e2969. doi:10.7717/peerj.2969. ISSN 2167-8359. PMC 5345826. PMID 28289558.
Martiny, Jennifer B. H.; Jones, Stuart E.; Lennon, Jay T.; Martiny, Adam C. (2015-11-06). "Microbiomes in light of traits: A phylogenetic perspective". Science. 350 (6261). doi:10.1126/science.aac9323. ISSN 0036-8075. PMID 26542581.

escholarship.org

Eisen, J. (2000). "Horizontal gene transfer among microbial genomes: new insights from complete genome analysis". Current Opinion in Genetics & Development. 10 (6): 606–611. doi:10.1016/S0959-437X(00)00143-X. PMID 11088009.

harvard.edu

ui.adsabs.harvard.edu

Woese, C.R.; Fox, G.E. (1977). "Phylogenetic structure of the procaryote domain: The primary kingdoms". Proceedings of the National Academy of Sciences. 75 (11): 5088–5090. Bibcode:1977PNAS...74.5088W. doi:10.1073/pnas.74.11.5088. PMC 432104. PMID 270744.
Sanger, F.; Nicklen, S.; Coulson, A.R. (1977). "DNA sequencing with chain-terminating inhibitors". Proceedings of the National Academy of Sciences. 74 (12): 5463–5467. Bibcode:1977PNAS...74.5463S. doi:10.1073/pnas.74.12.5463. PMC 431765. PMID 271968.
Maxam, A.M. (1977). "A new method for sequencing DNA". Proceedings of the National Academy of Sciences. 74 (2): 560–564. Bibcode:1977PNAS...74..560M. doi:10.1073/pnas.74.2.560. PMC 392330. PMID 265521.
Woese, C.R.; et al. (1990). "Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya". Proceedings of the National Academy of Sciences. 87 (12): 4576–4579. Bibcode:1990PNAS...87.4576W. doi:10.1073/pnas.87.12.4576. PMC 54159. PMID 2112744.
Whitman, W. B; et al. (1998). "Procaryotes: The unseen majority". Proceedings of the National Academy of Sciences. 95 (12): 6578–6583. Bibcode:1998PNAS...95.6578W. doi:10.1073/pnas.95.12.6578. PMC 33863. PMID 9618454.
Ochman, H.; Lawrence, J.G.; Groisman, E.A. (2000). "Lateral gene transfer and the nature of bacterial innovation". Nature. 405 (6784): 299–304. Bibcode:2000Natur.405..299O. doi:10.1038/35012500. PMID 10830951. S2CID 85739173.

nature.com

Washburne, Alex D.; Morton, James T.; Sanders, Jon; McDonald, Daniel; Zhu, Qiyun; Oliverio, Angela M.; Knight, Rob (2018-05-24). "Methods for phylogenetic analysis of microbiome data". Nature Microbiology. 3 (6): 652–661. doi:10.1038/s41564-018-0156-0. ISSN 2058-5276. PMID 29795540. S2CID 43962376.

nih.gov

pubmed.ncbi.nlm.nih.gov

Sapp, J. (2007). "The structure of microbial evolutionary theory". Stud. Hist. Phil. Biol. & Biomed. Sci. 38 (4): 780–795. doi:10.1016/j.shpsc.2007.09.011. PMID 18053933.
Dietrich, M. (1998). "Paradox and persuasion: Negotiating the place of molecular evolution within evolutionary biology". Journal of the History of Biology. 31 (1): 85–111. doi:10.1023/A:1004257523100. PMID 11619919. S2CID 29935487.
Dietrich, M. (1994). "The origins of the neutral theory of molecular evolution". Journal of the History of Biology. 27 (1): 21–59. doi:10.1007/BF01058626. PMID 11639258. S2CID 367102.
Woese, C.R.; Fox, G.E. (1977). "Phylogenetic structure of the procaryote domain: The primary kingdoms". Proceedings of the National Academy of Sciences. 75 (11): 5088–5090. Bibcode:1977PNAS...74.5088W. doi:10.1073/pnas.74.11.5088. PMC 432104. PMID 270744.
Sanger, F.; Nicklen, S.; Coulson, A.R. (1977). "DNA sequencing with chain-terminating inhibitors". Proceedings of the National Academy of Sciences. 74 (12): 5463–5467. Bibcode:1977PNAS...74.5463S. doi:10.1073/pnas.74.12.5463. PMC 431765. PMID 271968.
Maxam, A.M. (1977). "A new method for sequencing DNA". Proceedings of the National Academy of Sciences. 74 (2): 560–564. Bibcode:1977PNAS...74..560M. doi:10.1073/pnas.74.2.560. PMC 392330. PMID 265521.
Mullis, K.F.; et al. (1986). "Specific enzymatic amplification of DNA in vitro: The polymerase chain reaction". Cold Spring Harbor Symposia on Quantitative Biology. 51: 263–273. doi:10.1101/SQB.1986.051.01.032. PMID 3472723. S2CID 26180176.
Woese, C.R.; et al. (1990). "Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya". Proceedings of the National Academy of Sciences. 87 (12): 4576–4579. Bibcode:1990PNAS...87.4576W. doi:10.1073/pnas.87.12.4576. PMC 54159. PMID 2112744.
Pace, N (1997). "A molecular view of microbial diversity and the biosphere". Science. 276 (5313): 734–740. doi:10.1126/science.276.5313.734. PMID 9115194.
Whitman, W. B; et al. (1998). "Procaryotes: The unseen majority". Proceedings of the National Academy of Sciences. 95 (12): 6578–6583. Bibcode:1998PNAS...95.6578W. doi:10.1073/pnas.95.12.6578. PMC 33863. PMID 9618454.
Delusc, F.; Brinkmann, H.; Philippe, H. (2005). "Phylogenomics and the reconstruction of the tree of life" (PDF). Nature Reviews Genetics. 6 (5): 361–375. doi:10.1038/nrg1603. PMID 15861208. S2CID 16379422.
Doolittle, W.F. (1999). "Phylogenetic classification and the universal tree". Science. 284 (5423): 2124–2128. doi:10.1126/science.284.5423.2124. PMID 10381871.
Andam, Cheryl P.; Williams, David; Gogarten, J. Peter (2010-06-08). "Biased gene transfer mimics patterns created through shared ancestry". Proceedings of the National Academy of Sciences. 107 (23): 10679–10684. doi:10.1073/pnas.1001418107. ISSN 0027-8424. PMC 2890805. PMID 20495090.
Ochman, H.; Lawrence, J.G.; Groisman, E.A. (2000). "Lateral gene transfer and the nature of bacterial innovation". Nature. 405 (6784): 299–304. Bibcode:2000Natur.405..299O. doi:10.1038/35012500. PMID 10830951. S2CID 85739173.
Eisen, J. (2000). "Horizontal gene transfer among microbial genomes: new insights from complete genome analysis". Current Opinion in Genetics & Development. 10 (6): 606–611. doi:10.1016/S0959-437X(00)00143-X. PMID 11088009.
Kunin, V.; Goldovsky, L.; Darzentas, N.; Ouzounis, C. A. (2005). "The net of life: Reconstructing the microbial phylogenetic network". Genome Research. 15 (7): 954–959. doi:10.1101/gr.3666505. PMC 1172039. PMID 15965028.
Washburne, Alex D.; Morton, James T.; Sanders, Jon; McDonald, Daniel; Zhu, Qiyun; Oliverio, Angela M.; Knight, Rob (2018-05-24). "Methods for phylogenetic analysis of microbiome data". Nature Microbiology. 3 (6): 652–661. doi:10.1038/s41564-018-0156-0. ISSN 2058-5276. PMID 29795540. S2CID 43962376.
Wu, Martin; Eisen, Jonathan A (2008). "A simple, fast, and accurate method of phylogenomic inference". Genome Biology. 9 (10): R151. doi:10.1186/gb-2008-9-10-r151. ISSN 1465-6906. PMC 2760878. PMID 18851752.
Hillis, David M.; Dixon, Michael T. (1991). "Ribosomal DNA: Molecular Evolution and Phylogenetic Inference". The Quarterly Review of Biology. 66 (4): 411–453. doi:10.1086/417338. ISSN 0033-5770. PMID 1784710. S2CID 32027097.
Bradley, Patrick H.; Nayfach, Stephen; Pollard, Katherine S. (2018-08-09). "Phylogeny-corrected identification of microbial gene families relevant to human gut colonization". PLOS Computational Biology. 14 (8): e1006242. doi:10.1371/journal.pcbi.1006242. ISSN 1553-7358. PMC 6084841. PMID 30091981.
Langille, Morgan G I; Zaneveld, Jesse; Caporaso, J Gregory; McDonald, Daniel; Knights, Dan; Reyes, Joshua A; Clemente, Jose C; Burkepile, Deron E; Vega Thurber, Rebecca L; Knight, Rob; Beiko, Robert G; Huttenhower, Curtis (2013). "Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences". Nature Biotechnology. 31 (9): 814–821. doi:10.1038/nbt.2676. ISSN 1087-0156. PMC 3819121. PMID 23975157.
Silverman, Justin D; Washburne, Alex D; Mukherjee, Sayan; David, Lawrence A (2017-02-15). "A phylogenetic transform enhances analysis of compositional microbiota data". eLife. 6. doi:10.7554/eLife.21887. ISSN 2050-084X. PMC 5328592. PMID 28198697.
Washburne, Alex D.; Silverman, Justin D.; Leff, Jonathan W.; Bennett, Dominic J.; Darcy, John L.; Mukherjee, Sayan; Fierer, Noah; David, Lawrence A. (2017-02-09). "Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets". PeerJ. 5: e2969. doi:10.7717/peerj.2969. ISSN 2167-8359. PMC 5345826. PMID 28289558.
Martiny, Jennifer B. H.; Jones, Stuart E.; Lennon, Jay T.; Martiny, Adam C. (2015-11-06). "Microbiomes in light of traits: A phylogenetic perspective". Science. 350 (6261). doi:10.1126/science.aac9323. ISSN 0036-8075. PMID 26542581.

ncbi.nlm.nih.gov

Woese, C.R.; Fox, G.E. (1977). "Phylogenetic structure of the procaryote domain: The primary kingdoms". Proceedings of the National Academy of Sciences. 75 (11): 5088–5090. Bibcode:1977PNAS...74.5088W. doi:10.1073/pnas.74.11.5088. PMC 432104. PMID 270744.
Sanger, F.; Nicklen, S.; Coulson, A.R. (1977). "DNA sequencing with chain-terminating inhibitors". Proceedings of the National Academy of Sciences. 74 (12): 5463–5467. Bibcode:1977PNAS...74.5463S. doi:10.1073/pnas.74.12.5463. PMC 431765. PMID 271968.
Maxam, A.M. (1977). "A new method for sequencing DNA". Proceedings of the National Academy of Sciences. 74 (2): 560–564. Bibcode:1977PNAS...74..560M. doi:10.1073/pnas.74.2.560. PMC 392330. PMID 265521.
Woese, C.R.; et al. (1990). "Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya". Proceedings of the National Academy of Sciences. 87 (12): 4576–4579. Bibcode:1990PNAS...87.4576W. doi:10.1073/pnas.87.12.4576. PMC 54159. PMID 2112744.
Whitman, W. B; et al. (1998). "Procaryotes: The unseen majority". Proceedings of the National Academy of Sciences. 95 (12): 6578–6583. Bibcode:1998PNAS...95.6578W. doi:10.1073/pnas.95.12.6578. PMC 33863. PMID 9618454.
Andam, Cheryl P.; Williams, David; Gogarten, J. Peter (2010-06-08). "Biased gene transfer mimics patterns created through shared ancestry". Proceedings of the National Academy of Sciences. 107 (23): 10679–10684. doi:10.1073/pnas.1001418107. ISSN 0027-8424. PMC 2890805. PMID 20495090.
Kunin, V.; Goldovsky, L.; Darzentas, N.; Ouzounis, C. A. (2005). "The net of life: Reconstructing the microbial phylogenetic network". Genome Research. 15 (7): 954–959. doi:10.1101/gr.3666505. PMC 1172039. PMID 15965028.
Wu, Martin; Eisen, Jonathan A (2008). "A simple, fast, and accurate method of phylogenomic inference". Genome Biology. 9 (10): R151. doi:10.1186/gb-2008-9-10-r151. ISSN 1465-6906. PMC 2760878. PMID 18851752.
Bradley, Patrick H.; Nayfach, Stephen; Pollard, Katherine S. (2018-08-09). "Phylogeny-corrected identification of microbial gene families relevant to human gut colonization". PLOS Computational Biology. 14 (8): e1006242. doi:10.1371/journal.pcbi.1006242. ISSN 1553-7358. PMC 6084841. PMID 30091981.
Langille, Morgan G I; Zaneveld, Jesse; Caporaso, J Gregory; McDonald, Daniel; Knights, Dan; Reyes, Joshua A; Clemente, Jose C; Burkepile, Deron E; Vega Thurber, Rebecca L; Knight, Rob; Beiko, Robert G; Huttenhower, Curtis (2013). "Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences". Nature Biotechnology. 31 (9): 814–821. doi:10.1038/nbt.2676. ISSN 1087-0156. PMC 3819121. PMID 23975157.
Silverman, Justin D; Washburne, Alex D; Mukherjee, Sayan; David, Lawrence A (2017-02-15). "A phylogenetic transform enhances analysis of compositional microbiota data". eLife. 6. doi:10.7554/eLife.21887. ISSN 2050-084X. PMC 5328592. PMID 28198697.
Washburne, Alex D.; Silverman, Justin D.; Leff, Jonathan W.; Bennett, Dominic J.; Darcy, John L.; Mukherjee, Sayan; Fierer, Noah; David, Lawrence A. (2017-02-09). "Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets". PeerJ. 5: e2969. doi:10.7717/peerj.2969. ISSN 2167-8359. PMC 5345826. PMID 28289558.

semanticscholar.org

api.semanticscholar.org

Dietrich, M. (1998). "Paradox and persuasion: Negotiating the place of molecular evolution within evolutionary biology". Journal of the History of Biology. 31 (1): 85–111. doi:10.1023/A:1004257523100. PMID 11619919. S2CID 29935487.
Dietrich, M. (1994). "The origins of the neutral theory of molecular evolution". Journal of the History of Biology. 27 (1): 21–59. doi:10.1007/BF01058626. PMID 11639258. S2CID 367102.
Mullis, K.F.; et al. (1986). "Specific enzymatic amplification of DNA in vitro: The polymerase chain reaction". Cold Spring Harbor Symposia on Quantitative Biology. 51: 263–273. doi:10.1101/SQB.1986.051.01.032. PMID 3472723. S2CID 26180176.
Delusc, F.; Brinkmann, H.; Philippe, H. (2005). "Phylogenomics and the reconstruction of the tree of life" (PDF). Nature Reviews Genetics. 6 (5): 361–375. doi:10.1038/nrg1603. PMID 15861208. S2CID 16379422.
Ochman, H.; Lawrence, J.G.; Groisman, E.A. (2000). "Lateral gene transfer and the nature of bacterial innovation". Nature. 405 (6784): 299–304. Bibcode:2000Natur.405..299O. doi:10.1038/35012500. PMID 10830951. S2CID 85739173.
Washburne, Alex D.; Morton, James T.; Sanders, Jon; McDonald, Daniel; Zhu, Qiyun; Oliverio, Angela M.; Knight, Rob (2018-05-24). "Methods for phylogenetic analysis of microbiome data". Nature Microbiology. 3 (6): 652–661. doi:10.1038/s41564-018-0156-0. ISSN 2058-5276. PMID 29795540. S2CID 43962376.
Hillis, David M.; Dixon, Michael T. (1991). "Ribosomal DNA: Molecular Evolution and Phylogenetic Inference". The Quarterly Review of Biology. 66 (4): 411–453. doi:10.1086/417338. ISSN 0033-5770. PMID 1784710. S2CID 32027097.

uchicago.edu

journals.uchicago.edu

Hillis, David M.; Dixon, Michael T. (1991). "Ribosomal DNA: Molecular Evolution and Phylogenetic Inference". The Quarterly Review of Biology. 66 (4): 411–453. doi:10.1086/417338. ISSN 0033-5770. PMID 1784710. S2CID 32027097.

worldcat.org

search.worldcat.org

Andam, Cheryl P.; Williams, David; Gogarten, J. Peter (2010-06-08). "Biased gene transfer mimics patterns created through shared ancestry". Proceedings of the National Academy of Sciences. 107 (23): 10679–10684. doi:10.1073/pnas.1001418107. ISSN 0027-8424. PMC 2890805. PMID 20495090.
Washburne, Alex D.; Morton, James T.; Sanders, Jon; McDonald, Daniel; Zhu, Qiyun; Oliverio, Angela M.; Knight, Rob (2018-05-24). "Methods for phylogenetic analysis of microbiome data". Nature Microbiology. 3 (6): 652–661. doi:10.1038/s41564-018-0156-0. ISSN 2058-5276. PMID 29795540. S2CID 43962376.
Wu, Martin; Eisen, Jonathan A (2008). "A simple, fast, and accurate method of phylogenomic inference". Genome Biology. 9 (10): R151. doi:10.1186/gb-2008-9-10-r151. ISSN 1465-6906. PMC 2760878. PMID 18851752.
Hillis, David M.; Dixon, Michael T. (1991). "Ribosomal DNA: Molecular Evolution and Phylogenetic Inference". The Quarterly Review of Biology. 66 (4): 411–453. doi:10.1086/417338. ISSN 0033-5770. PMID 1784710. S2CID 32027097.
Bradley, Patrick H.; Nayfach, Stephen; Pollard, Katherine S. (2018-08-09). "Phylogeny-corrected identification of microbial gene families relevant to human gut colonization". PLOS Computational Biology. 14 (8): e1006242. doi:10.1371/journal.pcbi.1006242. ISSN 1553-7358. PMC 6084841. PMID 30091981.
Langille, Morgan G I; Zaneveld, Jesse; Caporaso, J Gregory; McDonald, Daniel; Knights, Dan; Reyes, Joshua A; Clemente, Jose C; Burkepile, Deron E; Vega Thurber, Rebecca L; Knight, Rob; Beiko, Robert G; Huttenhower, Curtis (2013). "Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences". Nature Biotechnology. 31 (9): 814–821. doi:10.1038/nbt.2676. ISSN 1087-0156. PMC 3819121. PMID 23975157.
Silverman, Justin D; Washburne, Alex D; Mukherjee, Sayan; David, Lawrence A (2017-02-15). "A phylogenetic transform enhances analysis of compositional microbiota data". eLife. 6. doi:10.7554/eLife.21887. ISSN 2050-084X. PMC 5328592. PMID 28198697.
Washburne, Alex D.; Silverman, Justin D.; Leff, Jonathan W.; Bennett, Dominic J.; Darcy, John L.; Mukherjee, Sayan; Fierer, Noah; David, Lawrence A. (2017-02-09). "Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets". PeerJ. 5: e2969. doi:10.7717/peerj.2969. ISSN 2167-8359. PMC 5345826. PMID 28289558.
Martiny, Jennifer B. H.; Jones, Stuart E.; Lennon, Jay T.; Martiny, Adam C. (2015-11-06). "Microbiomes in light of traits: A phylogenetic perspective". Science. 350 (6261). doi:10.1126/science.aac9323. ISSN 0036-8075. PMID 26542581.