Publications

Also see Citations by Method

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

• Huse, S. M., D. Mark Welch, H. G. Morrison, and M. L. Sogin. (2010). Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environmental Microbiology 12:1889-1898.
  

      Template sequences used for analysis: IroningWrinkles_fasta.tar.gz

• 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.
  
  
• 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.
  

      Additional data file 4. Text translation of the original GS20 binary output (sff) file for the second
      of three regions (compressed file corrupted on Genome Biology website). Download File

• 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.
  
  
• 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.
  
  
• 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.
  
  
• 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.
  
  
• Edgar RC (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32(5): 1792-1797.
  
  

Citations By Method:

Illumina Av6:
• Meyer, J. L., Akerman, N. H., Proskurowski, G., and Huber, J. A. (2013). "Microbiological characterization of post-eruption “snowblower” vents at Axial Seamount, Juan de Fuca Ridge." Front Microbiol, 4, 153.

Illumina Bv6:
• Eren, A. M., Vineis, J. H., Morrison, H. G., and Sogin, M. L. (2013). "A filtering method to generate high quality short reads using illumina paired-end technology." PLoS One, 8(6), e66643.

Illumina Av4v5:
• Topçuoğlu BD, Stewart LC, Morrison HG, Butterfield DA, Huber JA, Holden JF. "Hydrogen Limitation and Syntrophic Growth among Natural Assemblages of Thermophilic Methanogens at Deep-sea Hydrothermal Vents." Frontiers in Microbiology. 2016;7:1240. doi:10.3389/fmicb.2016.01240.

Illumina Bv4v5:
• Newton R.J., McLellan S.L., Dila D.K., Vineis J.H., Morrison H.G., Eren A.M., Sogin M.L. (2015). "Sewage reflects the microbiomes of human populations." mBio 6(2):e02574-14. doi:10.1128/mBio.02574-14.


• Nelson, M. C., Morrison, H. G., Benjamino, J., Grim, S. L., and Graf, J. (2014). "Analysis, optimization and verification of Illumina-generated 16S rRNA gene amplicon surveys." PLoS One, 9(4), e94249.


• Huse, S. M., Young, V. B., Morrison, H. G., Antonopoulos, D. A., Kwon, J., Dalal, S., Arrieta, R., Hubert, N. A., Shen, L., Vineis, J. H., Koval, J. C., Sogin, M. L., Chang, E. B., and Raffals, L. E. (2014). "Comparison of brush and biopsy sampling methods of the ileal pouch for assessment of mucosa-associated microbiota of human subjects." Microbiome, 2(1), 5.



454 pyrosequencing Bv3v5 and Bv6v4:

• Viggó Thór Marteinsson, Árni Rúnarsson, Andri Stefánsson, Thorsteinn Thorsteinsson, Tómas Jóhannesson, Sveinn H Magnússon, Eyjólfur Reynisson, Bergur Einarsson, Nicole Wade, Hilary G Morrison and Eric Gaidos (2013) "Microbial communities in the subglacial waters of the Vatnajökull ice cap, Iceland" The ISME Journal (2013) 7, 427–437; doi:10.1038/ismej.2012.97; published online 13 September 2012