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Items: 1 to 20 of 168

1.

OptCom: a multi-level optimization framework for the metabolic modeling and analysis of microbial communities.

Zomorrodi AR, Maranas CD.

PLoS Comput Biol. 2012 Feb;8(2):e1002363. doi: 10.1371/journal.pcbi.1002363. Epub 2012 Feb 2.

2.

d-OptCom: Dynamic multi-level and multi-objective metabolic modeling of microbial communities.

Zomorrodi AR, Islam MM, Maranas CD.

ACS Synth Biol. 2014 Apr 18;3(4):247-57. doi: 10.1021/sb4001307. Epub 2014 Feb 28.

PMID:
24742179
3.

Metabolic dependencies drive species co-occurrence in diverse microbial communities.

Zelezniak A, Andrejev S, Ponomarova O, Mende DR, Bork P, Patil KR.

Proc Natl Acad Sci U S A. 2015 May 19;112(20):6449-54. doi: 10.1073/pnas.1421834112. Epub 2015 May 4. Erratum in: Proc Natl Acad Sci U S A. 2015 Dec 22;112(51):E7156.

4.

Community flux balance analysis for microbial consortia at balanced growth.

Khandelwal RA, Olivier BG, Röling WF, Teusink B, Bruggeman FJ.

PLoS One. 2013 May 31;8(5):e64567. doi: 10.1371/journal.pone.0064567. Print 2013.

5.

Genome-scale metabolic flux analysis of Streptomyces lividans growing on a complex medium.

D'Huys PJ, Lule I, Vercammen D, Anné J, Van Impe JF, Bernaerts K.

J Biotechnol. 2012 Sep 15;161(1):1-13. doi: 10.1016/j.jbiotec.2012.04.010. Epub 2012 May 26.

PMID:
22641041
6.

A computational exploration of bacterial metabolic diversity identifying metabolic interactions and growth-efficient strain communities.

Tzamali E, Poirazi P, Tollis IG, Reczko M.

BMC Syst Biol. 2011 Oct 18;5:167. doi: 10.1186/1752-0509-5-167.

7.

Metabolic Network Modeling of Microbial Interactions in Natural and Engineered Environmental Systems.

Perez-Garcia O, Lear G, Singhal N.

Front Microbiol. 2016 May 18;7:673. doi: 10.3389/fmicb.2016.00673. eCollection 2016. Review.

8.

Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association.

Nagarajan H, Embree M, Rotaru AE, Shrestha PM, Feist AM, Palsson BØ, Lovley DR, Zengler K.

Nat Commun. 2013;4:2809. doi: 10.1038/ncomms3809.

PMID:
24264237
9.

In silico approaches to study mass and energy flows in microbial consortia: a syntrophic case study.

Taffs R, Aston JE, Brileya K, Jay Z, Klatt CG, McGlynn S, Mallette N, Montross S, Gerlach R, Inskeep WP, Ward DM, Carlson RP.

BMC Syst Biol. 2009 Dec 10;3:114. doi: 10.1186/1752-0509-3-114.

10.

Ecosystems biology of microbial metabolism.

Klitgord N, Segrè D.

Curr Opin Biotechnol. 2011 Aug;22(4):541-6. doi: 10.1016/j.copbio.2011.04.018. Epub 2011 May 16. Review.

PMID:
21592777
11.
12.

Genome-scale constraint-based modeling of Geobacter metallireducens.

Sun J, Sayyar B, Butler JE, Pharkya P, Fahland TR, Famili I, Schilling CH, Lovley DR, Mahadevan R.

BMC Syst Biol. 2009 Jan 28;3:15. doi: 10.1186/1752-0509-3-15.

13.

Genome-based Modeling and Design of Metabolic Interactions in Microbial Communities.

Mahadevan R, Henson MA.

Comput Struct Biotechnol J. 2012 Nov 12;3:e201210008. doi: 10.5936/csbj.201210008. eCollection 2012. Review.

14.

MultiMetEval: comparative and multi-objective analysis of genome-scale metabolic models.

Zakrzewski P, Medema MH, Gevorgyan A, Kierzek AM, Breitling R, Takano E.

PLoS One. 2012;7(12):e51511. doi: 10.1371/journal.pone.0051511. Epub 2012 Dec 14.

15.

The large-scale organization of the bacterial network of ecological co-occurrence interactions.

Freilich S, Kreimer A, Meilijson I, Gophna U, Sharan R, Ruppin E.

Nucleic Acids Res. 2010 Jul;38(12):3857-68. doi: 10.1093/nar/gkq118. Epub 2010 Mar 1.

16.

Syntrophic exchange in synthetic microbial communities.

Mee MT, Collins JJ, Church GM, Wang HH.

Proc Natl Acad Sci U S A. 2014 May 20;111(20):E2149-56. doi: 10.1073/pnas.1405641111. Epub 2014 Apr 28.

17.

Microbial communities and their interactions in biofilm systems: an overview.

Wuertz S, Okabe S, Hausner M.

Water Sci Technol. 2004;49(11-12):327-36. Review.

PMID:
15303758
18.

Systems approaches to microbial communities and their functioning.

Röling WF, Ferrer M, Golyshin PN.

Curr Opin Biotechnol. 2010 Aug;21(4):532-8. doi: 10.1016/j.copbio.2010.06.007. Epub 2010 Jul 14. Review.

PMID:
20637597
19.

Metabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic Variation.

Noecker C, Eng A, Srinivasan S, Theriot CM, Young VB, Jansson JK, Fredricks DN, Borenstein E.

mSystems. 2016 Jan-Feb;1(1). pii: e00013-15. Epub 2016 Jan 19.

20.

Upflow anaerobic sludge blanket reactor--a review.

Bal AS, Dhagat NN.

Indian J Environ Health. 2001 Apr;43(2):1-82. Review.

PMID:
12397675
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