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Bioprospecting metagenomics for new glycoside hydrolases.

Gilbert J, Li LL, Taghavi S, McCorkle SM, Tringe S, van der Lelie D.

Methods Mol Biol. 2012;908:141-51. doi: 10.1007/978-1-61779-956-3_14.


Bioprospecting metagenomics of decaying wood: mining for new glycoside hydrolases.

Li LL, Taghavi S, McCorkle SM, Zhang YB, Blewitt MG, Brunecky R, Adney WS, Himmel ME, Brumm P, Drinkwater C, Mead DA, Tringe SG, Lelie Dv.

Biotechnol Biofuels. 2011 Aug 4;4(1):23. doi: 10.1186/1754-6834-4-23.


Bioprospecting metagenomes: glycosyl hydrolases for converting biomass.

Li LL, McCorkle SR, Monchy S, Taghavi S, van der Lelie D.

Biotechnol Biofuels. 2009 May 18;2:10. doi: 10.1186/1754-6834-2-10.


GASdb: a large-scale and comparative exploration database of glycosyl hydrolysis systems.

Zhou F, Chen H, Xu Y.

BMC Microbiol. 2010 Mar 4;10:69. doi: 10.1186/1471-2180-10-69.


Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores.

Pope PB, Denman SE, Jones M, Tringe SG, Barry K, Malfatti SA, McHardy AC, Cheng JF, Hugenholtz P, McSweeney CS, Morrison M.

Proc Natl Acad Sci U S A. 2010 Aug 17;107(33):14793-8. doi: 10.1073/pnas.1005297107. Epub 2010 Jul 28.


Multisubstrate isotope labeling and metagenomic analysis of active soil bacterial communities.

Verastegui Y, Cheng J, Engel K, Kolczynski D, Mortimer S, Lavigne J, Montalibet J, Romantsov T, Hall M, McConkey BJ, Rose DR, Tomashek JJ, Scott BR, Charles TC, Neufeld JD.

MBio. 2014 Jul 15;5(4):e01157-14. doi: 10.1128/mBio.01157-14.


Application of metagenomic techniques in mining enzymes from microbial communities for biofuel synthesis.

Xing MN, Zhang XZ, Huang H.

Biotechnol Adv. 2012 Jul-Aug;30(4):920-9. doi: 10.1016/j.biotechadv.2012.01.021. Epub 2012 Jan 28. Review.


Mining of novel thermo-stable cellulolytic genes from a thermophilic cellulose-degrading consortium by metagenomics.

Xia Y, Ju F, Fang HH, Zhang T.

PLoS One. 2013;8(1):e53779. doi: 10.1371/journal.pone.0053779. Epub 2013 Jan 14.


Reference databases for taxonomic assignment in metagenomics.

Santamaria M, Fosso B, Consiglio A, De Caro G, Grillo G, Licciulli F, Liuni S, Marzano M, Alonso-Alemany D, Valiente G, Pesole G.

Brief Bioinform. 2012 Nov;13(6):682-95. doi: 10.1093/bib/bbs036. Epub 2012 Jul 10. Review.


Glycoside hydrolases from a targeted compost metagenome, activity-screening and functional characterization.

Dougherty MJ, D'haeseleer P, Hazen TC, Simmons BA, Adams PD, Hadi MZ.

BMC Biotechnol. 2012 Jul 3;12:38. doi: 10.1186/1472-6750-12-38.


Use of metagenomic approaches to isolate lipolytic genes from activated sludge.

Liaw RB, Cheng MP, Wu MC, Lee CY.

Bioresour Technol. 2010 Nov;101(21):8323-9. doi: 10.1016/j.biortech.2010.05.091.


Metagenomic analysis reveals a functional signature for biomass degradation by cecal microbiota in the leaf-eating flying squirrel (Petaurista alborufus lena).

Lu HP, Wang YB, Huang SW, Lin CY, Wu M, Hsieh CH, Yu HT.

BMC Genomics. 2012 Sep 10;13:466. doi: 10.1186/1471-2164-13-466.


Achievements and new knowledge unraveled by metagenomic approaches.

Simon C, Daniel R.

Appl Microbiol Biotechnol. 2009 Nov;85(2):265-76. doi: 10.1007/s00253-009-2233-z. Epub 2009 Sep 16. Review.


Snapshot of the eukaryotic gene expression in muskoxen rumen--a metatranscriptomic approach.

Qi M, Wang P, O'Toole N, Barboza PS, Ungerfeld E, Leigh MB, Selinger LB, Butler G, Tsang A, McAllister TA, Forster RJ.

PLoS One. 2011;6(5):e20521. doi: 10.1371/journal.pone.0020521. Epub 2011 May 31.


Metagenomic discovery of biomass-degrading genes and genomes from cow rumen.

Hess M, Sczyrba A, Egan R, Kim TW, Chokhawala H, Schroth G, Luo S, Clark DS, Chen F, Zhang T, Mackie RI, Pennacchio LA, Tringe SG, Visel A, Woyke T, Wang Z, Rubin EM.

Science. 2011 Jan 28;331(6016):463-7. doi: 10.1126/science.1200387.


Molecular methods to study complex microbial communities.

Vieites JM, Guazzaroni ME, Beloqui A, Golyshin PN, Ferrer M.

Methods Mol Biol. 2010;668:1-37. doi: 10.1007/978-1-60761-823-2_1.


i-rDNA: alignment-free algorithm for rapid in silico detection of ribosomal gene fragments from metagenomic sequence data sets.

Mohammed MH, Ghosh TS, Chadaram S, Mande SS.

BMC Genomics. 2011 Nov 30;12 Suppl 3:S12. doi: 10.1186/1471-2164-12-S3-S12. Epub 2011 Nov 30.


Exploration of community traits as ecological markers in microbial metagenomes.

Barberán A, Fernández-Guerra A, Bohannan BJ, Casamayor EO.

Mol Ecol. 2012 Apr;21(8):1909-17. doi: 10.1111/j.1365-294X.2011.05383.x. Epub 2011 Nov 28.


Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes.

Tasse L, Bercovici J, Pizzut-Serin S, Robe P, Tap J, Klopp C, Cantarel BL, Coutinho PM, Henrissat B, Leclerc M, Doré J, Monsan P, Remaud-Simeon M, Potocki-Veronese G.

Genome Res. 2010 Nov;20(11):1605-12. doi: 10.1101/gr.108332.110. Epub 2010 Sep 14.


Unlocking the potential of metagenomics through replicated experimental design.

Knight R, Jansson J, Field D, Fierer N, Desai N, Fuhrman JA, Hugenholtz P, van der Lelie D, Meyer F, Stevens R, Bailey MJ, Gordon JI, Kowalchuk GA, Gilbert JA.

Nat Biotechnol. 2012 Jun 7;30(6):513-20. doi: 10.1038/nbt.2235.

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