Kreft Lab: University of Birmingham

Please see my Google Scholar page for further or more recent publications!

If you don't have access to one of these publications, just email me for a pdf (j.kreft@bham.ac.uk)

Kreft JU, Schink B (1993). Demethylation and degradation of phenylmethylethers by the sulfide-methylating homoacetogenic bacterium strain TMBS4. Archives of Microbiology 159: 308-315
Kreft JU, Schink B (1994). O-Demethylation by the homoacetogenic anaerobe Holophaga foetida studied by a new photometric methylation assay using electrochemically produced cob(I)alamin. European Journal of Biochemistry 226: 945-951
Liesack W, Bak F, Kreft JU, Stackebrandt E (1994). Holophaga foetida gen. nov., sp. nov., a new, homoacetogenic bacterium degrading methoxylated aromatic compounds. Archives of Microbiology 162: 85-90
Kappler O, Janssen PH, Kreft JU, Schink B (1997). Effects of alternative methyl group acceptors on the growth energetics of the O-demethylating anaerobe Holophaga foetida. Microbiology 143: 1105-1114
Kreft JU, Schink B (1997). Specificity of O-demethylation in extracts of the homoacetogenic Holophaga foetida and demethylation kinetics measured by a coupled photometric assay. Archives of Microbiology 167: 363-368
Kreft JU, Booth G, Wimpenny JWT (1998). BacSim, a simulator for individual-based modelling of bacterial colony growth. Microbiology 144: 3275-3287
Kreft JU, Picioreanu C, Wimpenny JWT, van Loosdrecht MCM (2001). Individual-based modelling of biofilms. Microbiology 147: 2897-2912
Faculty of 1000 evaluation of Kreft et al. (2001)
Kreft JU, Wimpenny JWT (2001). Effect of EPS on biofilm structure and function as revealed by an individual-based model of biofilm growth. Water Science and Technology 43(6): 135-141
Faculty of 1000 evaluation of Kreft & Wimpenny (2001)
van Loosdrecht MCM, Heijnen JJ, Eberl HJ, Kreft JU, Picioreanu C (2002). Mathematical modelling of biofilm structures. Antonie van Leeuwenhoek 81: 245-256
Picioreanu C, Kreft JU, van Loosdrecht MCM (2004). Particle-based multidimensional multispecies biofilm model. Applied and Environmental Microbiology 70: 3024-3040
Kreft JU (2004). Biofilms promote altruism. Microbiology 150: 2751-2760
Kreft JU (2004). Conflicts of interest in biofilms. Biofilms 1: 265-276
Kreft JU, Bonhoeffer S (2005). The evolution of groups of cooperating bacteria and the growth rate versus yield trade-off. Microbiology 151: 637-641
Grijspeerdt K, Kreft JU, Messens W (2005). Individual-based modelling of growth and migration of Salmonella enteritidis in hen's eggs. International Journal of Food Microbiology 100: 323-333
Dens EJ, Bernaerts K, Standaert AR, Kreft JU, Van Impe JF (2005). Cell division theory and individual-based modeling of microbial lag. Part II. Modeling lag phenomena induced by temperature shifts. International Journal of Food Microbiology 101: 319-332
Costa E, Pérez J, Kreft JU (2006). Why is metabolic labour divided in nitrification? Trends in Microbiology 14: 213-219
Faculty of 1000 evaluation of Costa et al. (2006)
Klausen M, Gjermansen M, Kreft JU, Tolker-Nielsen T (2006). Dynamics of development and dispersal in sessile microbial communities: examples from Pseudomonas aeruginosa and Pseudomonas putida model biofilms. FEMS Microbiology Letters 261: 1-11
Hense BA, Kuttler C, Müller J, Rothballer M, Hartmann A, Kreft JU (2007). Does efficiency sensing unify quorum and diffusion sensing? Nature Reviews Microbiology 5: 230-239
Faculty of 1000 evaluation of Hense et al. (2007)
Picioreanu C, Kreft JU, Klausen M, Haagensen JAJ, Tolker-Nielsen T, Molin S (2007). Microbial motility involvement in biofilm structure formation – a 3D modelling study. Water Science and Technology 55: 337-343
Dötsch A, Severin J, Alt W, Galinski EA, Kreft JU (2008). A mathematical model for growth and osmoregulation in halophilic bacteria. Microbiology 154: 2956-2969
Schuster S, Kreft JU, Schroeter A, Pfeiffer T (2008). Use of game-theoretical methods in biochemistry and biophysics. Journal of Biological Physics 34: 1-17
Pérez J, Costa E, Kreft JU (2009). Conditions for partial nitrification in biofilm reactors and a kinetic explanation. Biotechnology and Bioengineering 103: 282-295
Kreft JU (2009). Mathematical modeling of microbial ecology: spatial dynamics of interactions in biofilms and guts. In Foodborne Microbes: Shaping the Host Ecosystem. Jaykus LA, Wang HH, Schlesinger LS (eds), pp 347-377. Washington, DC: ASM Press
Bock M, Tyagi AK, Kreft JU, Alt W (2010). Generalized Voronoi tessellation as a model of two-dimensional cell tissue dynamics. Bulletin of Mathematical Biology 72: 1696-1731
Schuster S, Kreft JU, Brenner N, Wessely F, Theißen G, Ruppin E, Schroeter A (2010). Cooperation and cheating in microbial exoenzyme production - Theoretical analysis for biotechnological applications. Biotechnology Journal 5: 751-758
Lardon LA, Merkey BV, Martins S, Dötsch A, Picioreanu C, Kreft JU, Smets BF (2011). iDynoMiCS: next-generation individual-based modelling of biofilms. Environmental Microbiology 13: 2416-2434
Faculty of 1000 evaluation of Lardon et al. (2011)
Costello C, Kreft JU, Thomas CM, Mendes PM (2011).Protein nanoarrays for high resolution patterning of bacteria on gold surfaces.In: Toms S, Weil R (eds) Nanoproteomics: Methods and Protocols. Springer Protocols, Methods in Molecular Biology Series. Humana Press, New York
Merkey BV, Lardon LA, Seoane JM, Kreft JU, Smets BF (2011). Growth dependence of conjugation explains limited plasmid invasion in biofilms: an individual-based modelling study. Environmental Microbiology 13: 2435-2452
Schmidt SI, Picioreanu C, Craenen B, Mackay R, Kreft JU, Theodoropoulos G (2011). A multi-scale agent-based distributed simulation framework for groundwater pollution management. Proceedings of the 15th IEEE International Symposium on Distributed Simulation and Real Time Applications (DS-RT'11), Salford, Manchester, UK, September 4-7 2011. IEEE Computer Society, Los Alamitos, CA, USA, pp 18-27
Costello CM, Kreft JU, Thomas CM, Hammes DM, Bao P, Evans SD, Mendes PM (2012). Exploiting additive and subtractive patterning for spatially controlled and robust bacterial co-cultures. Soft Matter 8: 9147-9155
van der Wal A, Tecon R, Kreft JU, Mooij WM, Leveau JHJ (2013). Explaining bacterial dispersion on leaf surfaces with an individual-based model (PHYLLOSIM). PLoS ONE 8: e75633
Kreft JU, Plugge CM, Grimm V, Prats C, Leveau JHJ, Banitz T, Baines S, Clark J, Ros A, Klapper I, Topping CJ, Field AJ, Schuler A, Litchman E, Hellweger FL (2013). Mighty small: Observing and modeling individual microbes becomes big science. PNAS 110: 18027-18028
Clegg RJ, Dyson RJ, Kreft JU (2014). Repair rather than segregation of damage is the optimal unicellular aging strategy. BMC Biology 12: 52
Kreft JU (2014). Mathematical modelling of plasmid dynamics. Molecular Life Sciences: An Encyclopedic Reference, (Bell E, Bond J, Klinman J, Masters B, Wells R, eds). Springer-Verlag, Berlin Heidelberg
Sinden NJ, Baker MJ, Smith DJ, Kreft JU, Dafforn TR, Stockley RA (2015). Alpha-1-Antitrypsin Variants and the Proteinase/Anti-Proteinase Imbalance in Chronic Obstructive Pulmonary Disease. Am J Physiol Lung Cell Mol Physiol 308: L179-190
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, Großkopf T, Huisman J, Free A, Picioreanu C, Quince C, Klapper I, Labarthe S, Smets BF, Wang H, Isaac Newton Institute Fellows, Soyer OS (2016). Challenges in microbial ecology: building predictive understanding of community function and dynamics. ISME Journal 10: 2557–2568
Hellweger FL, Clegg RJ, Clark JR, Plugge CM, Kreft JU (2016). Advancing microbial sciences by individual-based modelling. Nature Reviews Microbiology 14: 461–471
Dong F, Valsami-Jones E, Kreft JU (2016). New, rapid method to measure dissolved silver concentration in silver nanoparticle suspensions by aggregation combined with centrifugation. Journal of Nanoparticle Research 18: 259
Clegg RJ, Kreft JU (2017). Reducing discrepancies between 3D and 2D simulations due to cell packing density. Journal of Theoretical Biology 423: 26–30
Dong F, Mohd Zaidi NF, Valsami-Jones E, Kreft JU (2017). Time-resolved toxicity study reveals the dynamic interactions between uncoated silver nanoparticles and bacteria. Nanotoxicology 11: 637–646
Kreft JU, Plugge CM, Prats C, Leveau JHJ, Zhang W, Hellweger FL (2017). From Genes to Ecosystems in Microbiology: Modeling Approaches and the Importance of Individuality. Frontiers in Microbiology 8: 2299
Kreft JU (2017). Mathematical modelling of the microbiota for manipulating its membership (Part of editorial series: The microbiome as a source of new enterprises and job creation). Microbial Biotechnology 11: 145–148
Leveau JHJ, Hellweger FL, Kreft JU, Prats C, Zhang W (2018). Editorial: The Individual Microbe: Single-Cell Analysis and Agent-Based Modelling. Frontiers in Microbiology 9: 2825
Schmidt SI, Kreft JU, Mackay R, Picioreanu C, Thullner M (2018). Elucidating the impact of micro-scale heterogeneous bacterial distribution on biodegradation. Advances in Water Resources 116: 67–76
Kreft JU, Gülez G (2019). Microbiology and Mathematics: microbiological meaning from mathematical models (feature article). Microbiologist (SfAM magazine) 20: 24-29