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Fast and sensitive protein alignment using DIAMOND.
Buchfink B, Xie C, Huson DH. Buchfink B, et al. Nat Methods. 2015 Jan;12(1):59-60. doi: 10.1038/nmeth.3176. Epub 2014 Nov 17. Nat Methods. 2015. PMID: 25402007
A poor man's BLASTX--high-throughput metagenomic protein database search using PAUDA.
Huson DH, Xie C. Huson DH, et al. Bioinformatics. 2014 Jan 1;30(1):38-9. doi: 10.1093/bioinformatics/btt254. Epub 2013 May 7. Bioinformatics. 2014. PMID: 23658416 Free PMC article.
Spatially extensive microbial biogeography of the Indian Ocean provides insights into the unique community structure of a pristine coral atoll.
Jeffries TC, Ostrowski M, Williams RB, Xie C, Jensen RM, Grzymski JJ, Senstius SJ, Givskov M, Hoeke R, Philip GK, Neches RY, Drautz-Moses DI, Chénard C, Paulsen IT, Lauro FM. Jeffries TC, et al. Sci Rep. 2015 Oct 20;5:15383. doi: 10.1038/srep15383. Sci Rep. 2015. PMID: 26481089 Free PMC article.
Integrative microbial community analysis reveals full-scale enhanced biological phosphorus removal under tropical conditions.
Law Y, Kirkegaard RH, Cokro AA, Liu X, Arumugam K, Xie C, Stokholm-Bjerregaard M, Drautz-Moses DI, Nielsen PH, Wuertz S, Williams RB. Law Y, et al. Sci Rep. 2016 May 19;6:25719. doi: 10.1038/srep25719. Sci Rep. 2016. PMID: 27193869 Free PMC article.
Primer-free FISH probes from metagenomics/metatranscriptomics data permit the study of uncharacterised taxa in complex microbial communities.
Tan SM, Yung PYM, Hutchinson PE, Xie C, Teo GH, Ismail MH, Drautz-Moses DI, Little PFR, Williams RBH, Cohen Y. Tan SM, et al. NPJ Biofilms Microbiomes. 2019 Jun 25;5:17. doi: 10.1038/s41522-019-0090-9. eCollection 2019. NPJ Biofilms Microbiomes. 2019. PMID: 31263569 Free PMC article.
The role of quorum sensing signalling in EPS production and the assembly of a sludge community into aerobic granules.
Tan CH, Koh KS, Xie C, Tay M, Zhou Y, Williams R, Ng WJ, Rice SA, Kjelleberg S. Tan CH, et al. ISME J. 2014 Jun;8(6):1186-97. doi: 10.1038/ismej.2013.240. Epub 2014 Jan 16. ISME J. 2014. PMID: 24430488 Free PMC article.
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