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Items: 1 to 50 of 54

1.

Acetate Metabolism and the Inhibition of Bacterial Growth by Acetate.

Pinhal S, Ropers D, Geiselmann J, de Jong H.

J Bacteriol. 2019 Jun 10;201(13). pii: e00147-19. doi: 10.1128/JB.00147-19. Print 2019 Jul 1.

2.

An ensemble of mathematical models showing diauxic growth behaviour.

Kremling A, Geiselmann J, Ropers D, de Jong H.

BMC Syst Biol. 2018 Sep 21;12(1):82. doi: 10.1186/s12918-018-0604-8.

3.

Mathematical modelling of microbes: metabolism, gene expression and growth.

de Jong H, Casagranda S, Giordano N, Cinquemani E, Ropers D, Geiselmann J, Gouzé JL.

J R Soc Interface. 2017 Nov;14(136). pii: 20170502. doi: 10.1098/rsif.2017.0502. Review.

4.

Resource Reallocation in Bacteria by Reengineering the Gene Expression Machinery.

de Jong H, Geiselmann J, Ropers D.

Trends Microbiol. 2017 Jun;25(6):480-493. doi: 10.1016/j.tim.2016.12.009. Epub 2017 Jan 16. Review.

PMID:
28110800
5.

Dynamical Allocation of Cellular Resources as an Optimal Control Problem: Novel Insights into Microbial Growth Strategies.

Giordano N, Mairet F, Gouzé JL, Geiselmann J, de Jong H.

PLoS Comput Biol. 2016 Mar 9;12(3):e1004802. doi: 10.1371/journal.pcbi.1004802. eCollection 2016 Mar.

6.

A synthetic growth switch based on controlled expression of RNA polymerase.

Izard J, Gomez Balderas CD, Ropers D, Lacour S, Song X, Yang Y, Lindner AB, Geiselmann J, de Jong H.

Mol Syst Biol. 2015 Nov 23;11(11):840. doi: 10.15252/msb.20156382.

7.

Robust reconstruction of gene expression profiles from reporter gene data using linear inversion.

Zulkower V, Page M, Ropers D, Geiselmann J, de Jong H.

Bioinformatics. 2015 Jun 15;31(12):i71-9. doi: 10.1093/bioinformatics/btv246.

8.

Characterization of the Escherichia coli σ(S) core regulon by Chromatin Immunoprecipitation-sequencing (ChIP-seq) analysis.

Peano C, Wolf J, Demol J, Rossi E, Petiti L, De Bellis G, Geiselmann J, Egli T, Lacour S, Landini P.

Sci Rep. 2015 May 28;5:10469. doi: 10.1038/srep10469.

9.

Inference of quantitative models of bacterial promoters from time-series reporter gene data.

Stefan D, Pinel C, Pinhal S, Cinquemani E, Geiselmann J, de Jong H.

PLoS Comput Biol. 2015 Jan 15;11(1):e1004028. doi: 10.1371/journal.pcbi.1004028. eCollection 2015 Jan. Erratum in: PLoS Comput Biol. 2017 Mar 8;13(3):e1005402.

10.

Understanding carbon catabolite repression in Escherichia coli using quantitative models.

Kremling A, Geiselmann J, Ropers D, de Jong H.

Trends Microbiol. 2015 Feb;23(2):99-109. doi: 10.1016/j.tim.2014.11.002. Epub 2014 Dec 2. Review.

PMID:
25475882
11.

Repression of flagellar genes in exponential phase by CsgD and CpxR, two crucial modulators of Escherichia coli biofilm formation.

Dudin O, Geiselmann J, Ogasawara H, Ishihama A, Lacour S.

J Bacteriol. 2014 Feb;196(3):707-15. doi: 10.1128/JB.00938-13. Epub 2013 Nov 22.

12.

A genome-wide screen for identifying all regulators of a target gene.

Baptist G, Pinel C, Ranquet C, Izard J, Ropers D, de Jong H, Geiselmann J.

Nucleic Acids Res. 2013 Sep;41(17):e164. doi: 10.1093/nar/gkt655. Epub 2013 Jul 26.

13.

Expression dynamics of RpoS/Crl-dependent genes in Escherichia coli.

Dudin O, Lacour S, Geiselmann J.

Res Microbiol. 2013 Oct;164(8):838-47. doi: 10.1016/j.resmic.2013.07.002. Epub 2013 Jul 16.

PMID:
23867204
14.

Shared control of gene expression in bacteria by transcription factors and global physiology of the cell.

Berthoumieux S, de Jong H, Baptist G, Pinel C, Ranquet C, Ropers D, Geiselmann J.

Mol Syst Biol. 2013;9:634. doi: 10.1038/msb.2012.70.

15.

Genetic network analyzer: a tool for the qualitative modeling and simulation of bacterial regulatory networks.

Batt G, Besson B, Ciron PE, de Jong H, Dumas E, Geiselmann J, Monte R, Monteiro PT, Page M, Rechenmann F, Ropers D.

Methods Mol Biol. 2012;804:439-62. doi: 10.1007/978-1-61779-361-5_22.

PMID:
22144166
16.

Importance of metabolic coupling for the dynamics of gene expression following a diauxic shift in Escherichia coli.

Baldazzi V, Ropers D, Geiselmann J, Kahn D, de Jong H.

J Theor Biol. 2012 Feb 21;295:100-15. doi: 10.1016/j.jtbi.2011.11.010. Epub 2011 Nov 28.

PMID:
22138386
17.

The carbon assimilation network in Escherichia coli is densely connected and largely sign-determined by directions of metabolic fluxes.

Baldazzi V, Ropers D, Markowicz Y, Kahn D, Geiselmann J, de Jong H.

PLoS Comput Biol. 2010 Jun 10;6(6):e1000812. doi: 10.1371/journal.pcbi.1000812. Erratum in: PLoS Comput Biol. 2010 Aug;6(8). doi: 10.1371/annotation/ed46bce4-e4e1-4df5-bad3-fac0770efeac.

18.

Experimental and computational validation of models of fluorescent and luminescent reporter genes in bacteria.

de Jong H, Ranquet C, Ropers D, Pinel C, Geiselmann J.

BMC Syst Biol. 2010 Apr 29;4:55. doi: 10.1186/1752-0509-4-55.

19.

WellReader: a MATLAB program for the analysis of fluorescence and luminescence reporter gene data.

Boyer F, Besson B, Baptist G, Izard J, Pinel C, Ropers D, Geiselmann J, de Jong H.

Bioinformatics. 2010 May 1;26(9):1262-3. doi: 10.1093/bioinformatics/btq016. Epub 2010 Jan 22.

PMID:
20097915
20.

The Crl-RpoS regulon of Escherichia coli.

Lelong C, Aguiluz K, Luche S, Kuhn L, Garin J, Rabilloud T, Geiselmann J.

Mol Cell Proteomics. 2007 Apr;6(4):648-59. Epub 2007 Jan 15.

21.

Mutual regulation of Crl and Fur in Escherichia coli W3110.

Lelong C, Rolland M, Louwagie M, Garin J, Geiselmann J.

Mol Cell Proteomics. 2007 Apr;6(4):660-8. Epub 2007 Jan 15.

22.

Parallel changes in global protein profiles during long-term experimental evolution in Escherichia coli.

Pelosi L, Kühn L, Guetta D, Garin J, Geiselmann J, Lenski RE, Schneider D.

Genetics. 2006 Aug;173(4):1851-69. Epub 2006 May 15.

23.

Qualitative simulation of the carbon starvation response in Escherichia coli.

Ropers D, de Jong H, Page M, Schneider D, Geiselmann J.

Biosystems. 2006 May;84(2):124-52. Epub 2005 Dec 1.

PMID:
16325332
24.

Control of bacteriophage mu lysogenic repression.

Ranquet C, Toussaint A, de Jong H, Maenhaut-Michel G, Geiselmann J.

J Mol Biol. 2005 Oct 14;353(1):186-95.

PMID:
16154589
25.

Validation of qualitative models of genetic regulatory networks by model checking: analysis of the nutritional stress response in Escherichia coli.

Batt G, Ropers D, de Jong H, Geiselmann J, Mateescu R, Page M, Schneider D.

Bioinformatics. 2005 Jun;21 Suppl 1:i19-28.

PMID:
15961457
26.

Inferring the connectivity of a regulatory network from mRNA quantification in Synechocystis PCC6803.

Lemeille S, Latifi A, Geiselmann J.

Nucleic Acids Res. 2005 Jun 8;33(10):3381-9. Print 2005.

27.

Crosstalk regulation among group 2-sigma factors in Synechocystis PCC6803.

Lemeille S, Geiselmann J, Latifi A.

BMC Microbiol. 2005 Apr 22;5:18.

28.

The glucosyl-1-phosphate transferase WchA (Cap8E) primes the capsular polysaccharide repeat unit biosynthesis of Streptococcus pneumoniae serotype 8.

Pelosi L, Boumedienne M, Saksouk N, Geiselmann J, Geremia RA.

Biochem Biophys Res Commun. 2005 Feb 18;327(3):857-65.

PMID:
15649424
29.

Long-term experimental evolution in Escherichia coli. XII. DNA topology as a key target of selection.

Crozat E, Philippe N, Lenski RE, Geiselmann J, Schneider D.

Genetics. 2005 Feb;169(2):523-32. Epub 2004 Oct 16.

30.

Improvement of pCVD442, a suicide plasmid for gene allele exchange in bacteria.

Philippe N, Alcaraz JP, Coursange E, Geiselmann J, Schneider D.

Plasmid. 2004 May;51(3):246-55.

PMID:
15109831
31.

Crl, a low temperature-induced protein in Escherichia coli that binds directly to the stationary phase sigma subunit of RNA polymerase.

Bougdour A, Lelong C, Geiselmann J.

J Biol Chem. 2004 May 7;279(19):19540-50. Epub 2004 Feb 21.

32.

Qualitative simulation of genetic regulatory networks using piecewise-linear models.

De Jong H, Gouzé JL, Hernandez C, Page M, Sari T, Geiselmann J.

Bull Math Biol. 2004 Mar;66(2):301-40.

PMID:
14871568
33.

Qualitative simulation of the initiation of sporulation in Bacillus subtilis.

De Jong H, Geiselmann J, Batt G, Hernandez C, Page M.

Bull Math Biol. 2004 Mar;66(2):261-99.

PMID:
14871567
34.

Genetic Network Analyzer: qualitative simulation of genetic regulatory networks.

de Jong H, Geiselmann J, Hernandez C, Page M.

Bioinformatics. 2003 Feb 12;19(3):336-44.

PMID:
12584118
35.

The tRNA function of SsrA contributes to controlling repression of bacteriophage Mu prophage.

Ranquet C, Geiselmann J, Toussaint A.

Proc Natl Acad Sci U S A. 2001 Aug 28;98(18):10220-5. Epub 2001 Aug 21.

36.

Ultraviolet-laser footprinting.

Geiselmann J, Boccard F.

Methods Mol Biol. 2001;148:161-73. No abstract available.

PMID:
11357584
37.
38.

Participation of IHF and a distant UP element in the stimulation of the phage lambda PL promoter.

Giladi H, Koby S, Prag G, Engelhorn M, Geiselmann J, Oppenheim AB.

Mol Microbiol. 1998 Oct;30(2):443-51.

39.
40.

A simple polypyrimidine repeat acts as an artificial Rho-dependent terminator in vivo and in vitro.

Guérin M, Robichon N, Geiselmann J, Rahmouni AR.

Nucleic Acids Res. 1998 Nov 1;26(21):4895-900.

41.

Structural kinetics of transcription activation at the malT promoter of Escherichia coli by UV laser footprinting.

Eichenberger P, Déthiollaz S, Buc H, Geiselmann J.

Proc Natl Acad Sci U S A. 1997 Aug 19;94(17):9022-7.

42.
43.
44.

Influence of the location of the cAMP receptor protein binding site on the geometry of a transcriptional activation complex in Escherichia coli.

Eichenberger P, Déthiollaz S, Fujita N, Ishihama A, Geiselmann J.

Biochemistry. 1996 Dec 3;35(48):15302-12.

PMID:
8952481
45.

Influence of DNA geometry on transcriptional activation in Escherichia coli.

Déthiollaz S, Eichenberger P, Geiselmann J.

EMBO J. 1996 Oct 1;15(19):5449-58.

46.

In vivo interaction of the Escherichia coli integration host factor with its specific binding sites.

Engelhorn M, Boccard F, Murtin C, Prentki P, Geiselmann J.

Nucleic Acids Res. 1995 Sep 11;23(17):2959-65.

PMID:
7567442
47.

In vivo interaction of the Escherichia coli integration host factor with its specific binding sites.

Engelhorn M, Boccard F, Murtin C, Prentki P, Geiselmann J.

Nucleic Acids Res. 1995 Aug 11;23(15):2959-65. Corrected and republished in: Nucleic Acids Res. 1995 Sep 11;23(17):2959-65.

48.

A physical model for the translocation and helicase activities of Escherichia coli transcription termination protein Rho.

Geiselmann J, Wang Y, Seifried SE, von Hippel PH.

Proc Natl Acad Sci U S A. 1993 Aug 15;90(16):7754-8.

50.

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