66
A. Meyerdierks and F.O. Glöckner
Karlin S, Campbell AM, Mrazek J (1998) Comparative DNA analysis across diverse genomes.
Ann Rev Genet 32:185–225
Kaufmann SHE, Schaible UE (2005) 100th anniversary of Robert Koch’s Nobel Prize for the
discovery of the tubercle bacillus. Trends Microbiol 13:469–475
Kim UJ, Birren BW, Slepak T et al (1996) Construction and characterization of a human bacterial
artificial chromosome library. Genomics 34:213–218
Kim UJ, Shizuya H, Dejong PJ et al (1992) Stable propagation of cosmid sized human DNA inserts
in an F-factor based vector. Nucleic Acids Res 20:1083–1085
Krause L, Diaz NN, Bartels D et al (2006) Finding novel genes in bacterial communities isolated
from the environment. Bioinformatics 22:E281–E289
Krogh A, Larsson B, von Heijne G et al (2001) Predicting transmembrane protein topology with a
hidden Markov model: application to complete genomes. J Mol Biol 305:567–580
Krüger M, Meyerdierks A, Glockner FO et al (2003) A conspicuous nickel protein in microbial
mats that oxidize methane anaerobically. Nature 426:878–881
Kube M, Beck A, Meyerdierks A et al (2005) A catabolic gene cluster for anaerobic benzoate
degradation in methanotrophic microbial Black Sea mats. Syst Appl Microbiol 28:287–294
Kvist T, Ahring BK, Lasken RS et al (2007) Specific single-cell isolation and genomic amplification of uncultured microorganisms. Appl Microbiol Biotechnol 74:926–935
Lasken RS (2007) Single-cell genomic sequencing using Multiple Displacement Amplification.
Curr Opin Microbiol 10:510–516
Lasken RS, Stockwell TB (2007) Mechanism of chimera formation during the Multiple
Displacement Amplification reaction. BMC Biotechnol 7:19
Leininger S, Urich T, Schloter M et al (2006) Archaea predominate among ammonia-oxidizing
prokaryotes in soils. Nature 442:806–809
Leonardo ED, Sedivy JM (1990) A new vector for cloning large eukaryotic DNA segments in
Escherichia coli. Bio-Technology 8:841–844
Liles MR, Manske BF, Bintrim SB et al (2003) A census of rRNA genes and linked genomic
sequences within a soil metagenomic library. Appl Environ Microbiol 69:2684–2691
Liles MR, Williamson LL, Rodbumrer J et al (2008) Recovery, purification, and cloning of highmolecular-weight DNA from soil microorganisms. Appl Environ Microbiol 74:3302–3305
Liu DY, Daubendiek SL, Zillman MA et al (1996) Rolling circle DNA synthesis: small circular
oligonucleotides as efficient templates for DNA polymerases. J Am Chem Soc 118:1587–1594
Lombardot T, Kottmann R, Pfeffer H et al (2006) Megx.net – database resource for marine
ecological genomics. Nucleic Acids Res 34:D390–D393
Lopez-Garcia P, Brochier C, Moreira D et al (2004) Comparative analysis of a genome fragment of
an uncultivated mesopelagic crenarchaeote reveals multiple horizontal gene transfers. Environ
Microbiol 6:19–34
Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA
genes in genomic sequence. Nucleic Acids Res 25:955–964
Ludwig W, Strunk O, Westram R et al (2004) ARB: a software environment for sequence data.
Nucleic Acids Res 32:1363–1371
MacNeil IA, Tiong CL, Minor C et al (2001) Expression and isolation of antimicrobial small
molecules from soil DNA libraries. J Mol Microbiol Biotechnol 3:301–308
Maltsev N, Glass E, Sulakhe D et al (2006) PUMA2 – grid-based high-throughput analysis of
genomes and metabolic pathways. Nucleic Acids Res 34:D369–D372
Marcy Y, Ouverney C, Bik EM et al (2007) Dissecting biological “dark matter” with single-cell
genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proc Natl Acad
Sci U S A 104:11889–11894
Mardis ER (2008) Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet
9:387–402
Margulies M, Egholm M, Altman WE et al (2005) Genome sequencing in microfabricated highdensity picolitre reactors. Nature 437:376–380
Markowitz VM (2007) Microbial genome data resources. Curr Opin Biotechnol 18:267–272
A. Meyerdierks and F.O. Glöckner
Karlin S, Campbell AM, Mrazek J (1998) Comparative DNA analysis across diverse genomes.
Ann Rev Genet 32:185–225
Kaufmann SHE, Schaible UE (2005) 100th anniversary of Robert Koch’s Nobel Prize for the
discovery of the tubercle bacillus. Trends Microbiol 13:469–475
Kim UJ, Birren BW, Slepak T et al (1996) Construction and characterization of a human bacterial
artificial chromosome library. Genomics 34:213–218
Kim UJ, Shizuya H, Dejong PJ et al (1992) Stable propagation of cosmid sized human DNA inserts
in an F-factor based vector. Nucleic Acids Res 20:1083–1085
Krause L, Diaz NN, Bartels D et al (2006) Finding novel genes in bacterial communities isolated
from the environment. Bioinformatics 22:E281–E289
Krogh A, Larsson B, von Heijne G et al (2001) Predicting transmembrane protein topology with a
hidden Markov model: application to complete genomes. J Mol Biol 305:567–580
Krüger M, Meyerdierks A, Glockner FO et al (2003) A conspicuous nickel protein in microbial
mats that oxidize methane anaerobically. Nature 426:878–881
Kube M, Beck A, Meyerdierks A et al (2005) A catabolic gene cluster for anaerobic benzoate
degradation in methanotrophic microbial Black Sea mats. Syst Appl Microbiol 28:287–294
Kvist T, Ahring BK, Lasken RS et al (2007) Specific single-cell isolation and genomic amplification of uncultured microorganisms. Appl Microbiol Biotechnol 74:926–935
Lasken RS (2007) Single-cell genomic sequencing using Multiple Displacement Amplification.
Curr Opin Microbiol 10:510–516
Lasken RS, Stockwell TB (2007) Mechanism of chimera formation during the Multiple
Displacement Amplification reaction. BMC Biotechnol 7:19
Leininger S, Urich T, Schloter M et al (2006) Archaea predominate among ammonia-oxidizing
prokaryotes in soils. Nature 442:806–809
Leonardo ED, Sedivy JM (1990) A new vector for cloning large eukaryotic DNA segments in
Escherichia coli. Bio-Technology 8:841–844
Liles MR, Manske BF, Bintrim SB et al (2003) A census of rRNA genes and linked genomic
sequences within a soil metagenomic library. Appl Environ Microbiol 69:2684–2691
Liles MR, Williamson LL, Rodbumrer J et al (2008) Recovery, purification, and cloning of highmolecular-weight DNA from soil microorganisms. Appl Environ Microbiol 74:3302–3305
Liu DY, Daubendiek SL, Zillman MA et al (1996) Rolling circle DNA synthesis: small circular
oligonucleotides as efficient templates for DNA polymerases. J Am Chem Soc 118:1587–1594
Lombardot T, Kottmann R, Pfeffer H et al (2006) Megx.net – database resource for marine
ecological genomics. Nucleic Acids Res 34:D390–D393
Lopez-Garcia P, Brochier C, Moreira D et al (2004) Comparative analysis of a genome fragment of
an uncultivated mesopelagic crenarchaeote reveals multiple horizontal gene transfers. Environ
Microbiol 6:19–34
Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA
genes in genomic sequence. Nucleic Acids Res 25:955–964
Ludwig W, Strunk O, Westram R et al (2004) ARB: a software environment for sequence data.
Nucleic Acids Res 32:1363–1371
MacNeil IA, Tiong CL, Minor C et al (2001) Expression and isolation of antimicrobial small
molecules from soil DNA libraries. J Mol Microbiol Biotechnol 3:301–308
Maltsev N, Glass E, Sulakhe D et al (2006) PUMA2 – grid-based high-throughput analysis of
genomes and metabolic pathways. Nucleic Acids Res 34:D369–D372
Marcy Y, Ouverney C, Bik EM et al (2007) Dissecting biological “dark matter” with single-cell
genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proc Natl Acad
Sci U S A 104:11889–11894
Mardis ER (2008) Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet
9:387–402
Margulies M, Egholm M, Altman WE et al (2005) Genome sequencing in microfabricated highdensity picolitre reactors. Nature 437:376–380
Markowitz VM (2007) Microbial genome data resources. Curr Opin Biotechnol 18:267–272