References.bib

@article{handelsman2004metagenomics,
  title={Metagenomics: application of genomics to uncultured microorganisms},
  author={Handelsman, Jo},
  journal={Microbiology and molecular biology reviews},
  volume={68},
  number={4},
  pages={669--685},
  year={2004},
  publisher={Am Soc Microbiol}
}

@article{staley1985measurement,
  title={Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats},
  author={Staley, James T and Konopka, Allan},
  journal={Annual Reviews in Microbiology},
  volume={39},
  number={1},
  pages={321--346},
  year={1985},
  publisher={Annual Reviews 4139 El Camino Way, PO Box 10139, Palo Alto, CA 94303-0139, USA}
}

@article{hugenholtz2002exploring,
  title={Exploring prokaryotic diversity in the genomic era},
  author={Hugenholtz, Philip and others},
  journal={Genome Biol},
  volume={3},
  number={2},
  pages={1--0003},
  year={2002}
}

@article{sanger1977dna,
  title={DNA sequencing with chain-terminating inhibitors},
  author={Sanger, Frederick and Nicklen, Steven and Coulson, Alan R},
  journal={Proceedings of the National Academy of Sciences},
  volume={74},
  number={12},
  pages={5463--5467},
  year={1977},
  publisher={National Acad Sciences}
}

@article{smith1986fluorescence,
  title={Fluorescence detection in automated DNA sequence analysis},
  author={Smith, Lloyd M and Sanders, Jane Z and Kaiser, Robert J and Hughes, Peter and Dodd, Chris and Connell, Charles R and Heiner, Cheryl and Kent, Stephen BH and Hood, Leroy E},
  year={1986},
  publisher={Nature Publishing Group}
}

@article{prober1987system,
  title={A system for rapid DNA sequencing with fluorescent chain-terminating dideoxynucleotides},
  author={Prober, James M and Trainor, George L and Dam, Rudy J and Hobbs, Frank W and Robertson, Charles W and Zagursky, Robert J and Cocuzza, Anthony J and Jensen, Mark A and Baumeister, Kirk},
  journal={Science},
  volume={238},
  number={4825},
  pages={336--341},
  year={1987},
  publisher={American Association for the Advancement of Science}
}

@article{ronaghi1996real,
  title={Real-time DNA sequencing using detection of pyrophosphate release},
  author={Ronaghi, Mostafa and Karamohamed, Samer and Pettersson, Bertil and Uhl{\'e}n, Mathias and Nyr{\'e}n, P{\aa}l},
  journal={Analytical biochemistry},
  volume={242},
  number={1},
  pages={84--89},
  year={1996},
  publisher={Elsevier}
}

@article{ewing1998base,
  title={Base-calling of automated sequencer traces using phred. II. Error probabilities},
  author={Ewing, Brent and Green, Phil},
  journal={Genome research},
  volume={8},
  number={3},
  pages={186--194},
  year={1998},
  publisher={Cold Spring Harbor Lab}
}

@article{brenner2000gene,
  title={Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays},
  author={Brenner, Sydney and Johnson, Maria and Bridgham, John and Golda, George and Lloyd, David H and Johnson, Davida and Luo, Shujun and McCurdy, Sarah and Foy, Michael and Ewan, Mark and others},
  journal={Nature biotechnology},
  volume={18},
  number={6},
  pages={630--634},
  year={2000},
  publisher={Nature Publishing Group}
}

@article{wang2007naive,
  title={Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy},
  author={Wang, Qiong and Garrity, George M and Tiedje, James M and Cole, James R},
  journal={Applied and environmental microbiology},
  volume={73},
  number={16},
  pages={5261--5267},
  year={2007},
  publisher={Am Soc Microbiol}
}

@article{van2001graph,
  title={Graph clustering by flow simulation},
  author={Van Dongen, Stijn Marinus},
  year={2001}
}