Publications

The following is a list of publications that may be of interest for anyone wishing to perform similar data analysis:

• Amaral-Zettler L.A., McCliment E.A., Ducklow H.W., Huse S.M. (2009) A Method for Studying Protistan Diversity Using Massively Parallel Sequencing of V9 Hypervariable Regions of Small-Subunit Ribosomal RNA Genes. PLoS ONE 4(7): e6372. doi:10.1371/journal.pone.0006372
  
  
• Huse, S.M., L. Dethlefsen, J.A. Huber, D. Mark Welch, D.A. Relman, M.L. Sogin (2008). Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. PLoS Genetics.4(11): e1000255 doi:10.1371/journal.pgen.1000255.
  
  
• Binladen J, Gilbert MTP, Bollback JP, Panitz F, Bendixen C et al. (2007). The Use of Coded PCR Primers Enables High-Throughput Sequencing of Multiple Homolog Amplification Products by 454 Parallel Sequencing. PLoS ONE 2(2): e197.
  
  
• Edgar RC (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32(5): 1792-1797.
  
  
• Huber JA, Mark Welch DB, Morrison HG, Huse SM, Neal PR et al. (2007). Microbial Population Structures in the Deep Marine Biosphere. Science 318(5847): 97-100.
  
  
• Huse S, Huber J, Morrison H, Sogin M, Welch D (2007). Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biology 8(7): R143.
  
  
• Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W et al. (2007). SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Research: gkm864.
  
  
• Schloss PD, Handelsman J (2005). Introducing DOTUR, a Computer Program for Defining Operational Taxonomic Units and Estimating Species Richness. Applied and Environmental Microbiology 71(3): 1501-1506.
  
  
• Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM et al. (2006). Microbial diversity in the deep sea and the underexplored "rare biosphere". Proceedings of the National Academy of Sciences 103(32): 12115-12120.
  
  
• Wang Q, Garrity GM, Tiedje JM, Cole JR (2007). A Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy. Applied and Environmental Microbiology: AEM.00062-00007.