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Probabilistic inference of biochemical reactions in microbial communities from metagenomic sequences.

Jiao D, Ye Y, Tang H.

PLoS Comput Biol. 2013;9(3):e1002981. doi: 10.1371/journal.pcbi.1002981. Epub 2013 Mar 21.


A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes.

Ye Y, Doak TG.

PLoS Comput Biol. 2009 Aug;5(8):e1000465. doi: 10.1371/journal.pcbi.1000465. Epub 2009 Aug 14.


Fragment recruitment on metabolic pathways: comparative metabolic profiling of metagenomes and metatranscriptomes.

Desai DK, Schunck H, Löser JW, Laroche J.

Bioinformatics. 2013 Mar 15;29(6):790-1. doi: 10.1093/bioinformatics/bts721. Epub 2013 Jan 9.


Prediction and identification of sequences coding for orphan enzymes using genomic and metagenomic neighbours.

Yamada T, Waller AS, Raes J, Zelezniak A, Perchat N, Perret A, Salanoubat M, Patil KR, Weissenbach J, Bork P.

Mol Syst Biol. 2012 May 8;8:581. doi: 10.1038/msb.2012.13.


Coordinating environmental genomics and geochemistry reveals metabolic transitions in a hot spring ecosystem.

Swingley WD, Meyer-Dombard DR, Shock EL, Alsop EB, Falenski HD, Havig JR, Raymond J.

PLoS One. 2012;7(6):e38108. doi: 10.1371/journal.pone.0038108. Epub 2012 Jun 4.


Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease.

Greenblum S, Turnbaugh PJ, Borenstein E.

Proc Natl Acad Sci U S A. 2012 Jan 10;109(2):594-9. doi: 10.1073/pnas.1116053109. Epub 2011 Dec 19.


Classification of metagenomic sequences: methods and challenges.

Mande SS, Mohammed MH, Ghosh TS.

Brief Bioinform. 2012 Nov;13(6):669-81. doi: 10.1093/bib/bbs054. Epub 2012 Sep 8. Review.


Metagenomic annotation networks: construction and applications.

Vey G, Moreno-Hagelsieb G.

PLoS One. 2012;7(8):e41283. doi: 10.1371/journal.pone.0041283. Epub 2012 Aug 7.


Identifying biologically relevant differences between metagenomic communities.

Parks DH, Beiko RG.

Bioinformatics. 2010 Mar 15;26(6):715-21. doi: 10.1093/bioinformatics/btq041. Epub 2010 Feb 3.


Metagenomic analysis of Surti buffalo (Bubalus bubalis) rumen: a preliminary study.

Singh KM, Ahir VB, Tripathi AK, Ramani UV, Sajnani M, Koringa PG, Jakhesara S, Pandya PR, Rank DN, Murty DS, Kothari RK, Joshi CG.

Mol Biol Rep. 2012 Apr;39(4):4841-8. doi: 10.1007/s11033-011-1278-0. Epub 2011 Sep 27.


The phylogenetic diversity of metagenomes.

Kembel SW, Eisen JA, Pollard KS, Green JL.

PLoS One. 2011;6(8):e23214. doi: 10.1371/journal.pone.0023214. Epub 2011 Aug 31.


Metabolic reconstruction for metagenomic data and its application to the human microbiome.

Abubucker S, Segata N, Goll J, Schubert AM, Izard J, Cantarel BL, Rodriguez-Mueller B, Zucker J, Thiagarajan M, Henrissat B, White O, Kelley ST, Methé B, Schloss PD, Gevers D, Mitreva M, Huttenhower C.

PLoS Comput Biol. 2012;8(6):e1002358. doi: 10.1371/journal.pcbi.1002358. Epub 2012 Jun 13.


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.


Metagenomic analysis of the pygmy loris fecal microbiome reveals unique functional capacity related to metabolism of aromatic compounds.

Xu B, Xu W, Yang F, Li J, Yang Y, Tang X, Mu Y, Zhou J, Huang Z.

PLoS One. 2013;8(2):e56565. doi: 10.1371/journal.pone.0056565. Epub 2013 Feb 15.


Comparative metagenomic analysis of plasmid encoded functions in the human gut microbiome.

Jones BV, Sun F, Marchesi JR.

BMC Genomics. 2010 Jan 19;11:46. doi: 10.1186/1471-2164-11-46.


Our second genome-human metagenome: how next-generation sequencer changes our life through microbiology.

Song S, Jarvie T, Hattori M.

Adv Microb Physiol. 2013;62:119-44. doi: 10.1016/B978-0-12-410515-7.00003-2.


Stitching gene fragments with a network matching algorithm improves gene assembly for metagenomics.

Wu YW, Rho M, Doak TG, Ye Y.

Bioinformatics. 2012 Sep 15;28(18):i363-i369. doi: 10.1093/bioinformatics/bts388.


A user's guide to quantitative and comparative analysis of metagenomic datasets.

Luo C, Rodriguez-R LM, Konstantinidis KT.

Methods Enzymol. 2013;531:525-47. doi: 10.1016/B978-0-12-407863-5.00023-X.


Metagenomics using next-generation sequencing.

Bragg L, Tyson GW.

Methods Mol Biol. 2014;1096:183-201. doi: 10.1007/978-1-62703-712-9_15.


MetaProx: the database of metagenomic proximons.

Vey G, Charles TC.

Database (Oxford). 2014 Oct 6;2014. pii: bau097. doi: 10.1093/database/bau097. Print 2014.

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