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A user's guide to quantitative and comparative analysis of metagenomic datasets.
Luo C, Rodriguez-R LM, Konstantinidis KT. Luo C, et al. Methods Enzymol. 2013;531:525-47. doi: 10.1016/B978-0-12-407863-5.00023-X. Methods Enzymol. 2013. PMID: 24060135
Soil microbial community responses to a decade of warming as revealed by comparative metagenomics.
Luo C, Rodriguez-R LM, Johnston ER, Wu L, Cheng L, Xue K, Tu Q, Deng Y, He Z, Shi JZ, Yuan MM, Sherry RA, Li D, Luo Y, Schuur EA, Chain P, Tiedje JM, Zhou J, Konstantinidis KT. Luo C, et al. Appl Environ Microbiol. 2014 Mar;80(5):1777-86. doi: 10.1128/AEM.03712-13. Epub 2013 Dec 27. Appl Environ Microbiol. 2014. PMID: 24375144 Free PMC article.
MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences.
Luo C, Rodriguez-R LM, Konstantinidis KT. Luo C, et al. Nucleic Acids Res. 2014 Apr;42(8):e73. doi: 10.1093/nar/gku169. Epub 2014 Mar 3. Nucleic Acids Res. 2014. PMID: 24589583 Free PMC article.
Strengths and limitations of 16S rRNA gene amplicon sequencing in revealing temporal microbial community dynamics.
Poretsky R, Rodriguez-R LM, Luo C, Tsementzi D, Konstantinidis KT. Poretsky R, et al. PLoS One. 2014 Apr 8;9(4):e93827. doi: 10.1371/journal.pone.0093827. eCollection 2014. PLoS One. 2014. PMID: 24714158 Free PMC article.
Estimating coverage in metagenomic data sets and why it matters.
Rodriguez-R LM, Konstantinidis KT. Rodriguez-R LM, et al. ISME J. 2014 Nov;8(11):2349-51. doi: 10.1038/ismej.2014.76. Epub 2014 May 13. ISME J. 2014. PMID: 24824669 Free PMC article. No abstract available.
Detecting nitrous oxide reductase (NosZ) genes in soil metagenomes: method development and implications for the nitrogen cycle.
Orellana LH, Rodriguez-R LM, Higgins S, Chee-Sanford JC, Sanford RA, Ritalahti KM, Löffler FE, Konstantinidis KT. Orellana LH, et al. mBio. 2014 Jun 3;5(3):e01193-14. doi: 10.1128/mBio.01193-14. mBio. 2014. PMID: 24895307 Free PMC article.
Biofilms on Hospital Shower Hoses: Characterization and Implications for Nosocomial Infections.
Soto-Giron MJ, Rodriguez-R LM, Luo C, Elk M, Ryu H, Hoelle J, Santo Domingo JW, Konstantinidis KT. Soto-Giron MJ, et al. Appl Environ Microbiol. 2016 Apr 18;82(9):2872-2883. doi: 10.1128/AEM.03529-15. Print 2016 May. Appl Environ Microbiol. 2016. PMID: 26969701 Free PMC article.
Metagenomics Reveals Pervasive Bacterial Populations and Reduced Community Diversity across the Alaska Tundra Ecosystem.
Johnston ER, Rodriguez-R LM, Luo C, Yuan MM, Wu L, He Z, Schuur EA, Luo Y, Tiedje JM, Zhou J, Konstantinidis KT. Johnston ER, et al. Front Microbiol. 2016 Apr 25;7:579. doi: 10.3389/fmicb.2016.00579. eCollection 2016. Front Microbiol. 2016. PMID: 27199914 Free PMC article.
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