-
1
-
-
0000286531
-
An ordination of the upland forest communities in southern Wisconsin
-
Bray, J. & Curtis, J. (1957) An ordination of the upland forest communities in southern Wisconsin. Ecology Monographs, 27, 325–349.
-
(1957)
Ecology Monographs
, vol.27
, pp. 325-349
-
-
Bray, J.1
Curtis, J.2
-
2
-
-
84865082160
-
Associating microbiome composition with environmental covariates using generalized UniFrac distances
-
Chen, J., Bittinger, K., Charlson, E.S., Hoffmann, C., Lewis, J., Wu, G.D., Collman, R.G., Bushman, F.D. & Li, H. (2012) Associating microbiome composition with environmental covariates using generalized UniFrac distances. Bioinformatics, 28, 2106–2113.
-
(2012)
Bioinformatics
, vol.28
, pp. 2106-2113
-
-
Chen, J.1
Bittinger, K.2
Charlson, E.S.3
Hoffmann, C.4
Lewis, J.5
Wu, G.D.6
Collman, R.G.7
Bushman, F.D.8
Li, H.9
-
3
-
-
53749096964
-
Environmental genomics reveals a single-species ecosystem deep within Earth
-
Chivian, D., Broidie, E.L., Alm, E.J., Culley, D.E., Dehal, P.S., DeSantis, T.Z. et al. (2008) Environmental genomics reveals a single-species ecosystem deep within Earth. Science, 322, 275–278.
-
(2008)
Science
, vol.322
, pp. 275-278
-
-
Chivian, D.1
Broidie, E.L.2
Alm, E.J.3
Culley, D.E.4
Dehal, P.S.5
DeSantis, T.Z.6
-
4
-
-
77954547447
-
Second-generation sequencing derived insights into the temporal biodiversity dynamics of freshwater protists
-
Creer, S. (2010) Second-generation sequencing derived insights into the temporal biodiversity dynamics of freshwater protists. Molecular Ecology, 19, 2829–2831.
-
(2010)
Molecular Ecology
, vol.19
, pp. 2829-2831
-
-
Creer, S.1
-
5
-
-
79961181125
-
UCHIME improves sensitivity and speed of chimera detection
-
Edgar, R.C., Haas, B.J., Clemente, J.C., Quince, C. & Knight, R. (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics, 27, 2194–2200.
-
(2011)
Bioinformatics
, vol.27
, pp. 2194-2200
-
-
Edgar, R.C.1
Haas, B.J.2
Clemente, J.C.3
Quince, C.4
Knight, R.5
-
6
-
-
84880321899
-
Second-generation environmental sequencing unmasks marine metazoan biodiversity
-
Fonseca, V.G., Carvalho, G.R., Sung, W., Johnson, H.F., Power, D.M., Neill, S.P. et al. (2010) Second-generation environmental sequencing unmasks marine metazoan biodiversity. Nature Communications, 1, 98.
-
(2010)
Nature Communications
, vol.1
, pp. 98
-
-
Fonseca, V.G.1
Carvalho, G.R.2
Sung, W.3
Johnson, H.F.4
Power, D.M.5
Neill, S.P.6
-
7
-
-
84856563821
-
Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library
-
Gihring, T.M., Green, S.J. & Schadt, C.W. (2012) Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library. Environmental Microbiology, 14, 285–290.
-
(2012)
Environmental Microbiology
, vol.14
, pp. 285-290
-
-
Gihring, T.M.1
Green, S.J.2
Schadt, C.W.3
-
8
-
-
70350294348
-
Systematic artifacts in metagenomes from complex microbial communities
-
Gomez-Alvarez, V., Teal, T.K. & Schmidt, T.M. (2009) Systematic artifacts in metagenomes from complex microbial communities. The ISME Journal, 3, 1314–1317.
-
(2009)
The ISME Journal
, vol.3
, pp. 1314-1317
-
-
Gomez-Alvarez, V.1
Teal, T.K.2
Schmidt, T.M.3
-
9
-
-
0003816899
-
-
&, Acquired Intelligence Inc. and Kesey-Bear, Jericho, VT, 05465
-
Gotelli, N.J. & Entsminger, G.L. (2006) EcoSim: Null Models Software for Ecology. Version 7. Acquired Intelligence Inc. and Kesey-Bear, Jericho, VT 05465. http://garyents-minger.com/ecosim.ht.
-
(2006)
EcoSim: Null Models Software for Ecology. Version 7
-
-
Gotelli, N.J.1
Entsminger, G.L.2
-
10
-
-
0036590014
-
Estimation of single nucleotide polymorphism allele frequency in DNA pools by using pyrosequencing
-
Gruber, J.D., Colligan, P.B. & Wolford, J.K. (2002) Estimation of single nucleotide polymorphism allele frequency in DNA pools by using pyrosequencing. Human Genetics, 110, 395–401.
-
(2002)
Human Genetics
, vol.110
, pp. 395-401
-
-
Gruber, J.D.1
Colligan, P.B.2
Wolford, J.K.3
-
11
-
-
79954587407
-
Environmental barcoding: a next-generation sequencing approach for biomonitoring applications using river benthos
-
Hajibabaei, M., Shokralla, S., Zhou, X., Singer, G.A.C. & Baird, D.J. (2011) Environmental barcoding: a next-generation sequencing approach for biomonitoring applications using river benthos. PLoS ONE, 6, e17497.
-
(2011)
PLoS ONE
, vol.6
-
-
Hajibabaei, M.1
Shokralla, S.2
Zhou, X.3
Singer, G.A.C.4
Baird, D.J.5
-
12
-
-
84883816660
-
Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding
-
Ji, Y., Ashton, L., Pedley, S.M., Edwards, D.P., Tang, Y., Nakamura, A. et al. (2013) Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding. Ecology Letters, 16, 1245–1257.
-
(2013)
Ecology Letters
, vol.16
, pp. 1245-1257
-
-
Ji, Y.1
Ashton, L.2
Pedley, S.M.3
Edwards, D.P.4
Tang, Y.5
Nakamura, A.6
-
13
-
-
84875619226
-
MAFFT multiple sequence alignment software version 7: improvements in performance and usability
-
Katoh, K. & Standley, D.M. (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution, 30, 772–780.
-
(2013)
Molecular Biology and Evolution
, vol.30
, pp. 772-780
-
-
Katoh, K.1
Standley, D.M.2
-
14
-
-
84859829470
-
High consistency between replicate 454 pyrosequencing analyses of ectomycorrhizal plant root samples
-
Kauserud, H., Kumar, S., Brysting, A.K., Norden, J. & Carlsen, T. (2012) High consistency between replicate 454 pyrosequencing analyses of ectomycorrhizal plant root samples. Mycorrhiza, 22, 309–315.
-
(2012)
Mycorrhiza
, vol.22
, pp. 309-315
-
-
Kauserud, H.1
Kumar, S.2
Brysting, A.K.3
Norden, J.4
Carlsen, T.5
-
15
-
-
79956216816
-
CLOTU: an online pipeline for processing and clustering of 454 amplicon reads into OTUs followed by taxonomic annotation
-
Kumar, S., Carlsen, T., Mevik, B., Enger, P., Blaalid, R., Shalchian-Tabrizi, K. & Kauserud, H. (2011) CLOTU: an online pipeline for processing and clustering of 454 amplicon reads into OTUs followed by taxonomic annotation. BMC Bioinformatics, 12, 182.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 182
-
-
Kumar, S.1
Carlsen, T.2
Mevik, B.3
Enger, P.4
Blaalid, R.5
Shalchian-Tabrizi, K.6
Kauserud, H.7
-
16
-
-
73349110099
-
Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates
-
Kunin, V., Engelbrektson, A., Ochman, H. & Hugenholtz, P. (2010) Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environmental Microbiology, 12, 118–123.
-
(2010)
Environmental Microbiology
, vol.12
, pp. 118-123
-
-
Kunin, V.1
Engelbrektson, A.2
Ochman, H.3
Hugenholtz, P.4
-
17
-
-
33745634395
-
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
-
Li, W. & Godzik, A. (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics, 22, 1658–1659.
-
(2006)
Bioinformatics
, vol.22
, pp. 1658-1659
-
-
Li, W.1
Godzik, A.2
-
18
-
-
0020685956
-
Autotrophic picoplankton in the tropical ocean
-
Li, W.K.W., Subba Rao, D.V., Harrison, W.G., Smith, J.C., Cullen, J.J., Irwin, B. & Platt, T. (1983) Autotrophic picoplankton in the tropical ocean. Science, 219, 292–295.
-
(1983)
Science
, vol.219
, pp. 292-295
-
-
Li, W.K.W.1
Subba Rao, D.V.2
Harrison, W.G.3
Smith, J.C.4
Cullen, J.J.5
Irwin, B.6
Platt, T.7
-
19
-
-
29144464937
-
UniFrac: a new phylogenetic method for comparing microbial communities
-
Lozupone, C. & Knight, R. (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Applied and Environmental Microbiology, 71, 8228–8235.
-
(2005)
Applied and Environmental Microbiology
, vol.71
, pp. 8228-8235
-
-
Lozupone, C.1
Knight, R.2
-
20
-
-
78751575501
-
UniFrac: an effective distance metric for microbial community comparison
-
Lozupone, C., Lladser, M.E., Knights, D., Stombaugh, J. & Knight, R. (2011) UniFrac: an effective distance metric for microbial community comparison. The ISME Journal, 5, 169–172.
-
(2011)
The ISME Journal
, vol.5
, pp. 169-172
-
-
Lozupone, C.1
Lladser, M.E.2
Knights, D.3
Stombaugh, J.4
Knight, R.5
-
21
-
-
0034879220
-
Rare species loss alters ecosystem function - invasion resistance
-
Lyons, K.G. & Schwartz, M.W. (2001) Rare species loss alters ecosystem function - invasion resistance. Ecology Letters, 4, 358–365.
-
(2001)
Ecology Letters
, vol.4
, pp. 358-365
-
-
Lyons, K.G.1
Schwartz, M.W.2
-
22
-
-
84874557284
-
From molecules to dynamic biological communities
-
McDonald, D., Vázquez-Baeza, Y., Walters, W.A., Caporaso, J.G. & Knight, R. (2013) From molecules to dynamic biological communities. Biology and Philosophy, 28, 241–259.
-
(2013)
Biology and Philosophy
, vol.28
, pp. 241-259
-
-
McDonald, D.1
Vázquez-Baeza, Y.2
Walters, W.A.3
Caporaso, J.G.4
Knight, R.5
-
23
-
-
78650868863
-
Spatial patterns of bacterial richness and evenness in the NW Mediterranean Sea explored by pyrosequencing of the 16S rRNA
-
Pommier, T., Neal, P.R., Gasol, J.M., Coll, M., Acinas, S.G. & Pedrós-Alió, C. (2010) Spatial patterns of bacterial richness and evenness in the NW Mediterranean Sea explored by pyrosequencing of the 16S rRNA. Aquatic Microbial Ecology, 61, 221–233.
-
(2010)
Aquatic Microbial Ecology
, vol.61
, pp. 221-233
-
-
Pommier, T.1
Neal, P.R.2
Gasol, J.M.3
Coll, M.4
Acinas, S.G.5
Pedrós-Alió, C.6
-
24
-
-
67649327176
-
FastTree: computing large minimum evolution trees with profiles instead of a distance matrix
-
Price, M.N., Dehal, P.S. & Arkin, A.P. (2009) FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Molecular Biology and Evolution, 26, 1641–1650.
-
(2009)
Molecular Biology and Evolution
, vol.26
, pp. 1641-1650
-
-
Price, M.N.1
Dehal, P.S.2
Arkin, A.P.3
-
26
-
-
53849104257
-
The rational exploration of microbial diversity
-
Quince, C., Curtis, T.P. & Sloan, W.T. (2008) The rational exploration of microbial diversity. The ISME Journal, 2, 997–1006.
-
(2008)
The ISME Journal
, vol.2
, pp. 997-1006
-
-
Quince, C.1
Curtis, T.P.2
Sloan, W.T.3
-
27
-
-
77956996314
-
Soil bacterial and fungal communities across a pH gradient in an arable soil
-
Rousk, J., Bååth, E., Brookes, P.C., Lauber, C.L., Lozupone, C., Caporaso, J.G., Knight, R. & Fierer, N. (2010) Soil bacterial and fungal communities across a pH gradient in an arable soil. The ISME Journal, 4, 1340–1351.
-
(2010)
The ISME Journal
, vol.4
, pp. 1340-1351
-
-
Rousk, J.1
Bååth, E.2
Brookes, P.C.3
Lauber, C.L.4
Lozupone, C.5
Caporaso, J.G.6
Knight, R.7
Fierer, N.8
-
28
-
-
72949107142
-
Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities
-
Schloss, P.D., Westcott, S.L., Ryabin, T., Hall, J.R., Hartmann, M., Hollister, E.B. et al. (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology, 75, 7537–7541.
-
(2009)
Applied and Environmental Microbiology
, vol.75
, pp. 7537-7541
-
-
Schloss, P.D.1
Westcott, S.L.2
Ryabin, T.3
Hall, J.R.4
Hartmann, M.5
Hollister, E.B.6
-
29
-
-
37749031255
-
Next-generation sequencing transforms today's biology
-
Schuster, S.C. (2008) Next-generation sequencing transforms today's biology. Nature Methods, 5, 16–18.
-
(2008)
Nature Methods
, vol.5
, pp. 16-18
-
-
Schuster, S.C.1
-
30
-
-
77951919587
-
Bacterial diversity in a glacier foreland of the high Arctic
-
Schütte, U.M.E., Abdo, Z., Foster, J., Ravel, J., Bunge, J., Solheim, B. & Forney, L.J. (2010) Bacterial diversity in a glacier foreland of the high Arctic. Molecular Ecology, 19, 54–66.
-
(2010)
Molecular Ecology
, vol.19
, pp. 54-66
-
-
Schütte, U.M.E.1
Abdo, Z.2
Foster, J.3
Ravel, J.4
Bunge, J.5
Solheim, B.6
Forney, L.J.7
-
31
-
-
0002969802
-
A method of establishing groups of equal amplitude in plant sociology based on similarity of species content, and its application to analyses of the vegetation on Danish commons
-
Sørensen, T.A. (1948) A method of establishing groups of equal amplitude in plant sociology based on similarity of species content, and its application to analyses of the vegetation on Danish commons. Kongelige Danske Videnskabernes Selskabs Biologiske Skrifter, 5, 1–34.
-
(1948)
Kongelige Danske Videnskabernes Selskabs Biologiske Skrifter
, vol.5
, pp. 1-34
-
-
Sørensen, T.A.1
-
32
-
-
84867065778
-
The widely used small subunit 18S rDNA molecule greatly underestimates true diversity in biodiversity surveys of the meiofauna
-
Tang, C.Q., Leasi, F., Obertegger, U., Kieneke, A., Barraclough, T.G. & Fontaneto, D. (2012) The widely used small subunit 18S rDNA molecule greatly underestimates true diversity in biodiversity surveys of the meiofauna. Proceedings of the National Academy of Sciences of the United States of America, 109, 16208–16212.
-
(2012)
Proceedings of the National Academy of Sciences of the United States of America
, vol.109
, pp. 16208-16212
-
-
Tang, C.Q.1
Leasi, F.2
Obertegger, U.3
Kieneke, A.4
Barraclough, T.G.5
Fontaneto, D.6
-
33
-
-
77956283658
-
454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases
-
Tedersoo, L., Nilsson, R.H., Abarenkov, K., Jairus, T., Sadam, A., Saar, I. et al. (2010) 454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases. New Phytologist, 188, 291–301.
-
(2010)
New Phytologist
, vol.188
, pp. 291-301
-
-
Tedersoo, L.1
Nilsson, R.H.2
Abarenkov, K.3
Jairus, T.4
Sadam, A.5
Saar, I.6
-
34
-
-
84888007223
-
Analysis of soil fungal communities by amplicon pyrosequencing: current approaches to data analysis and the introduction of the pipeline SEED
-
Větrovský, T. & Baldrian, P. (2013) Analysis of soil fungal communities by amplicon pyrosequencing: current approaches to data analysis and the introduction of the pipeline SEED. Biology and Fertility of Soils, 49, 1027–1037.
-
(2013)
Biology and Fertility of Soils
, vol.49
, pp. 1027-1037
-
-
Větrovský, T.1
Baldrian, P.2
-
35
-
-
57749195712
-
RNA-Seq: a revolutionary tool for transcriptomics
-
Wang, Z., Gerstein, M. & Snyder, M. (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nature Reviews Genetics, 10, 57–63.
-
(2009)
Nature Reviews Genetics
, vol.10
, pp. 57-63
-
-
Wang, Z.1
Gerstein, M.2
Snyder, M.3
-
36
-
-
84866642478
-
Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring
-
Yu, D.W., Ji, Y., Emerson, B.C., Wang, X., Ye, C., Yang, C. & Ding, Z. (2012) Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring. Methods in Ecology and Evolution, 3, 613–623.
-
(2012)
Methods in Ecology and Evolution
, vol.3
, pp. 613-623
-
-
Yu, D.W.1
Ji, Y.2
Emerson, B.C.3
Wang, X.4
Ye, C.5
Yang, C.6
Ding, Z.7
-
37
-
-
84878914141
-
High sensitivity of 454 pyrosequencing for detection of rare species in aquatic communities
-
Zhan, A., Hulák, M., Sylvester, F., Huang, X., Adebayo, A., Abbott, C.L. et al. (2013) High sensitivity of 454 pyrosequencing for detection of rare species in aquatic communities. Methods in Ecology and Evolution, 4, 558–565.
-
(2013)
Methods in Ecology and Evolution
, vol.4
, pp. 558-565
-
-
Zhan, A.1
Hulák, M.2
Sylvester, F.3
Huang, X.4
Adebayo, A.5
Abbott, C.L.6
-
38
-
-
84905983626
-
Performance comparison of genetic markers for high-throughput sequencing-based biodiversity assessment in complex communities
-
Zhan, A., Bailey, S.A., Heath, D.D. & MacIsaac, H.J. (2014a) Performance comparison of genetic markers for high-throughput sequencing-based biodiversity assessment in complex communities. Molecular Ecology Resources, doi:10.1111/1755-0998.12254.
-
(2014)
Molecular Ecology Resources
-
-
Zhan, A.1
Bailey, S.A.2
Heath, D.D.3
MacIsaac, H.J.4
-
39
-
-
84900458220
-
Influence of artifact removal on rare species recovery in natural complex communities using high-throughput sequencing
-
Zhan, A., Xiong, W., He, S. & MacIsaac, H.J. (2014b) Influence of artifact removal on rare species recovery in natural complex communities using high-throughput sequencing. PLoS ONE, 9, e96928.
-
(2014)
PLoS ONE
, vol.9
-
-
Zhan, A.1
Xiong, W.2
He, S.3
MacIsaac, H.J.4
-
40
-
-
45549097485
-
Spatial scaling of functional gene diversity across various microbial taxa
-
Zhou, J., Kang, S., Schadt, C.W. & Garten, C.T. (2008) Spatial scaling of functional gene diversity across various microbial taxa. Proceedings of the National Academy of Sciences of the United States of America, 105, 7768–7773.
-
(2008)
Proceedings of the National Academy of Sciences of the United States of America
, vol.105
, pp. 7768-7773
-
-
Zhou, J.1
Kang, S.2
Schadt, C.W.3
Garten, C.T.4
-
41
-
-
79960557827
-
Reproducibility and quantitation of amplicon sequencing-based detection
-
Zhou, J., Wu, L., Deng, Y., Zhi, X., Jiang, Y., Tu, Q. et al. (2011) Reproducibility and quantitation of amplicon sequencing-based detection. The ISME Journal, 5, 1303–1313.
-
(2011)
The ISME Journal
, vol.5
, pp. 1303-1313
-
-
Zhou, J.1
Wu, L.2
Deng, Y.3
Zhi, X.4
Jiang, Y.5
Tu, Q.6
|