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Cited In for PubMed (Select 19052320)


InteMAP: Integrated metagenomic assembly pipeline for NGS short reads.

Lai B, Wang F, Wang X, Duan L, Zhu H.

BMC Bioinformatics. 2015 Aug 7;16:244. doi: 10.1186/s12859-015-0686-x.


Xander: employing a novel method for efficient gene-targeted metagenomic assembly.

Wang Q, Fish JA, Gilman M, Sun Y, Brown CT, Tiedje JM, Cole JR.

Microbiome. 2015 Aug 5;3:32. doi: 10.1186/s40168-015-0093-6. eCollection 2015.


Elviz - exploration of metagenome assemblies with an interactive visualization tool.

Cantor M, Nordberg H, Smirnova T, Hess M, Tringe S, Dubchak I.

BMC Bioinformatics. 2015 Apr 28;16:130. doi: 10.1186/s12859-015-0566-4.


CoMeta: classification of metagenomes using k-mers.

Kawulok J, Deorowicz S.

PLoS One. 2015 Apr 17;10(4):e0121453. doi: 10.1371/journal.pone.0121453. eCollection 2015.


Microbiology of diabetic foot infections: from Louis Pasteur to 'crime scene investigation'.

Spichler A, Hurwitz BL, Armstrong DG, Lipsky BA.

BMC Med. 2015 Jan 7;13:2. doi: 10.1186/s12916-014-0232-0. Review.


AKE - the Accelerated k-mer Exploration web-tool for rapid taxonomic classification and visualization.

Langenkämper D, Goesmann A, Nattkemper TW.

BMC Bioinformatics. 2014 Dec 13;15:384. doi: 10.1186/s12859-014-0384-0.


Taxator-tk: precise taxonomic assignment of metagenomes by fast approximation of evolutionary neighborhoods.

Dröge J, Gregor I, McHardy AC.

Bioinformatics. 2015 Mar 15;31(6):817-24. doi: 10.1093/bioinformatics/btu745. Epub 2014 Nov 10.


MetaGeniE: characterizing human clinical samples using deep metagenomic sequencing.

Rawat A, Engelthaler DM, Driebe EM, Keim P, Foster JT.

PLoS One. 2014 Nov 3;9(11):e110915. doi: 10.1371/journal.pone.0110915. eCollection 2014.


Metaphylogenomic and potential functionality of the limpet Patella pellucida's gastrointestinal tract microbiome.

Dudek M, Adams J, Swain M, Hegarty M, Huws S, Gallagher J.

Int J Mol Sci. 2014 Oct 20;15(10):18819-39. doi: 10.3390/ijms151018819.


Sequencing and computational approaches to identification and characterization of microbial organisms.

Yadav BS, Ronda V, Vashista DP, Sharma B.

Biomed Eng Comput Biol. 2013 May 20;5:43-9. doi: 10.4137/BECB.S10886. eCollection 2013. Review.


Insights into novel antimicrobial compounds and antibiotic resistance genes from soil metagenomes.

de Castro AP, Fernandes Gda R, Franco OL.

Front Microbiol. 2014 Sep 18;5:489. doi: 10.3389/fmicb.2014.00489. eCollection 2014. Review.


A two-stage statistical procedure for feature selection and comparison in functional analysis of metagenomes.

Pookhao N, Sohn MB, Li Q, Jenkins I, Du R, Jiang H, An L.

Bioinformatics. 2015 Jan 15;31(2):158-65. doi: 10.1093/bioinformatics/btu635. Epub 2014 Sep 24.


Microbiome analysis - from technical advances to biological relevance.

Smith MI, Turpin W, Tyler AD, Silverberg MS, Croitoru K.

F1000Prime Rep. 2014 Jul 8;6:51. doi: 10.12703/P6-51. eCollection 2014. Review.


Metagenomic survey for viruses in Western Arctic caribou, Alaska, through iterative assembly of taxonomic units.

Schürch AC, Schipper D, Bijl MA, Dau J, Beckmen KB, Schapendonk CM, Raj VS, Osterhaus AD, Haagmans BL, Tryland M, Smits SL.

PLoS One. 2014 Aug 20;9(8):e105227. doi: 10.1371/journal.pone.0105227. eCollection 2014.


The rhizosphere microbiota of plant invaders: an overview of recent advances in the microbiomics of invasive plants.

Coats VC, Rumpho ME.

Front Microbiol. 2014 Jul 23;5:368. doi: 10.3389/fmicb.2014.00368. eCollection 2014. Review.


An introduction to the analysis of shotgun metagenomic data.

Sharpton TJ.

Front Plant Sci. 2014 Jun 16;5:209. doi: 10.3389/fpls.2014.00209. eCollection 2014. Review.


Standardized metadata for human pathogen/vector genomic sequences.

Dugan VG, Emrich SJ, Giraldo-Calderón GI, Harb OS, Newman RM, Pickett BE, Schriml LM, Stockwell TB, Stoeckert CJ Jr, Sullivan DE, Singh I, Ward DV, Yao A, Zheng J, Barrett T, Birren B, Brinkac L, Bruno VM, Caler E, Chapman S, Collins FH, Cuomo CA, Di Francesco V, Durkin S, Eppinger M, Feldgarden M, Fraser C, Fricke WF, Giovanni M, Henn MR, Hine E, Hotopp JD, Karsch-Mizrachi I, Kissinger JC, Lee EM, Mathur P, Mongodin EF, Murphy CI, Myers G, Neafsey DE, Nelson KE, Nierman WC, Puzak J, Rasko D, Roos DS, Sadzewicz L, Silva JC, Sobral B, Squires RB, Stevens RL, Tallon L, Tettelin H, Wentworth D, White O, Will R, Wortman J, Zhang Y, Scheuermann RH.

PLoS One. 2014 Jun 17;9(6):e99979. doi: 10.1371/journal.pone.0099979. eCollection 2014.


Analysis of plant microbe interactions in the era of next generation sequencing technologies.

Knief C.

Front Plant Sci. 2014 May 21;5:216. doi: 10.3389/fpls.2014.00216. eCollection 2014. Review.


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.

MBio. 2014 Jun 3;5(3):e01193-14. doi: 10.1128/mBio.01193-14.

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