Jaguc - a Software package for Environmental Diversity Analyses
Nebel M, Wild S, Holzhauser M, Hüttenberger L, Reitzig R, Sperber M, Stoeck T (2011)
J. Bioinformatics and Computational Biology 9(6): 749--773.
Zeitschriftenaufsatz | Englisch
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Autor*in
Nebel, MarkusUniBi;
Wild, Sebastian;
Holzhauser, Michael;
Hüttenberger, Lars;
Reitzig, Raphael;
Sperber, Matthias;
Stoeck, Thorsten
Einrichtung
Erscheinungsjahr
2011
Zeitschriftentitel
J. Bioinformatics and Computational Biology
Band
9
Ausgabe
6
Seite(n)
749--773
ISSN
0219-7200
Page URI
https://pub.uni-bielefeld.de/record/2910019
Zitieren
Nebel M, Wild S, Holzhauser M, et al. Jaguc - a Software package for Environmental Diversity Analyses. J. Bioinformatics and Computational Biology. 2011;9(6):749--773.
Nebel, M., Wild, S., Holzhauser, M., Hüttenberger, L., Reitzig, R., Sperber, M., & Stoeck, T. (2011). Jaguc - a Software package for Environmental Diversity Analyses. J. Bioinformatics and Computational Biology, 9(6), 749--773. doi:10.1142/S0219720011005781
Nebel, Markus, Wild, Sebastian, Holzhauser, Michael, Hüttenberger, Lars, Reitzig, Raphael, Sperber, Matthias, and Stoeck, Thorsten. 2011. “Jaguc - a Software package for Environmental Diversity Analyses”. J. Bioinformatics and Computational Biology 9 (6): 749--773.
Nebel, M., Wild, S., Holzhauser, M., Hüttenberger, L., Reitzig, R., Sperber, M., and Stoeck, T. (2011). Jaguc - a Software package for Environmental Diversity Analyses. J. Bioinformatics and Computational Biology 9, 749--773.
Nebel, M., et al., 2011. Jaguc - a Software package for Environmental Diversity Analyses. J. Bioinformatics and Computational Biology, 9(6), p 749--773.
M. Nebel, et al., “Jaguc - a Software package for Environmental Diversity Analyses”, J. Bioinformatics and Computational Biology, vol. 9, 2011, pp. 749--773.
Nebel, M., Wild, S., Holzhauser, M., Hüttenberger, L., Reitzig, R., Sperber, M., Stoeck, T.: Jaguc - a Software package for Environmental Diversity Analyses. J. Bioinformatics and Computational Biology. 9, 749--773 (2011).
Nebel, Markus, Wild, Sebastian, Holzhauser, Michael, Hüttenberger, Lars, Reitzig, Raphael, Sperber, Matthias, and Stoeck, Thorsten. “Jaguc - a Software package for Environmental Diversity Analyses”. J. Bioinformatics and Computational Biology 9.6 (2011): 749--773.
Daten bereitgestellt von European Bioinformatics Institute (EBI)
25 Zitationen in Europe PMC
Daten bereitgestellt von Europe PubMed Central.
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Wieczorek AS, Schmidt O, Chatzinotas A, von Bergen M, Gorissen A, Kolb S., Front Microbiol 10(), 2019
PMID: 31281293
Wieczorek AS, Schmidt O, Chatzinotas A, von Bergen M, Gorissen A, Kolb S., Front Microbiol 10(), 2019
PMID: 31281293
Identifying protist consumers of photosynthetic picoeukaryotes in the surface ocean using stable isotope probing.
Orsi WD, Wilken S, Del Campo J, Heger T, James E, Richards TA, Keeling PJ, Worden AZ, Santoro AE., Environ Microbiol 20(2), 2018
PMID: 29215213
Orsi WD, Wilken S, Del Campo J, Heger T, James E, Richards TA, Keeling PJ, Worden AZ, Santoro AE., Environ Microbiol 20(2), 2018
PMID: 29215213
Acidotolerant Bacteria and Fungi as a Sink of Methanol-Derived Carbon in a Deciduous Forest Soil.
Morawe M, Hoeke H, Wissenbach DK, Lentendu G, Wubet T, Kröber E, Kolb S., Front Microbiol 8(), 2017
PMID: 28790984
Morawe M, Hoeke H, Wissenbach DK, Lentendu G, Wubet T, Kröber E, Kolb S., Front Microbiol 8(), 2017
PMID: 28790984
A clinician's guide to microbiome analysis.
Claesson MJ, Clooney AG, O'Toole PW., Nat Rev Gastroenterol Hepatol 14(10), 2017
PMID: 28790452
Claesson MJ, Clooney AG, O'Toole PW., Nat Rev Gastroenterol Hepatol 14(10), 2017
PMID: 28790452
Microbial eukaryote plankton communities of high-mountain lakes from three continents exhibit strong biogeographic patterns.
Filker S, Sommaruga R, Vila I, Stoeck T., Mol Ecol 25(10), 2016
PMID: 27029537
Filker S, Sommaruga R, Vila I, Stoeck T., Mol Ecol 25(10), 2016
PMID: 27029537
The Tara Oceans voyage reveals global diversity and distribution patterns of marine planktonic ciliates.
Gimmler A, Korn R, de Vargas C, Audic S, Stoeck T., Sci Rep 6(), 2016
PMID: 27633177
Gimmler A, Korn R, de Vargas C, Audic S, Stoeck T., Sci Rep 6(), 2016
PMID: 27633177
Associative nitrogen fixation in nodules of the conifer Lepidothamnus fonkii (Podocarpaceae) inhabiting ombrotrophic bogs in southern Patagonia.
Borken W, Horn MA, Geimer S, Aguilar NA, Knorr KH., Sci Rep 6(), 2016
PMID: 27976730
Borken W, Horn MA, Geimer S, Aguilar NA, Knorr KH., Sci Rep 6(), 2016
PMID: 27976730
Deep sequencing uncovers protistan plankton diversity in the Portuguese Ria Formosa solar saltern ponds.
Filker S, Gimmler A, Dunthorn M, Mahé F, Stoeck T., Extremophiles 19(2), 2015
PMID: 25472012
Filker S, Gimmler A, Dunthorn M, Mahé F, Stoeck T., Extremophiles 19(2), 2015
PMID: 25472012
High diversity of protistan plankton communities in remote high mountain lakes in the European Alps and the Himalayan mountains.
Kammerlander B, Breiner HW, Filker S, Sommaruga R, Sonntag B, Stoeck T., FEMS Microbiol Ecol 91(4), 2015
PMID: 25764458
Kammerlander B, Breiner HW, Filker S, Sommaruga R, Sonntag B, Stoeck T., FEMS Microbiol Ecol 91(4), 2015
PMID: 25764458
Metagenomics: tools and insights for analyzing next-generation sequencing data derived from biodiversity studies.
Oulas A, Pavloudi C, Polymenakou P, Pavlopoulos GA, Papanikolaou N, Kotoulas G, Arvanitidis C, Iliopoulos I., Bioinform Biol Insights 9(), 2015
PMID: 25983555
Oulas A, Pavloudi C, Polymenakou P, Pavlopoulos GA, Papanikolaou N, Kotoulas G, Arvanitidis C, Iliopoulos I., Bioinform Biol Insights 9(), 2015
PMID: 25983555
A morphogenetic survey on ciliate plankton from a mountain lake pinpoints the necessity of lineage-specific barcode markers in microbial ecology.
Stoeck T, Breiner HW, Filker S, Ostermaier V, Kammerlander B, Sonntag B., Environ Microbiol 16(2), 2014
PMID: 23848238
Stoeck T, Breiner HW, Filker S, Ostermaier V, Kammerlander B, Sonntag B., Environ Microbiol 16(2), 2014
PMID: 23848238
Agricultural soil and drilosphere as reservoirs of new and unusual assimilators of 2,4-dichlorophenol carbon.
Dallinger A, Horn MA., Environ Microbiol 16(1), 2014
PMID: 23919434
Dallinger A, Horn MA., Environ Microbiol 16(1), 2014
PMID: 23919434
The D1-D2 region of the large subunit ribosomal DNA as barcode for ciliates.
Stoeck T, Przybos E, Dunthorn M., Mol Ecol Resour 14(3), 2014
PMID: 24165195
Stoeck T, Przybos E, Dunthorn M., Mol Ecol Resour 14(3), 2014
PMID: 24165195
Placing environmental next-generation sequencing amplicons from microbial eukaryotes into a phylogenetic context.
Dunthorn M, Otto J, Berger SA, Stamatakis A, Mahé F, Romac S, de Vargas C, Audic S, Biomarks Consortium, Stock A, Kauff F, Stoeck T., Mol Biol Evol 31(4), 2014
PMID: 24473288
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PMID: 24473288
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Stoeck T, Przybos E, Dunthorn M., Mol Ecol Resour 14(3), 2014
PMID: IND500859450
Stoeck T, Przybos E, Dunthorn M., Mol Ecol Resour 14(3), 2014
PMID: IND500859450
Investigating microbial eukaryotic diversity from a global census: insights from a comparison of pyrotag and full-length sequences of 18S rRNA genes.
Lie AA, Liu Z, Hu SK, Jones AC, Kim DY, Countway PD, Amaral-Zettler LA, Cary SC, Sherr EB, Sherr BF, Gast RJ, Caron DA., Appl Environ Microbiol 80(14), 2014
PMID: 24814788
Lie AA, Liu Z, Hu SK, Jones AC, Kim DY, Countway PD, Amaral-Zettler LA, Cary SC, Sherr EB, Sherr BF, Gast RJ, Caron DA., Appl Environ Microbiol 80(14), 2014
PMID: 24814788
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PMID: 22928867
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PMID: 22928867
Morphology of Bromeliophrya quadristicha n. spec., an inhabitant of tank bromeliads (Bromeliaceae), and phylogeny of the Bromeliophryidae (Ciliophora, Tetrahymenida).
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PMID: 23346872
Foissner W, Stoeck T., J Eukaryot Microbiol 60(3), 2013
PMID: 23346872
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PMID: 23398981
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PMID: 23398981
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PMID: 25369746
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PMID: 25369746
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PMID: 23716649
Bernhard JM, Edgcomb VP, Visscher PT, McIntyre-Wressnig A, Summons RE, Bouxsein ML, Louis L, Jeglinski M., Proc Natl Acad Sci U S A 110(24), 2013
PMID: 23716649
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PMID: 23834625
Stock A, Edgcomb V, Orsi W, Filker S, Breiner HW, Yakimov MM, Stoeck T., BMC Microbiol 13(), 2013
PMID: 23834625
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PMID: 22134649
Palmer K, Biasi C, Horn MA., ISME J 6(5), 2012
PMID: 22134649
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PMID: 22660709
Palmer K, Horn MA., Appl Environ Microbiol 78(16), 2012
PMID: 22660709
Introduction--some new results and tools for protein function prediction, RNA target site prediction, genotype calling, environmental genomics, and more.
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PMID: 22187755
Wong L., J Bioinform Comput Biol 9(6), 2011
PMID: 22187755
23 References
Daten bereitgestellt von Europe PubMed Central.
Margulies, Nature 437(), 0
Ecology of the rare microbial biosphere of the Arctic Ocean.
Galand PE, Casamayor EO, Kirchman DL, Lovejoy C., Proc. Natl. Acad. Sci. U.S.A. 106(52), 2009
PMID: 20018741
Galand PE, Casamayor EO, Kirchman DL, Lovejoy C., Proc. Natl. Acad. Sci. U.S.A. 106(52), 2009
PMID: 20018741
Microbial diversity in the deep sea and the underexplored "rare biosphere".
Sogin ML, Morrison HG, Huber JA, Mark Welch D, Huse SM, Neal PR, Arrieta JM, Herndl GJ., Proc. Natl. Acad. Sci. U.S.A. 103(32), 2006
PMID: 16880384
Sogin ML, Morrison HG, Huber JA, Mark Welch D, Huse SM, Neal PR, Arrieta JM, Herndl GJ., Proc. Natl. Acad. Sci. U.S.A. 103(32), 2006
PMID: 16880384
Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water.
Stoeck T, Bass D, Nebel M, Christen R, Jones MD, Breiner HW, Richards TA., Mol. Ecol. 19 Suppl 1(), 2010
PMID: 20331767
Stoeck T, Bass D, Nebel M, Christen R, Jones MD, Breiner HW, Richards TA., Mol. Ecol. 19 Suppl 1(), 2010
PMID: 20331767
Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities.
Stoeck T, Behnke A, Christen R, Amaral-Zettler L, Rodriguez-Mora MJ, Chistoserdov A, Orsi W, Edgcomb VP., BMC Biol. 7(), 2009
PMID: 19886985
Stoeck T, Behnke A, Christen R, Amaral-Zettler L, Rodriguez-Mora MJ, Chistoserdov A, Orsi W, Edgcomb VP., BMC Biol. 7(), 2009
PMID: 19886985
Stoeck, Crystal Ball Environ. Microbiol. Reports 1(), 0
Myers, Comput. Appl. Biosci. 4(), 0
Mahmoud, 1992
Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness.
Schloss PD, Handelsman J., Appl. Environ. Microbiol. 71(3), 2005
PMID: 15746353
Schloss PD, Handelsman J., Appl. Environ. Microbiol. 71(3), 2005
PMID: 15746353
A greedy algorithm for aligning DNA sequences.
Zhang Z, Schwartz S, Wagner L, Miller W., J. Comput. Biol. 7(1-2), 2000
PMID: 10890397
Zhang Z, Schwartz S, Wagner L, Miller W., J. Comput. Biol. 7(1-2), 2000
PMID: 10890397
PANGEA: pipeline for analysis of next generation amplicons.
Giongo A, Crabb DB, Davis-Richardson AG, Chauliac D, Mobberley JM, Gano KA, Mukherjee N, Casella G, Roesch LF, Walts B, Riva A, King G, Triplett EW., ISME J 4(7), 2010
PMID: 20182525
Giongo A, Crabb DB, Davis-Richardson AG, Chauliac D, Mobberley JM, Gano KA, Mukherjee N, Casella G, Roesch LF, Walts B, Riva A, King G, Triplett EW., ISME J 4(7), 2010
PMID: 20182525
QIIME allows analysis of high-throughput community sequencing data.
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R., Nat. Methods 7(5), 2010
PMID: 20383131
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R., Nat. Methods 7(5), 2010
PMID: 20383131
ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences.
Sun Y, Cai Y, Liu L, Yu F, Farrell ML, McKendree W, Farmerie W., Nucleic Acids Res. 37(10), 2009
PMID: 19417062
Sun Y, Cai Y, Liu L, Yu F, Farrell ML, McKendree W, Farmerie W., Nucleic Acids Res. 37(10), 2009
PMID: 19417062
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences.
Li W, Godzik A., Bioinformatics 22(13), 2006
PMID: 16731699
Li W, Godzik A., Bioinformatics 22(13), 2006
PMID: 16731699
Ironing out the wrinkles in the rare biosphere through improved OTU clustering.
Huse SM, Welch DM, Morrison HG, Sogin ML., Environ. Microbiol. 12(7), 2010
PMID: 20236171
Huse SM, Welch DM, Morrison HG, Sogin ML., Environ. Microbiol. 12(7), 2010
PMID: 20236171
MUSCLE: a multiple sequence alignment method with reduced time and space complexity.
Edgar RC., BMC Bioinformatics 5(), 2004
PMID: 15318951
Edgar RC., BMC Bioinformatics 5(), 2004
PMID: 15318951
Depicting more accurate pictures of protistan community complexity using pyrosequencing of hypervariable SSU rRNA gene regions.
Behnke A, Engel M, Christen R, Nebel M, Klein RR, Stoeck T., Environ. Microbiol. 13(2), 2010
PMID: 21281421
Behnke A, Engel M, Christen R, Nebel M, Klein RR, Stoeck T., Environ. Microbiol. 13(2), 2010
PMID: 21281421
The correlation between rDNA copy number and genome size in eukaryotes.
Prokopowich CD, Gregory TR, Crease TJ., Genome 46(1), 2003
PMID: 12669795
Prokopowich CD, Gregory TR, Crease TJ., Genome 46(1), 2003
PMID: 12669795
Mapping of picoeucaryotes in marine ecosystems with quantitative PCR of the 18S rRNA gene.
Zhu F, Massana R, Not F, Marie D, Vaulot D., FEMS Microbiol. Ecol. 52(1), 2004
PMID: 16329895
Zhu F, Massana R, Not F, Marie D, Vaulot D., FEMS Microbiol. Ecol. 52(1), 2004
PMID: 16329895
Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates.
Kunin V, Engelbrektson A, Ochman H, Hugenholtz P., Environ. Microbiol. 12(1), 2009
PMID: 19725865
Kunin V, Engelbrektson A, Ochman H, Hugenholtz P., Environ. Microbiol. 12(1), 2009
PMID: 19725865
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