-
1
-
-
0036909621
-
Phylogenies and community ecology
-
Webb CO, Ackerly DD, McPeek MA, Donoghue MJ, (2002) Phylogenies and community ecology. Annual Review of Ecology and Systematics 33: 475-505.
-
(2002)
Annual Review of Ecology and Systematics
, vol.33
, pp. 475-505
-
-
Webb, C.O.1
Ackerly, D.D.2
McPeek, M.A.3
Donoghue, M.J.4
-
2
-
-
68849099915
-
Disentangling niche and neutral influences on community assembly: assessing the performance of community phylogenetic structure tests
-
doi: 10.1111/j.1461-0248.2009.01354.x
-
Kembel SW, (2009) Disentangling niche and neutral influences on community assembly: assessing the performance of community phylogenetic structure tests. Ecology Letters 12: 949-960 doi:10.1111/j.1461-0248.2009.01354.x.
-
(2009)
Ecology Letters
, vol.12
, pp. 949-960
-
-
Kembel, S.W.1
-
3
-
-
50049085522
-
Microbes on mountainsides: Contrasting elevational patterns of bacterial and plant diversity
-
Bryant JA, Lamanna C, Morlon H, Kerkhoff AJ, Enquist BJ, et al. (2008) Microbes on mountainsides: Contrasting elevational patterns of bacterial and plant diversity. Proceedings of the National Academy of Sciences 105: 11505-11511.
-
(2008)
Proceedings of the National Academy of Sciences
, vol.105
, pp. 11505-11511
-
-
Bryant, J.A.1
Lamanna, C.2
Morlon, H.3
Kerkhoff, A.J.4
Enquist, B.J.5
-
4
-
-
33749859789
-
Phylogenetic clustering and overdispersion in bacterial communities
-
Horner-Devine MC, Bohannan BJM, (2006) Phylogenetic clustering and overdispersion in bacterial communities. Ecology 87: 100-108.
-
(2006)
Ecology
, vol.87
, pp. 100-108
-
-
Horner-Devine, M.C.1
Bohannan, B.J.M.2
-
6
-
-
31444447130
-
The diversity and biogeography of soil bacterial communities
-
doi: 10.1073/pnas.0507535103
-
Fierer N, Jackson RB, (2006) The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci U S A 103: 626-631 doi:10.1073/pnas.0507535103.
-
(2006)
Proc Natl Acad Sci U S A
, vol.103
, pp. 626-631
-
-
Fierer, N.1
Jackson, R.B.2
-
7
-
-
67651247607
-
Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale
-
doi: 10.1128/AEM.00335-09
-
Lauber CL, Hamady M, Knight R, Fierer N, (2009) Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale. Appl. Environ. Microbiol 75: 5111-5120 doi:10.1128/AEM.00335-09.
-
(2009)
Appl. Environ. Microbiol
, vol.75
, pp. 5111-5120
-
-
Lauber, C.L.1
Hamady, M.2
Knight, R.3
Fierer, N.4
-
8
-
-
72949091232
-
Bacterial community variation in human body habitats across space and time
-
doi: 10.1126/science.1177486
-
Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, et al. (2009) Bacterial community variation in human body habitats across space and time. Science 326: 1694-1697 doi:10.1126/science.1177486.
-
(2009)
Science
, vol.326
, pp. 1694-1697
-
-
Costello, E.K.1
Lauber, C.L.2
Hamady, M.3
Fierer, N.4
Gordon, J.I.5
-
9
-
-
77957885485
-
The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leaves
-
doi: 10.1111/j.1462-2920.2010.02258.x
-
Redford AJ, Bowers RM, Knight R, Linhart Y, Fierer N, (2010) The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leaves. Environmental Microbiology 12: 2885-2893 doi:10.1111/j.1462-2920.2010.02258.x.
-
(2010)
Environmental Microbiology
, vol.12
, pp. 2885-2893
-
-
Redford, A.J.1
Bowers, R.M.2
Knight, R.3
Linhart, Y.4
Fierer, N.5
-
10
-
-
0030982247
-
A molecular view of microbial diversity and the biosphere
-
Pace NR, (1997) A molecular view of microbial diversity and the biosphere. Science 276: 734-740.
-
(1997)
Science
, vol.276
, pp. 734-740
-
-
Pace, N.R.1
-
11
-
-
0036324293
-
Phylogenetic approaches for describing and comparing the diversity of microbial communities
-
Martin AP, (2002) Phylogenetic approaches for describing and comparing the diversity of microbial communities. Applied and Environmental Microbiology 68: 3673-3682.
-
(2002)
Applied and Environmental Microbiology
, vol.68
, pp. 3673-3682
-
-
Martin, A.P.1
-
12
-
-
44849128805
-
Species divergence and the measurement of microbial diversity
-
Lozupone CA, Knight R, (2008) Species divergence and the measurement of microbial diversity. FEMS Microbiology Reviews 32: 557-578.
-
(2008)
FEMS Microbiology Reviews
, vol.32
, pp. 557-578
-
-
Lozupone, C.A.1
Knight, R.2
-
13
-
-
33947221422
-
Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes
-
Eisen JA, (2007) Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes. PLoS Biology 5: e82.
-
(2007)
PLoS Biology
, vol.5
-
-
Eisen, J.A.1
-
14
-
-
10344227692
-
Metagenomics: application of genomics to uncultured microorganisms
-
Handelsman J, (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiology and Molecular Biology Reviews 68: 669-685.
-
(2004)
Microbiology and Molecular Biology Reviews
, vol.68
, pp. 669-685
-
-
Handelsman, J.1
-
15
-
-
19544377549
-
Genomic analysis of Hyphomonas neptunium contradicts 16S rRNA gene-based phylogenetic analysis: implications for the taxonomy of the orders "Rhodobacterales" and Caulobacterales
-
doi: 10.1099/ijs.0.63510-0
-
Badger JH, Eisen JA, Ward NL, (2005) Genomic analysis of Hyphomonas neptunium contradicts 16S rRNA gene-based phylogenetic analysis: implications for the taxonomy of the orders "Rhodobacterales" and Caulobacterales. Int J Syst Evol Microbiol 55: 1021-1026 doi:10.1099/ijs.0.63510-0.
-
(2005)
Int J Syst Evol Microbiol
, vol.55
, pp. 1021-1026
-
-
Badger, J.H.1
Eisen, J.A.2
Ward, N.L.3
-
16
-
-
11144354360
-
Environmental genome shotgun sequencing of the Sargasso Sea
-
doi: 10.1126/science.1093857
-
Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, et al. (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66-74 doi:10.1126/science.1093857.
-
(2004)
Science
, vol.304
, pp. 66-74
-
-
Venter, J.C.1
Remington, K.2
Heidelberg, J.F.3
Halpern, A.L.4
Rusch, D.5
-
17
-
-
67949095970
-
Bias in assessments of marine microbial biodiversity in fosmid libraries as evaluated by pyrosequencing
-
Temperton B, Field D, Oliver A, Tiwari B, Muhling M, et al. (2009) Bias in assessments of marine microbial biodiversity in fosmid libraries as evaluated by pyrosequencing. ISME J 3: 792-796.
-
(2009)
ISME J
, vol.3
, pp. 792-796
-
-
Temperton, B.1
Field, D.2
Oliver, A.3
Tiwari, B.4
Muhling, M.5
-
18
-
-
77950251400
-
A human gut microbial gene catalogue established by metagenomic sequencing
-
doi: 10.1038/nature08821
-
Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, et al. (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464: 59-65 doi:10.1038/nature08821.
-
(2010)
Nature
, vol.464
, pp. 59-65
-
-
Qin, J.1
Li, R.2
Raes, J.3
Arumugam, M.4
Burgdorf, K.S.5
-
19
-
-
79952005915
-
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample
-
doi: 10.1073/pnas.1000080107
-
Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, et al. (2010) Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci U S A 108 (Suppl 1): 4516-4522 doi:10.1073/pnas.1000080107.
-
(2010)
Proc Natl Acad Sci U S A
, vol.108
, Issue.SUPPL. 1
, pp. 4516-4522
-
-
Caporaso, J.G.1
Lauber, C.L.2
Walters, W.A.3
Berg-Lyons, D.4
Lozupone, C.A.5
-
20
-
-
72949101201
-
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
-
doi: 10.1038/nature08656
-
Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, et al. (2009) A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 462: 1056-1060 doi:10.1038/nature08656.
-
(2009)
Nature
, vol.462
, pp. 1056-1060
-
-
Wu, D.1
Hugenholtz, P.2
Mavromatis, K.3
Pukall, R.4
Dalin, E.5
-
21
-
-
62849096845
-
Harnessing genomics for evolutionary insights
-
Rokas A, Abbot P, (2009) Harnessing genomics for evolutionary insights. Trends in Ecology & Evolution 24: 192-200.
-
(2009)
Trends in Ecology & Evolution
, vol.24
, pp. 192-200
-
-
Rokas, A.1
Abbot, P.2
-
22
-
-
31544483932
-
Community genomics among stratified microbial assemblages in the ocean's interior
-
DeLong EF, Preston CM, Mincer T, Rich V, Hallam SJ, et al. (2006) Community genomics among stratified microbial assemblages in the ocean's interior. Science 311: 496-503.
-
(2006)
Science
, vol.311
, pp. 496-503
-
-
DeLong, E.F.1
Preston, C.M.2
Mincer, T.3
Rich, V.4
Hallam, S.J.5
-
23
-
-
33744804299
-
Metagenomic analysis of the human distal gut microbiome
-
Gill SR, Pop M, DeBoy RT, Eckburg PB, Turnbaugh PJ, et al. (2006) Metagenomic analysis of the human distal gut microbiome. Science 312: 1355-1359.
-
(2006)
Science
, vol.312
, pp. 1355-1359
-
-
Gill, S.R.1
Pop, M.2
DeBoy, R.T.3
Eckburg, P.B.4
Turnbaugh, P.J.5
-
24
-
-
33947238287
-
The Sorcerer II Global Ocean Sampling expedition: Northwest Atlantic through eastern tropical Pacific
-
Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, et al. (2007) The Sorcerer II Global Ocean Sampling expedition: Northwest Atlantic through eastern tropical Pacific. PLoS Biol 5: e77.
-
(2007)
PLoS Biol
, vol.5
-
-
Rusch, D.B.1
Halpern, A.L.2
Sutton, G.3
Heidelberg, K.B.4
Williamson, S.5
-
25
-
-
33947235074
-
The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families
-
Yooseph S, Sutton G, Rusch DB, Halpern AL, Williamson SJ, et al. (2007) The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol 5: e16.
-
(2007)
PLoS Biol
, vol.5
-
-
Yooseph, S.1
Sutton, G.2
Rusch, D.B.3
Halpern, A.L.4
Williamson, S.J.5
-
26
-
-
55649110049
-
A simple, fast, and accurate method of phylogenomic inference
-
Wu M, Eisen J, (2008) A simple, fast, and accurate method of phylogenomic inference. Genome Biology 9: R151.
-
(2008)
Genome Biology
, vol.9
-
-
Wu, M.1
Eisen, J.2
-
27
-
-
33847291893
-
Quantitative phylogenetic assessment of microbial communities in diverse environments
-
doi: 10.1126/science.1133420
-
von Mering C, Hugenholtz P, Raes J, Tringe SG, Doerks T, et al. (2007) Quantitative phylogenetic assessment of microbial communities in diverse environments. Science 315: 1126-1130 doi:10.1126/science.1133420.
-
(2007)
Science
, vol.315
, pp. 1126-1130
-
-
von Mering, C.1
Hugenholtz, P.2
Raes, J.3
Tringe, S.G.4
Doerks, T.5
-
28
-
-
77955179934
-
MLTreeMap - accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies
-
doi: 10.1186/1471-2164-11-461
-
Stark M, Berger S, Stamatakis A, von Mering C, (2010) MLTreeMap- accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies. BMC Genomics 11: 461 doi:10.1186/1471-2164-11-461.
-
(2010)
BMC Genomics
, vol.11
, pp. 461
-
-
Stark, M.1
Berger, S.2
Stamatakis, A.3
von Mering, C.4
-
29
-
-
33750403801
-
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
-
Stamatakis A, (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-2690.
-
(2006)
Bioinformatics
, vol.22
, pp. 2688-2690
-
-
Stamatakis, A.1
-
30
-
-
51749095104
-
Phylocom: software for the analysis of phylogenetic community structure and trait evolution
-
doi: 10.1093/bioinformatics/btn358
-
Webb CO, Ackerly DD, Kembel SW, (2008) Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Bioinformatics 24: 2098-2100 doi:10.1093/bioinformatics/btn358.
-
(2008)
Bioinformatics
, vol.24
, pp. 2098-2100
-
-
Webb, C.O.1
Ackerly, D.D.2
Kembel, S.W.3
-
31
-
-
58849095783
-
Emerging patterns in the comparative analysis of phylogenetic community structure
-
doi: 10.1111/j.1365-294X.2008.04001.x
-
Vamosi SM, Heard SB, Vamosi JC, Webb CO, (2009) Emerging patterns in the comparative analysis of phylogenetic community structure. Molecular Ecology 18: 572-592 doi:10.1111/j.1365-294X.2008.04001.x.
-
(2009)
Molecular Ecology
, vol.18
, pp. 572-592
-
-
Vamosi, S.M.1
Heard, S.B.2
Vamosi, J.C.3
Webb, C.O.4
-
32
-
-
72949108886
-
Phylogenetic diversity metrics for ecological communities: integrating species richness, abundance and evolutionary history
-
doi: 10.1111/j.1461-0248.2009.01405.x
-
Cadotte MW, Davies TJ, Regetz J, Kembel SW, Cleland E, et al. (2010) Phylogenetic diversity metrics for ecological communities: integrating species richness, abundance and evolutionary history. Ecology Letters 13: 96-105 doi:10.1111/j.1461-0248.2009.01405.x.
-
(2010)
Ecology Letters
, vol.13
, pp. 96-105
-
-
Cadotte, M.W.1
Davies, T.J.2
Regetz, J.3
Kembel, S.W.4
Cleland, E.5
-
33
-
-
77953882250
-
Picante: R tools for integrating phylogenies and ecology
-
doi: 10.1093/bioinformatics/btq166
-
Kembel SW, Cowan PD, Helmus MR, Cornwell WK, Morlon H, et al. (2010) Picante: R tools for integrating phylogenies and ecology. Bioinformatics 26: 1463-1464 doi:10.1093/bioinformatics/btq166.
-
(2010)
Bioinformatics
, vol.26
, pp. 1463-1464
-
-
Kembel, S.W.1
Cowan, P.D.2
Helmus, M.R.3
Cornwell, W.K.4
Morlon, H.5
-
34
-
-
66349134056
-
The merging of community ecology and phylogenetic biology
-
doi: 10.1111/j.1461-0248.2009.01314.x
-
Cavender-Bares J, Kozak KH, Fine PV, Kembel SW, (2009) The merging of community ecology and phylogenetic biology. Ecology Letters 12: 693-715 doi:10.1111/j.1461-0248.2009.01314.x.
-
(2009)
Ecology Letters
, vol.12
, pp. 693-715
-
-
Cavender-Bares, J.1
Kozak, K.H.2
Fine, P.V.3
Kembel, S.W.4
-
35
-
-
53649083413
-
Phylogenetic analysis of community assembly and structure over space and time
-
Emerson BC, Gillespie RG, (2008) Phylogenetic analysis of community assembly and structure over space and time. Trends in Ecology & Evolution 23: 619-630.
-
(2008)
Trends in Ecology & Evolution
, vol.23
, pp. 619-630
-
-
Emerson, B.C.1
Gillespie, R.G.2
-
36
-
-
33744923681
-
Remarkable heterogeneity in meso- and bathypelagic bacterioplankton assemblage composition
-
Hewson I, Steele JA, Capone DG, Fuhrman JA, (2006) Remarkable heterogeneity in meso- and bathypelagic bacterioplankton assemblage composition. Limnology and Oceanography 51: 1274-1283.
-
(2006)
Limnology and Oceanography
, vol.51
, pp. 1274-1283
-
-
Hewson, I.1
Steele, J.A.2
Capone, D.G.3
Fuhrman, J.A.4
-
37
-
-
70349472694
-
Seasonality and vertical structure of microbial communities in an ocean gyre
-
Treusch AH, Vergin KL, Finlay LA, Donatz MG, Burton RM, et al. (2009) Seasonality and vertical structure of microbial communities in an ocean gyre. The ISME Journal pp. 1-16.
-
(2009)
The ISME Journal
, pp. 1-16
-
-
Treusch, A.H.1
Vergin, K.L.2
Finlay, L.A.3
Donatz, M.G.4
Burton, R.M.5
-
38
-
-
72649092768
-
Microbial community structure in the North Pacific ocean
-
Brown MV, Philip GK, Bunge JA, Smith MC, Bissett A, et al. (2009) Microbial community structure in the North Pacific ocean. The ISME Journal pp. 1-13.
-
(2009)
The ISME Journal
, pp. 1-13
-
-
Brown, M.V.1
Philip, G.K.2
Bunge, J.A.3
Smith, M.C.4
Bissett, A.5
-
40
-
-
33847702910
-
MEGAN analysis of metagenomic data
-
doi: 10.1101/gr.5969107
-
Huson DH, Auch AF, Qi J, Schuster SC, (2007) MEGAN analysis of metagenomic data. Genome Res 17: 377-386 doi:10.1101/gr.5969107.
-
(2007)
Genome Res
, vol.17
, pp. 377-386
-
-
Huson, D.H.1
Auch, A.F.2
Qi, J.3
Schuster, S.C.4
-
41
-
-
77949494823
-
Covariation of branch lengths in phylogenies of functionally related genes
-
Li W, Rodrigo A, (2009) Covariation of branch lengths in phylogenies of functionally related genes. PLoS ONE 4: e8487.
-
(2009)
PLoS ONE
, vol.4
-
-
Li, W.1
Rodrigo, A.2
-
42
-
-
50149086330
-
An automated phylogenetic tree-based small subunit rRNA taxonomy and alignment pipeline (STAP)
-
Wu D, Hartman A, Ward N, Eisen J, (2008) An automated phylogenetic tree-based small subunit rRNA taxonomy and alignment pipeline (STAP). PLoS ONE 3: e2566.
-
(2008)
PLoS ONE
, vol.3
-
-
Wu, D.1
Hartman, A.2
Ward, N.3
Eisen, J.4
-
43
-
-
67649327176
-
FastTree: computing large minimum evolution trees with profiles instead of a distance matrix
-
doi: 10.1093/molbev/msp077
-
Price MN, Dehal PS, Arkin AP, (2009) FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 26: 1641-1650 doi:10.1093/molbev/msp077.
-
(2009)
Mol Biol Evol
, vol.26
, pp. 1641-1650
-
-
Price, M.N.1
Dehal, P.S.2
Arkin, A.P.3
-
44
-
-
79960414804
-
Aligning short Reads to Reference Alignments and Trees
-
doi: 10.1093/bioinformatics/btr320
-
Berger SA, Stamatakis A, (2011) Aligning short Reads to Reference Alignments and Trees. Bioinformatics 27: 2068-2075 doi:10.1093/bioinformatics/btr320.
-
(2011)
Bioinformatics
, vol.27
, pp. 2068-2075
-
-
Berger, S.A.1
Stamatakis, A.2
-
45
-
-
0000461280
-
Confidence limits on phylogenies: an approach using the bootstrap
-
Felsenstein J, (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783-791.
-
(1985)
Evolution
, vol.39
, pp. 783-791
-
-
Felsenstein, J.1
-
46
-
-
72949107142
-
Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ
-
doi: 10.1128/AEM.01541-09
-
Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, et al. (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol 75: 7537-7541 doi:10.1128/AEM.01541-09.
-
(2009)
Microbiol
, vol.75
, pp. 7537-7541
-
-
Schloss, P.D.1
Westcott, S.L.2
Ryabin, T.3
Hall, J.R.4
Hartmann, M.5
|