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Quality control and preprocessing of metagenomic datasets.
Schmieder R, Edwards R. Schmieder R, et al. Bioinformatics. 2011 Mar 15;27(6):863-4. doi: 10.1093/bioinformatics/btr026. Epub 2011 Jan 28. Bioinformatics. 2011. PMID: 21278185 Free PMC article.
An application of statistics to comparative metagenomics.
Rodriguez-Brito B, Rohwer F, Edwards RA. Rodriguez-Brito B, et al. BMC Bioinformatics. 2006 Mar 20;7:162. doi: 10.1186/1471-2105-7-162. BMC Bioinformatics. 2006. PMID: 16549025 Free PMC article.
Metagenomic analysis indicates that stressors induce production of herpes-like viruses in the coral Porites compressa.
Vega Thurber RL, Barott KL, Hall D, Liu H, Rodriguez-Mueller B, Desnues C, Edwards RA, Haynes M, Angly FE, Wegley L, Rohwer FL. Vega Thurber RL, et al. Proc Natl Acad Sci U S A. 2008 Nov 25;105(47):18413-8. doi: 10.1073/pnas.0808985105. Epub 2008 Nov 18. Proc Natl Acad Sci U S A. 2008. PMID: 19017800 Free PMC article.
Metagenomic analysis of stressed coral holobionts.
Vega Thurber R, Willner-Hall D, Rodriguez-Mueller B, Desnues C, Edwards RA, Angly F, Dinsdale E, Kelly L, Rohwer F. Vega Thurber R, et al. Environ Microbiol. 2009 Aug;11(8):2148-63. doi: 10.1111/j.1462-2920.2009.01935.x. Epub 2009 Apr 22. Environ Microbiol. 2009. PMID: 19397678
Accessing the SEED genome databases via Web services API: tools for programmers.
Disz T, Akhter S, Cuevas D, Olson R, Overbeek R, Vonstein V, Stevens R, Edwards RA. Disz T, et al. BMC Bioinformatics. 2010 Jun 14;11:319. doi: 10.1186/1471-2105-11-319. BMC Bioinformatics. 2010. PMID: 20546611 Free PMC article.
TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets.
Schmieder R, Lim YW, Rohwer F, Edwards R. Schmieder R, et al. BMC Bioinformatics. 2010 Jun 23;11:341. doi: 10.1186/1471-2105-11-341. BMC Bioinformatics. 2010. PMID: 20573248 Free PMC article.
The interactive web interface facilitates export functionality for subsequent data processing, and is available at http://edwards.sdsu.edu/tagcleaner....
The interactive web interface facilitates export functionality for subsequent data processing, and is available at http://edwards.sds …
Identification and removal of ribosomal RNA sequences from metatranscriptomes.
Schmieder R, Lim YW, Edwards R. Schmieder R, et al. Bioinformatics. 2012 Feb 1;28(3):433-5. doi: 10.1093/bioinformatics/btr669. Epub 2011 Dec 6. Bioinformatics. 2012. PMID: 22155869 Free PMC article.
Insights into antibiotic resistance through metagenomic approaches.
Schmieder R, Edwards R. Schmieder R, et al. Future Microbiol. 2012 Jan;7(1):73-89. doi: 10.2217/fmb.11.135. Future Microbiol. 2012. PMID: 22191448 Review.
PHACTS, a computational approach to classifying the lifestyle of phages.
McNair K, Bailey BA, Edwards RA. McNair K, et al. Bioinformatics. 2012 Mar 1;28(5):614-8. doi: 10.1093/bioinformatics/bts014. Epub 2012 Jan 11. Bioinformatics. 2012. PMID: 22238260 Free PMC article.
AVAILABILITY AND IMPLEMENTATION: PHACTS was implemented in the PERL programming language and utilizes the FASTA program (Pearson and Lipman, 1988) and the R programming language library 'Random Forest' (Liaw and Weiner, 2010). ...
AVAILABILITY AND IMPLEMENTATION: PHACTS was implemented in the PERL programming language and utilizes the FASTA program (Pearson and Lipman, …
Real time metagenomics: using k-mers to annotate metagenomes.
Edwards RA, Olson R, Disz T, Pusch GD, Vonstein V, Stevens R, Overbeek R. Edwards RA, et al. Bioinformatics. 2012 Dec 15;28(24):3316-7. doi: 10.1093/bioinformatics/bts599. Epub 2012 Oct 9. Bioinformatics. 2012. PMID: 23047562 Free PMC article.
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