-
1
-
-
0030801002
-
Gapped BLAST and PSIBLAST: A new generation of protein database search programs
-
doi:10.1093/nar/25.17.3389
-
Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J.H., Zhang, Z., Miller, W., and Lipman, D.J. 1997. Gapped BLAST and PSIBLAST: a new generation of protein database search programs. Nucleic Acids Res. 25(17): 3389-3402. doi:10.1093/nar/25.17.3389.
-
(1997)
Nucleic Acids Res
, vol.25
, Issue.17
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.H.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
2
-
-
78650161976
-
Quantifying microbial communities with 454 pyrosequencing: Does read abundance count?
-
doi:10.1111/j.1365-294X.2010.04898.x
-
Amend, A.S., Seifert, K.A., and Bruns, T.D. 2010. Quantifying microbial communities with 454 pyrosequencing: Does read abundance count? Mol. Ecol. 19(24): 5555-5565. doi:10.1111/j.1365-294X.2010.04898.x.
-
(2010)
Mol. Ecol.
, vol.19
, Issue.24
, pp. 5555-5565
-
-
Amend, A.S.1
Seifert, K.A.2
Bruns, T.D.3
-
3
-
-
77954336858
-
ITS as an environmental DNA barcode for fungi: An in silico approach reveals potential PCR biases
-
doi:10.1186/1471-2180-10-189
-
Bellemain, E., Carlsen, T., Brochmann, C., Coissac, E., Taberlet, P., and Kauserud, H. 2010. ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases. BMC Microbiol. 10(1): 189. doi:10.1186/1471-2180-10-189.
-
(2010)
BMC Microbiol
, vol.10
, Issue.1
, pp. 189
-
-
Bellemain, E.1
Carlsen, T.2
Brochmann, C.3
Coissac, E.4
Taberlet, P.5
Kauserud, H.6
-
4
-
-
25444439861
-
GenBank
-
doi:10.1093/nar/gkq1079
-
Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., and Sayers, E.W. 2011. GenBank. Nucleic Acids Res. 39(Suppl. 1): D32-D37. doi:10.1093/nar/gkq1079.
-
(2011)
Nucleic Acids Res
, vol.39
, Issue.SUPPL. 1
-
-
Benson, D.A.1
Karsch-Mizrachi, I.2
Lipman, D.J.3
Ostell, J.4
Sayers, E.W.5
-
5
-
-
33645781099
-
Defining operational taxonomic units using DNA barcode data
-
doi:10.1098/rstb.2005.1725
-
Blaxter, M., Mann, J., Chapman, T., Thomas, F., Whitton, C., Floyd, R., and Abebe, E. 2005. Defining operational taxonomic units using DNA barcode data. Philos. Trans. R. Soc. B Biol. Sci. 360(1462): 1935-1943. doi:10.1098/rstb.2005.1725.
-
(2005)
Philos. Trans. R. Soc. B Biol. Sci.
, vol.360
, Issue.1462
, pp. 1935-1943
-
-
Blaxter, M.1
Mann, J.2
Chapman, T.3
Thomas, F.4
Whitton, C.5
Floyd, R.6
Abebe, E.7
-
6
-
-
0011298785
-
Foliar diseases caused by fungi: Ascochyta spp
-
2nd ed. Edited by J.M. Kraft and F.L. Pfleger. APS Press, St. Paul, Minn
-
Bretag, T.W., and Ramsey, M. 2001. Foliar diseases caused by fungi: Ascochyta spp. In Compendium of pea diseases and pests. 2nd ed. Edited by J.M. Kraft and F.L. Pfleger. APS Press, St. Paul, Minn. pp. 24-28.
-
(2001)
Compendium of Pea Diseases and Pests
, pp. 24-28
-
-
Bretag, T.W.1
Ramsey, M.2
-
7
-
-
70349482733
-
454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity
-
doi:10.1111/j.1469-8137.2009.03003.x
-
Buée, M., Reich, M., Murat, C., Morin, E., Nilsson, R.H., Uroz, S., and Martin, F. 2009. 454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity. New Phytol. 184(2): 449-456. doi:10.1111/j.1469-8137.2009.03003.x.
-
(2009)
New Phytol
, vol.184
, Issue.2
, pp. 449-456
-
-
Buée, M.1
Reich, M.2
Murat, C.3
Morin, E.4
Nilsson, R.H.5
Uroz, S.6
Martin, F.7
-
8
-
-
13544268567
-
A new statistical approach for assessing similarity of species composition with incidence and abundance data
-
doi:10.1111/j.1461-0248.2004.00707.x
-
Chao, A., Chazdon, R.L., Colwell, R.K., and Shen, T.J. 2005. A new statistical approach for assessing similarity of species composition with incidence and abundance data. Ecol. Lett. 8(2): 148-159. doi:10.1111/j.1461-0248.2004.00707.x.
-
(2005)
Ecol. Lett.
, vol.8
, Issue.2
, pp. 148-159
-
-
Chao, A.1
Chazdon, R.L.2
Colwell, R.K.3
Shen, T.J.4
-
10
-
-
77951498638
-
Experimental factors affecting PCR-based estimates of microbial species richness and evenness
-
doi:10.1038/ismej.2009.153
-
Engelbrektson, A., Kunin, V., Wrighton, K.C., Zvenigorodsky, N., Chen, F., Ochman, H., and Hugenholtz, P. 2010. Experimental factors affecting PCR-based estimates of microbial species richness and evenness. ISME J. 4(5): 642-647. doi:10.1038/ismej.2009.153.
-
(2010)
ISME J
, vol.4
, Issue.5
, pp. 642-647
-
-
Engelbrektson, A.1
Kunin, V.2
Wrighton, K.C.3
Zvenigorodsky, N.4
Chen, F.5
Ochman, H.6
Hugenholtz, P.7
-
11
-
-
68549132517
-
Assessment of bias associated with incomplete extraction of microbial DNA from soil
-
doi:10.1128/AEM.00120-09
-
Feinstein, L.M., Sul, W.J., and Blackwood, C.B. 2009. Assessment of bias associated with incomplete extraction of microbial DNA from soil. Appl. Environ. Microbiol. 75(16): 5428-5433. doi:10.1128/AEM.00120-09.
-
(2009)
Appl. Environ. Microbiol.
, vol.75
, Issue.16
, pp. 5428-5433
-
-
Feinstein, L.M.1
Sul, W.J.2
Blackwood, C.B.3
-
12
-
-
79952447866
-
Progress in molecular and morphological taxon discovery in Fungi and options for formal classification of environmental sequences
-
doi:10.1016/j.fbr.2011.01.001
-
Hibbett, D.S., Ohman, A., Glotzer, D., Nuhn, M., Kirk, P., and Nilsson, R. 2011. Progress in molecular and morphological taxon discovery in Fungi and options for formal classification of environmental sequences. Fungal Biol. Rev. 25(1): 38-47. doi:10.1016/j.fbr.2011.01.001.
-
(2011)
Fungal Biol. Rev.
, vol.25
, Issue.1
, pp. 38-47
-
-
Hibbett, D.S.1
Ohman, A.2
Glotzer, D.3
Nuhn, M.4
Kirk, P.5
Nilsson, R.6
-
13
-
-
34948842866
-
Accuracy and quality of massively parallel DNA pyrosequencing
-
doi:10.1186/gb-2007-8-7-r143
-
Huse, S.M., Huber, J.A., Morrison, H.G., Sogin, M.L., and Welch, D. 2007. Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol. 8(7): R143. doi:10.1186/gb-2007-8-7-r143.
-
(2007)
Genome Biol
, vol.8
, Issue.7
-
-
Huse, S.M.1
Huber, J.A.2
Morrison, H.G.3
Sogin, M.L.4
Welch, D.5
-
14
-
-
77955251092
-
Ironing out the wrinkles in the rare biosphere through improved OTU clustering
-
doi:10.1111/j.1462-2920.2010.02193.x
-
Huse, S.M., Welch, D.M., Morrison, H.G., and Sogin, M.L. 2010. Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ. Microbiol. 12(7): 1889-1898. doi:10.1111/j.1462-2920.2010.02193.x.
-
(2010)
Environ. Microbiol.
, vol.12
, Issue.7
, pp. 1889-1898
-
-
Huse, S.M.1
Welch, D.M.2
Morrison, H.G.3
Sogin, M.L.4
-
15
-
-
77957672841
-
Microbial community resemblance methods differ in their ability to detect biologically relevant patterns
-
doi:10.1038/nmeth.1499
-
Kuczynski, J., Liu, Z.Z., Lozupone, C., McDonald, D., Fierer, N., and Knight, R. 2010. Microbial community resemblance methods differ in their ability to detect biologically relevant patterns. Nat. Methods, 7(10): 813-819. doi:10.1038/nmeth.1499.
-
(2010)
Nat. Methods
, vol.7
, Issue.10
, pp. 813-819
-
-
Kuczynski, J.1
Liu, Z.Z.2
Lozupone, C.3
McDonald, D.4
Fierer, N.5
Knight, R.6
-
16
-
-
79956216816
-
CLOTU: An online pipeline for processing and clustering of 454 amplicon reads into OTUs followed by taxonomic annotation
-
doi:10.1186/1471-2105-12-182
-
Kumar, S., Carlsen, T., Mevik, B.H., Enger, P., Blaalid, R., Shalchian-Tabrizi, K., and Kauserud, H. 2011. CLOTU: an online pipeline for processing and clustering of 454 amplicon reads into OTUs followed by taxonomic annotation. BMC Bioinformatics, 12(1): 182. doi:10.1186/1471-2105-12-182.
-
(2011)
BMC Bioinformatics
, vol.12
, Issue.1
, pp. 182
-
-
Kumar, S.1
Carlsen, T.2
Mevik, B.H.3
Enger, P.4
Blaalid, R.5
Shalchian-Tabrizi, K.6
Kauserud, H.7
-
17
-
-
73349110099
-
Wrinkles in the rare biosphere: Pyrosequencing errors can lead to artificial inflation of diversity estimates
-
doi:10.1111/j.1462-2920.2009.02051.x
-
Kunin, V., Engelbrektson, A., Ochman, H., and Hugenholtz, P. 2010. Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ. Microbiol. 12(1): 118-123. doi:10.1111/j.1462-2920.2009.02051.x.
-
(2010)
Environ. Microbiol.
, vol.12
, Issue.1
, pp. 118-123
-
-
Kunin, V.1
Engelbrektson, A.2
Ochman, H.3
Hugenholtz, P.4
-
18
-
-
80051698839
-
Intragenomic variation in the ITS rDNA region obscures phylogenetic relationships and inflates estimates of operational taxonomic units in genus Laetiporus
-
doi:10.3852/10-331
-
Lindner, D.L., and Banik, M.T. 2011. Intragenomic variation in the ITS rDNA region obscures phylogenetic relationships and inflates estimates of operational taxonomic units in genus Laetiporus. Mycologia, 103(4): 731-740. doi:10.3852/10-331.
-
(2011)
Mycologia
, vol.103
, Issue.4
, pp. 731-740
-
-
Lindner, D.L.1
Banik, M.T.2
-
19
-
-
77955262221
-
Disclosing arbuscular mycorrhizal fungal biodiversity in soil through a land-use gradient using a pyrosequencing approach
-
Lumini, E., Orgiazzi, A., Borriello, R., Bonfante, P., and Bianciotto, V. 2010. Disclosing arbuscular mycorrhizal fungal biodiversity in soil through a land-use gradient using a pyrosequencing approach. Environ. Microbiol. 12(8): 2165-2179.
-
(2010)
Environ. Microbiol.
, vol.12
, Issue.8
, pp. 2165-2179
-
-
Lumini, E.1
Orgiazzi, A.2
Borriello, R.3
Bonfante, P.4
Bianciotto, V.5
-
20
-
-
24044455869
-
Genome sequencing in microfabricated high-density picolitre reactors
-
Margulies, M., Egholm, M., Altman, W.E., Attiya, S., Bader, J.S., Bemben, L.A., et al. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature (Lond.), 437(7057): 376-380.
-
(2005)
Nature (Lond.)
, vol.437
, Issue.7057
, pp. 376-380
-
-
Margulies, M.1
Egholm, M.2
Altman, W.E.3
Attiya, S.4
Bader, J.S.5
Bemben, L.A.6
-
21
-
-
23044485088
-
Fungal-specific PCR primers developed for analysis of the ITS region of environmental DNA extracts
-
doi:10.1186/1471-2180-5-28
-
Martin, K.J., and Rygiewicz, P.T. 2005. Fungal-specific PCR primers developed for analysis of the ITS region of environmental DNA extracts. BMC Microbiol. 5(1): 28. doi:10.1186/1471-2180-5-28.
-
(2005)
BMC Microbiol
, vol.5
, Issue.1
, pp. 28
-
-
Martin, K.J.1
Rygiewicz, P.T.2
-
22
-
-
0031050585
-
Prevalence and pathogenicity of foot and root rot pathogens of pea in southern Scandinavia
-
doi:10.1094/PDIS.1997.81.2.171
-
Persson, L., Bødker, L., and Larsson-Wikström, M. 1997. Prevalence and pathogenicity of foot and root rot pathogens of pea in southern Scandinavia. Plant Dis. 81(2): 171-174. doi:10.1094/PDIS.1997.81.2.171.
-
(1997)
Plant Dis
, vol.81
, Issue.2
, pp. 171-174
-
-
Persson, L.1
Bødker, L.2
Larsson-Wikström, M.3
-
23
-
-
77954025874
-
Reproducibility of read numbers in high-throughput sequencing analysis of nematode community composition and structure
-
doi:10.1111/j.1755-0998.2009.02819.x
-
Porazinska, D.L., Sung, W., Giblin-Davis, R.M., and Thomas, W.K. 2010. Reproducibility of read numbers in high-throughput sequencing analysis of nematode community composition and structure. Mol. Ecol. Resour. 10(4): 666-676. doi:10.1111/j.1755-0998.2009.02819.x.
-
(2010)
Mol. Ecol. Resour.
, vol.10
, Issue.4
, pp. 666-676
-
-
Porazinska, D.L.1
Sung, W.2
Giblin-Davis, R.M.3
Thomas, W.K.4
-
24
-
-
77956996314
-
Soil bacterial and fungal communities across a pH gradient in an arable soil
-
doi:10.1038/ismej.2010.58
-
Rousk, J., Bååth, E., Brookes, P.C., Lauber, C.L., Lozupone, C., Caporaso, J.G., et al. 2010. Soil bacterial and fungal communities across a pH gradient in an arable soil. ISME J. 4(10): 1340-1351. doi:10.1038/ismej.2010.58.
-
(2010)
ISME J
, vol.4
, Issue.10
, pp. 1340-1351
-
-
Rousk, J.1
Bååth, E.2
Brookes, P.C.3
Lauber, C.L.4
Lozupone, C.5
Caporaso, J.G.6
-
25
-
-
65349088516
-
Progress towards DNA barcoding of fungi
-
doi:10.1111/j.1755-0998.2009.02635.x
-
Seifert, K.A. 2009. Progress towards DNA barcoding of fungi. Mol. Ecol. Resour. 9(Suppl. s1): 83-89. doi:10.1111/j.1755-0998.2009.02635.x.
-
(2009)
Mol. Ecol. Resour.
, vol.9
, Issue.SUPPL. s1
, pp. 83-89
-
-
Seifert, K.A.1
-
26
-
-
78149334241
-
Pyrosequencing assessment of soil microbial communities in organic and conventional potato farms
-
doi:10.1094/PDIS-02-10-0090
-
Sugiyama, A., Vivanco, J.M., Jayanty, S.S., and Manter, D.K. 2010. Pyrosequencing assessment of soil microbial communities in organic and conventional potato farms. Plant Dis. 94(11): 1329-1335. doi:10.1094/PDIS-02-10-0090.
-
(2010)
Plant Dis
, vol.94
, Issue.11
, pp. 1329-1335
-
-
Sugiyama, A.1
Vivanco, J.M.2
Jayanty, S.S.3
Manter, D.K.4
-
27
-
-
77956283658
-
454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases
-
doi:10.1111/j.1469-8137.2010.03373.x
-
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 Phytol. 188(1): 291-301. doi:10.1111/j.1469-8137.2010.03373.x.
-
(2010)
New Phytol
, vol.188
, Issue.1
, pp. 291-301
-
-
Tedersoo, L.1
Nilsson, R.H.2
Abarenkov, K.3
Jairus, T.4
Sadam, A.5
Saar, I.6
-
28
-
-
78651322088
-
Species abundance distributions and richness estimations in fungal metagenomics - lessons learned from community ecology
-
doi:10.1111/j.1365-294X.2010.04948.x
-
Unterseher, M., Jumpponen, A., Öpik, M., Tedersoo, L., Moora, M., Dormann, C.F., et al. 2011. Species abundance distributions and richness estimations in fungal metagenomics - lessons learned from community ecology. Mol. Ecol. 20(2): 275-285. doi:10.1111/j.1365-294X.2010.04948.x.
-
(2011)
Mol. Ecol.
, vol.20
, Issue.2
, pp. 275-285
-
-
Unterseher, M.1
Jumpponen, A.2
Öpik, M.3
Tedersoo, L.4
Moora, M.5
Dormann, C.F.6
-
29
-
-
0000432452
-
Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics
-
Edited by M.A. Innis, D.H. Gelfand, J.J. Sninsky, and T.J. White. Academic Press, New York
-
White, T.J., Bruns, T.D., Lee, S.B., and Taylor, J.W. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In PCR protocols: a guide to methods and applications. Edited by M.A. Innis, D.H. Gelfand, J.J. Sninsky, and T.J. White. Academic Press, New York. pp. 315-322.
-
(1990)
PCR Protocols: A Guide to Methods and Applications
, pp. 315-322
-
-
White, T.J.1
Bruns, T.D.2
Lee, S.B.3
Taylor, J.W.4
-
30
-
-
79960557827
-
Reproducibility and quantitation of amplicon sequencing-based detection
-
doi:10.1038/ismej.2011.11
-
Zhou, J., Wu, L., Deng, Y., Zhi, X., Jiang, Y.H., Tu, Q., et al. 2011. Reproducibility and quantitation of amplicon sequencing-based detection. ISME J. 5(8): 1303-1313. doi:10.1038/ismej.2011.11.
-
(2011)
ISME J
, vol.5
, Issue.8
, pp. 1303-1313
-
-
Zhou, J.1
Wu, L.2
Deng, Y.3
Zhi, X.4
Jiang, Y.H.5
Tu, Q.6
|