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DirtyGenes: testing for significant changes in gene or bacterial population compositions from a small number of samples (2019)
Journal Article
Shaw, L. M., Blanchard, A., Chen, Q., An, X., Davies, P., Totemeyer, S., …Stekel, D. J. (2019). DirtyGenes: testing for significant changes in gene or bacterial population compositions from a small number of samples. Scientific Reports, 9, doi:10.1038/s41598-019-38873-4

High throughput genomics technologies are applied widely to microbiomes in humans, animals, soil and water, to detect changes in bacterial communities or the genes they carry, between different environments or treatments. We describe a method to test... Read More about DirtyGenes: testing for significant changes in gene or bacterial population compositions from a small number of samples.

Removal of copper from cattle footbath wastewater with layered double hydroxide adsorbents as a route to antimicrobial resistance mitigation on dairy farms (2018)
Journal Article
Williams, O., Clark, I., Gomes, R. L., Perehinec, T., Hobman, J. L., Stekel, D. J., …Lester, E. (2019). Removal of copper from cattle footbath wastewater with layered double hydroxide adsorbents as a route to antimicrobial resistance mitigation on dairy farms. Science of the Total Environment, 655, 1139-1149. doi:10.1016/j.scitotenv.2018.11.330

Copper and zinc are routinely used in livestock antimicrobial footbaths in commercial farming. The footbath mix is a cost to farmers, and the disposal of spent footbath into slurry tanks leads to soil contamination, as well as the potential for antim... Read More about Removal of copper from cattle footbath wastewater with layered double hydroxide adsorbents as a route to antimicrobial resistance mitigation on dairy farms.

Investigating the association between the caecal microbiomes of broilers and Campylobacter burden (2018)
Journal Article
Sakaridis, I., Ellis, R. J., Cawthraw, S. A., van Vliet, A. H. M., Stekel, D. J., Penell, J., …Cook, A. J. (2018). Investigating the association between the caecal microbiomes of broilers and Campylobacter burden. Frontiers in Microbiology, 9, doi:10.3389/fmicb.2018.00927

One of the major transmission routes for the foodborne bacterial pathogen Campylobacter is undercooked poultry meat, contaminated from intestinal contents during processing. In broilers, Campylobacter can grow to very high densities in the caeca, and... Read More about Investigating the association between the caecal microbiomes of broilers and Campylobacter burden.

Regulatory feedback response mechanisms to phosphate starvation in rice (2018)
Journal Article
Ajmera, I., Shi, J., Giri, J., Wu, P., Stekel, D. J., Lu, C., & Hodgman, C. (in press). Regulatory feedback response mechanisms to phosphate starvation in rice. npj Systems Biology and Applications, 4(4), https://doi.org/10.1038/s41540-017-0041-0

Phosphorus is a growth-limiting nutrient for plants. The growing scarcity of phosphate stocks threatens global food security. Phosphate-uptake regulation is so complex and incompletely known that attempts to improve phosphorus use efficiency have had... Read More about Regulatory feedback response mechanisms to phosphate starvation in rice.

Human dissemination of genes and microorganisms in Earth's Critical Zone (2017)
Journal Article
Zhu, Y., Gillings, M., Simonet, P., Stekel, D., Banwart, S., & Penuelas, J. (2018). Human dissemination of genes and microorganisms in Earth's Critical Zone. Global Change Biology, 24(4), 1488-1499. doi:10.1111/gcb.14003

Earth's Critical Zone sustains terrestrial life and consists of the thin planetary surface layer between unaltered rock and the atmospheric boundary. Within this zone, flows of energy and materials are mediated by physical processes and by the action... Read More about Human dissemination of genes and microorganisms in Earth's Critical Zone.

Reconstructing promoter activity from Lux bioluminescent reporters (2017)
Journal Article
Iqbal, M., Doherty, N., Page, A. M., Qazi, S. N., Ajmera, I., Lund, P. A., …Stekel, D. J. (2017). Reconstructing promoter activity from Lux bioluminescent reporters. PLoS Computational Biology, 13(9), https://doi.org/10.1371/journal.pcbi.1005731

The bacterial Lux system is used as a gene expression reporter. It is fast, sensitive and non-destructive, enabling high frequency measurements. Originally developed for bacterial cells, it has also been adapted for eukaryotic cells, and can be used... Read More about Reconstructing promoter activity from Lux bioluminescent reporters.

Microbial mass movements (2017)
Journal Article
Zhu, Y., Gillings, M., Simonet, P., Stekel, D., Banwart, S., & Penuelas, J. (2017). Microbial mass movements. Science, 357(6356), 1099-1100. doi:10.1126/science.aao3007

Metal resistance and its association with antibiotic resistance (2017)
Book Chapter
Asiani, K., Pal, C., Asiani, K. R., Arya, S., Rensing, C., Stekel, D. J., …Hobman, J. L. (2017). Metal resistance and its association with antibiotic resistance. In R. K. Poole (Ed.), Microbiology of metal ions, 261-313. Academic Press. https://doi.org/10.1016/bs.ampbs.2017.02.001

Antibiotic resistance is recognised as a major global threat to public health by the World Health Organization. Currently, several hundred thousand deaths yearly can be attributed to infections with antibiotic-resistant bacteria. The major driver for... Read More about Metal resistance and its association with antibiotic resistance.

So why have you added me? Adolescent girls’ technology-mediated attachments and relationships (2016)
Journal Article
Levine, D. T., & Stekel, D. J. (2016). So why have you added me? Adolescent girls’ technology-mediated attachments and relationships. Computers in Human Behavior, 63, 25-34. doi:10.1016/j.chb.2016.05.011

Technology plays an almost ubiquitous role in contemporary British society. Despite this, we do not have a well-theorised understanding of the ways adolescent girls use digital devices in the context of their developing secure relationships with thei... Read More about So why have you added me? Adolescent girls’ technology-mediated attachments and relationships.

Mathematical modelling of antimicrobial resistance in agricultural waste highlights importance of gene transfer rate (2016)
Journal Article
Baker, M., Hobman, J. L., Dodd, C. E., Ramsden, S. J., & Stekel, D. J. (2016). Mathematical modelling of antimicrobial resistance in agricultural waste highlights importance of gene transfer rate. FEMS Microbiology Ecology, 92(4), doi:10.1093/femsec/fiw040

Antimicrobial resistance is of global concern. Most antimicrobial use is in agriculture; manures and slurry are especially important because they contain a mix of bacteria, including potential pathogens, antimicrobial resistance genes and antimicrobi... Read More about Mathematical modelling of antimicrobial resistance in agricultural waste highlights importance of gene transfer rate.

Multidrug resistant, extended spectrum β-lactamase (ESBL)-producing Escherichia coli isolated from a dairy farm (2016)
Journal Article
Ibrahim, D. R., Ibrahim, D., Dodd, C. E. R., Stekel, D. J., Ramsden, S. J., & Hobman, J. L. (2016). Multidrug resistant, extended spectrum β-lactamase (ESBL)-producing Escherichia coli isolated from a dairy farm. FEMS Microbiology Ecology, 92(4), https://doi.org/10.1093/femsec/fiw013

Escherichia coli strains were isolated from a single dairy farm as a sentinel organism for the persistence of antibiotic resistance genes in the farm environment. Selective microbiological media were used to isolate 126 E. coli isolates from slurry a... Read More about Multidrug resistant, extended spectrum β-lactamase (ESBL)-producing Escherichia coli isolated from a dairy farm.

A Bayesian approach to analyzing phenotype microarray data enables estimation of microbial growth parameters (2016)
Journal Article
Gerstgrasser, M., Nicholls, S., Stout, M., Smart, K., Powell, C., Kypraios, T., & Stekel, D. J. (2016). A Bayesian approach to analyzing phenotype microarray data enables estimation of microbial growth parameters. Journal of Bioinformatics and Computational Biology, 14(03), 1-23. doi:10.1142/S0219720016500074

Biolog phenotype microarrays enable simultaneous, high throughput analysis of cell cultures in different environments. The output is high-density time-course data showing redox curves (approximating growth) for each experimental condition. The softwa... Read More about A Bayesian approach to analyzing phenotype microarray data enables estimation of microbial growth parameters.

The dynamic balance of import and export of zinc in Escherichia coli suggests a heterogeneous population response to stress (2015)
Journal Article
Takahashi, H., Oshima, T., Hobman, J. L., Doherty, N., Clayton, S. R., Iqbal, M., …Stekel, D. J. (2015). The dynamic balance of import and export of zinc in Escherichia coli suggests a heterogeneous population response to stress. Interface, 12(106), doi:10.1098/rsif.2015.0069

Zinc is essential for life, but toxic in excess. Thus all cells must control their internal zinc concentration. We used a systems approach, alternating rounds of experiments and models, to further elucidate the zinc control systems in Escherichia col... Read More about The dynamic balance of import and export of zinc in Escherichia coli suggests a heterogeneous population response to stress.

A machine learning heuristic to identify biologically relevant and minimal biomarker panels from omics data (2015)
Journal Article
Swan, A. L., Stekel, D. J., Hodgman, C., Allaway, D., Alqahtani, M. H., Mobasheri, A., & Bacardit, J. (2015). A machine learning heuristic to identify biologically relevant and minimal biomarker panels from omics data. BMC Genomics, 16(Suppl 1), doi:10.1186/1471-2164-16-s1-s2

Background: Investigations into novel biomarkers using omics techniques generate large amounts of data. Due to their size and numbers of attributes, these data are suitable for analysis with machine learning methods. A key component of typical machin... Read More about A machine learning heuristic to identify biologically relevant and minimal biomarker panels from omics data.

Analysis of occludin trafficking, demonstrating continuous endocytosis, degradation, recycling and biosynthetic secretory trafficking (2014)
Journal Article
Stekel, D., Fletcher, S., Iqbal, M., Jabbari, S., & Rappoport, J. (2014). Analysis of occludin trafficking, demonstrating continuous endocytosis, degradation, recycling and biosynthetic secretory trafficking. PLoS ONE, 9(11), https://doi.org/10.1371/journal.pone.0111176

© 2014 Fletcher et al. Tight junctions (TJs) link adjacent cells and are critical for maintenance of apicalbasolateral polarity in epithelial monolayers. The TJ protein occludin functions in disparate processes, including wound healing and Hepatitis... Read More about Analysis of occludin trafficking, demonstrating continuous endocytosis, degradation, recycling and biosynthetic secretory trafficking.

Lipidomic analysis of plasma samples from women with polycystic ovary syndrome (2014)
Journal Article
Haoula, Z., Ravipati, S., Stekel, D. J., Ortori, C. A., Hodgman, C., Daykin, C., …Atiomo, W. (2015). Lipidomic analysis of plasma samples from women with polycystic ovary syndrome. Metabolomics, 11(3), 657-666. https://doi.org/10.1007/s11306-014-0726-y

Abstract Polycystic ovary syndrome (PCOS) is a common disorder affecting between 5 and 18 % of females of reproductive age and can be diagnosed based on a combination of clinical, ultrasound and biochemical features, none of which on its own is diagn... Read More about Lipidomic analysis of plasma samples from women with polycystic ovary syndrome.