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Items: 1 to 50 of 89

1.

Editorial: The Individual Microbe: Single-Cell Analysis and Agent-Based Modelling.

Leveau JHJ, Hellweger FL, Kreft JU, Prats C, Zhang W.

Front Microbiol. 2018 Nov 21;9:2825. doi: 10.3389/fmicb.2018.02825. eCollection 2018. No abstract available.

2.

From Genes to Ecosystems in Microbiology: Modeling Approaches and the Importance of Individuality.

Kreft JU, Plugge CM, Prats C, Leveau JHJ, Zhang W, Hellweger FL.

Front Microbiol. 2017 Nov 27;8:2299. doi: 10.3389/fmicb.2017.02299. eCollection 2017. Review.

3.

Editorial: The microbiome as a source of new enterprises and job creation.

Kreft JU.

Microb Biotechnol. 2018 Jan;11(1):145-148. doi: 10.1111/1751-7915.13026. Epub 2017 Dec 4. No abstract available.

4.

Time-resolved toxicity study reveals the dynamic interactions between uncoated silver nanoparticles and bacteria.

Dong F, Mohd Zaidi NF, Valsami-Jones E, Kreft JU.

Nanotoxicology. 2017 Jun;11(5):637-646. doi: 10.1080/17435390.2017.1342010.

PMID:
28608745
5.

Reducing discrepancies between 3D and 2D simulations due to cell packing density.

Clegg RJ, Kreft JU.

J Theor Biol. 2017 Jun 21;423:26-30. doi: 10.1016/j.jtbi.2017.04.016. Epub 2017 Apr 17.

PMID:
28427817
6.

Challenges in microbial ecology: building predictive understanding of community function and dynamics.

Widder S, Allen RJ, Pfeiffer T, Curtis TP, Wiuf C, Sloan WT, Cordero OX, Brown SP, Momeni B, Shou W, Kettle H, Flint HJ, Haas AF, Laroche B, Kreft JU, Rainey PB, Freilich S, Schuster S, Milferstedt K, van der Meer JR, Groβkopf T, Huisman J, Free A, Picioreanu C, Quince C, Klapper I, Labarthe S, Smets BF, Wang H; Isaac Newton Institute Fellows, Soyer OS.

ISME J. 2016 Nov;10(11):2557-2568. doi: 10.1038/ismej.2016.45. Epub 2016 Mar 29. Review.

7.
8.

Advancing microbial sciences by individual-based modelling.

Hellweger FL, Clegg RJ, Clark JR, Plugge CM, Kreft JU.

Nat Rev Microbiol. 2016 Jul;14(7):461-71. doi: 10.1038/nrmicro.2016.62. Epub 2016 Jun 6. Review.

PMID:
27265769
9.

Backbone circularization of Bacillus subtilis family 11 xylanase increases its thermostability and its resistance against aggregation.

Waldhauer MC, Schmitz SN, Ahlmann-Eltze C, Gleixner JG, Schmelas CC, Huhn AG, Bunne C, Büscher M, Horn M, Klughammer N, Kreft J, Schäfer E, Bayer PA, Krämer SG, Neugebauer J, Wehler P, Mayer MP, Eils R, Di Ventura B.

Mol Biosyst. 2015 Dec;11(12):3231-43. doi: 10.1039/c5mb00341e.

PMID:
26434634
10.

α-1-antitrypsin variants and the proteinase/antiproteinase imbalance in chronic obstructive pulmonary disease.

Sinden NJ, Baker MJ, Smith DJ, Kreft JU, Dafforn TR, Stockley RA.

Am J Physiol Lung Cell Mol Physiol. 2015 Jan 15;308(2):L179-90.

11.

Repair rather than segregation of damage is the optimal unicellular aging strategy.

Clegg RJ, Dyson RJ, Kreft JU.

BMC Biol. 2014 Aug 16;12:52. doi: 10.1186/s12915-014-0052-x.

12.

Mighty small: Observing and modeling individual microbes becomes big science.

Kreft JU, Plugge CM, Grimm V, Prats C, Leveau JH, Banitz T, Baines S, Clark J, Ros A, Klapper I, Topping CJ, Field AJ, Schuler A, Litchman E, Hellweger FL.

Proc Natl Acad Sci U S A. 2013 Nov 5;110(45):18027-8. doi: 10.1073/pnas.1317472110. No abstract available.

13.

Explaining bacterial dispersion on leaf surfaces with an individual-based model (PHYLLOSIM).

van der Wal A, Tecon R, Kreft JU, Mooij WM, Leveau JH.

PLoS One. 2013 Oct 4;8(10):e75633. doi: 10.1371/journal.pone.0075633. eCollection 2013.

14.

Complete genome sequence of the animal pathogen Listeria ivanovii, which provides insights into host specificities and evolution of the genus Listeria.

Buchrieser C, Rusniok C, Garrido P, Hain T, Scortti M, Lampidis R, Kärst U, Chakraborty T, Cossart P, Kreft J, Vazquez-Boland JA, Goebel W, Glaser P.

J Bacteriol. 2011 Dec;193(23):6787-8. doi: 10.1128/JB.06120-11.

15.

Protein nanoarrays for high-resolution patterning of bacteria on gold surfaces.

Costello C, Kreft JU, Thomas CM, Mendes PM.

Methods Mol Biol. 2011;790:191-200. doi: 10.1007/978-1-61779-319-6_15.

PMID:
21948416
16.

Growth dependence of conjugation explains limited plasmid invasion in biofilms: an individual-based modelling study.

Merkey BV, Lardon LA, Seoane JM, Kreft JU, Smets BF.

Environ Microbiol. 2011 Sep;13(9):2435-52. doi: 10.1111/j.1462-2920.2011.02535.x.

PMID:
21906217
17.

Implications of the inability of Listeria monocytogenes EGD-e to grow anaerobically due to a deletion in the class III NrdD ribonucleotide reductase for its use as a model laboratory strain.

Ofer A, Kreft J, Logan DT, Cohen G, Borovok I, Aharonowitz Y.

J Bacteriol. 2011 Jun;193(12):2931-40. doi: 10.1128/JB.01405-10. Epub 2011 Apr 8.

18.

iDynoMiCS: next-generation individual-based modelling of biofilms.

Lardon LA, Merkey BV, Martins S, Dötsch A, Picioreanu C, Kreft JU, Smets BF.

Environ Microbiol. 2011 Sep;13(9):2416-34. doi: 10.1111/j.1462-2920.2011.02414.x. Epub 2011 Mar 16.

PMID:
21410622
19.

Blue and red light modulates SigB-dependent gene transcription, swimming motility and invasiveness in Listeria monocytogenes.

Ondrusch N, Kreft J.

PLoS One. 2011 Jan 11;6(1):e16151. doi: 10.1371/journal.pone.0016151.

20.

Cooperation and cheating in microbial exoenzyme production--theoretical analysis for biotechnological applications.

Schuster S, Kreft JU, Brenner N, Wessely F, Theissen G, Ruppin E, Schroeter A.

Biotechnol J. 2010 Jul;5(7):751-8. doi: 10.1002/biot.200900303.

PMID:
20540107
21.

Maltose and maltodextrin utilization by Listeria monocytogenes depend on an inducible ABC transporter which is repressed by glucose.

Gopal S, Berg D, Hagen N, Schriefer EM, Stoll R, Goebel W, Kreft J.

PLoS One. 2010 Apr 27;5(4):e10349. doi: 10.1371/journal.pone.0010349.

22.

Generalized voronoi tessellation as a model of two-dimensional cell tissue dynamics.

Bock M, Tyagi AK, Kreft JU, Alt W.

Bull Math Biol. 2010 Oct;72(7):1696-731. doi: 10.1007/s11538-009-9498-3. Epub 2010 Jan 16.

PMID:
20082148
23.

Complete genome sequence of Listeria seeligeri, a nonpathogenic member of the genus Listeria.

Steinweg C, Kuenne CT, Billion A, Mraheil MA, Domann E, Ghai R, Barbuddhe SB, Kärst U, Goesmann A, Pühler A, Weisshaar B, Wehland J, Lampidis R, Kreft J, Goebel W, Chakraborty T, Hain T.

J Bacteriol. 2010 Mar;192(5):1473-4. doi: 10.1128/JB.01415-09. Epub 2010 Jan 8.

24.

Conditions for partial nitrification in biofilm reactors and a kinetic explanation.

Pérez J, Costa E, Kreft JU.

Biotechnol Bioeng. 2009 Jun 1;103(2):282-95. doi: 10.1002/bit.22249.

PMID:
19189394
25.

Prediction of proteins putatively involved in the thiol: disulfide redox metabolism of a bacterium (Listeria): the CXXC motif as query sequence.

Gopal S, Srinivas V, Zameer F, Kreft J.

In Silico Biol. 2009;9(5-6):407-14. doi: 10.3233/ISB-2009-0409.

PMID:
22430441
26.

A mathematical model for growth and osmoregulation in halophilic bacteria.

Dötsch A, Severin J, Alt W, Galinski EA, Kreft JU.

Microbiology. 2008 Oct;154(Pt 10):2956-69. doi: 10.1099/mic.0.2007/012237-0.

PMID:
18832302
27.

Conformation and trapping rate of DNA at a convergent stagnation point.

Kreft J, Chen YL, Chang HC.

Phys Rev E Stat Nonlin Soft Matter Phys. 2008 Mar;77(3 Pt 1):030801. Epub 2008 Mar 5.

PMID:
18517319
28.

Use of game-theoretical methods in biochemistry and biophysics.

Schuster S, Kreft JU, Schroeter A, Pfeiffer T.

J Biol Phys. 2008 Apr;34(1-2):1-17. doi: 10.1007/s10867-008-9101-4. Epub 2008 Aug 6.

29.

Gastric bypass: post-operative complications in individuals with and without preoperative dietary guidance.

Kreft JS, Montebelo J, Fogaça KC, Rasera I, Oliveira MR.

J Eval Clin Pract. 2008 Feb;14(1):169-71. doi: 10.1111/j.1365-2753.2007.00815.x. No abstract available.

PMID:
18211665
30.

Thermal diffusion by Brownian-motion-induced fluid stress.

Kreft J, Chen YL.

Phys Rev E Stat Nonlin Soft Matter Phys. 2007 Aug;76(2 Pt 1):021912. Epub 2007 Aug 10.

PMID:
17930070
31.

Microbial motility involvement in biofilm structure formation--a 3D modelling study.

Picioreanu C, Kreft JU, Klausen M, Haagensen JA, Tolker-Nielsen T, Molin S.

Water Sci Technol. 2007;55(8-9):337-43.

PMID:
17547003
32.

Pathogenomics of Listeria spp.

Hain T, Chatterjee SS, Ghai R, Kuenne CT, Billion A, Steinweg C, Domann E, Kärst U, Jänsch L, Wehland J, Eisenreich W, Bacher A, Joseph B, Schär J, Kreft J, Klumpp J, Loessner MJ, Dorscht J, Neuhaus K, Fuchs TM, Scherer S, Doumith M, Jacquet C, Martin P, Cossart P, Rusniock C, Glaser P, Buchrieser C, Goebel W, Chakraborty T.

Int J Med Microbiol. 2007 Nov;297(7-8):541-57. Epub 2007 May 7. Review.

PMID:
17482873
33.

Does efficiency sensing unify diffusion and quorum sensing?

Hense BA, Kuttler C, Müller J, Rothballer M, Hartmann A, Kreft JU.

Nat Rev Microbiol. 2007 Mar;5(3):230-9. Review.

PMID:
17304251
34.

Whole-genome sequence of Listeria welshimeri reveals common steps in genome reduction with Listeria innocua as compared to Listeria monocytogenes.

Hain T, Steinweg C, Kuenne CT, Billion A, Ghai R, Chatterjee SS, Domann E, Kärst U, Goesmann A, Bekel T, Bartels D, Kaiser O, Meyer F, Pühler A, Weisshaar B, Wehland J, Liang C, Dandekar T, Lampidis R, Kreft J, Goebel W, Chakraborty T.

J Bacteriol. 2006 Nov;188(21):7405-15. Epub 2006 Aug 25.

35.

Mechanisms in the size segregation of a binary granular mixture.

Schröter M, Ulrich S, Kreft J, Swift JB, Swinney HL.

Phys Rev E Stat Nonlin Soft Matter Phys. 2006 Jul;74(1 Pt 1):011307. Epub 2006 Jul 26.

PMID:
16907089
36.

Dynamics of development and dispersal in sessile microbial communities: examples from Pseudomonas aeruginosa and Pseudomonas putida model biofilms.

Klausen M, Gjermansen M, Kreft JU, Tolker-Nielsen T.

FEMS Microbiol Lett. 2006 Aug;261(1):1-11. Review.

37.

Three-dimensional on-line reconstruction of coronary bifurcated lesions to optimize side-branch stenting.

Schlundt C, Kreft JG, Fuchs F, Achenbach S, Daniel WG, Ludwig J.

Catheter Cardiovasc Interv. 2006 Aug;68(2):249-53. No abstract available.

PMID:
16830353
38.

Why is metabolic labour divided in nitrification?

Costa E, Pérez J, Kreft JU.

Trends Microbiol. 2006 May;14(5):213-9. Epub 2006 Apr 18.

PMID:
16621570
39.

A spontaneous genomic deletion in Listeria ivanovii identifies LIPI-2, a species-specific pathogenicity island encoding sphingomyelinase and numerous internalins.

Domínguez-Bernal G, Müller-Altrock S, González-Zorn B, Scortti M, Herrmann P, Monzó HJ, Lacharme L, Kreft J, Vázquez-Boland JA.

Mol Microbiol. 2006 Jan;59(2):415-32.

40.

Sublimation of a vibrated granular monolayer: coexistence of gas and solid.

Götzendorfer A, Kreft J, Kruelle CA, Rehberg I.

Phys Rev Lett. 2005 Sep 23;95(13):135704. Epub 2005 Sep 23.

PMID:
16197150
41.

Cell division theory and individual-based modeling of microbial lag: part II. Modeling lag phenomena induced by temperature shifts.

Dens EJ, Bernaerts K, Standaert AR, Kreft JU, Van Impe JF.

Int J Food Microbiol. 2005 Jun 15;101(3):319-32.

PMID:
15913823
42.

A multidomain fusion protein in Listeria monocytogenes catalyzes the two primary activities for glutathione biosynthesis.

Gopal S, Borovok I, Ofer A, Yanku M, Cohen G, Goebel W, Kreft J, Aharonowitz Y.

J Bacteriol. 2005 Jun;187(11):3839-47.

43.

Individual-based modelling of growth and migration of Salmonella enteritidis in hens' eggs.

Grijspeerdt K, Kreft JU, Messens W.

Int J Food Microbiol. 2005 Apr 15;100(1-3):323-33. Epub 2004 Dec 8.

PMID:
15854715
44.

Onset of patterns in an oscillated granular layer: continuum and molecular dynamics simulations.

Bougie J, Kreft J, Swift JB, Swinney HL.

Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Feb;71(2 Pt 1):021301. Epub 2005 Feb 8.

PMID:
15783318
45.

The evolution of groups of cooperating bacteria and the growth rate versus yield trade-off.

Kreft JU, Bonhoeffer S.

Microbiology. 2005 Mar;151(Pt 3):637-41. No abstract available.

PMID:
15758209
46.

Evolutionary history of the genus Listeria and its virulence genes.

Schmid MW, Ng EY, Lampidis R, Emmerth M, Walcher M, Kreft J, Goebel W, Wagner M, Schleifer KH.

Syst Appl Microbiol. 2005 Jan;28(1):1-18.

PMID:
15709360
47.

Crucial role of sidewalls in velocity distributions in quasi-two-dimensional granular gases.

van Zon JS, Kreft J, Goldman DI, Miracle D, Swift JB, Swinney HL.

Phys Rev E Stat Nonlin Soft Matter Phys. 2004 Oct;70(4 Pt 1):040301. Epub 2004 Oct 19.

PMID:
15600385
48.

Biofilms promote altruism.

Kreft JU.

Microbiology. 2004 Aug;150(Pt 8):2751-60.

PMID:
15289571
49.

Particle-based multidimensional multispecies biofilm model.

Picioreanu C, Kreft JU, Van Loosdrecht MC.

Appl Environ Microbiol. 2004 May;70(5):3024-40.

50.

Mathematical modelling of biofilm structures.

van Loosdrecht MC, Heijnen JJ, Eberl H, Kreft J, Picioreanu C.

Antonie Van Leeuwenhoek. 2002 Aug;81(1-4):245-56. Review.

PMID:
12448723

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