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Items: 27

1.

Structure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience.

Mandakovic D, Rojas C, Maldonado J, Latorre M, Travisany D, Delage E, Bihouée A, Jean G, Díaz FP, Fernández-Gómez B, Cabrera P, Gaete A, Latorre C, Gutiérrez RA, Maass A, Cambiazo V, Navarrete SA, Eveillard D, González M.

Sci Rep. 2018 Apr 12;8(1):5875. doi: 10.1038/s41598-018-23931-0.

2.

On the Power of Uncertainties in Microbial System Modeling: No Need To Hide Them Anymore.

Delahaye B, Eveillard D, Bouskill N.

mSystems. 2017 Dec 5;2(6). pii: e00169-17. doi: 10.1128/mSystems.00169-17. eCollection 2017 Nov-Dec. Review.

3.

Combining graph and flux-based structures to decipher phenotypic essential metabolites within metabolic networks.

Laniau J, Frioux C, Nicolas J, Baroukh C, Cortes MP, Got J, Trottier C, Eveillard D, Siegel A.

PeerJ. 2017 Oct 12;5:e3860. doi: 10.7717/peerj.3860. eCollection 2017.

4.

Gene Expression Analysis of Zobellia galactanivorans during the Degradation of Algal Polysaccharides Reveals both Substrate-Specific and Shared Transcriptome-Wide Responses.

Thomas F, Bordron P, Eveillard D, Michel G.

Front Microbiol. 2017 Sep 21;8:1808. doi: 10.3389/fmicb.2017.01808. eCollection 2017.

5.

A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems.

Budinich M, Bourdon J, Larhlimi A, Eveillard D.

PLoS One. 2017 Feb 10;12(2):e0171744. doi: 10.1371/journal.pone.0171744. eCollection 2017.

6.

Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks.

Prigent S, Frioux C, Dittami SM, Thiele S, Larhlimi A, Collet G, Gutknecht F, Got J, Eveillard D, Bourdon J, Plewniak F, Tonon T, Siegel A.

PLoS Comput Biol. 2017 Jan 27;13(1):e1005276. doi: 10.1371/journal.pcbi.1005276. eCollection 2017 Jan.

7.

Beyond the Black Queen Hypothesis.

Mas A, Jamshidi S, Lagadeuc Y, Eveillard D, Vandenkoornhuyse P.

ISME J. 2016 Sep;10(9):2085-91. doi: 10.1038/ismej.2016.22. Epub 2016 Mar 8. Review.

8.

Plankton networks driving carbon export in the oligotrophic ocean.

Guidi L, Chaffron S, Bittner L, Eveillard D, Larhlimi A, Roux S, Darzi Y, Audic S, Berline L, Brum J, Coelho LP, Espinoza JCI, Malviya S, Sunagawa S, Dimier C, Kandels-Lewis S, Picheral M, Poulain J, Searson S; Tara Oceans coordinators, Stemmann L, Not F, Hingamp P, Speich S, Follows M, Karp-Boss L, Boss E, Ogata H, Pesant S, Weissenbach J, Wincker P, Acinas SG, Bork P, de Vargas C, Iudicone D, Sullivan MB, Raes J, Karsenti E, Bowler C, Gorsky G.

Nature. 2016 Apr 28;532(7600):465-470. doi: 10.1038/nature16942. Epub 2016 Feb 10.

9.

Deciphering transcriptional regulations coordinating the response to environmental changes.

Acuña V, Aravena A, Guziolowski C, Eveillard D, Siegel A, Maass A.

BMC Bioinformatics. 2016 Jan 16;17:35. doi: 10.1186/s12859-016-0885-0.

10.

Putative bacterial interactions from metagenomic knowledge with an integrative systems ecology approach.

Bordron P, Latorre M, Cortés MP, González M, Thiele S, Siegel A, Maass A, Eveillard D.

Microbiologyopen. 2016 Feb;5(1):106-17. doi: 10.1002/mbo3.315. Epub 2015 Dec 17.

11.

Marine systems biology.

Tonon T, Eveillard D.

Front Genet. 2015 May 13;6:181. doi: 10.3389/fgene.2015.00181. eCollection 2015. No abstract available.

12.

The genome-scale metabolic network of Ectocarpus siliculosus (EctoGEM): a resource to study brown algal physiology and beyond.

Prigent S, Collet G, Dittami SM, Delage L, Ethis de Corny F, Dameron O, Eveillard D, Thiele S, Cambefort J, Boyen C, Siegel A, Tonon T.

Plant J. 2014 Oct;80(2):367-81. doi: 10.1111/tpj.12627. Epub 2014 Aug 27.

13.

A shift in the archaeal nitrifier community in response to natural and anthropogenic disturbances in the northern Gulf of Mexico.

Newell SE, Eveillard D, McCarthy MJ, Gardner WS, Liu Z, Ward BB.

Environ Microbiol Rep. 2014 Feb;6(1):106-12. doi: 10.1111/1758-2229.12114. Epub 2013 Nov 12.

PMID:
24596268
14.

A metabolic approach to study algal-bacterial interactions in changing environments.

Dittami SM, Eveillard D, Tonon T.

Mol Ecol. 2014 Apr;23(7):1656-60. doi: 10.1111/mec.12670. Epub 2014 Mar 13.

PMID:
24447216
15.

Antagonistic interactions between heterotrophic bacteria as a potential regulator of community structure of hypersaline microbial mats.

Long RA, Eveillard D, Franco SL, Reeves E, Pinckney JL.

FEMS Microbiol Ecol. 2013 Jan;83(1):74-81. doi: 10.1111/j.1574-6941.2012.01457.x. Epub 2012 Aug 6.

16.

Toward systems biology in brown algae to explore acclimation and adaptation to the shore environment.

Tonon T, Eveillard D, Prigent S, Bourdon J, Potin P, Boyen C, Siegel A.

OMICS. 2011 Dec;15(12):883-92. doi: 10.1089/omi.2011.0089. Epub 2011 Dec 2. Review. Erratum in: OMICS. 2012 Apr;16(4):229.

PMID:
22136637
17.

Environmental factors determining ammonia-oxidizing organism distribution and diversity in marine environments.

Bouskill NJ, Eveillard D, Chien D, Jayakumar A, Ward BB.

Environ Microbiol. 2012 Mar;14(3):714-29. doi: 10.1111/j.1462-2920.2011.02623.x. Epub 2011 Nov 3.

PMID:
22050634
18.

Integrating quantitative knowledge into a qualitative gene regulatory network.

Bourdon J, Eveillard D, Siegel A.

PLoS Comput Biol. 2011 Sep;7(9):e1002157. doi: 10.1371/journal.pcbi.1002157. Epub 2011 Sep 15.

19.

Integrated analysis of the gene neighbouring impact on bacterial metabolic networks.

Bordron P, Eveillard D, Rusu I.

IET Syst Biol. 2011 Jul;5(4):261-8. doi: 10.1049/iet-syb.2010.0070.

PMID:
21823757
20.

Using logic programming for modeling the one-carbon metabolism network to study the impact of folate deficiency on methylation processes.

Gnimpieba EZ, Eveillard D, Guéant JL, Chango A.

Mol Biosyst. 2011 Aug;7(8):2508-21. doi: 10.1039/c1mb05102d. Epub 2011 Jun 7.

PMID:
21647531
21.

Seasonal and annual reoccurrence in betaproteobacterial ammonia-oxidizing bacterial population structure.

Bouskill NJ, Eveillard D, O'Mullan G, Jackson GA, Ward BB.

Environ Microbiol. 2011 Apr;13(4):872-86. doi: 10.1111/j.1462-2920.2010.02362.x. Epub 2010 Nov 5.

PMID:
21054735
22.

Targeting human Rad51 by specific DNA aptamers induces inhibition of homologous recombination.

Martinez SF, Renodon-Cornière A, Nomme J, Eveillard D, Fleury F, Takahashi M, Weigel P.

Biochimie. 2010 Dec;92(12):1832-8. doi: 10.1016/j.biochi.2010.08.006. Epub 2010 Aug 14.

PMID:
20713120
23.

Hybrid modeling of biological networks: mixing temporal and qualitative biological properties.

Fromentin J, Eveillard D, Roux O.

BMC Syst Biol. 2010 Jun 4;4:79. doi: 10.1186/1752-0509-4-79.

24.

Temporal constraints of a gene regulatory network: Refining a qualitative simulation.

Ahmad J, Bourdon J, Eveillard D, Fromentin J, Roux O, Sinoquet C.

Biosystems. 2009 Dec;98(3):149-59. doi: 10.1016/j.biosystems.2009.05.002. Epub 2009 May 13.

PMID:
19446002
25.

Homogeneous decomposition of protein interaction networks: refining the description of intra-modular interactions.

Del Mondo G, Eveillard D, Rusu I.

Bioinformatics. 2009 Apr 1;25(7):926-32. doi: 10.1093/bioinformatics/btp083. Epub 2009 Feb 17.

PMID:
19223451
26.

Time course gene expression in the one-carbon metabolism network using HepG2 cell line grown in folate-deficient medium.

Chango A, Nour AA, Bousserouel S, Eveillard D, Anton PM, Guéant JL.

J Nutr Biochem. 2009 Apr;20(4):312-20. doi: 10.1016/j.jnutbio.2008.04.004. Epub 2008 Jul 7.

PMID:
18602821
27.

Ammonia-oxidizing bacterial community composition in estuarine and oceanic environments assessed using a functional gene microarray.

Ward BB, Eveillard D, Kirshtein JD, Nelson JD, Voytek MA, Jackson GA.

Environ Microbiol. 2007 Oct;9(10):2522-38.

PMID:
17803777

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