Dov J Stekel
Affiliation: University of Nottingham
- Adaptation for protein synthesis efficiency in a naturally occurring self-regulating operonDorota 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...
- Evolution of resource and energy management in biologically realistic gene regulatory network modelsDov 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...
- De novo evolution of complex, global and hierarchical gene regulatory mechanismsDafyd 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...
- A new model for investigating the evolution of transcription control networksDafyd 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...
- A non-independent energy-based multiple sequence alignment improves prediction of transcription factor binding sitesRafik 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...
- Inclusion of neighboring base interdependencies substantially improves genome-wide prokaryotic transcription factor binding site predictionRafik 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...
- Stochasticity versus determinism: consequences for realistic gene regulatory network modelling and evolutionDafyd 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...
- Molecular circuits for associative learning in single-celled organismsChrisantha 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...
- Bioinformatic methods for finding differentially expressed genes in cDNA libraries, applied to the identification of tumour vascular targetsJohn 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...
- 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 explorationDorota 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...
- Strong negative self regulation of prokaryotic transcription factors increases the intrinsic noise of protein expressionDov 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...
- xBASE2: a comprehensive resource for comparative bacterial genomicsRoy 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...
- Three-dimensional images of choanoflagellate loricaeBarry S C Leadbeater
School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
Proc Biol Sci 276:3-11. 2009....