-
1
-
-
84885611996
-
Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data
-
Bengtsson-Palme J., Ryberg M., Hartmann M., Branco S., Wang Z., Godhe A., De Wit P., Sánchez-García M., Edersberger I., de Sousa F., Amend A.S., Jumpponen A., Unterseher M., Kristiansson E., Abarenkov K., Bertrand Y.J.K., Sanli K., Eriksson K.M., Vik U., Veldre V., Nilsson R.H. Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data. Methods in Ecology and Evolution 2013, 4:914-919.
-
(2013)
Methods in Ecology and Evolution
, vol.4
, pp. 914-919
-
-
Bengtsson-Palme, J.1
Ryberg, M.2
Hartmann, M.3
Branco, S.4
Wang, Z.5
Godhe, A.6
De Wit, P.7
Sánchez-García, M.8
Edersberger, I.9
de Sousa, F.10
Amend, A.S.11
Jumpponen, A.12
Unterseher, M.13
Kristiansson, E.14
Abarenkov, K.15
Bertrand, Y.J.K.16
Sanli, K.17
Eriksson, K.M.18
Vik, U.19
Veldre, V.20
Nilsson, R.H.21
more..
-
2
-
-
84900322856
-
Analyses of ITS and LSU gene regions provide congruent results on fungal community responses
-
Brown S.P., Rigdon-Huss A.R., Jumpponen A. Analyses of ITS and LSU gene regions provide congruent results on fungal community responses. Fungal Ecology 2014, 9:65-68.
-
(2014)
Fungal Ecology
, vol.9
, pp. 65-68
-
-
Brown, S.P.1
Rigdon-Huss, A.R.2
Jumpponen, A.3
-
3
-
-
70349482733
-
454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity
-
Buée M., Reich M., Murat C., Morin E., Nilsson R.H., Uroz S., Martin F. 454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity. New Phytologist 2009, 184:449-456.
-
(2009)
New Phytologist
, vol.184
, 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
-
4
-
-
84863981120
-
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
-
Caporaso J.G., Lauber C.L., Walters W.A., Berg-Lyons D., Huntley J., Fierer N., Owens S.M., Betley J., Fraser L., Bauer M., Gormley N., Gilbert J.A., Smith G., Knight R. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. The ISME Journal 2012, 6:1621-1624.
-
(2012)
The ISME Journal
, vol.6
, pp. 1621-1624
-
-
Caporaso, J.G.1
Lauber, C.L.2
Walters, W.A.3
Berg-Lyons, D.4
Huntley, J.5
Fierer, N.6
Owens, S.M.7
Betley, J.8
Fraser, L.9
Bauer, M.10
Gormley, N.11
Gilbert, J.A.12
Smith, G.13
Knight, R.14
-
5
-
-
0026207466
-
DNA polymerase fidelity and the polymerase chain reaction
-
Eckert K.A., Kunkel T.A. DNA polymerase fidelity and the polymerase chain reaction. Genome Research 1991, 1:17-24.
-
(1991)
Genome Research
, vol.1
, pp. 17-24
-
-
Eckert, K.A.1
Kunkel, T.A.2
-
6
-
-
79961181125
-
UCHIME improves sensitivity and speed of chimera detection
-
Edgar R.C., Haas B.J., Clemente J.C., Quince C., Knight R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 2011, 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
-
7
-
-
84879414990
-
Topographic diversity of fungal and bacterial communities in human skin
-
NIH Intramural Sequencing Center Comparative Sequencing Program
-
Findley K., Oh J., Yang J., Conlan S., Deming C., Meyer J.A., Schoenfeld D., Nomicos E., Park M., Kong H.H., Segre J.A. Topographic diversity of fungal and bacterial communities in human skin. Nature 2013, 498:367-370. NIH Intramural Sequencing Center Comparative Sequencing Program.
-
(2013)
Nature
, vol.498
, pp. 367-370
-
-
Findley, K.1
Oh, J.2
Yang, J.3
Conlan, S.4
Deming, C.5
Meyer, J.A.6
Schoenfeld, D.7
Nomicos, E.8
Park, M.9
Kong, H.H.10
Segre, J.A.11
-
8
-
-
77956096764
-
Multivariate cutoff levels analysis (MultoCoLA) of large community data sets
-
Gobet A., Quince C., Ramette A. Multivariate cutoff levels analysis (MultoCoLA) of large community data sets. Nucleic Acid Research 2010, 38(15):e155.
-
(2010)
Nucleic Acid Research
, vol.38
, Issue.15
, pp. e155
-
-
Gobet, A.1
Quince, C.2
Ramette, A.3
-
9
-
-
84878270728
-
Robust estimation of microbial diversity in theory and practice
-
Haegeman B., Hamelin J., Moriarty J., Neal P., Dushoff J., Weitz J.S. Robust estimation of microbial diversity in theory and practice. The ISME Journal 2013, 7:1092-1101.
-
(2013)
The ISME Journal
, vol.7
, pp. 1092-1101
-
-
Haegeman, B.1
Hamelin, J.2
Moriarty, J.3
Neal, P.4
Dushoff, J.5
Weitz, J.S.6
-
11
-
-
77955251092
-
Ironing out the wrinkles in the rare biosphere through improved OTU clustering
-
Huse S.M., Welch D.M., Morrison H.G., Sogin M.L. Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environmental Microbiology 2010, 12:1889-1898.
-
(2010)
Environmental Microbiology
, vol.12
, pp. 1889-1898
-
-
Huse, S.M.1
Welch, D.M.2
Morrison, H.G.3
Sogin, M.L.4
-
12
-
-
33750329972
-
Reconstructing the early evolution of fungi using a six-gene phylogeny
-
James T.Y., Kauff F., Schoch C.L., Matteny P.B., Hofstetter V., Cox C.J., Celia G., Gueidas C., Fraker E., Miadlikowska J., Lumbsch H.T., Rauhut A., Reeb V., Arnold A.E., et al. Reconstructing the early evolution of fungi using a six-gene phylogeny. Nature 2006, 443:818-822.
-
(2006)
Nature
, vol.443
, pp. 818-822
-
-
James, T.Y.1
Kauff, F.2
Schoch, C.L.3
Matteny, P.B.4
Hofstetter, V.5
Cox, C.J.6
Celia, G.7
Gueidas, C.8
Fraker, E.9
Miadlikowska, J.10
Lumbsch, H.T.11
Rauhut, A.12
Reeb, V.13
Arnold, A.E.14
-
13
-
-
70349493057
-
Massively parallel 454 sequencing indicated hyperdiverse fungal communities in temperate Quercus macrocarpa phyllosphere
-
Jumpponen A., Jones K.L. Massively parallel 454 sequencing indicated hyperdiverse fungal communities in temperate Quercus macrocarpa phyllosphere. New Phytologist 2009, 184:438-448.
-
(2009)
New Phytologist
, vol.184
, pp. 438-448
-
-
Jumpponen, A.1
Jones, K.L.2
-
14
-
-
84886099720
-
Toward a unified paradigm for sequence-based identification of fungi
-
Kõljalg U., Nilsson R.H., Abarenkov K., Tedersoo L., Taylor A.F.S., Bahram M., Bates S.T., Bruns T.D., Bengtsson-Palme J., Callaghan T.M., Douglas B., Drenkhan T., Eberhardt U., Dueñas M., Grebenc T., Griffith G.W., Hartmann M., Kirk P.M., Kohout P., Larsson E., Lindahl B.D., Lücking R., Nguyen N.H., Niskanen T., Oja J., Peay K.G., Peintner U., Peterson M., Põldmaa K., Saag L., Saar I., Schüßler A., Scott J.A., Senés C., Smith M.E., Suija A., Taylor D.L., Telleria M.T., Weiss M., Larsson K. Toward a unified paradigm for sequence-based identification of fungi. Molecular Ecology 2013, 22:5271-5277.
-
(2013)
Molecular Ecology
, vol.22
, pp. 5271-5277
-
-
Kõljalg, U.1
Nilsson, R.H.2
Abarenkov, K.3
Tedersoo, L.4
Taylor, A.F.S.5
Bahram, M.6
Bates, S.T.7
Bruns, T.D.8
Bengtsson-Palme, J.9
Callaghan, T.M.10
Douglas, B.11
Drenkhan, T.12
Eberhardt, U.13
Dueñas, M.14
Grebenc, T.15
Griffith, G.W.16
Hartmann, M.17
Kirk, P.M.18
Kohout, P.19
Larsson, E.20
Lindahl, B.D.21
Lücking, R.22
Nguyen, N.H.23
Niskanen, T.24
Oja, J.25
Peay, K.G.26
Peintner, U.27
Peterson, M.28
Põldmaa, K.29
Saag, L.30
Saar, I.31
Schüßler, A.32
Scott, J.A.33
Senés, C.34
Smith, M.E.35
Suija, A.36
Taylor, D.L.37
Telleria, M.T.38
Weiss, M.39
Larsson, K.40
more..
-
15
-
-
73349110099
-
Wrinkles in the rare biosphere: pyrosequencing errors lead to artificial inflation of diversity estimates
-
Kunin V., Engelbrektson A., Ochman H., Hugenholtz P. Wrinkles in the rare biosphere: pyrosequencing errors lead to artificial inflation of diversity estimates. Environmental Microbiology 2010, 12:118-123.
-
(2010)
Environmental Microbiology
, vol.12
, pp. 118-123
-
-
Kunin, V.1
Engelbrektson, A.2
Ochman, H.3
Hugenholtz, P.4
-
16
-
-
84878360700
-
Fungal community analysis by high-throughput sequencing of amplified markers - a user's guide
-
Lindahl B.D., Nilsson R.H., Tedersoo L., Abarenkov K., Carlsen T., Kjøller R., Kõljalg U., Pennanen T., Rosendahl S., Stenlid J., Kauserud H. Fungal community analysis by high-throughput sequencing of amplified markers - a user's guide. New Phytologist 2013, 199:288-299.
-
(2013)
New Phytologist
, vol.199
, pp. 288-299
-
-
Lindahl, B.D.1
Nilsson, R.H.2
Tedersoo, L.3
Abarenkov, K.4
Carlsen, T.5
Kjøller, R.6
Kõljalg, U.7
Pennanen, T.8
Rosendahl, S.9
Stenlid, J.10
Kauserud, H.11
-
17
-
-
84890806831
-
Meta-analysis of deep-sequenced fungal communities indicates limited taxon sharing between studies and the presence of biogeographic patterns
-
Meiser A., Bálint M., Schmitt I. Meta-analysis of deep-sequenced fungal communities indicates limited taxon sharing between studies and the presence of biogeographic patterns. New Phytologist 2014, 201:623-635.
-
(2014)
New Phytologist
, vol.201
, pp. 623-635
-
-
Meiser, A.1
Bálint, M.2
Schmitt, I.3
-
18
-
-
77956292565
-
An open source software package for automated extraction of ITS1 and ITS2 from fungal ITS sequences for use in high-throughput community assays and molecular ecology
-
Nilsson R.H., Veldre V., Hartmann M., Unterseher M., Amend A., Bergsten J., Kristiansson E., Ruberg M., Jumpponen A., Abarenkov K. An open source software package for automated extraction of ITS1 and ITS2 from fungal ITS sequences for use in high-throughput community assays and molecular ecology. Fungal Ecology 2010, 3:284-287.
-
(2010)
Fungal Ecology
, vol.3
, pp. 284-287
-
-
Nilsson, R.H.1
Veldre, V.2
Hartmann, M.3
Unterseher, M.4
Amend, A.5
Bergsten, J.6
Kristiansson, E.7
Ruberg, M.8
Jumpponen, A.9
Abarenkov, K.10
-
19
-
-
79959874811
-
Towards standardization of the description and publication of next-generation sequencing datasets of fungal communities
-
Nilsson R.H., Tedersoo L., Lindahl B.D., Kjøller R., Carlsen T., Quince C., Abarenkov K., Pennanen T., Stenlid J., Bruns T., Larsson K., Kõljalg U., Kauserud H. Towards standardization of the description and publication of next-generation sequencing datasets of fungal communities. New Phytologist 2011, 191:314-318.
-
(2011)
New Phytologist
, vol.191
, pp. 314-318
-
-
Nilsson, R.H.1
Tedersoo, L.2
Lindahl, B.D.3
Kjøller, R.4
Carlsen, T.5
Quince, C.6
Abarenkov, K.7
Pennanen, T.8
Stenlid, J.9
Bruns, T.10
Larsson, K.11
Kõljalg, U.12
Kauserud, H.13
-
20
-
-
79251565226
-
Removing noise from Pyrosequenced amplicons
-
Quince C., Lanzen A., Davenport R.J., Turnbaugh P.J. Removing noise from Pyrosequenced amplicons. BMC Bioinformatics 2011, 12:38.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 38
-
-
Quince, C.1
Lanzen, A.2
Davenport, R.J.3
Turnbaugh, P.J.4
-
21
-
-
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., Lesniewski R.A., Oakley B.B., Parks E.B., Robinson C.J., Sahl J.W., Stres B., Thallinger G.G., Van Horn D.J., Weber C.F. Introducing mothur: open-source, platform independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology 2009, 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
Lesniewski, R.A.7
Oakley, B.B.8
Parks, E.B.9
Robinson, C.J.10
Sahl, J.W.11
Stres, B.12
Thallinger, G.G.13
Van Horn, D.J.14
Weber, C.F.15
-
22
-
-
84865720868
-
Culturing captures members of the soil rare biosphere
-
Shade A., Hogan C.S., Klimowicz A.K., Linske M., McManus P.S., Handelsman J. Culturing captures members of the soil rare biosphere. Environmental Microbiology 2012, 14:2247-2252.
-
(2012)
Environmental Microbiology
, vol.14
, pp. 2247-2252
-
-
Shade, A.1
Hogan, C.S.2
Klimowicz, A.K.3
Linske, M.4
McManus, P.S.5
Handelsman, J.6
-
23
-
-
33747073504
-
Microbial diversity in the deep sea and the underexplored "rare biosphere."
-
Sogin M.L., Morrison H.G., Huber J.A., Welch D.M., Huse A.M., Neal P.R., Arrieta J.M., Herndl G.J. Microbial diversity in the deep sea and the underexplored "rare biosphere.". Proceedings of the National Academy of Science 2006, 103:12115-12120.
-
(2006)
Proceedings of the National Academy of Science
, vol.103
, pp. 12115-12120
-
-
Sogin, M.L.1
Morrison, H.G.2
Huber, J.A.3
Welch, D.M.4
Huse, A.M.5
Neal, P.R.6
Arrieta, J.M.7
Herndl, G.J.8
-
24
-
-
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., Bahram M., Bechem E., Chuyong G., Kõljalg U. 454 pyrosequencing and sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases. New Phytologist 2010, 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
Bahram, M.7
Bechem, E.8
Chuyong, G.9
Kõljalg, U.10
-
25
-
-
78651322088
-
Species abundance distributions and richness estimations in fungal metagenomics - lessons learned from community ecology
-
Unterseher M., Jumpponen A., Öpik M., Tedersoo L., Moora M., Dormann C.F., Schnittler M. Species abundance distributions and richness estimations in fungal metagenomics - lessons learned from community ecology. Molecular Ecology 2011, 20:275-285.
-
(2011)
Molecular Ecology
, vol.20
, pp. 275-285
-
-
Unterseher, M.1
Jumpponen, A.2
Öpik, M.3
Tedersoo, L.4
Moora, M.5
Dormann, C.F.6
Schnittler, M.7
-
26
-
-
34548293679
-
Naïve Bayesian classifier for rapid assignment of rRNA sequences into new bacterial taxonomy
-
Wang Q., Garrity G.M., Tiedje J.M., Cole J.R. Naïve Bayesian classifier for rapid assignment of rRNA sequences into new bacterial taxonomy. Applied and Environmental Microbiology 2007, 73. 5261-5267.
-
(2007)
Applied and Environmental Microbiology
, vol.73
, pp. 5261-5267
-
-
Wang, Q.1
Garrity, G.M.2
Tiedje, J.M.3
Cole, J.R.4
-
27
-
-
84878914141
-
High-sensitivity pyrosequencing of detection of rare species in aquatic communities
-
Zhan A., Hulák M., Sylvester F., Huang X., Adebayo A.A., Abbot C.L., Adamowicz S.J., Heath D.D., Cristescu M.E., Maclsaac H.J. High-sensitivity pyrosequencing of detection of rare species in aquatic communities. Methods in Ecology and Evolution 2013, 4:58-565.
-
(2013)
Methods in Ecology and Evolution
, vol.4
, pp. 58-565
-
-
Zhan, A.1
Hulák, M.2
Sylvester, F.3
Huang, X.4
Adebayo, A.A.5
Abbot, C.L.6
Adamowicz, S.J.7
Heath, D.D.8
Cristescu, M.E.9
Maclsaac, H.J.10
|