2 Metagenome Analysis
69
Rondon MR, Raffel SJ, Goodman RM et al (1999) Toward functional genomics in bacteria: analysis of gene expression in Escherichia coli from a bacterial artificial chromosome library of
Bacillus cereus. Proc Natl Acad Sci U S A 96:6451–6455
Rusch DB, Halpern AL, Sutton G et al (2007) The Sorcerer II Global Ocean Sampling expedition:
Northwest Atlantic through Eastern Tropical Pacific. PLoS Biol 5:398–431
Rutherford K, Parkhill J, Crook J et al (2000) Artemis: sequence visualization and annotation.
Bioinformatics 16:944–945
Sabehi G, Kirkup BC, Rozenberg M et al (2007) Adaptation and spectral tuning in divergent marine
proteorhodopsins from the eastern Mediterranean and the Sargasso Seas. ISME J 1:48–55
Salzberg SL, Yorke JA (2005) Beware of mis-assembled genomes. Bioinformatics 21:4320–4321
Sambrook J, Russel DW (2001) Molecular cloning: a laboratory manual, 3rd edn. Cold Spring
Harbor Laboratory Press, Cold Spring Harbor, New York
Sandberg R, Winberg G, Branden CI et al (2001) Capturing whole-genome characteristics in short
sequences using a naive Bayesian classifier. Genome Res 11:1404–1409
Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc
Natl Acad Sci U S A 74:5463–5467
Schirmer A, Gadkari R, Reeves CD et al (2005) Metagenomic analysis reveals diverse polyketide synthase gene clusters in microorganisms associated with the marine sponge Discodermia
dissoluta. Appl Environ Microbiol 71:4840–4849
Schlegel HG (1996) Winogradsky discovered a new Modus vivendi. Anaerobe 2:129–136
Schleper C, Delong EF, Preston CM et al (1998) Genomic analysis reveals chromosomal variation
in natural populations of the uncultured psychrophilic archaeon Cenarchaeum symbiosum. J
Bacteriol 180:5003–5009
Schleper C, Swanson RV, Mathur EJ et al (1997) Characterization of a DNA polymerase
from the uncultivated psychrophilic archaeon Cenarchaeum symbiosum. J Bacteriol 179:
7803–7811
Schloss PD, Handelsman J (2008) A statistical toolbox for metagenomics: assessing functional
diversity in microbial communities. BMC Bioinformatics 9:34
Schmeisser C, Stockigt C, Raasch C et al (2003) Metagenome survey of biofilms in drinking-water
networks. Appl Environ Microbiol 69:7298–7309
Schmidt TM, Delong EF, Pace NR (1991) Analysis of a marine picoplankton community by 16s
ribosomal-RNA gene cloning and sequencing. J Bacteriol 173:4371–4378
Schwartz M (2001) The life and works of Louis Pasteur. J Appl Microbiol 91:597–601
Schübbe S, Kube M, Scheffel A et al (2003) Characterization of a spontaneous nonmagnetic
mutant of Magnetospirillum gryphiswaldense reveals a large deletion comprising a putative
magnetosome island. J Bacteriol 185:5779–5790
Sebat JL, Colwell FS, Crawford RL (2003) Metagenomic profiling: microarray analysis of an
environmental genomic library. Appl Environ Microbiol 69:4927–4934
Seshadri R, Kravitz SA, Smarr L et al (2007) CAMERA: a Community Resource for
Metagenomics. PLoS Biol 5:e75
Sheng Y, Mancino V, Birren B (1995) Transformation of Escherichia coli with large DNA
molecules by electroporation. Nucleic Acids Res 23:1990–1996
Shizuya H, Birren B, Kim UJ et al (1992) Cloning and stable maintenance of 300-kilobase-pair
fragments of human DNA in Escherichia coli using an F-factor-based vector. Proc Natl Acad
Sci U S A 89:8794–8797
Sogin ML, Morrison HG, Huber JA et al (2006) Microbial diversity in the deep sea and the
underexplored “rare biosphere”. Proc Natl Acad Sci U S A 103:12115–12120
Stahl DA, Amann R (1991) Development and application of nucleic acid probes. In: Stackebrandt
E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. John Wiley & Sons
Ltd., Chichester, UK, pp 205–248
Stein JL, Marsh TL, Wu KY et al (1996) Characterization of uncultivated prokaryotes: isolation
and analysis of a 40-kilobase-pair genome fragment front a planktonic marine archaeon. J
Bacteriol 178:591–599
69
Rondon MR, Raffel SJ, Goodman RM et al (1999) Toward functional genomics in bacteria: analysis of gene expression in Escherichia coli from a bacterial artificial chromosome library of
Bacillus cereus. Proc Natl Acad Sci U S A 96:6451–6455
Rusch DB, Halpern AL, Sutton G et al (2007) The Sorcerer II Global Ocean Sampling expedition:
Northwest Atlantic through Eastern Tropical Pacific. PLoS Biol 5:398–431
Rutherford K, Parkhill J, Crook J et al (2000) Artemis: sequence visualization and annotation.
Bioinformatics 16:944–945
Sabehi G, Kirkup BC, Rozenberg M et al (2007) Adaptation and spectral tuning in divergent marine
proteorhodopsins from the eastern Mediterranean and the Sargasso Seas. ISME J 1:48–55
Salzberg SL, Yorke JA (2005) Beware of mis-assembled genomes. Bioinformatics 21:4320–4321
Sambrook J, Russel DW (2001) Molecular cloning: a laboratory manual, 3rd edn. Cold Spring
Harbor Laboratory Press, Cold Spring Harbor, New York
Sandberg R, Winberg G, Branden CI et al (2001) Capturing whole-genome characteristics in short
sequences using a naive Bayesian classifier. Genome Res 11:1404–1409
Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc
Natl Acad Sci U S A 74:5463–5467
Schirmer A, Gadkari R, Reeves CD et al (2005) Metagenomic analysis reveals diverse polyketide synthase gene clusters in microorganisms associated with the marine sponge Discodermia
dissoluta. Appl Environ Microbiol 71:4840–4849
Schlegel HG (1996) Winogradsky discovered a new Modus vivendi. Anaerobe 2:129–136
Schleper C, Delong EF, Preston CM et al (1998) Genomic analysis reveals chromosomal variation
in natural populations of the uncultured psychrophilic archaeon Cenarchaeum symbiosum. J
Bacteriol 180:5003–5009
Schleper C, Swanson RV, Mathur EJ et al (1997) Characterization of a DNA polymerase
from the uncultivated psychrophilic archaeon Cenarchaeum symbiosum. J Bacteriol 179:
7803–7811
Schloss PD, Handelsman J (2008) A statistical toolbox for metagenomics: assessing functional
diversity in microbial communities. BMC Bioinformatics 9:34
Schmeisser C, Stockigt C, Raasch C et al (2003) Metagenome survey of biofilms in drinking-water
networks. Appl Environ Microbiol 69:7298–7309
Schmidt TM, Delong EF, Pace NR (1991) Analysis of a marine picoplankton community by 16s
ribosomal-RNA gene cloning and sequencing. J Bacteriol 173:4371–4378
Schwartz M (2001) The life and works of Louis Pasteur. J Appl Microbiol 91:597–601
Schübbe S, Kube M, Scheffel A et al (2003) Characterization of a spontaneous nonmagnetic
mutant of Magnetospirillum gryphiswaldense reveals a large deletion comprising a putative
magnetosome island. J Bacteriol 185:5779–5790
Sebat JL, Colwell FS, Crawford RL (2003) Metagenomic profiling: microarray analysis of an
environmental genomic library. Appl Environ Microbiol 69:4927–4934
Seshadri R, Kravitz SA, Smarr L et al (2007) CAMERA: a Community Resource for
Metagenomics. PLoS Biol 5:e75
Sheng Y, Mancino V, Birren B (1995) Transformation of Escherichia coli with large DNA
molecules by electroporation. Nucleic Acids Res 23:1990–1996
Shizuya H, Birren B, Kim UJ et al (1992) Cloning and stable maintenance of 300-kilobase-pair
fragments of human DNA in Escherichia coli using an F-factor-based vector. Proc Natl Acad
Sci U S A 89:8794–8797
Sogin ML, Morrison HG, Huber JA et al (2006) Microbial diversity in the deep sea and the
underexplored “rare biosphere”. Proc Natl Acad Sci U S A 103:12115–12120
Stahl DA, Amann R (1991) Development and application of nucleic acid probes. In: Stackebrandt
E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. John Wiley & Sons
Ltd., Chichester, UK, pp 205–248
Stein JL, Marsh TL, Wu KY et al (1996) Characterization of uncultivated prokaryotes: isolation
and analysis of a 40-kilobase-pair genome fragment front a planktonic marine archaeon. J
Bacteriol 178:591–599