A5014444761- Gene Regulatory Network Analysis
- Circadian rhythm and melatonin
- Light effects on plants
- Microbial Metabolic Engineering and Bioproduction
- Vestibular and auditory disorders
- Evolution and Genetic Dynamics
- Advanced Multi-Objective Optimization Algorithms
- Neural dynamics and brain function
- Visual perception and processing mechanisms
- Photoreceptor and optogenetics research
- Glaucoma and retinal disorders
- Plant Molecular Biology Research
- Evolutionary Algorithms and Applications
- Metaheuristic Optimization Algorithms Research
- Photosynthetic Processes and Mechanisms
- Bioinformatics and Genomic Networks
- Fungal and yeast genetics research
- Functional Brain Connectivity Studies
- Plant and Biological Electrophysiology Studies
- Simulation Techniques and Applications
- Ocular Surface and Contact Lens
- Gaussian Processes and Bayesian Inference
- Viral Infectious Diseases and Gene Expression in Insects
- Plant nutrient uptake and metabolism
- Parallel Computing and Optimization Techniques
University of Exeter
2014-2023
Karabük University
2021
University of Edinburgh
2008-2015
University of California, San Diego
2015
Institute of Genetics and Cancer
2015
Systems Biology Institute
2013
University of Nottingham
2013
Google (United States)
2012
University of Warwick
2005-2008
University of Manchester
2002-2006
Abstract In higher plants, plasmodesmata (PD) are major conduits for cell–cell communication. Primary PD laid down at cytokinesis, while secondary arise during wall extension. During leaf development, the basal cell walls of trichomes extend radially without division, providing a convenient system studying origin PD. We devised simple freeze-fracture protocol examining large numbers in surface view. postcytokinetic wall, were distributed randomly. As extended, became twinned periphery....
The circadian clock controls 24‐h rhythms in many biological processes, allowing appropriate timing of relative to dawn and dusk. Known circuits include multiple, interlocked feedback loops. Theory suggested that multiple loops contribute the flexibility for molecular track phases external cycle. Clear dawn‐ dusk‐tracking illustrate Ipomoea nil . Molecular components Arabidopsis thaliana showed complex, photoperiod‐dependent regulation, which was analysed by comparison with three contrasting...
The gene networks that comprise the circadian clock modulate biological function across a range of scales, from expression to performance and adaptive behaviour. functions by generating endogenous rhythms can be entrained external 24-h day–night cycle, enabling organisms optimally time biochemical processes relative dawn dusk. In recent years, computational models based on differential equations have become useful tools for dissecting quantifying complex regulatory relationships underlying...
Abstract Background Robustness is a central property of living systems, enabling function to be maintained against environmental perturbations. A key challenge identify the structures in biological circuits that confer system-level properties such as robustness. Circadian clocks allow organisms adapt predictable changes 24-hour day/night cycle by generating endogenous rhythms can entrained external cycle. In all organisms, clock typically comprise multiple interlocked feedback loops...
Model selection and parameter inference are complex problems that have yet to be fully addressed in systems biology. In contrast with optimisation, computes both the means their standard deviations (or full posterior distributions), thus yielding important information on extent which data model topology constrain inferred values.We report application of nested sampling, a statistical approach computing Bayesian evidence Z, parameters, estimation log Z an established circadian rhythms. A...
Network models of brain dynamics provide valuable insight into the healthy functioning and how this breaks down in disease. A pertinent example is use network to understand seizure generation (ictogenesis) epilepsy. Recently, computational have emerged aid our understanding seizures predict outcome surgical perturbations networks. Such approaches opportunity quantify effect removing regions tissue from networks thereby search for optimal resection strategy. Here, we elucidate sets nodes...
Cellular phenotypes underpinned by regulatory networks need to respond evolutionary pressures allow adaptation, but at the same time be robust perturbations. This creates a conflict in which mutations affecting must both generate variance also tolerated phenotype level. Here, we perform mathematical analyses and simulations of better understand potential trade-off between robustness evolvability. Examining phenotypic effects mutations, find an inverse correlation evolvability that breaks...
Article12 February 2008Open Access Isoform switching facilitates period control in the Neurospora crassa circadian clock Ozgur E Akman Interdisciplinary Programme for Cellular Regulation, University of Warwick, Coventry, UK Systems Biology Centre, Mathematics Institute, Search more papers by this author James C W Locke Department Physics, Sanyi Tang Isabelle Carré Biological Sciences, Andrew J Millar School Edinburgh, David A Rand Corresponding Author Information Akman1,2,3, Locke1,4,...
Circadian clocks are oscillatory genetic networks that help organisms adapt to the 24-hour day/night cycle. The clock of green alga Ostreococcus tauri is simplest plant discovered so far. Its many advantages as an experimental system facilitate testing computational predictions. We present a model in stochastic process algebra Bio-PEPA and exploit its mapping different analysis techniques, such ordinary differential equations, simulation algorithms model-checking. small number molecules...
Summary The circadian clock measures time across a 24 h period, increasing fitness by phasing biological processes to the most appropriate of day. interlocking feedback loop mechanism is conserved species; however, number loops varies. Mathematical and computational analyses have suggested that complexity affects overall flexibility oscillator, including its responses entrainment signals. We used discriminating experimental assay, at transition between different photoperiods, in order test...
Abstract The potential for epigenetic changes in host cells following microbial infection has been widely suggested, but few examples have reported. We assessed genome-wide patterns of DNA methylation human macrophage-like U937 with Burkholderia pseudomallei , an intracellular bacterial pathogen and the causative agent melioidosis. Our analyses revealed significant cell methylation, at multiple CpG sites genome, infection. Infection induced differentially methylated probes (iDMPs) showing...
Many of the most important potential applications Synthetic Biology will require ability to design and implement high performance feedback control systems that can accurately regulate dynamics multiple molecular species within cell. Here, we argue use strategies based on combining ultrasensitive response with negative represents a natural approach this problem fully exploits strongly nonlinear nature cellular information processing. We propose such mechanisms explain adaptive responses...
BackgroundAssessing circadian rhythmicity from infrequently sampled data is challenging; however, these types of are often encountered when measuring transcripts in hospitalized patients.MethodsWe present ClinCirc. This method combines 2 existing mathematical methods (Lomb-Scargle periodogram and cosinor) sequentially designed to measure oscillations clinical data. The accuracy this was compared against 9 other using simulated frequently biological ClinCirc then evaluated 13 intensive care...
Neural mass models (NMMs) are important for helping us interpret observations of brain dynamics. They provide a means to understand data in terms mechanisms such as synaptic interactions between excitatory and inhibitory neuronal populations. To using NMMs we need quantitatively compare the output with data, thereby find parameter values which model can produce observed Mapping dynamics NMM this way has potential improve our understanding health disease. Though abstract, still comprise many...
Abstract Summary: Complex computational experiments in Systems Biology, such as fitting model parameters to experimental data, can be challenging perform. Not only do they frequently require a high level of power, but the software needed run experiment needs usable by scientists with varying levels expertise, and modellers need able obtain up-to-date data resources easily. We have developed suite, Biology Software Infrastructure (SBSI), facilitate parameter-fitting process. SBSI is modular...
The circadian clock orchestrates biological processes so that they occur at specific times of the day, thereby facilitating adaptation to diurnal and seasonal environmental changes. In plants, mathematical modelling has been comprehensively integrated with experimental studies gain a better mechanistic understanding complex genetic regulatory network comprising clock. However, an increasing number genes being discovered, there is pressing need for methods expansion computational models...
Rhythmic behavior is essential for plants; example, daily (circadian) rhythms control photosynthesis and seasonal regulate their life cycle. The core of the circadian clock a genetic network that coordinates expression specific genes in rhythm reflecting 24-h day/night Circadian clocks exhibit stochastic noise due to low copy numbers consequent cell-to-cell variation: this intrinsic plays major role by inducing more robust oscillatory behavior. Another source environment, which causes...
The circadian system-an organism's built-in biological clock-is responsible for orchestrating processes to adapt diurnal and seasonal variations. Perturbations the system (e.g., pathogen attack, sudden environmental change) often result in pathophysiological responses jetlag humans, stunted growth plants, etc.) In view of this, synthetic biologists are progressively adapting idea employing feedback control circuits alleviate effects perturbations on systems. To facilitate design such...