-
1
-
-
77954748234
-
The UNITE database for molecular identification of fungi-recent updates and future perspectives
-
Abarenkov K., Henrik Nilsson R., Larsson K.H., Alexander I.J., Eberhardt U., Erland S., Hoiland K., Kjoller R., Larsson E., Pennanen T., Sen R., Taylor A.F., Tedersoo L., Ursing B.M., Vralstad T., Liimatainen K., Peintner U., Koljalg U. The UNITE database for molecular identification of fungi-recent updates and future perspectives. New Phytol. 2010, 186:281.
-
(2010)
New Phytol.
, vol.186
, pp. 281
-
-
Abarenkov, K.1
Henrik Nilsson, R.2
Larsson, K.H.3
Alexander, I.J.4
Eberhardt, U.5
Erland, S.6
Hoiland, K.7
Kjoller, R.8
Larsson, E.9
Pennanen, T.10
Sen, R.11
Taylor, A.F.12
Tedersoo, L.13
Ursing, B.M.14
Vralstad, T.15
Liimatainen, K.16
Peintner, U.17
Koljalg, U.18
-
2
-
-
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., Ebersberger I., de Sousa F., Amend A., 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 Ecol. Evol. 2013, 4:914.
-
(2013)
Methods Ecol. Evol.
, vol.4
, pp. 914
-
-
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
Ebersberger, I.9
de Sousa, F.10
Amend, A.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..
-
3
-
-
77952243141
-
QIIME allows analysis of high-throughput community sequencing data
-
Caporaso J.G., Kuczynski J., Stombaugh J., Bittinger K., Bushman F.D., Costello E.K., Fierer N., Pena A.G., Goodrich J.K., Gordon J.I., Huttley G.A., Kelley S.T., Knights D., Koenig J.E., Ley R.E., Lozupone C.A., McDonald D., Muegge B.D., Pirrung M., Reeder J., Sevinsky J.R., Turnbaugh P.J., Walters W.A., Widmann J., Yatsunenko T., Zaneveld J., Knight R. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 2010, 7:335.
-
(2010)
Nat. Methods
, vol.7
, pp. 335
-
-
Caporaso, J.G.1
Kuczynski, J.2
Stombaugh, J.3
Bittinger, K.4
Bushman, F.D.5
Costello, E.K.6
Fierer, N.7
Pena, A.G.8
Goodrich, J.K.9
Gordon, J.I.10
Huttley, G.A.11
Kelley, S.T.12
Knights, D.13
Koenig, J.E.14
Ley, R.E.15
Lozupone, C.A.16
McDonald, D.17
Muegge, B.D.18
Pirrung, M.19
Reeder, J.20
Sevinsky, J.R.21
Turnbaugh, P.J.22
Walters, W.A.23
Widmann, J.24
Yatsunenko, T.25
Zaneveld, J.26
Knight, R.27
more..
-
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. ISME J. 2012, 6:1621.
-
(2012)
ISME J.
, vol.6
, pp. 1621
-
-
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
-
-
84858376593
-
The impact of the gut microbiota on human health: an integrative view
-
Clemente J.C., Ursell L.K., Parfrey L.W., Knight R. The impact of the gut microbiota on human health: an integrative view. Cell 2012, 148:1258.
-
(2012)
Cell
, vol.148
, pp. 1258
-
-
Clemente, J.C.1
Ursell, L.K.2
Parfrey, L.W.3
Knight, R.4
-
6
-
-
84894626268
-
Fungi of the murine gut: episodic variation and proliferation during antibiotic treatment
-
Dollive S., Chen Y.Y., Grunberg S., Bittinger K., Hoffmann C., Vandivier L., Cuff C., Lewis J.D., Wu G.D., Bushman F.D. Fungi of the murine gut: episodic variation and proliferation during antibiotic treatment. PLoS One 2013, 8:e71806.
-
(2013)
PLoS One
, vol.8
, pp. e71806
-
-
Dollive, S.1
Chen, Y.Y.2
Grunberg, S.3
Bittinger, K.4
Hoffmann, C.5
Vandivier, L.6
Cuff, C.7
Lewis, J.D.8
Wu, G.D.9
Bushman, F.D.10
-
7
-
-
84879414990
-
Topographic diversity of fungal and bacterial communities in human skin
-
Findley K., Oh J., Yang J., Conlan S., Deming C., Meyer J.A., Schoenfeld D., Nomicos E., Park M., Program N.I.H.I.S.C.C.S., Kong H.H., Segre J.A. Topographic diversity of fungal and bacterial communities in human skin. Nature 2013, 498:367.
-
(2013)
Nature
, vol.498
, pp. 367
-
-
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
Program, N.I.H.I.S.C.C.S.10
Kong, H.H.11
Segre, J.A.12
-
8
-
-
0027580147
-
ITS primers with enhanced specificity for basidiomycetes-application to the identification of mycorrhizae and rusts
-
Gardes M., Bruns T.D. ITS primers with enhanced specificity for basidiomycetes-application to the identification of mycorrhizae and rusts. Mol. Ecol. 1993, 2:113.
-
(1993)
Mol. Ecol.
, vol.2
, pp. 113
-
-
Gardes, M.1
Bruns, T.D.2
-
9
-
-
84879148662
-
Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents
-
Hoffmann C., Dollive S., Grunberg S., Chen J., Li H., Wu G.D., Lewis J.D., Bushman F.D. Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents. PLoS One 2013, 8:e66019.
-
(2013)
PLoS One
, vol.8
, pp. e66019
-
-
Hoffmann, C.1
Dollive, S.2
Grunberg, S.3
Chen, J.4
Li, H.5
Wu, G.D.6
Lewis, J.D.7
Bushman, F.D.8
-
10
-
-
84861964286
-
Interactions between commensal fungi and the C-type lectin receptor Dectin-1 influence colitis
-
Iliev I.D., Funari V.A., Taylor K.D., Nguyen Q., Reyes C.N., Strom S.P., Brown J., Becker C.A., Fleshner P.R., Dubinsky M., Rotter J.I., Wang H.L., McGovern D.P., Brown G.D., Underhill D.M. Interactions between commensal fungi and the C-type lectin receptor Dectin-1 influence colitis. Science 2012, 336:1314.
-
(2012)
Science
, vol.336
, pp. 1314
-
-
Iliev, I.D.1
Funari, V.A.2
Taylor, K.D.3
Nguyen, Q.4
Reyes, C.N.5
Strom, S.P.6
Brown, J.7
Becker, C.A.8
Fleshner, P.R.9
Dubinsky, M.10
Rotter, J.I.11
Wang, H.L.12
McGovern, D.P.13
Brown, G.D.14
Underhill, D.M.15
-
11
-
-
84884273778
-
Advances in inflammatory bowel disease pathogenesis: linking host genetics and the microbiome
-
Knights D., Lassen K.G., Xavier R.J. Advances in inflammatory bowel disease pathogenesis: linking host genetics and the microbiome. Gut 2013, 62:1505.
-
(2013)
Gut
, vol.62
, pp. 1505
-
-
Knights, D.1
Lassen, K.G.2
Xavier, R.J.3
-
12
-
-
84860756398
-
Performance comparison of benchtop high-throughput sequencing platforms
-
Loman N.J., Misra R.V., Dallman T.J., Constantinidou C., Gharbia S.E., Wain J., Pallen M.J. Performance comparison of benchtop high-throughput sequencing platforms. Nat. Biotechnol. 2012, 30:434.
-
(2012)
Nat. Biotechnol.
, vol.30
, pp. 434
-
-
Loman, N.J.1
Misra, R.V.2
Dallman, T.J.3
Constantinidou, C.4
Gharbia, S.E.5
Wain, J.6
Pallen, M.J.7
-
13
-
-
80255127234
-
Cutadapt removes adapter sequences from high-throughput sequencing reads
-
Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. journal 2011, 17.
-
(2011)
EMBnet. journal
, vol.17
-
-
Martin, M.1
-
14
-
-
84862286169
-
A framework for human microbiome research
-
Methé B.A., Nelson K.E., Pop M., Creasy H.H., Giglio M.G., Huttenhower C., Gevers D., Petrosino J.F., Abubucker S., Badger J.H., Chinwalla A.T., Earl A.M., FitzGerald M.G., Fulton R.S., Hallsworth-Pepin K., Lobos E.A., Madupu R., Magrini V., Martin J.C., Mitreva M., Muzny D.M., Sodergren E.J., Versalovic J., Wollam A.M., Worley K.C., Wortman J.R., Young S.K., Zeng Q., Aagaard K.M., Abolude O.O., Allen-Vercoe E., Alm E.J., Alvarado L., Andersen G.L., Anderson S., Appelbaum E., Arachchi H.M., Armitage G., Arze C.A., Ayvaz T., Baker C.C., Begg L., Belachew T., Bhonagiri V., Bihan M., Blaser M.J., Bloom T., Bonazzi J.V., Brooks P., Buck G.A., Buhay C.J., Busam D.A., Campbell J.L., Canon S.R., Cantarel B.L., Chain P.S., Chen I.-M.A., Chen L., Chhibba S., Chu K., Ciulla D.M., Clemente J.C., Clifton S.W., Conlan S., Crabtree J., Cutting M.A., Davidovics N.J., Davis C.C., DeSantis T.Z., Deal C., Delehaunty K.D., Dewhirst F.E., Deych E., Ding Y., Dooling D.J., Dugan S.P., Dunne W.M., Durkin A.S., Edgar R.C., Erlich R.L., Farmer C.N., Farrell R.M., Faust K., Feldgarden M., Felix V.M., Fisher S., Fodor A.A., Forney L., Foster L., Francesco V.D., Friedman J., Friedrich D.C., Fronick C.C., Fulton L.L., Gao H., Garcia N., Giannoukos G., Giblin C., Giovanni M.Y., et al. A framework for human microbiome research. Nature 2012, 486:215.
-
(2012)
Nature
, vol.486
, pp. 215
-
-
Methé, B.A.1
Nelson, K.E.2
Pop, M.3
Creasy, H.H.4
Giglio, M.G.5
Huttenhower, C.6
Gevers, D.7
Petrosino, J.F.8
Abubucker, S.9
Badger, J.H.10
Chinwalla, A.T.11
Earl, A.M.12
FitzGerald, M.G.13
Fulton, R.S.14
Hallsworth-Pepin, K.15
Lobos, E.A.16
Madupu, R.17
Magrini, V.18
Martin, J.C.19
Mitreva, M.20
Muzny, D.M.21
Sodergren, E.J.22
Versalovic, J.23
Wollam, A.M.24
Worley, K.C.25
Wortman, J.R.26
Young, S.K.27
Zeng, Q.28
Aagaard, K.M.29
Abolude, O.O.30
Allen-Vercoe, E.31
Alm, E.J.32
Alvarado, L.33
Andersen, G.L.34
Anderson, S.35
Appelbaum, E.36
Arachchi, H.M.37
Armitage, G.38
Arze, C.A.39
Ayvaz, T.40
Baker, C.C.41
Begg, L.42
Belachew, T.43
Bhonagiri, V.44
Bihan, M.45
Blaser, M.J.46
Bloom, T.47
Bonazzi, J.V.48
Brooks, P.49
Buck, G.A.50
Buhay, C.J.51
Busam, D.A.52
Campbell, J.L.53
Canon, S.R.54
Cantarel, B.L.55
Chain, P.S.56
Chen, I.-M.A.57
Chen, L.58
Chhibba, S.59
Chu, K.60
Ciulla, D.M.61
Clemente, J.C.62
Clifton, S.W.63
Conlan, S.64
Crabtree, J.65
Cutting, M.A.66
Davidovics, N.J.67
Davis, C.C.68
DeSantis, T.Z.69
Deal, C.70
Delehaunty, K.D.71
Dewhirst, F.E.72
Deych, E.73
Ding, Y.74
Dooling, D.J.75
Dugan, S.P.76
Dunne, W.M.77
Durkin, A.S.78
Edgar, R.C.79
Erlich, R.L.80
Farmer, C.N.81
Farrell, R.M.82
Faust, K.83
Feldgarden, M.84
Felix, V.M.85
Fisher, S.86
Fodor, A.A.87
Forney, L.88
Foster, L.89
Francesco, V.D.90
Friedman, J.91
Friedrich, D.C.92
Fronick, C.C.93
Fulton, L.L.94
Gao, H.95
Garcia, N.96
Giannoukos, G.97
Giblin, C.98
Giovanni, M.Y.99
more..
-
15
-
-
84898808700
-
Meta'omic analytic techniques for studying the intestinal microbiome
-
(e1)
-
Morgan X.C., Huttenhower C. Meta'omic analytic techniques for studying the intestinal microbiome. Gastroenterology 2014, 146:1437. (e1).
-
(2014)
Gastroenterology
, vol.146
, pp. 1437
-
-
Morgan, X.C.1
Huttenhower, C.2
-
16
-
-
36049004436
-
Taxonomic reliability of DNA sequences in public sequence databases: a fungal perspective
-
Nilsson R.H., Ryberg M., Kristiansson E., Abarenkov K., Larsson K.H., Koljalg U. Taxonomic reliability of DNA sequences in public sequence databases: a fungal perspective. PLoS One 2006, 1:e59.
-
(2006)
PLoS One
, vol.1
, pp. e59
-
-
Nilsson, R.H.1
Ryberg, M.2
Kristiansson, E.3
Abarenkov, K.4
Larsson, K.H.5
Koljalg, U.6
-
17
-
-
84869045574
-
Reference databases for taxonomic assignment in metagenomics
-
Santamaria M., Fosso B., Consiglio A., De Caro G., Grillo G., Licciulli F., Liuni S., Marzano M., Alonso-Alemany D., Valiente G., Pesole G. Reference databases for taxonomic assignment in metagenomics. Brief. Bioinform. 2012, 13:682.
-
(2012)
Brief. Bioinform.
, vol.13
, pp. 682
-
-
Santamaria, M.1
Fosso, B.2
Consiglio, A.3
De Caro, G.4
Grillo, G.5
Licciulli, F.6
Liuni, S.7
Marzano, M.8
Alonso-Alemany, D.9
Valiente, G.10
Pesole, G.11
-
18
-
-
84924853303
-
Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi
-
Schoch C.L., Robbertse B., Robert V., Vu D., Cardinali G., Irinyi L., Meyer W., Nilsson R.H., Hughes K., Miller A.N., Kirk P.M., Abarenkov K., Aime M.C., Ariyawansa H.A., Bidartondo M., Boekhout T., Buyck B., Cai Q., Chen J., Crespo A., Crous P.W., Damm U., De Beer Z.W., Dentinger B.T., Divakar P.K., Duenas M., Feau N., Fliegerova K., Garcia M.A., Ge Z.W., Griffith G.W., Groenewald J.Z., Groenewald M., Grube M., Gryzenhout M., Gueidan C., Guo L., Hambleton S., Hamelin R., Hansen K., Hofstetter V., Hong S.B., Houbraken J., Hyde K.D., Inderbitzin P., Johnston P.R., Karunarathna S.C., Koljalg U., Kovacs G.M., Kraichak E., Krizsan K., Kurtzman C.P., Larsson K.H., Leavitt S., Letcher P.M., Liimatainen K., Liu J.K., Lodge D.J., Luangsa-ard J.J., Lumbsch H.T., Maharachchikumbura S.S., Manamgoda D., Martin M.P., Minnis A.M., Moncalvo J.M., Mule G., Nakasone K.K., Niskanen T., Olariaga I., Papp T., Petkovits T., Pino-Bodas R., Powell M.J., Raja H.A., Redecker D., Sarmiento-Ramirez J.M., Seifert K.A., Shrestha B., Stenroos S., Stielow B., Suh S.O., Tanaka K., Tedersoo L., Telleria M.T., Udayanga D., Untereiner W.A., Dieguez Uribeondo J., Subbarao K.V., Vagvolgyi C., Visagie C., Voigt K., Walker D.M., Weir B.S., Weiss M., Wijayawardene N.N., Wingfield M.J., Xu J.P., Yang Z.L., Zhang N., Zhuang W.Y., et al. Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi. Database: the Journal of Biological Databases and Curation 2014, 2014.
-
(2014)
Database: the Journal of Biological Databases and Curation
, vol.2014
-
-
Schoch, C.L.1
Robbertse, B.2
Robert, V.3
Vu, D.4
Cardinali, G.5
Irinyi, L.6
Meyer, W.7
Nilsson, R.H.8
Hughes, K.9
Miller, A.N.10
Kirk, P.M.11
Abarenkov, K.12
Aime, M.C.13
Ariyawansa, H.A.14
Bidartondo, M.15
Boekhout, T.16
Buyck, B.17
Cai, Q.18
Chen, J.19
Crespo, A.20
Crous, P.W.21
Damm, U.22
De Beer, Z.W.23
Dentinger, B.T.24
Divakar, P.K.25
Duenas, M.26
Feau, N.27
Fliegerova, K.28
Garcia, M.A.29
Ge, Z.W.30
Griffith, G.W.31
Groenewald, J.Z.32
Groenewald, M.33
Grube, M.34
Gryzenhout, M.35
Gueidan, C.36
Guo, L.37
Hambleton, S.38
Hamelin, R.39
Hansen, K.40
Hofstetter, V.41
Hong, S.B.42
Houbraken, J.43
Hyde, K.D.44
Inderbitzin, P.45
Johnston, P.R.46
Karunarathna, S.C.47
Koljalg, U.48
Kovacs, G.M.49
Kraichak, E.50
Krizsan, K.51
Kurtzman, C.P.52
Larsson, K.H.53
Leavitt, S.54
Letcher, P.M.55
Liimatainen, K.56
Liu, J.K.57
Lodge, D.J.58
Luangsa-ard, J.J.59
Lumbsch, H.T.60
Maharachchikumbura, S.S.61
Manamgoda, D.62
Martin, M.P.63
Minnis, A.M.64
Moncalvo, J.M.65
Mule, G.66
Nakasone, K.K.67
Niskanen, T.68
Olariaga, I.69
Papp, T.70
Petkovits, T.71
Pino-Bodas, R.72
Powell, M.J.73
Raja, H.A.74
Redecker, D.75
Sarmiento-Ramirez, J.M.76
Seifert, K.A.77
Shrestha, B.78
Stenroos, S.79
Stielow, B.80
Suh, S.O.81
Tanaka, K.82
Tedersoo, L.83
Telleria, M.T.84
Udayanga, D.85
Untereiner, W.A.86
Dieguez Uribeondo, J.87
Subbarao, K.V.88
Vagvolgyi, C.89
Visagie, C.90
Voigt, K.91
Walker, D.M.92
Weir, B.S.93
Weiss, M.94
Wijayawardene, N.N.95
Wingfield, M.J.96
Xu, J.P.97
Yang, Z.L.98
Zhang, N.99
more..
-
19
-
-
84859972408
-
Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi
-
Schoch C.L., Seifert K.A., Huhndorf S., Robert V., Spouge J.L., Levesque C.A., Chen W., Fungal Barcoding C., Fungal Barcoding Consortium Author L. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc. Natl. Acad. Sci. U. S. A. 2012, 109:6241.
-
(2012)
Proc. Natl. Acad. Sci. U. S. A.
, vol.109
, pp. 6241
-
-
Schoch, C.L.1
Seifert, K.A.2
Huhndorf, S.3
Robert, V.4
Spouge, J.L.5
Levesque, C.A.6
Chen, W.7
Fungal Barcoding, C.8
Fungal Barcoding Consortium Author, L.9
-
20
-
-
32944459814
-
Abundant and diverse fungal microbiota in the murine intestine
-
Scupham A.J., Presley L.L., Wei B., Bent E., Griffith N., McPherson M., Zhu F., Oluwadara O., Rao N., Braun J., Borneman J. Abundant and diverse fungal microbiota in the murine intestine. Appl. Environ. Microbiol. 2006, 72:793.
-
(2006)
Appl. Environ. Microbiol.
, vol.72
, pp. 793
-
-
Scupham, A.J.1
Presley, L.L.2
Wei, B.3
Bent, E.4
Griffith, N.5
McPherson, M.6
Zhu, F.7
Oluwadara, O.8
Rao, N.9
Braun, J.10
Borneman, J.11
-
21
-
-
79959383523
-
Metagenomic biomarker discovery and explanation
-
Segata N., Izard J., Waldron L., Gevers D., Miropolsky L., Garrett W.S., Huttenhower C. Metagenomic biomarker discovery and explanation. Genome Biol. 2011, 12:R60.
-
(2011)
Genome Biol.
, vol.12
, pp. R60
-
-
Segata, N.1
Izard, J.2
Waldron, L.3
Gevers, D.4
Miropolsky, L.5
Garrett, W.S.6
Huttenhower, C.7
-
22
-
-
84901296354
-
The mycobiota: interactions between commensal fungi and the host immune system
-
Underhill D.M., Iliev I.D. The mycobiota: interactions between commensal fungi and the host immune system. Nat. Rev. Immunol. 2014, 14:405.
-
(2014)
Nat. Rev. Immunol.
, vol.14
, pp. 405
-
-
Underhill, D.M.1
Iliev, I.D.2
|