Our scientific publications
We’ve published dozens of peer-reviewed scientific papers across a number of areas.
More than half of our work is proprietary. This post summarises some of our publicly-available work.
Drug Discovery and Uptake Transporters
Drug uptake is largely transporter-mediated rather than passive, and metabolite-likeness offers a design principle for drug libraries.
Carrier-mediated cellular uptake of pharmaceutical drugs: an exception or the rule? | Nat Rev Drug Discov | 2008
‘Metabolite-likeness’ as a criterion in the design and selection of pharmaceutical drug libraries | Drug Discov Today | 2009
Implications of the dominant role of transporters in drug uptake by cells | Curr Top Med Chem | 2009
Pharmaceutical drug transport: the issues and the implications that it is essentially carrier-mediated only | Drug Discov Today | 2011
The promiscuous binding of pharmaceutical drugs and their transporter-mediated uptake into cells | Drug Discov Today | 2013
Genome-wide assessment of the carriers involved in the cellular uptake of drugs: a model system in yeast | BMC Biol | 2011
Systems Biology & Metabolic Network Reconstructions
Comprehensive genome-scale metabolic reconstructions for yeast, humans, Arabidopsis, and C. elegans, alongside databases like biochem4j, enable flux modeling and metabolic engineering.
A consensus yeast metabolic network reconstruction obtained from a community approach | Nat Biotechnol | 2008
Further developments towards a genome-scale metabolic model of yeast | BMC Syst Biol | 2010
Mining metabolites: extracting the yeast metabolome from the literature | Metabolomics | 2011
A community-driven global reconstruction of human metabolism (Recon 2) | Nat Biotechnol | 2013
A genome-scale metabolic network reconstruction of Arabidopsis thaliana and its applications in plant metabolism | Plant J | 2015
Recon 2.2: from reconstruction to model of human metabolism | Metabolomics | 2016
biochem4j: Integrated and extensible biochemical knowledge through graph databases | PLoS One | 2017
WormJam: A consensus C. elegans metabolic reconstruction and its integration with gene expression data | Mol Syst Biol | 2018
Aptamers and Diagnostics
Aptamer arrays and fitness landscape modeling provide antibody alternatives for diagnostics, while resistive pulse sensing offers rapid DNA methylation assays.
Analysis of aptamer sequence activity relationships | Integr Biol (Camb) | 2009
Array-based evolution of DNA aptamers allows modelling of an explicit sequence-fitness landscape | Nucleic Acids Res | 2009
Aptamer evolution for array-based diagnostics | Anal Biochem | 2009
Advances and perspectives in aptamer arrays | Integr Biol (Camb) | 2009
Convergent evolution to an aptamer observed in small populations on DNA microarrays | Phys Biol | 2010
Rapid assessment of site specific DNA methylation through resistive pulse sensing | ACS Sens | 2018
Directed Evolution and Fitness Landscape Modeling
Models of evolutionary dynamics and optimization frameworks support rational experimental design in biomolecule engineering and analytical chemistry.
In silico modelling of directed evolution: implications for experimental design and stepwise evolution | J Theor Biol | 2009
Predictive models for population performance on real biological fitness landscapes | Bioinformatics | 2010
Multiobjective evolutionary optimisation for surface-enhanced Raman scattering (SERS) | Anal Bioanal Chem | 2010
Immune Signaling and Inflammation Control
Quantitative imaging and modeling reveal how NF-κB and cytokine dynamics, refractory states, and temperature shape immune responses.
Quantitative dynamic imaging of immune cell signalling using lentiviral gene transfer | Integr Biol (Camb) | 2015
Signal transduction controls heterogeneous NF-κB dynamics and target gene expression through cytokine-specific refractory states | Nat Commun | 2016
Integration of kinase and calcium signaling at the level of chromatin underlies inducible gene activation in T cells | J Immunol | 2017
Quantitative analysis of competitive cytokine signaling predicts tissue thresholds for the propagation of macrophage activation | Sci Signal | 2018
Temperature regulates NF-κB dynamics and function through timing of A20 transcription | Proc Natl Acad Sci USA | 2018
Gene-specific linear trends constrain transcriptional variability of the Toll-like receptor signaling | Cell Syst | 2020
Translational Regulation
RNA-binding proteins such as Puf3p, Slf1p, and eIF4E-BPs control translation under stress and oxidative conditions, linking gene expression programs to stress resilience and disease.
Identifying eIF4E-binding protein translationally-controlled transcripts reveals links to mRNAs bound by specific PUF proteins | Nucleic Acids Res | 2010
Puf3p induces translational repression of genes linked to oxidative stress | Nucleic Acids Res | 2014
Integrated multi-omics analyses reveal the pleiotropic nature of the control of gene expression by Puf3p | Sci Rep | 2015
The yeast La related protein Slf1p is a key activator of translation during the oxidative stress response | PLoS Genet | 2015
Dynamic changes in eIF4F-mRNA interactions revealed by global analyses of environmental stress responses | Genome Biol | 2017
Analytical and Experimental Optimization Tools
Metabolomics databases and evolutionary optimization approaches improve metabolite identification and experimental reproducibility.