2 Metagenome Analysis
65
Glöckner FO, Meyerdierks A (2006) Metagenome analysis. In: Stackebrandt E (ed) Molecular
identification, systematics, and population structure of prokaryotes. Springer-Verlag,
Heidelberg
Gloess S, Grossart HP, Allgaier M et al (2008) Use of laser microdissection for phylogenetic characterization of polyphosphate-accumulating bacteria. Appl Environ Microbiol 74:4231–4235
Goldberg SMD, Johnson J, Busam D et al (2006) A Sanger/pyrosequencing hybrid approach for
the generation of high-quality draft assemblies of marine microbial genomes. Proc Natl Acad
Sci U S A 103:11240–11245
Goodman RM, Liles M (2001) Template specific termination in a polymerase chain reaction. US
Patent 6,248,567
Green ED, Birren B, Klapholz S et al (1997) Genome analysis: a laboratory manual, 1st edn. Cold
Spring Harbor Laboratory Press, New York
Guo FB, Ou HY, Zhang CT (2003) ZCURVE: a new system for recognizing protein-coding genes
in bacterial and archaeal genomes. Nucleic Acids Res 31:1780–1789
Hall AR (1989) The Leeuwenhoek Lecture, 1988 – Antoni van Leeuwenhoek 1632–1723. Notes
Rec R Soc Lond 43:249–273
Hallam SJ, Girguis PR, Preston CM et al (2003) Identification of methyl coenzyme M reductase A (mcrA) genes associated with methane-oxidizing archaea. Appl Environ Microbiol 69:
5483–5491
Handelsman JRM (1998) Molecular biological access to the chemistry of unknown soil microbes –
a new frontier for natural products. Chem Biol 5:R245–R249
Handelsman J, Liles M, Mann D et al (2002) Cloning the metagenome: culture-independent access
to the diversity and functions of the uncultivated microbial world. In: Functional microbial
genomics. Academic Press Inc., San Diego, pp 241–255
Harrington ED, Singh AH, Doerks T et al (2007) Quantitative assessment of protein function prediction from metagenomics shotgun sequences. Proc Natl Acad Sci U S A 104:
13913–13918
Henne A, Daniel R, Schmitz RA et al (1999) Construction of environmental DNA libraries
in Escherichia coli and screening for the presence of genes conferring utilization of
4-hydroxybutyrate. Appl Environ Microbiol 65:3901–3907
Hosono S, Faruqi AF, Dean FB et al (2003) Unbiased whole-genome amplification directly from
clinical samples. Genome Res 13:954–964
Huber R, Burggraf S, Mayer T et al (1995) Isolation of a hyperthermophilic archaeum predicted
by in situ RNA Analysis. Nature 376:57–58
Hughes DS, Felbeck H, Stein JL (1997) A histidine protein kinase homolog from the endosymbiont
of the hydrothermal vent tubeworm Riftia pachyptila. Appl Environ Microbiol 63:3494–3498
Huse SM, Huber JA, Morrison HG et al (2007) Accuracy and quality of massively parallel DNA
pyrosequencing. Genome Biol 8:9
Huson DH, Auch AF, Qi J et al (2007) MEGAN analysis of metagenomic data. Genome Res
17:377–386
Hutchison CA, Venter JC (2006) Single-cell genomics. Nat Biotechnol 24:657–658
Ishoy T, Kvist T, Westermann P et al (2006) An improved method for single cell isolation of
prokaryotes from meso-, thermo- and hyperthermophilic environments using micromanipulation. Appl Microbiol Biotechnol 69:510–514
Jaffe DB, Butler J, Gnerre S et al (2003) Whole-genome sequence assembly for mammalian
genomes: Arachne 2. Genome Res 13:91–96
Johnson PLF, Slatkin M (2006) Inference of population genetic parameters in metagenomics: a
clean look at messy data. Genome Res 16:1320–1327
Kagan J, Sharon I, Beja O et al (2008) The tryptophan pathway genes of the Sargasso Sea
metagenome: new operon structures and the prevalence of non-operon organization. Genome
Biol 9:R20
Kanehisa M, Goto S, Kawashima S et al (2004) The KEGG resource for deciphering the genome.
Nucleic Acids Res 32:D277–D280
65
Glöckner FO, Meyerdierks A (2006) Metagenome analysis. In: Stackebrandt E (ed) Molecular
identification, systematics, and population structure of prokaryotes. Springer-Verlag,
Heidelberg
Gloess S, Grossart HP, Allgaier M et al (2008) Use of laser microdissection for phylogenetic characterization of polyphosphate-accumulating bacteria. Appl Environ Microbiol 74:4231–4235
Goldberg SMD, Johnson J, Busam D et al (2006) A Sanger/pyrosequencing hybrid approach for
the generation of high-quality draft assemblies of marine microbial genomes. Proc Natl Acad
Sci U S A 103:11240–11245
Goodman RM, Liles M (2001) Template specific termination in a polymerase chain reaction. US
Patent 6,248,567
Green ED, Birren B, Klapholz S et al (1997) Genome analysis: a laboratory manual, 1st edn. Cold
Spring Harbor Laboratory Press, New York
Guo FB, Ou HY, Zhang CT (2003) ZCURVE: a new system for recognizing protein-coding genes
in bacterial and archaeal genomes. Nucleic Acids Res 31:1780–1789
Hall AR (1989) The Leeuwenhoek Lecture, 1988 – Antoni van Leeuwenhoek 1632–1723. Notes
Rec R Soc Lond 43:249–273
Hallam SJ, Girguis PR, Preston CM et al (2003) Identification of methyl coenzyme M reductase A (mcrA) genes associated with methane-oxidizing archaea. Appl Environ Microbiol 69:
5483–5491
Handelsman JRM (1998) Molecular biological access to the chemistry of unknown soil microbes –
a new frontier for natural products. Chem Biol 5:R245–R249
Handelsman J, Liles M, Mann D et al (2002) Cloning the metagenome: culture-independent access
to the diversity and functions of the uncultivated microbial world. In: Functional microbial
genomics. Academic Press Inc., San Diego, pp 241–255
Harrington ED, Singh AH, Doerks T et al (2007) Quantitative assessment of protein function prediction from metagenomics shotgun sequences. Proc Natl Acad Sci U S A 104:
13913–13918
Henne A, Daniel R, Schmitz RA et al (1999) Construction of environmental DNA libraries
in Escherichia coli and screening for the presence of genes conferring utilization of
4-hydroxybutyrate. Appl Environ Microbiol 65:3901–3907
Hosono S, Faruqi AF, Dean FB et al (2003) Unbiased whole-genome amplification directly from
clinical samples. Genome Res 13:954–964
Huber R, Burggraf S, Mayer T et al (1995) Isolation of a hyperthermophilic archaeum predicted
by in situ RNA Analysis. Nature 376:57–58
Hughes DS, Felbeck H, Stein JL (1997) A histidine protein kinase homolog from the endosymbiont
of the hydrothermal vent tubeworm Riftia pachyptila. Appl Environ Microbiol 63:3494–3498
Huse SM, Huber JA, Morrison HG et al (2007) Accuracy and quality of massively parallel DNA
pyrosequencing. Genome Biol 8:9
Huson DH, Auch AF, Qi J et al (2007) MEGAN analysis of metagenomic data. Genome Res
17:377–386
Hutchison CA, Venter JC (2006) Single-cell genomics. Nat Biotechnol 24:657–658
Ishoy T, Kvist T, Westermann P et al (2006) An improved method for single cell isolation of
prokaryotes from meso-, thermo- and hyperthermophilic environments using micromanipulation. Appl Microbiol Biotechnol 69:510–514
Jaffe DB, Butler J, Gnerre S et al (2003) Whole-genome sequence assembly for mammalian
genomes: Arachne 2. Genome Res 13:91–96
Johnson PLF, Slatkin M (2006) Inference of population genetic parameters in metagenomics: a
clean look at messy data. Genome Res 16:1320–1327
Kagan J, Sharon I, Beja O et al (2008) The tryptophan pathway genes of the Sargasso Sea
metagenome: new operon structures and the prevalence of non-operon organization. Genome
Biol 9:R20
Kanehisa M, Goto S, Kawashima S et al (2004) The KEGG resource for deciphering the genome.
Nucleic Acids Res 32:D277–D280