Dov J Stekel

Summary

Affiliation: University of Nottingham
Country: UK

Publications

  1. pmc Adaptation for protein synthesis efficiency in a naturally occurring self-regulating operon
    Dorota Herman
    School of Biosciences, University of Birmingham, Birmingham, United Kingdom
    PLoS ONE 7:e49678. 2012
  2. doi request reprint Evolution of resource and energy management in biologically realistic gene regulatory network models
    Dov J Stekel
    School of Biosciences, University of Nottingham, Leicestershire, UK
    Adv Exp Med Biol 751:301-28. 2012
  3. pmc De novo evolution of complex, global and hierarchical gene regulatory mechanisms
    Dafyd J Jenkins
    Centre for Systems Biology, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
    J Mol Evol 71:128-40. 2010
  4. doi request reprint A new model for investigating the evolution of transcription control networks
    Dafyd J Jenkins
    Centre for Systems Biology, School of Biosciences, University of Birmingham, Edgbaston, UK
    Artif Life 15:259-91. 2009
  5. doi request reprint A non-independent energy-based multiple sequence alignment improves prediction of transcription factor binding sites
    Rafik A Salama
    Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK and School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, UK
    Bioinformatics 29:2699-704. 2013
  6. pmc Inclusion of neighboring base interdependencies substantially improves genome-wide prokaryotic transcription factor binding site prediction
    Rafik A Salama
    Centre of Systems Biology, School of Biosciences, University of Birmingham, B15 2TT, UK
    Nucleic Acids Res 38:e135. 2010
  7. doi request reprint Stochasticity versus determinism: consequences for realistic gene regulatory network modelling and evolution
    Dafyd J Jenkins
    Centre for Systems Biology, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
    J Mol Evol 70:215-31. 2010
  8. pmc Molecular circuits for associative learning in single-celled organisms
    Chrisantha T Fernando
    Systems Biology Centre, University of Birmingham, Birmingham B15 2TT, UK
    J R Soc Interface 6:463-9. 2009
  9. doi request reprint Bioinformatic methods for finding differentially expressed genes in cDNA libraries, applied to the identification of tumour vascular targets
    John M J Herbert
    Cancer Research UK Angiogenesis Group, Institute for Biomedical Research, Schools of Immunity and Infection and Cancer studies, College of Medicine and Dentistry, University of Birmingham, Birmingham, UK
    Methods Mol Biol 729:99-119. 2011
  10. pmc Global transcription regulation of RK2 plasmids: a case study in the combined use of dynamical mathematical models and statistical inference for integration of experimental data and hypothesis exploration
    Dorota Herman
    Center for Systems Biology, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
    BMC Syst Biol 5:119. 2011

Collaborators

Detail Information

Publications13

  1. pmc Adaptation for protein synthesis efficiency in a naturally occurring self-regulating operon
    Dorota Herman
    School of Biosciences, University of Birmingham, Birmingham, United Kingdom
    PLoS ONE 7:e49678. 2012
    ..We propose that an important evolutionary driver for negatively self-regulated genes is to improve the efficiency of protein synthesis...
  2. doi request reprint Evolution of resource and energy management in biologically realistic gene regulatory network models
    Dov J Stekel
    School of Biosciences, University of Nottingham, Leicestershire, UK
    Adv Exp Med Biol 751:301-28. 2012
    ..In summary, we demonstrate the value of biologically realistic computer evolution techniques, and the importance of energy and resource management in driving the topology and function of gene regulatory networks...
  3. pmc De novo evolution of complex, global and hierarchical gene regulatory mechanisms
    Dafyd J Jenkins
    Centre for Systems Biology, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
    J Mol Evol 71:128-40. 2010
    ..These results highlight the adaptive and incremental evolution of complex biological networks, and the value and potential of studying realistic in silico evolutionary systems as a way of understanding living systems...
  4. doi request reprint A new model for investigating the evolution of transcription control networks
    Dafyd J Jenkins
    Centre for Systems Biology, School of Biosciences, University of Birmingham, Edgbaston, UK
    Artif Life 15:259-91. 2009
    ..This study also highlights the importance of using in silico genetics techniques to investigate evolved model robustness...
  5. doi request reprint A non-independent energy-based multiple sequence alignment improves prediction of transcription factor binding sites
    Rafik A Salama
    Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK and School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, UK
    Bioinformatics 29:2699-704. 2013
    ..However, non-coding DNA binding sequences, such as transcription factor binding sites (TFBSs), are frequently not related by common descent, and so the existing alignment scoring methods are not well suited for aligning such sequences...
  6. pmc Inclusion of neighboring base interdependencies substantially improves genome-wide prokaryotic transcription factor binding site prediction
    Rafik A Salama
    Centre of Systems Biology, School of Biosciences, University of Birmingham, B15 2TT, UK
    Nucleic Acids Res 38:e135. 2010
    ..Finally we have developed the ungapped likelihood under positional background platform: a user friendly website that gives access to the prediction method devised in this work...
  7. doi request reprint Stochasticity versus determinism: consequences for realistic gene regulatory network modelling and evolution
    Dafyd J Jenkins
    Centre for Systems Biology, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
    J Mol Evol 70:215-31. 2010
    ..Moreover, there are trade-offs between efficiency and yield, indicating an inherent intertwining of fitness and evolutionary dynamics...
  8. pmc Molecular circuits for associative learning in single-celled organisms
    Chrisantha T Fernando
    Systems Biology Centre, University of Birmingham, Birmingham B15 2TT, UK
    J R Soc Interface 6:463-9. 2009
    ..A preliminary design for implementing this model using plasmids within Escherichia coli is presented, along with an alternative approach, based on double-phosphorylated protein kinases...
  9. doi request reprint Bioinformatic methods for finding differentially expressed genes in cDNA libraries, applied to the identification of tumour vascular targets
    John M J Herbert
    Cancer Research UK Angiogenesis Group, Institute for Biomedical Research, Schools of Immunity and Infection and Cancer studies, College of Medicine and Dentistry, University of Birmingham, Birmingham, UK
    Methods Mol Biol 729:99-119. 2011
    ..With the advent of next-generation sequencing, these or similar methods can be applied to find novel genes with this new source of data...
  10. pmc Global transcription regulation of RK2 plasmids: a case study in the combined use of dynamical mathematical models and statistical inference for integration of experimental data and hypothesis exploration
    Dorota Herman
    Center for Systems Biology, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
    BMC Syst Biol 5:119. 2011
    ..We also compared MCMC and Metabolic Control Analysis (MCA) as approaches for determining the sensitivity of model parameters...
  11. pmc Strong negative self regulation of prokaryotic transcription factors increases the intrinsic noise of protein expression
    Dov J Stekel
    Centre for Systems Biology, School of Biosciences, University of Birmingham, Edgbaston B15 2TT, UK
    BMC Syst Biol 2:6. 2008
    ..We explore the role of negative self regulation of transcription in regulating the variability of protein abundance using a variety of stochastic modeling techniques...
  12. pmc xBASE2: a comprehensive resource for comparative bacterial genomics
    Roy R Chaudhuri
    Centre for Systems Biology, University of Birmingham, Birmingham B15 2TT, UK
    Nucleic Acids Res 36:D543-6. 2008
    ..bham.ac.uk), now provides comprehensive coverage of all bacterial genomes and features an updated modularized backend and an improved user interface, which includes a taxonomy browser and a powerful full-text search facility...
  13. pmc Three-dimensional images of choanoflagellate loricae
    Barry S C Leadbeater
    School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
    Proc Biol Sci 276:3-11. 2009
    ....