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Items: 1 to 20 of 44


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. Review.


An algorithm for designing minimal microbial communities with desired metabolic capacities.

Eng A, Borenstein E.

Bioinformatics. 2016 Jul 1;32(13):2008-16. doi: 10.1093/bioinformatics/btw107.


Whole Cell Modeling: From Single Cells to Colonies.

Cole JA, Luthey-Schulten Z.

Isr J Chem. 2014 Aug;54(8-9):1219-1229.


Predicting compositions of microbial communities from stoichiometric models with applications for the biogas process.

Koch S, Benndorf D, Fronk K, Reichl U, Klamt S.

Biotechnol Biofuels. 2016 Jan 22;9:17. doi: 10.1186/s13068-016-0429-x.


The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases.

Caspi R, Billington R, Ferrer L, Foerster H, Fulcher CA, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Subhraveti P, Weaver DS, Karp PD.

Nucleic Acids Res. 2016 Jan 4;44(D1):D471-80. doi: 10.1093/nar/gkv1164.


Synthetic Ecology of Microbes: Mathematical Models and Applications.

Zomorrodi AR, Segrè D.

J Mol Biol. 2016 Feb 27;428(5 Pt B):837-61. doi: 10.1016/j.jmb.2015.10.019. Review.


Functional environmental proteomics: elucidating the role of a c-type cytochrome abundant during uranium bioremediation.

Yun J, Malvankar NS, Ueki T, Lovley DR.

ISME J. 2016 Feb;10(2):310-20. doi: 10.1038/ismej.2015.113.


Using Genome-scale Models to Predict Biological Capabilities.

O'Brien EJ, Monk JM, Palsson BO.

Cell. 2015 May 21;161(5):971-87. doi: 10.1016/j.cell.2015.05.019. Review.


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. Erratum in: Proc Natl Acad Sci U S A. 2015 Dec 22;112(51):E7156.


Systems biology of host-microbe metabolomics.

Heinken A, Thiele I.

Wiley Interdiscip Rev Syst Biol Med. 2015 Jul-Aug;7(4):195-219. doi: 10.1002/wsbm.1301. Review.


Systems modeling approaches for microbial community studies: from metagenomics to inference of the community structure.

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

Front Microbiol. 2015 Mar 19;6:213. doi: 10.3389/fmicb.2015.00213.


Anoxic Conditions Promote Species-Specific Mutualism between Gut Microbes In Silico.

Heinken A, Thiele I.

Appl Environ Microbiol. 2015 Jun 15;81(12):4049-61. doi: 10.1128/AEM.00101-15.


DFBAlab: a fast and reliable MATLAB code for dynamic flux balance analysis.

Gomez JA, Höffner K, Barton PI.

BMC Bioinformatics. 2014 Dec 18;15:409. doi: 10.1186/s12859-014-0409-8.


A peptide-based method for 13C Metabolic Flux Analysis in microbial communities.

Ghosh A, Nilmeier J, Weaver D, Adams PD, Keasling JD, Mukhopadhyay A, Petzold CJ, Martín HG.

PLoS Comput Biol. 2014 Sep 4;10(9):e1003827. doi: 10.1371/journal.pcbi.1003827.


Mapping the inner workings of the microbiome: genomic- and metagenomic-based study of metabolism and metabolic interactions in the human microbiome.

Manor O, Levy R, Borenstein E.

Cell Metab. 2014 Nov 4;20(5):742-52. doi: 10.1016/j.cmet.2014.07.021. Review.


Evidence of Geobacter-associated phage in a uranium-contaminated aquifer.

Holmes DE, Giloteaux L, Chaurasia AK, Williams KH, Luef B, Wilkins MJ, Wrighton KC, Thompson CA, Comolli LR, Lovley DR.

ISME J. 2015 Feb;9(2):333-46. doi: 10.1038/ismej.2014.128.


Emergent biosynthetic capacity in simple microbial communities.

Chiu HC, Levy R, Borenstein E.

PLoS Comput Biol. 2014 Jul 3;10(7):e1003695. doi: 10.1371/journal.pcbi.1003695.


Microbial Consortia Engineering for Cellular Factories: in vitro to in silico systems.

Bernstein HC, Carlson RP.

Comput Struct Biotechnol J. 2012 Dec 1;3:e201210017. doi: 10.5936/csbj.201210017. Review.

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