Project relations

• SYSTEMS BIOLOGY SOFTWARE INFRASTRUCTURE TM: ROUTES TO COMMDERCIALISATION

  Project: Research

Datasets

• Temporal analysis of RNA turnover in Interferon Gamma treated bone marrow-derived macrophages

  Dataset

• Data, Code and Models for Flis et al. RS Open Biology 2015

  Dataset

Activities

• SynthSys Practical Course on O.tauri transformation

  Activity: Participating in or organising an event types › Participation in workshop, seminar, course

• Freiburg Systems Biology Centre conference on Plant Systems Biology

  Activity: Participating in or organising an event types › Participation in conference

• Frontiers in Systems Biology

  Activity: Participating in or organising an event types › Participation in conference

• CISBIC Systems and Synthetic biology symposium

  Activity: Participating in or organising an event types › Participation in conference

• ICSB2012 - 12th International Conference on Systems Biology

  Activity: Participating in or organising an event types › Participation in conference

• From Bench to Clinic: UCSD Chronobiology Conference

  Activity: Participating in or organising an event types › Participation in conference

• UK Plant Systems Biology Workshop

  Activity: Participating in or organising an event types › Participation in workshop, seminar, course

• World Congress on Chronobiology

  Activity: Participating in or organising an event types › Participation in conference

• UK Circadian Clock Club

  Activity: Participating in or organising an event types › Participation in workshop, seminar, course

• Hutton seminar: "Watching plant clock genes run the organism, to understand growth and selection in crops"

  Activity: Academic talk or presentation types › Invited talk

• External examiner for Ph.D.: Understanding the Complex Dynamics of the Molecular Circadian Clock and Designing a Metric of Clock Disruption in Cancer

  Activity: Examination types › External Examiner or Assessor

• Society for Experimental Biology Annual Meeting, symposium on Algal Biology

  Activity: Participating in or organising an event types › Participation in conference

• Gordon conference on Chronobiology

  Activity: Participating in or organising an event types › Participation in conference

• European Biological Rhythms Society conference

  Activity: Participating in or organising an event types › Participation in conference

• CSBE Practical Course on O.tauri transformation

  Activity: Participating in or organising an event types › Participation in workshop, seminar, course

• Plant Systems Biology Workshop

  Activity: Participating in or organising an event types › Participation in workshop, seminar, course

• UK Circadian Clock Club

  Activity: Participating in or organising an event types › Participation in workshop, seminar, course

• Egenis/GARNet "Making Data Accessible to All” workshop

  Activity: Participating in or organising an event types › Participation in conference

• UK Plant Science Federation, inaugural conference

  Activity: Participating in or organising an event types › Participation in workshop, seminar, course

• UK Circadian Clock Club

  Activity: Participating in or organising an event types › Participation in workshop, seminar, course

• 20th International Conference on Arabidopsis Research

  Activity: Participating in or organising an event types › Participation in conference

• Chronobiology: Past, Present and Future

  Activity: Participating in or organising an event types › Participation in conference

• BBSRC Expert Working Group on Digital Organisms

  Activity: Consultancy types › Contribution to the work of national or international committees and working groups

• BioDynamics workshop

  Activity: Participating in or organising an event types › Participation in workshop, seminar, course

• FACCE MACSUR CropM International Symposium and Workshop: Modelling climate change impacts on crop production for food security.

  Activity: Participating in or organising an event types › Participation in conference

• Society for Experimental Biology Annual Main Meeting, 2015

  Activity: Participating in or organising an event types › Participation in conference

• Research visit from Mr. Bram Verhelst to SynthSys

  Activity: Other activity types › Types of External academic engagement - Hosting an academic visitor

• Research visit of Prof. Philippe de Reffye to SynthSys

  Activity: Other activity types › Types of External academic engagement - Hosting an academic visitor

• Seminar title: Systems analysis of biological timing in Arabidopsis

  Activity: Academic talk or presentation types › Invited talk

• Co-chaired the global working group developing "An International Model for Plant Science", a decadal vision document.

  Activity: Consultancy types › Contribution to the work of national or international committees and working groups

• Second meeting of the BBSRC Expert Working Group on Digital Organisms

  Activity: Consultancy types › Contribution to the work of national or international committees and working groups

Press/Media

• Study of plants may reveal the impact of jet lag and shift work on people

  Press/Media: Research

• Research reveals rhythms in blood cells which control sleep patterns

  Press/Media: Research

• Research breakthrough could help combat illnesses related to the disruption of the body clock

  Press/Media: Research

• Curbing cholesterol could help combat infections, says Edinburgh research

  Press/Media: Research

Research outputs

• Adaptable integration, analysis and data-sharing of diverse multi-omic and low-throughput data: computational platforms from European consortia.

  Research output: Contribution to conference › Poster

• A Loss of Function Analysis of Host Factors Influencing Vaccinia virus Replication by RNA Interference

  Research output: Contribution to journal › Article

• Processivity and Coupling in Messenger RNA Transcription

  Research output: Contribution to journal › Article

• Prp43 Bound at Different Sites on the Pre-rRNA Performs Distinct Functions in Ribosome Synthesis

  Research output: Contribution to journal › Article

• Protocol: high throughput silica-based purification of RNA from Arabidopsis seedlings in a 96-well format

  Research output: Contribution to journal › Article

• Improving the structure MCMC sampler for Bayesian networks by introducing a new edge reversal move

  Research output: Contribution to journal › Article

• Design and Development of Software Tools for Bio-PEPA

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

• A switchable light-input, light-output system modelled and constructed in yeast

  Research output: Contribution to journal › Article

• Modelling reveals kinetic advantages of co-transcriptional splicing.

  Research output: Contribution to journal › Article

• Time-resolved Interaction Proteomics of the GIGANTEA Protein Under Diurnal Cycles in Arabidopsis

  Research output: Contribution to journal › Article

• Extending signaling pathways with protein-interaction networks. Application to apoptosis

  Research output: Contribution to journal › Article

• A model of estrogen-related gene expression reveals non-linear effects in transcriptional response to tamoxifen

  Research output: Contribution to journal › Article

• Functional analysis of Casein Kinase 1 in a minimal circadian system

  Research output: Contribution to journal › Article

• A High-Level Language for Rule-Based Modelling

  Research output: Contribution to journal › Article

• Evolutionary Origin of the Interferon-Immune Metabolic Axis: The Sterol-Vitamin D Link

  Research output: Contribution to journal › Article

• Genomic Transformation of the Picoeukaryote Ostreococcus tauri

  Research output: Contribution to journal › Article

• Modelling and analysis of the NF-κB pathway in Bio-PEPA

  Research output: Chapter in Book/Report/Conference proceeding › Chapter (peer-reviewed)

• Online period estimation and determination of rhythmicity in circadian data, using the BioDare data infrastructure

  Research output: Chapter in Book/Report/Conference proceeding › Chapter

• A Temporal Gate for Viral Enhancers to Co-opt Toll-Like-Receptor Transcriptional Activation Pathways upon Acute Infection

  Research output: Contribution to journal › Article

• Muscle quality is maintained in healthy old women: Influence of muscle volume optimization

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

• The in silico macrophage: toward a better understanding of inflammatory disease

  Research output: Contribution to journal › Article

• Practical steps to digital organism models, from laboratory model species to ‘Crops in silico’

  Research output: Contribution to journal › Review article

• Mathematical model of Arabidopsis vegetative growth: the Framework Model

  Research output: Other contribution

• Temporal repression of core circadian genes is mediated through EARLY FLOWERING 3 in Arabidopsis

  Research output: Contribution to journal › Article

• Isoform switching facilitates period control in the Neurospora crassa circadian clock - Corrigendum

  Research output: Contribution to journal › Article

• Mathematical model of the clock gene circuit in the alga Ostreococcus tauri

  Research output: Other contribution

• Reversible inhibition of murine cytomegalovirus replication by gamma interferon (IFN-γ) in primary macrophages involves a primed type I IFN-signaling subnetwork for full establishment of an immediate-early antiviral state

  Research output: Contribution to journal › Article

• SBSI: An extensible distributed software infrastructure for parameter estimation in systems biology

  Research output: Contribution to journal › Article

• Virus resistance is not costly in a marine alga evolving under multiple environmental stressors

  Research output: Contribution to journal › Article

• Stochastic Modelling of the Kai-based Circadian Clock

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

• Temporal profiling of the coding and noncoding murine cytomegalovirus transcriptomes

  Research output: Contribution to journal › Article

• Cracking pre-40S ribosomal subunit structure by systematic analyses of RNA-protein cross-linking

  Research output: Contribution to journal › Article

• Label-free quantitative analysis of the casein kinase 2-responsive phosphoproteome of the marine minimal model species Ostreococcus tauri

  Research output: Contribution to journal › Article

• Integrated Simulation and Model-Checking for the Analysis of Biochemical Systems

  Research output: Contribution to journal › Article

• SPRINT: a new parallel framework for R

  Research output: Contribution to journal › Article

• Deciphering the modulation of gene expression by type I and II interferons combining 4sU-tagging, translational arrest and in silico promoter analysis

  Research output: Contribution to journal › Article

• Strengths and limitations of period estimation methods for circadian data

  Research output: Contribution to journal › Article

• Circadian protein regulation in the green lineage II. The clock gene circuit controls a phospho-dawn in Arabidopsis thaliana

  Research output: Working paper

• Consistent robustness analysis (CRA) identifies biologically relevant properties of regulatory network models

  Research output: Contribution to journal › Article

• Mapping the Core of the Arabidopsis Circadian Clock Defines the Network Structure of the Oscillator

  Research output: Contribution to journal › Article

• Peroxiredoxins are conserved markers of circadian rhythms

  Research output: Contribution to journal › Article

• Low-temperature-specific effects of PHYTOCHROME C on the circadian clock in Arabidopsis suggest that PHYC underlies natural variation in biological timing

  Research output: Working paper

• The reduced kinome of Ostreococcus tauri: core eukaryotic signalling components in a tractable model species

  Research output: Contribution to journal › Article

• Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism

  Research output: Working paper

• Use of logic theory in understanding regulatory pathway signaling in response to infection

  Research output: Contribution to journal › Literature review

• The use of a novel quantitation strategy based on Reductive Isotopic Di-Ethylation (RIDE) to evaluate the effect of glufosinate on the unicellular algae Ostreococcus tauri

  Research output: Contribution to journal › Article

• Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism

  Research output: Contribution to journal › Article

• Sarcopenic muscle shows distinct sex differences at the transcriptional level

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

• RiboSys, a high-resolution, quantitative approach to measure the in vivo kinetics of pre-mRNA splicing and 3 '-end processing in Saccharomyces cerevisiae

  Research output: Contribution to journal › Article

• Ablation of the Regulatory IE1 Protein of Murine Cytomegalovirus Alters In Vivo Pro-inflammatory TNF-alpha Production during Acute Infection

  Research output: Contribution to journal › Article

• Equivalence and discretisation in Bio-PEPA

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

• The contributions of interlocking loops and extensive nonlinearity to the properties of circadian clock models

  Research output: Contribution to journal › Article

• Interactions among mitochondrial proteins altered in glioblastoma

  Research output: Contribution to journal › Article

• SED-ED, a workflow editor for computational biology experiments written in SED-ML.

  Research output: Contribution to journal › Article

• Pathway biology approach to medicine

  Research output: Chapter in Book/Report/Conference proceeding › Chapter (peer-reviewed)

• Quantitative analysis of regulatory flexibility under changing environmental conditions

  Research output: Contribution to journal › Article

• PI3K/Akt1 signalling specifies foregut precursors by generating regionalized extra-cellular matrix.

  Research output: Contribution to journal › Article

• Circadian clock components control daily growth activities by modulating cytokinin levels and cell division-associated gene expression in Populus trees

  Research output: Contribution to journal › Article

• Complementary approaches to understanding the plant circadian clock

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

• The Transcription Factor STAT-1 Couples Macrophage Synthesis of 25-Hydroxycholesterol to the Interferon Antiviral Response

  Research output: Contribution to journal › Article

• Process Algebra Modelling Styles for Biomolecular Processes

  Research output: Chapter in Book/Report/Conference proceeding › Chapter (peer-reviewed)

• Translation from the Quantified Implicit Process Flow Abstraction in SBGN-PD Diagrams to Bio-PEPA Illustrated on the Cholesterol Pathway

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

• The Biodare Data Repository

  Research output: Other contribution

• Stochastic properties of the plant circadian clock

  Research output: Contribution to journal › Article

• The FERM-domain protein Expanded regulates Hippo pathway activity via direct interactions with the transcriptional activator Yorkie.

  Research output: Contribution to journal › Article

• Quantifying the implicit process flow abstraction in SBGN-PD diagrams with Bio-PEPA

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

• Using higher-order dynamic Bayesian networks to model periodic data from the circadian clock of Arabidopsis Thaliana.

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

• Gel free analysis of the proteome of intracellular Leishmania mexicana (vol 169, pg 108, 2010)

  Research output: Contribution to journal › Article

• Markov chain simulation with fewer random samples

  Research output: Contribution to journal › Article

• COMPUTATIONAL MODELING OF BIOLOGICAL PATHWAYS BY EXECUTABLE BIOLOGY

  Research output: Chapter in Book/Report/Conference proceeding › Other chapter contribution

• Proteasome Function Is Required for Biological Timing throughout the Twenty-Four Hour Cycle

  Research output: Contribution to journal › Article

• Data assimilation constrains new connections and components in a complex, eukaryotic circadian clock model

  Research output: Contribution to journal › Article

• Peeking into pit fields: a multiple twinning model of secondary plasmodesmata formation in tobacco

  Research output: Contribution to journal › Article

• Viral enhancer mimicry of host innate-immune promoters

  Research output: Contribution to journal › Comment/debate

• Identification of a human neonatal immune-metabolic network associated with bacterial infection

  Research output: Contribution to journal › Article

• Sample preparation for phosphoproteomic analysis of circadian time series in Arabidopsis thaliana

  Research output: Chapter in Book/Report/Conference proceeding › Chapter (peer-reviewed)

• Digital clocks: simple Boolean models can quantitatively describe circadian systems

  Research output: Contribution to journal › Article

• Modelling co-transcriptional cleavage in the synthesis of yeast pre-rRNA

  Research output: Contribution to journal › Article

• The proteomic response in glioblastoma in young patients

  Research output: Contribution to journal › Article

• Hybrid regulatory models: a statistically tractable approach to model regulatory network dynamics

  Research output: Contribution to journal › Article

• Impact of Age on the Cerebrovascular Proteomes of Wild-Type and Tg-SwDI Mice

  Research output: Contribution to journal › Article

• Formal Methods for Biochemical Signalling Pathways

  Research output: Chapter in Book/Report/Conference proceeding › Chapter

• Applying statistical inference in genomics with evidence-based pathways: Towards elucidating new functional correlations of biomarkers.

  Research output: Contribution to journal › Article

• Isoform switching facilitates period control in the Neurospora crassa circadian clock

  Research output: Contribution to journal › Article

• Prediction of photoperiodic regulators from quantitative gene circuit models

  Research output: Contribution to journal › Article

• Bio-PEPAd: A non-Markovian extension of Bio-PEPA

  Research output: Contribution to journal › Article

• Defining the robust behaviour of the plant clock gene circuit with absolute RNA timeseries and open infrastructure

  Research output: Contribution to journal › Article

• An interaction network of the mammalian COP9 signalosome identifies Dda1 as a core subunit of multiple Cul4-based E3 ligases

  Research output: Contribution to journal › Article

• A simulator for spatially extended kappa models

  Research output: Contribution to journal › Article

• Investigating modularity in the analysis of process algebra models of biochemical systems

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

• Host defense against viral infection involves interferon mediated down-regulation of sterol biosynthesis

  Research output: Contribution to journal › Article

• SCFCdc4 Enables Mating Type Switching in Yeast by Cyclin-Dependent Kinase-Mediated Elimination of the Ash1 Transcriptional Repressor

  Research output: Contribution to journal › Article

• Splicing-Dependent RNA Polymerase Pausing in Yeast

  Research output: Contribution to journal › Article

• Mathematical model of the Arabidopsis circadian clock: Pokhilko 2011 model

  Research output: Other contribution

• Changing planetary rotation rescues the biological clock mutant lhy cca1 of Arabidopsis thaliana

  Research output: Working paper

• Query-based verification of qualitative trends and oscillations in biochemical systems

  Research output: Contribution to journal › Article

• A cluster of ribosome synthesis factors regulate pre-rRNA folding and 5.8S rRNA maturation by the Rat1 exonuclease

  Research output: Contribution to journal › Article

• Photobacterium profundum under Pressure: A MS-Based Label-Free Quantitative Proteomics Study

  Research output: Contribution to journal › Article

• Modelling biological systems with delays in Bio-PEPA

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

• Light inputs shape the Arabidopsis circadian system

  Research output: Contribution to journal › Article

• Computational models in systems biology: A report of the 6th International Conference on Computational Methods in Systems Biology, Rostock, Germany, 12-15 October 2008.

  Research output: Contribution to journal › Article

• Identification of novel pathways linking epithelial-to-mesenchymal transition with resistance to HER2-targeted therapy

  Research output: Contribution to journal › Article

• Circadian clock parameter measurement: characterization of clock transcription factors using surface plasmon resonance

  Research output: Contribution to journal › Article

• Multiple light inputs to a simple clock circuit allow complex biological rhythms

  Research output: Contribution to journal › Article

• Quantitative analysis of low-abundance peptides in HeLa cell cytoplasm by targeted liquid chromatography/mass spectrometry and stable isotope dilution: emphasising the distinction between peptide detection and peptide identification

  Research output: Contribution to journal › Article

• A Systematic Analysis of Host Factors Reveals a Med23-Interferon-λ Regulatory Axis against Herpes Simplex Virus Type 1 Replication

  Research output: Contribution to journal › Article

• The Bio-PEPA Tool Suite

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

• Shotgun proteomic analysis of the unicellular alga Ostreococcus tauri

  Research output: Contribution to journal › Article

• Bio-PEPA: A framework for the modelling and analysis of biological systems

  Research output: Contribution to journal › Article

• Some Investigations Concerning the CTMC and the ODE Model Derived From Bio-PEPA

  Research output: Contribution to journal › Article

• A rule-based kinetic model of RNA polymerase II C-terminal domain phosphorylation

  Research output: Contribution to journal › Article

• CD200 receptor restriction of myeloid cell responses antagonizes antiviral immunity and facilitates cytomegalovirus persistence within mucosal tissue

  Research output: Contribution to journal › Article

• High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay

  Research output: Contribution to journal › Article

• The systems biology simulation core algorithm

  Research output: Contribution to journal › Article

• Combined genome-wide expression profiling and targeted RNA interference in primary mouse macrophages reveals perturbation of transcriptional networks associated with interferon signalling

  Research output: Contribution to journal › Article

• Whole blood gene expression profiling of neonates with confirmed bacterial sepsis

  Research output: Contribution to journal › Article

• The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops

  Research output: Contribution to journal › Article

• Cross-talk in transcription, splicing and chromatin: who makes the first call?

  Research output: Contribution to journal › Article

• Coding-Sequence Determinants of Gene Expression in Escherichia coli

  Research output: Contribution to journal › Article

• Adaptive changes in the neuronal proteome: mitochondrial energy production, endoplasmic reticulum stress, and ribosomal dysfunction in the cellular response to metabolic stress

  Research output: Contribution to journal › Article

• PROTEINCHALLENGE: Crowd sourcing in proteomics analysis and software development

  Research output: Contribution to journal › Article

• Network generation enhances interpretation of proteomic data from induced apoptosis

  Research output: Contribution to journal › Article

• A semantic equivalence for Bio-PEPA based on discretisation of continuous values

  Research output: Contribution to journal › Article

• The Input Signal Step Function (ISSF), a Standard Method to Encode Input Signals in SBML Models with Software Support, Applied to Circadian Clock Models

  Research output: Contribution to journal › Article

• Plant Systems Modelling portal, PlaSMo

  Research output: Non-textual form › Web publication/site

• S-nitrosylation of NADPH oxidase regulates cell death in plant immunity

  Research output: Contribution to journal › Article

• Reverse Engineering Gene Regulatory Networks with Various Machine Learning Methods: Analysis of Microarray Data

  Research output: Chapter in Book/Report/Conference proceeding › Chapter

• The mEPN scheme: an intuitive and flexible graphical system for rendering biological pathways: an intuitive and flexible graphical system for rendering biological pathways

  Research output: Contribution to journal › Article

• Corrigendum: Peroxiredoxins are conserved markers of circadian rhythms

  Research output: Contribution to journal › Article

• Network balance via CRY signalling controls the Arabidopsis circadian clock over ambient temperatures

  Research output: Contribution to journal › Article

• Verification and Testing of Biological Models

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

• A comprehensive machine-readable view of the mammalian cholesterol biosynthesis pathway

  Research output: Contribution to journal › Article

• A framework for evolutionary systems biology

  Research output: Contribution to journal › Article

• Coloured stochastic multilevel multiset rewriting

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

• Crossing the boundaries delivering trans-disciplinary science in a disciplinary world

  Research output: Contribution to journal › Article

• Inferring Boolean networks with perturbation from sparse gene expression data: a general model applied to the interferon regulatory network

  Research output: Contribution to journal › Article

• Identification of protein binding sites on U3 snoRNA and pre-rRNA by UV cross-linking and high-throughput analysis of cDNAs

  Research output: Contribution to journal › Article

• The Distribution of Mutational Effects on Fitness in a Simple Circadian Clock

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

• A logic-based diagram of signalling pathways central to macrophage activation

  Research output: Contribution to journal › Article

• Native gel electrophoresis of human telomerase distinguishes active complexes with or without dyskerin.

  Research output: Contribution to journal › Article

• The Systems Biology Graphical Notation

  Research output: Contribution to journal › Article

• Rapid proteasomal elimination of 3-hydroxy-3-methylglutaryl-CoA reductase by interferon-γ in primary macrophages requires endogenous 25-hydroxycholesterol synthesis

  Research output: Contribution to journal › Article

• Formal methods for checking the consistency of biological models

  Research output: Chapter in Book/Report/Conference proceeding › Chapter

• Avoiding Spurious Feedback Loops in the Reconstruction of Gene Regulatory Networks with Dynamic Bayesian Networks

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

• Reconstruction of transcriptional dynamics from gene reporter data using differential equations

  Research output: Contribution to journal › Article

• Proteomic analysis of mitochondria in APOE transgenic mice and in response to an ischemic challenge

  Research output: Contribution to journal › Article

• HYPE applied to the modelling of hybrid biological systems

  Research output: Contribution to journal › Article

• CPF-Associated Phosphatase Activity Opposes Condensin-Mediated Chromosome Condensation

  Research output: Contribution to journal › Article

• Total variance should drive data handling strategies in third generation proteomic studies

  Research output: Contribution to journal › Article

• An Interferon Regulated MicroRNA Provides Broad Cell-Intrinsic Antiviral Immunity through Multihit Host-Directed Targeting of the Sterol Pathway

  Research output: Contribution to journal › Article

• Multi-level modelling via stochastic multi-level multiset rewriting

  Research output: Contribution to journal › Article

• Cellular circadian pacemaking and the role of cytosolic rhythms

  Research output: Contribution to journal › Article

• A model of flux regulation in the cholesterol biosynthesis pathway: Immune mediated graduated flux reduction versus statin-like led stepped flux reduction

  Research output: Contribution to journal › Article

• Microarray data can predict diurnal changes of starch content in the picoalga Ostreococcus

  Research output: Contribution to journal › Article

• Statistical methods for analysis of high-throughput RNA interference screens

  Research output: Contribution to journal › Article

• Gel free analysis of the proteome of intracellular Leishmania mexicana

  Research output: Contribution to journal › Article

• Variation in plastic responses of a globally distributed picoplankton species to ocean acidification

  Research output: Contribution to journal › Article

• Modelling Biological Clocks with Bio-PEPA: Stochasticity and Robustness for the Neurospora crassa Circadian Network

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

• A semi-quantitative equivalence for abstracting from fast reactions

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

• Modelling the widespread effects of TOC1 signalling on the plant circadian clock and its outputs

  Research output: Contribution to journal › Article

• Light and circadian regulation of clock components aids flexible responses to environmental signals

  Research output: Contribution to journal › Article

• Non-transcriptional oscillators in circadian timekeeping

  Research output: Contribution to journal › Article

• Interferon control of the sterol metabolic network: bidirectional molecular circuitry mediating host protection

  Research output: Contribution to journal › Article

• Construction of a large scale integrated map of macrophage pathogen recognition and effector systems

  Research output: Contribution to journal › Article

• Proteome turnover in the green alga Ostreococcus tauri by time course ¹⁵N metabolic labeling mass spectrometry

  Research output: Contribution to journal › Article

• The impact of adhesion on cellular invasion processes in cancer and development

  Research output: Contribution to journal › Article

• Infection homeostasis: implications for therapeutic and immune programming of metabolism in controlling infection

  Research output: Contribution to journal › Article

• Model for starch polymerisation and degradation in the alga, Ostreococcus tauri.

  Research output: Other contribution

• Reproducible computational biology experiments with SED-ML-the Simulation Experiment Description Markup Language

  Research output: Contribution to journal › Article

• Minimum Information About a Simulation Experiment (MIASE)

  Research output: Contribution to journal › Article

• Circadian rhythms persist without transcription in a eukaryote

  Research output: Contribution to journal › Article

• A user-defined data type for the storage of time series data allowing efficient similarity screening

  Research output: Contribution to journal › Article

• Functional analysis of the rodent CK1tau mutation in the circadian clock of a marine unicellular alga

  Research output: Contribution to journal › Article

• Modelling non-stationary gene regulatory processes with a non-homogeneous Bayesian network and the allocation sampler

  Research output: Contribution to journal › Article

• Spontaneous spatiotemporal waves of gene expression from biological clocks in the leaf

  Research output: Contribution to journal › Article

• Regulatory principles and experimental approaches to the circadian control of starch turnover

  Research output: Contribution to journal › Article

• Logic models of pathway biology

  Research output: Contribution to journal › Literature review

• Real-time imaging of co-transcriptional splicing reveals a kinetic model that reduces noise: implications for alternative splicing regulation.

  Research output: Contribution to journal › Article

• Robustness from flexibility in the fungal circadian clock

  Research output: Contribution to journal › Article

• tbd (in Japanese)

  Research output: Contribution to journal › Literature review

• Conservation of Mass Analysis for Bio-PEPA

  Research output: Contribution to journal › Article