Dr Pawel Herzyk
- Honorary Senior Lecturer (School of Molecular Biosciences)
email:
Pawel.Herzyk@glasgow.ac.uk
Joseph Black Building, School of Molecular Biosciences, University of Glasgow, Glasgow, G12 8QQ
Research interests
'Analysis of data generated by -omics technologies, structural bioinformatics, molecular modelling of transmembrane proteins'
Publications
2024
Delles, C. et al. (2024) Response of blood pressure to renal denervation is not associated with genetic variants. Hypertension, (doi: 10.1161/HYPERTENSIONAHA.124.23393) (PMID:39569514) (Early Online Publication)
Kulkarni, J. et al. (2024) Early-responsive molecular signatures associated with halophytic adaptation in Sesuvium portulacastrum (L.). Plant, Cell and Environment, 47(3), pp. 961-975. (doi: 10.1111/pce.14767) (PMID:38044749)
Tobias, E. S. et al. (2024) SEC31A may be associated with pituitary hormone deficiency and gonadal dysgenesis. Endocrine, 84, pp. 345-349. (doi: 10.1007/s12020-024-03701-x) (PMID:38400880)
2023
Martin, T. P. et al. (2023) Ribonucleicacid interference or small molecule inhibition of Runx1 in the border zone prevents cardiac contractile dysfunction following myocardial infarction. Cardiovascular Research, 119(16), 2663–2671-2663–2671. (doi: 10.1093/cvr/cvad107) (PMID:37433039) (PMCID:PMC10730241)
Perrella, G., Fasano, C., Donald, N. A., Daddiego, L., Fang, W., Martignago, D., Carr, C., Conti, L., Herzyk, P. and Amtmann, A. (2023) Histone Deacetylase Complex 1 and Histone 1 epigenetically moderate stress responsiveness of Arabidopsis thaliana seedlings. New Phytologist, (doi: 10.1111/nph.19165) (PMID:37565540) (Early Online Publication)
McInnes, K. J., van der Hooft, J. J.J. , Sharma, A., Herzyk, P. , Hundleby, P. A.C., Schoonbeek, H.-J., Amtmann, A. , Ridout, C. and Jenkins, G. I. (2023) Overexpression of Brassica napus COMT1 in Arabidopsis heightens UV-B-mediated resistance to Plutella xylostella herbivory. Photochemical and Photobiological Sciences, 22, pp. 2341-2356. (doi: 10.1007/s43630-023-00455-9) (PMID:37505444) (PMCID:PMC10509076)
2022
Cousins, A. et al. (2022) Central nervous system involvement in childhood acute lymphoblastic leukemia is linked to upregulation of cholesterol biosynthetic pathways. Leukemia, 36(12), pp. 2903-2907. (doi: 10.1038/s41375-022-01722-x) (PMID:36289348) (PMCID:PMC9712090)
Dwomoh, L. et al. (2022) M1 muscarinic receptor activation reduces the molecular pathology and slows the progression of prion-mediated neurodegenerative disease. Science Signaling, 15(760), eabm3720. (doi: 10.1126/scisignal.abm3720) (PMID:36378750)
2021
Dow, J. A.T. , Krause, S. A. and Herzyk, P. (2021) Updates on ion and water transport by the Malpighian tubule. Current Opinion in Insect Science, 47, pp. 31-37. (doi: 10.1016/j.cois.2021.02.018) (PMID:33705976)
Madsen, M. A., Hamilton, G., Herzyk, P. and Amtmann, A. (2021) Environmental regulation of PndbA600, an auto-inducible promoter for two-stage industrial biotechnology in cyanobacteria. Frontiers in Bioengineering and Biotechnology, 8, 619055. (doi: 10.3389/fbioe.2020.619055) (PMID:33542914) (PMCID:PMC7853294)
2020
Savino, A. M. et al. (2020) Metabolic adaptation of acute lymphoblastic leukemia to the central nervous system microenvironment depends on Stearoyl CoA desaturase. Nature Cancer, 1(10), pp. 998-1009. (doi: 10.1038/s43018-020-00115-2) (PMID:33479702) (PMCID:PMC7116605)
2018
Cumming, S. A. et al. (2018) De novo repeat interruptions are associated with reduced somatic instability and mild or absent clinical features in myotonic dystrophy type 1. European Journal of Human Genetics, 26(11), pp. 1635-1647. (doi: 10.1038/s41431-018-0156-9) (PMID:29967337) (PMCID:PMC6189127)
Ciosi, M. , Cumming, S. A., Alshammari, A. M., Symeonidi, E., Herzyk, P. , Mcguinness, D. , Galbraith, J., Hamilton, G. and Monckton, D. G. (2018) Library preparation and MiSeq sequencing for the genotyping-by-sequencing of the Huntington disease HTT exon one trinucleotide repeat and the quantification of somatic mosaicism [Protocol]. Other. Springer Nature. (doi: 10.21203/rs.2.1581/v2).
Perrella, G., Davidson, M. L.H., O'Donnell, L. , Nastase, A.-M., Herzyk, P. , Breton, G., Pruneda-Paz, J. L., Kay, S. A., Chory, J. and Kaiserli, E. (2018) ZINC-FINGER interactions mediate transcriptional regulation of hypocotyl growth in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America, 115(19), E4503-E4511. (doi: 10.1073/pnas.1718099115) (PMID:29686058) (PMCID:PMC5948964)
Mitchell, R. et al. (2018) Targeting BCR-ABL independent TKI resistance in chronic myeloid leukaemia by mTOR and autophagy inhibition. Journal of the National Cancer Institute, 110(5), pp. 467-478. (doi: 10.1093/jnci/djx236) (PMID:29165716) (PMCID:PMC5946859)
Page, M. M., Schuster, E. F., Mudaliar, M. , Herzyk, P. , Withers, D. J. and Selman, C. (2018) Common and unique transcriptional responses to dietary restriction and loss of insulin receptor substrate 1 (IRS1) in mice. Aging, 10(5), pp. 1027-1052. (doi: 10.18632/aging.101446) (PMID:29779018) (PMCID:PMC5990393)
Carruthers, M., Yurchenko, A. A., Augley, J. J., Adams, C. E. , Herzyk, P. and Elmer, K. R. (2018) De novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish species. BMC Genomics, 19, 32. (doi: 10.1186/s12864-017-4379-x) (PMID:29310597) (PMCID:PMC5759245)
AlQarni, S. et al. (2018) Lymphomas driven by Epstein-Barr virus nuclear antigen-1 (EBNA1) are dependant upon Mdm2. Oncogene, 37, pp. 3998-4012. (doi: 10.1038/s41388-018-0147-x) (PMID:29691476) (PMCID:PMC6054874)
Connolly, J. P.R. et al. (2018) Host-associated niche metabolism controls enteric infection through fine-tuning the regulation of type 3 secretion. Nature Communications, 9, 4187. (doi: 10.1038/s41467-018-06701-4) (PMID:30305622) (PMCID:PMC6180029)
2017
Cousins, A. et al. (2017) Upregulated cholesterol biosynthesis is a biomarker for isolated central nervous system relapse in acute lymphoblastic leukaemia. Blood, 130(Sup 1), 3992.
Klymenko, T. et al. (2017) RNA-Seq analysis of differentiated keratinocytes reveals a massive response to late events during human papillomavirus 16 infection, including loss of epithelial barrier function. Journal of Virology, 91(24), e01001-17. (doi: 10.1128/JVI.01001-17) (PMID:29021401) (PMCID:PMC5709591)
Rodie, M.E., Mudaliar, M.A.V. , Herzyk, P. , McMillan, M., Boroujerdi, M., Chudleigh, S., Tobias, E.S. and Ahmed, S.F. (2017) Androgen-responsive non-coding small RNAs extend the potential of HCG stimulation to act as a bioassay of androgen sufficiency. European Journal of Endocrinology, 177(4), pp. 339-346. (doi: 10.1530/EJE-17-0404) (PMID:28733293)
Mwenechanya, R. et al. (2017) Sterol 14α-demethylase mutation leads to amphotericin B resistance in Leishmania mexicana. PLoS Neglected Tropical Diseases, 11(6), e0005649. (doi: 10.1371/journal.pntd.0005649) (PMID:28622334) (PMCID:PMC5498063)
2016
Mudaliar, M. et al. (2016) Mastitomics, the integrated omics of bovine milk in an experimental model of Streptococcus uberis mastitis: 2. Label-free relative quantitative proteomics. Molecular BioSystems, 12(9), pp. 2748-2761. (doi: 10.1039/C6MB00290K) (PMID:27412694) (PMCID:PMC5048399)
Thomas, F., Mudaliar, M. , Tassi, R., Mcneilly, T., Burchmore, R. , Burgess, K., Herzyk, P. , Zadoks, R. and Eckersall, P. (2016) Mastitomics, the integrated omics of bovine milk in an experimental model of Streptococcus uberis mastitis: 3. Untargeted metabolomics. Molecular BioSystems, 12(9), pp. 2762-2769. (doi: 10.1039/C6MB00289G) (PMID:27412568)
Marasco, V., Herzyk, P. , Robinson, J. and Spencer, K. A. (2016) Pre- and post-natal stress programming: developmental exposure to glucocorticoids causes long-term brain-region specific changes to transcriptome in the Japanese quail. Journal of Neuroendocrinology, 28(5), (doi: 10.1111/jne.12387) (PMID:26999292) (PMCID:PMC5103168)
Trewby, H. et al. (2016) Use of bacterial whole-genome sequencing to investigate local persistence and spread in bovine tuberculosis. Epidemics, 14, pp. 26-35. (doi: 10.1016/j.epidem.2015.08.003) (PMID:26972511) (PMCID:PMC4773590)
Gauson, E. J., Wang, X., Dornan, E. S., Herzyk, P. , Bristol, M. and Morgan, I. M. (2016) Failure to interact with Brd4 alters the ability of HPV16 E2 to regulate host genome expression and cellular movement. Virus Research, 211, pp. 1-8. (doi: 10.1016/j.virusres.2015.09.008) (PMID:26365679)
Velanis, C. N., Herzyk, P. and Jenkins, G. I. (2016) Regulation of transcription by the Arabidopsis UVR8 photoreceptor involves a specific histone modification. Plant Molecular Biology, 92(4), pp. 425-443. (doi: 10.1007/s11103-016-0522-3) (PMID:27534420) (PMCID:PMC5080334)
2015
Recknagel, H. , Jacobs, A., Herzyk, P. and Elmer, K. R. (2015) Double-digest RAD sequencing using Ion Proton semiconductor platform (ddRADseq-ion) with nonmodel organisms. Molecular Ecology Resources, 15(6), pp. 1316-1329. (doi: 10.1111/1755-0998.12406) (PMID:25808755)
Mudaliar, M. , Thomas, F., McLaughlin, M. , Burchmore, R. , Wilson, D., Herzyk, P. , Eckersall, P. and Zadoks, R. (2015) Using label-free quantitative proteomics and untargeted metabolomics to study bovine mastitis. In: Science with Impact – BSAS Annual Conference 2015, University of Chester, UK, 14-15 Apr 2015, p. 70. (doi: 10.1017/S2040470015000023)
2014
Mudaliar, M. , Thomas, F., McLaughlin, M. , Burchmore, R. , Herzyk, P. , Eckersall, P. and Zadoks, R. (2014) Integrative label-free quantitative proteomics study in mastitis. In: Final Showcase Meeting of Farm Animal Proteomics, Milan, Italy, 17-18 Nov 2014, pp. 98-101. ISBN 9789086868100 (doi: 10.3920/978-90-8686-810-0)
Gauson, E. J., Windle, B., Donaldson, M. , Cafarel, M. M., Dornan, E., Coleman, N., Herzyk, P. , Henderson, S. C., Wang, X. and Morgan, I. (2014) Regulation of human genome expression and RNA splicing by human papillomavirus 16 E2 protein. Virology, 468-70, pp. 10-18. (doi: 10.1016/j.virol.2014.07.022)
Tsimbouri, P. , Gadegaard, N., Burgess, K., White, K., Reynolds, P. , Herzyk, P. , Oreffo, R. and Dalby, M.J. (2014) Nanotopographical effects on mesenchymal stem cell morphology and phenotype. Journal of Cellular Biochemistry, 115(2), pp. 380-390. (doi: 10.1002/jcb.24673) (PMID:24123223)
Huser, C. A. et al. (2014) Insertional mutagenesis and deep profiling reveals gene hierarchies and a Myc/p53-dependent bottleneck in lymphomagenesis. PLoS Genetics, 10(2), e1004167. (doi: 10.1371/journal.pgen.1004167) (PMID:24586197) (PMCID:PMC3937229)
2013
Marasco, V., Spencer, K. A., Robinson, J. , Herzyk, P. and Costantini, D. (2013) Developmental post-natal stress can alter the effects of pre-natal stress on the adult redox balance. General and Comparative Endocrinology, 191, pp. 239-246. (doi: 10.1016/j.ygcen.2013.07.003)
Wiejak, J., Tsimbouri, P. M. , Herzyk, P. , Dalby, M. J. , Hamilton, G. and Yarwood, S. J. (2013) Genomic analysis of the role of transcription factor C/EBPδ in the regulation of cell behaviour on nanometric grooves. Biomaterials, 34(8), pp. 1967-1979. (doi: 10.1016/j.biomaterials.2012.11.036) (PMID:23245923) (PMCID:PMC3543902)
Tsimbouri, P. M. , Murawski, K., Hamilton, G., Herzyk, P. , Oreffo, R. O.C., Gadegaard, N. and Dalby, M. J. (2013) A genomics approach in determining nanotopographical effects on MSC phenotype. Biomaterials, 34(9), pp. 2177-2184. (doi: 10.1016/j.biomaterials.2012.12.019) (PMID:23312853) (PMCID:PMC3573234)
Robinson, S.W., Herzyk, P. , Dow, J.A.T. and Leader, D.P. (2013) FlyAtlas: database of gene expression in the tissues of drosophila melanogaster. Nucleic Acids Research, 41(D1), D744-D750. (doi: 10.1093/nar/gks1141) (PMID:23203866) (PMCID:PMC3531048)
Chintapalli, V.R., Wang, J., Herzyk, P. , Davies, S.A. and Dow, J.A.T. (2013) Data-mining the FlyAtlas online resource to identify core functional motifs across transporting epithelia. BMC Genomics, 14(518), (doi: 10.1186/1471-2164-14-518)
Sani, E., Herzyk, P. , Perrella, G., Colot, V. and Amtmann, A. (2013) Hyperosmotic priming of arabidopsis seedlings establishes a long-term somatic memory accompanied by specific changes of the epigenome. Genome Biology, 14(6), R59. (doi: 10.1186/gb-2013-14-6-r59) (PMID:23767915) (PMCID:PMC3707022)
2012
Reimer, M.M. et al. (2012) Rapid disruption of axon-glial integrity in response to mild cerebral hypoperfusion. Journal of Neuroscience, 31(49), pp. 18185-18194. (doi: 10.1523/JNEUROSCI.4936-11.2011)
Marasco, V., Robinson, J. , Herzyk, P. and Spencer, K. A. (2012) Pre- and post-natal stress in context: effects on the stress physiology in a precocial bird. Journal of Experimental Biology, 215(22), pp. 3955-3964. (doi: 10.1242/jeb.071423)
E-komon, T., Burchmore, R. , Herzyk, P. and Davies, R. (2012) Predicting the outer membrane proteome of Pasteurella multocida based on consensus prediction enhanced by results integration and manual confirmation. BMC Bioinformatics, 13(1), 63. (doi: 10.1186/1471-2105-13-63) (PMID:22540951) (PMCID:PMC3403877)
McNamara, L.E., Burchmore, R.J.S. , Riehle, M.O. , Herzyk, P. , Biggs, M.J.P., Wilkinson, C.D.W., Curtis, A.S.G. and Dalby, M.J. (2012) The role of microtopography in cellular mechanotransduction. Biomaterials, 33(10), pp. 2835-2847. (doi: 10.1016/j.biomaterials.2011.11.047)
James, A.B. , Syed, N.H., Bordage, S., Marshall, J., Nimmo, G.M., Jenkins, G.I. , Herzyk, P. , Brown, J.W.S. and Nimmo, H.G. (2012) Alternative splicing mediates responses of the arabidopsis circadian clock to temperature changes. Plant Cell, 24(3), pp. 961-981. (doi: 10.1105/tpc.111.093948) (PMID:22408072) (PMCID:PMC3336117)
Podar, D., Scherer, J., Noordally, Z., Herzyk, P. , Nies, D. and Sanders, D. (2012) Metal selectivity determinants in a family of transition metal transporters. Journal of Biological Chemistry, 287(5), pp. 3185-3196. (doi: 10.1074/jbc.M111.305649)
Chintapalli, V., Terhzaz, S. , Wang, J., Al Bratty, M., Watson, D.G., Herzyk, P. , Davies, S.A. and Dow, J.A.T. (2012) Functional correlates of positional and gender-specific renal asymmetry in drosophila. PLoS ONE, 7(4), e32577. (doi: 10.1371/journal.pone.0032577) (PMID:22496733) (PMCID:PMC3319558)
2011
Wang, D. et al. (2011) Identification of bacterial target proteins for the salicylidene acylhydrazide class of virulence blocking compounds. Journal of Biological Chemistry, 286(34), pp. 29922-29931. (doi: 10.1074/jbc.M111.233858) (PMID:21724850) (PMCID:PMC3191033)
Wright, C.F., Morelli, M.J., Thebaud, G., Knowles, N.J., Herzyk, P. , Paton, D.J., Haydon, D.T. and King, D.P. (2011) Beyond the consensus: dissecting within-host viral population diversity of foot-and-mouth disease virus using next-generation genome sequencing. Journal of Virology, 85(5), pp. 2266-2275. (doi: 10.1128/JVI.01396-10) (PMID:21159860) (PMCID:PMC3067773)
Gatherer, D. et al. (2011) High-resolution human cytomegalovirus transcriptome. Proceedings of the National Academy of Sciences of the United States of America, 108(49), pp. 19755-19760. (doi: 10.1073/pnas.1115861108)
Rogers, M.B. et al. (2011) Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania. Genome Research, 21(12), pp. 2129-2142. (doi: 10.1101/gr.122945.111)
2009
Gow, J.W., Hagan, S., Herzyk, P. , Cannon, C., Behan, P.O. and Chaudhuri, A. (2009) A gene signature for post-infectious chronic fatigue syndrome. BMC Medical Genomics, 2(38), (doi: 10.1186/1755-8794-2-38)
2008
James, A.B. , Monreal, J.A., Nimmo, G.A., Kelly, C.L., Herzyk, P. , Jenkins, G.I. and Nimmo, H.G. (2008) The circadian clock in Arabidopsis roots is a simplified slave version of the clock in shoots. Science, 322(5909), pp. 1832-1835. (doi: 10.1126/science.1161403)
Wotton, S., Terry, A., Kilbey, A., Jenkins, A., Herzyk, P. , Cameron, E. and Neil, J.C. (2008) Gene array analysis reveals a common Runx transcriptional programme controlling cell adhesion and survival. Oncogene, 27(44), pp. 5856-5866. (doi: 10.1038/onc.2008.195)
Wright, R.H.G., Dornan, E.S., Donaldson, M.M. , MacFarlane, M., Herzyk, P. and Morgan, I.M. (2008) TopBP1 contains transcriptional regulatory domains and regulates gene pathways involved in breast cancer. In: Breast Cancer Research 2008, London, UK, 13 May 2008, P21. (doi: 10.1186/bcr 1905)
Bridges, D.J., Pitt, A.R., Hanrahan, O., Brennan, K., Voorheis, H.P., Herzyk, P. , de Koning, H.P. and Burchmore, R.J.S. (2008) Characterisation of the plasma membrane subproteome of bloodstream form Trypanosoma brucei. Proteomics, 8(1), pp. 83-99. (doi: 10.1002/pmic.200700607)
2007
Nebel, J.C., Herzyk, P. and Gilbert, D.R. (2007) Automatic generation of 3D motifs for classification of protein binding sites. BMC Bioinformatics, 8(321), (doi: 10.1186/1471-2105-8-321)
Dalby, M.J. , Gadegaard, N. , Herzyk, P. , Agheli, H., Sutherland, D.S. and Wilkinson, C.D.W. (2007) Group analysis of regulation of fibroblast genome on low-adhesion nanostructures. Biomaterials, 28, pp. 1761-1769. (doi: 10.1016/j.biomaterials.2006.11.049)
Dalby, M.J. , Gadegaard, N. , Tare, R., Andar, A., Riehle, M.O. , Herzyk, P. , Wilkinson, C.D.W. and Oreffo, R.O.C. (2007) The control of human mesenchymal cell differentiation using nanoscale symmetry and disorder. Nature Materials, 6(12), pp. 997-1003. (doi: 10.1038/nmat2013)
Herzyk, P. (2007) Nanomechanotransduction and interphase nuclear organization influence on genomic control. Journal of Cellular Biochemistry, 102(5), pp. 1234-1244. (doi: 10.1002/jcb.21354)
Richardson, A., Boscari, A., Schreiber, L., Kerstiens, G., Jarvis, M., Herzyk, P. and Fricke, W. (2007) Cloning and expression analysis of candidate genes involved in wax deposition along the growing barley (Hordeum vulgare) leaf. Planta, 226, pp. 1459-1473. (doi: 10.1007/s00425-007-0585-0)
2006
Mackley, J., Ando, J., Herzyk, P. and Winder, S.J. (2006) Phenotypic responses to mechanical stress in fibroblasts from tendon, cornea and skin. Biochemical Journal, 396(Pt. 2), pp. 307-316.
Bolger, G.B. et al. (2006) Scanning peptide array analysis identify overlapping binding sites for the signaling scaffold proteins, beta-arestin and RACK1 in the cAMP-specific phosphodiesterase, PDE4D5. Biochemical Journal, 398(1), pp. 23-36. (doi: 10.1042/BJ20060423)
Hunter, K. et al. (2006) Divergent routes to oral cancer. Cancer Research, 66, pp. 7405-7413. (doi: 10.1158/0008-5472.CAN-06-0186)
2005
Breitling, R. and Herzyk, P. (2005) Biological master games: Using biologists' reasoning to guide algorithm development for integrated functional genomics. OMICS: A Journal of Integrative Biology, 9, pp. 225-232.
Brown, B. A., Cloix, C., Jiang, G. H., Kaiserli, E. , Herzyk, P., Kliebenstein, D. J. and Jenkins, G. I. (2005) A UV-B-specific signaling component orchestrates plant UV protection. Proceedings of the National Academy of Sciences of the United States of America, 102, pp. 18225-18230. (doi: 10.1073/pnas.0507187102) (PMID:16330762) (PMCID:PMC1312397)
Herzyk, P. (2005) Rank-based statistics as a non-parametric alternative of the t-statistic for the analysis of biological microarray data. Journal of Bioinformatics and Computational Biology, 3(5), pp. 1171-1189. (doi: 10.1142/S0219720005001442)
MacCallum, A., Herzyk, P., Young, C., Ketley, J. M. and Everest, P. (2005) Campylobacter jejuni interaction with enterocytes - using host gene expressionanalysis to unravel potential disease mechanisms. In: Ketley, J. M. and konkel, M. (eds.) In Campylobacter Cellular and Molecular Biology. Horizon Press, pp. 435-443.
2004
Breitling, R., Armengaud, P., Amtmann, A. and Herzyk, P. (2004) Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments. FEBS Letters, 573(1-3), pp. 83-92. (doi: 10.1016/j.febslet.2004.07.055)
Amtmann, A. , Armengaud, P., Breitling, R. and Herzyk, P. (2004) Recent advances in using microarray technology to study the role of hormonal control in plant responses to abiotic stress. Acta Physiologiae Plantarum, 26, p. 92.
Breitling, R., Amtmann, A. and Herzyk, P. (2004) Graph-based iterative Group Analysis enhances microarray interpretation. BMC Bioinformatics, 5, (doi: 10.1186/1471-2105-5-100)
Wang, J., Kean, L., Yang, J., Allan, A., Davies, S., Herzyk, P. and Dow, J. (2004) Function-informed transcriptome analysis of Drosophila renal tubule. Genome Biology, 5, (PMID:15345053) (PMCID:PMC522876)
2003
Maathuis, F. et al. (2003) Transcriptome analysis of root transporters reveals participation of multiple gene families in the response to cation stress. Plant Journal, 35, pp. 675-692. (doi: 10.1046/j.1365-313X.2003.01839.x)
2001
Herzyk, P. (2001) The dimerization interface of the metastasis-associated protein S100A4 (Mts1) - In vivo and in vitro studies. Journal of Biological Chemistry, 276(26), pp. 24212-24222. (doi: 10.1074/jbc.M009477200)
Articles
Delles, C. et al. (2024) Response of blood pressure to renal denervation is not associated with genetic variants. Hypertension, (doi: 10.1161/HYPERTENSIONAHA.124.23393) (PMID:39569514) (Early Online Publication)
Kulkarni, J. et al. (2024) Early-responsive molecular signatures associated with halophytic adaptation in Sesuvium portulacastrum (L.). Plant, Cell and Environment, 47(3), pp. 961-975. (doi: 10.1111/pce.14767) (PMID:38044749)
Tobias, E. S. et al. (2024) SEC31A may be associated with pituitary hormone deficiency and gonadal dysgenesis. Endocrine, 84, pp. 345-349. (doi: 10.1007/s12020-024-03701-x) (PMID:38400880)
Martin, T. P. et al. (2023) Ribonucleicacid interference or small molecule inhibition of Runx1 in the border zone prevents cardiac contractile dysfunction following myocardial infarction. Cardiovascular Research, 119(16), 2663–2671-2663–2671. (doi: 10.1093/cvr/cvad107) (PMID:37433039) (PMCID:PMC10730241)
Perrella, G., Fasano, C., Donald, N. A., Daddiego, L., Fang, W., Martignago, D., Carr, C., Conti, L., Herzyk, P. and Amtmann, A. (2023) Histone Deacetylase Complex 1 and Histone 1 epigenetically moderate stress responsiveness of Arabidopsis thaliana seedlings. New Phytologist, (doi: 10.1111/nph.19165) (PMID:37565540) (Early Online Publication)
McInnes, K. J., van der Hooft, J. J.J. , Sharma, A., Herzyk, P. , Hundleby, P. A.C., Schoonbeek, H.-J., Amtmann, A. , Ridout, C. and Jenkins, G. I. (2023) Overexpression of Brassica napus COMT1 in Arabidopsis heightens UV-B-mediated resistance to Plutella xylostella herbivory. Photochemical and Photobiological Sciences, 22, pp. 2341-2356. (doi: 10.1007/s43630-023-00455-9) (PMID:37505444) (PMCID:PMC10509076)
Cousins, A. et al. (2022) Central nervous system involvement in childhood acute lymphoblastic leukemia is linked to upregulation of cholesterol biosynthetic pathways. Leukemia, 36(12), pp. 2903-2907. (doi: 10.1038/s41375-022-01722-x) (PMID:36289348) (PMCID:PMC9712090)
Dwomoh, L. et al. (2022) M1 muscarinic receptor activation reduces the molecular pathology and slows the progression of prion-mediated neurodegenerative disease. Science Signaling, 15(760), eabm3720. (doi: 10.1126/scisignal.abm3720) (PMID:36378750)
Dow, J. A.T. , Krause, S. A. and Herzyk, P. (2021) Updates on ion and water transport by the Malpighian tubule. Current Opinion in Insect Science, 47, pp. 31-37. (doi: 10.1016/j.cois.2021.02.018) (PMID:33705976)
Madsen, M. A., Hamilton, G., Herzyk, P. and Amtmann, A. (2021) Environmental regulation of PndbA600, an auto-inducible promoter for two-stage industrial biotechnology in cyanobacteria. Frontiers in Bioengineering and Biotechnology, 8, 619055. (doi: 10.3389/fbioe.2020.619055) (PMID:33542914) (PMCID:PMC7853294)
Savino, A. M. et al. (2020) Metabolic adaptation of acute lymphoblastic leukemia to the central nervous system microenvironment depends on Stearoyl CoA desaturase. Nature Cancer, 1(10), pp. 998-1009. (doi: 10.1038/s43018-020-00115-2) (PMID:33479702) (PMCID:PMC7116605)
Cumming, S. A. et al. (2018) De novo repeat interruptions are associated with reduced somatic instability and mild or absent clinical features in myotonic dystrophy type 1. European Journal of Human Genetics, 26(11), pp. 1635-1647. (doi: 10.1038/s41431-018-0156-9) (PMID:29967337) (PMCID:PMC6189127)
Perrella, G., Davidson, M. L.H., O'Donnell, L. , Nastase, A.-M., Herzyk, P. , Breton, G., Pruneda-Paz, J. L., Kay, S. A., Chory, J. and Kaiserli, E. (2018) ZINC-FINGER interactions mediate transcriptional regulation of hypocotyl growth in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America, 115(19), E4503-E4511. (doi: 10.1073/pnas.1718099115) (PMID:29686058) (PMCID:PMC5948964)
Mitchell, R. et al. (2018) Targeting BCR-ABL independent TKI resistance in chronic myeloid leukaemia by mTOR and autophagy inhibition. Journal of the National Cancer Institute, 110(5), pp. 467-478. (doi: 10.1093/jnci/djx236) (PMID:29165716) (PMCID:PMC5946859)
Page, M. M., Schuster, E. F., Mudaliar, M. , Herzyk, P. , Withers, D. J. and Selman, C. (2018) Common and unique transcriptional responses to dietary restriction and loss of insulin receptor substrate 1 (IRS1) in mice. Aging, 10(5), pp. 1027-1052. (doi: 10.18632/aging.101446) (PMID:29779018) (PMCID:PMC5990393)
Carruthers, M., Yurchenko, A. A., Augley, J. J., Adams, C. E. , Herzyk, P. and Elmer, K. R. (2018) De novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish species. BMC Genomics, 19, 32. (doi: 10.1186/s12864-017-4379-x) (PMID:29310597) (PMCID:PMC5759245)
AlQarni, S. et al. (2018) Lymphomas driven by Epstein-Barr virus nuclear antigen-1 (EBNA1) are dependant upon Mdm2. Oncogene, 37, pp. 3998-4012. (doi: 10.1038/s41388-018-0147-x) (PMID:29691476) (PMCID:PMC6054874)
Connolly, J. P.R. et al. (2018) Host-associated niche metabolism controls enteric infection through fine-tuning the regulation of type 3 secretion. Nature Communications, 9, 4187. (doi: 10.1038/s41467-018-06701-4) (PMID:30305622) (PMCID:PMC6180029)
Cousins, A. et al. (2017) Upregulated cholesterol biosynthesis is a biomarker for isolated central nervous system relapse in acute lymphoblastic leukaemia. Blood, 130(Sup 1), 3992.
Klymenko, T. et al. (2017) RNA-Seq analysis of differentiated keratinocytes reveals a massive response to late events during human papillomavirus 16 infection, including loss of epithelial barrier function. Journal of Virology, 91(24), e01001-17. (doi: 10.1128/JVI.01001-17) (PMID:29021401) (PMCID:PMC5709591)
Rodie, M.E., Mudaliar, M.A.V. , Herzyk, P. , McMillan, M., Boroujerdi, M., Chudleigh, S., Tobias, E.S. and Ahmed, S.F. (2017) Androgen-responsive non-coding small RNAs extend the potential of HCG stimulation to act as a bioassay of androgen sufficiency. European Journal of Endocrinology, 177(4), pp. 339-346. (doi: 10.1530/EJE-17-0404) (PMID:28733293)
Mwenechanya, R. et al. (2017) Sterol 14α-demethylase mutation leads to amphotericin B resistance in Leishmania mexicana. PLoS Neglected Tropical Diseases, 11(6), e0005649. (doi: 10.1371/journal.pntd.0005649) (PMID:28622334) (PMCID:PMC5498063)
Mudaliar, M. et al. (2016) Mastitomics, the integrated omics of bovine milk in an experimental model of Streptococcus uberis mastitis: 2. Label-free relative quantitative proteomics. Molecular BioSystems, 12(9), pp. 2748-2761. (doi: 10.1039/C6MB00290K) (PMID:27412694) (PMCID:PMC5048399)
Thomas, F., Mudaliar, M. , Tassi, R., Mcneilly, T., Burchmore, R. , Burgess, K., Herzyk, P. , Zadoks, R. and Eckersall, P. (2016) Mastitomics, the integrated omics of bovine milk in an experimental model of Streptococcus uberis mastitis: 3. Untargeted metabolomics. Molecular BioSystems, 12(9), pp. 2762-2769. (doi: 10.1039/C6MB00289G) (PMID:27412568)
Marasco, V., Herzyk, P. , Robinson, J. and Spencer, K. A. (2016) Pre- and post-natal stress programming: developmental exposure to glucocorticoids causes long-term brain-region specific changes to transcriptome in the Japanese quail. Journal of Neuroendocrinology, 28(5), (doi: 10.1111/jne.12387) (PMID:26999292) (PMCID:PMC5103168)
Trewby, H. et al. (2016) Use of bacterial whole-genome sequencing to investigate local persistence and spread in bovine tuberculosis. Epidemics, 14, pp. 26-35. (doi: 10.1016/j.epidem.2015.08.003) (PMID:26972511) (PMCID:PMC4773590)
Gauson, E. J., Wang, X., Dornan, E. S., Herzyk, P. , Bristol, M. and Morgan, I. M. (2016) Failure to interact with Brd4 alters the ability of HPV16 E2 to regulate host genome expression and cellular movement. Virus Research, 211, pp. 1-8. (doi: 10.1016/j.virusres.2015.09.008) (PMID:26365679)
Velanis, C. N., Herzyk, P. and Jenkins, G. I. (2016) Regulation of transcription by the Arabidopsis UVR8 photoreceptor involves a specific histone modification. Plant Molecular Biology, 92(4), pp. 425-443. (doi: 10.1007/s11103-016-0522-3) (PMID:27534420) (PMCID:PMC5080334)
Recknagel, H. , Jacobs, A., Herzyk, P. and Elmer, K. R. (2015) Double-digest RAD sequencing using Ion Proton semiconductor platform (ddRADseq-ion) with nonmodel organisms. Molecular Ecology Resources, 15(6), pp. 1316-1329. (doi: 10.1111/1755-0998.12406) (PMID:25808755)
Gauson, E. J., Windle, B., Donaldson, M. , Cafarel, M. M., Dornan, E., Coleman, N., Herzyk, P. , Henderson, S. C., Wang, X. and Morgan, I. (2014) Regulation of human genome expression and RNA splicing by human papillomavirus 16 E2 protein. Virology, 468-70, pp. 10-18. (doi: 10.1016/j.virol.2014.07.022)
Tsimbouri, P. , Gadegaard, N., Burgess, K., White, K., Reynolds, P. , Herzyk, P. , Oreffo, R. and Dalby, M.J. (2014) Nanotopographical effects on mesenchymal stem cell morphology and phenotype. Journal of Cellular Biochemistry, 115(2), pp. 380-390. (doi: 10.1002/jcb.24673) (PMID:24123223)
Huser, C. A. et al. (2014) Insertional mutagenesis and deep profiling reveals gene hierarchies and a Myc/p53-dependent bottleneck in lymphomagenesis. PLoS Genetics, 10(2), e1004167. (doi: 10.1371/journal.pgen.1004167) (PMID:24586197) (PMCID:PMC3937229)
Marasco, V., Spencer, K. A., Robinson, J. , Herzyk, P. and Costantini, D. (2013) Developmental post-natal stress can alter the effects of pre-natal stress on the adult redox balance. General and Comparative Endocrinology, 191, pp. 239-246. (doi: 10.1016/j.ygcen.2013.07.003)
Wiejak, J., Tsimbouri, P. M. , Herzyk, P. , Dalby, M. J. , Hamilton, G. and Yarwood, S. J. (2013) Genomic analysis of the role of transcription factor C/EBPδ in the regulation of cell behaviour on nanometric grooves. Biomaterials, 34(8), pp. 1967-1979. (doi: 10.1016/j.biomaterials.2012.11.036) (PMID:23245923) (PMCID:PMC3543902)
Tsimbouri, P. M. , Murawski, K., Hamilton, G., Herzyk, P. , Oreffo, R. O.C., Gadegaard, N. and Dalby, M. J. (2013) A genomics approach in determining nanotopographical effects on MSC phenotype. Biomaterials, 34(9), pp. 2177-2184. (doi: 10.1016/j.biomaterials.2012.12.019) (PMID:23312853) (PMCID:PMC3573234)
Robinson, S.W., Herzyk, P. , Dow, J.A.T. and Leader, D.P. (2013) FlyAtlas: database of gene expression in the tissues of drosophila melanogaster. Nucleic Acids Research, 41(D1), D744-D750. (doi: 10.1093/nar/gks1141) (PMID:23203866) (PMCID:PMC3531048)
Chintapalli, V.R., Wang, J., Herzyk, P. , Davies, S.A. and Dow, J.A.T. (2013) Data-mining the FlyAtlas online resource to identify core functional motifs across transporting epithelia. BMC Genomics, 14(518), (doi: 10.1186/1471-2164-14-518)
Sani, E., Herzyk, P. , Perrella, G., Colot, V. and Amtmann, A. (2013) Hyperosmotic priming of arabidopsis seedlings establishes a long-term somatic memory accompanied by specific changes of the epigenome. Genome Biology, 14(6), R59. (doi: 10.1186/gb-2013-14-6-r59) (PMID:23767915) (PMCID:PMC3707022)
Reimer, M.M. et al. (2012) Rapid disruption of axon-glial integrity in response to mild cerebral hypoperfusion. Journal of Neuroscience, 31(49), pp. 18185-18194. (doi: 10.1523/JNEUROSCI.4936-11.2011)
Marasco, V., Robinson, J. , Herzyk, P. and Spencer, K. A. (2012) Pre- and post-natal stress in context: effects on the stress physiology in a precocial bird. Journal of Experimental Biology, 215(22), pp. 3955-3964. (doi: 10.1242/jeb.071423)
E-komon, T., Burchmore, R. , Herzyk, P. and Davies, R. (2012) Predicting the outer membrane proteome of Pasteurella multocida based on consensus prediction enhanced by results integration and manual confirmation. BMC Bioinformatics, 13(1), 63. (doi: 10.1186/1471-2105-13-63) (PMID:22540951) (PMCID:PMC3403877)
McNamara, L.E., Burchmore, R.J.S. , Riehle, M.O. , Herzyk, P. , Biggs, M.J.P., Wilkinson, C.D.W., Curtis, A.S.G. and Dalby, M.J. (2012) The role of microtopography in cellular mechanotransduction. Biomaterials, 33(10), pp. 2835-2847. (doi: 10.1016/j.biomaterials.2011.11.047)
James, A.B. , Syed, N.H., Bordage, S., Marshall, J., Nimmo, G.M., Jenkins, G.I. , Herzyk, P. , Brown, J.W.S. and Nimmo, H.G. (2012) Alternative splicing mediates responses of the arabidopsis circadian clock to temperature changes. Plant Cell, 24(3), pp. 961-981. (doi: 10.1105/tpc.111.093948) (PMID:22408072) (PMCID:PMC3336117)
Podar, D., Scherer, J., Noordally, Z., Herzyk, P. , Nies, D. and Sanders, D. (2012) Metal selectivity determinants in a family of transition metal transporters. Journal of Biological Chemistry, 287(5), pp. 3185-3196. (doi: 10.1074/jbc.M111.305649)
Chintapalli, V., Terhzaz, S. , Wang, J., Al Bratty, M., Watson, D.G., Herzyk, P. , Davies, S.A. and Dow, J.A.T. (2012) Functional correlates of positional and gender-specific renal asymmetry in drosophila. PLoS ONE, 7(4), e32577. (doi: 10.1371/journal.pone.0032577) (PMID:22496733) (PMCID:PMC3319558)
Wang, D. et al. (2011) Identification of bacterial target proteins for the salicylidene acylhydrazide class of virulence blocking compounds. Journal of Biological Chemistry, 286(34), pp. 29922-29931. (doi: 10.1074/jbc.M111.233858) (PMID:21724850) (PMCID:PMC3191033)
Wright, C.F., Morelli, M.J., Thebaud, G., Knowles, N.J., Herzyk, P. , Paton, D.J., Haydon, D.T. and King, D.P. (2011) Beyond the consensus: dissecting within-host viral population diversity of foot-and-mouth disease virus using next-generation genome sequencing. Journal of Virology, 85(5), pp. 2266-2275. (doi: 10.1128/JVI.01396-10) (PMID:21159860) (PMCID:PMC3067773)
Gatherer, D. et al. (2011) High-resolution human cytomegalovirus transcriptome. Proceedings of the National Academy of Sciences of the United States of America, 108(49), pp. 19755-19760. (doi: 10.1073/pnas.1115861108)
Rogers, M.B. et al. (2011) Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania. Genome Research, 21(12), pp. 2129-2142. (doi: 10.1101/gr.122945.111)
Gow, J.W., Hagan, S., Herzyk, P. , Cannon, C., Behan, P.O. and Chaudhuri, A. (2009) A gene signature for post-infectious chronic fatigue syndrome. BMC Medical Genomics, 2(38), (doi: 10.1186/1755-8794-2-38)
James, A.B. , Monreal, J.A., Nimmo, G.A., Kelly, C.L., Herzyk, P. , Jenkins, G.I. and Nimmo, H.G. (2008) The circadian clock in Arabidopsis roots is a simplified slave version of the clock in shoots. Science, 322(5909), pp. 1832-1835. (doi: 10.1126/science.1161403)
Wotton, S., Terry, A., Kilbey, A., Jenkins, A., Herzyk, P. , Cameron, E. and Neil, J.C. (2008) Gene array analysis reveals a common Runx transcriptional programme controlling cell adhesion and survival. Oncogene, 27(44), pp. 5856-5866. (doi: 10.1038/onc.2008.195)
Bridges, D.J., Pitt, A.R., Hanrahan, O., Brennan, K., Voorheis, H.P., Herzyk, P. , de Koning, H.P. and Burchmore, R.J.S. (2008) Characterisation of the plasma membrane subproteome of bloodstream form Trypanosoma brucei. Proteomics, 8(1), pp. 83-99. (doi: 10.1002/pmic.200700607)
Nebel, J.C., Herzyk, P. and Gilbert, D.R. (2007) Automatic generation of 3D motifs for classification of protein binding sites. BMC Bioinformatics, 8(321), (doi: 10.1186/1471-2105-8-321)
Dalby, M.J. , Gadegaard, N. , Herzyk, P. , Agheli, H., Sutherland, D.S. and Wilkinson, C.D.W. (2007) Group analysis of regulation of fibroblast genome on low-adhesion nanostructures. Biomaterials, 28, pp. 1761-1769. (doi: 10.1016/j.biomaterials.2006.11.049)
Dalby, M.J. , Gadegaard, N. , Tare, R., Andar, A., Riehle, M.O. , Herzyk, P. , Wilkinson, C.D.W. and Oreffo, R.O.C. (2007) The control of human mesenchymal cell differentiation using nanoscale symmetry and disorder. Nature Materials, 6(12), pp. 997-1003. (doi: 10.1038/nmat2013)
Herzyk, P. (2007) Nanomechanotransduction and interphase nuclear organization influence on genomic control. Journal of Cellular Biochemistry, 102(5), pp. 1234-1244. (doi: 10.1002/jcb.21354)
Richardson, A., Boscari, A., Schreiber, L., Kerstiens, G., Jarvis, M., Herzyk, P. and Fricke, W. (2007) Cloning and expression analysis of candidate genes involved in wax deposition along the growing barley (Hordeum vulgare) leaf. Planta, 226, pp. 1459-1473. (doi: 10.1007/s00425-007-0585-0)
Mackley, J., Ando, J., Herzyk, P. and Winder, S.J. (2006) Phenotypic responses to mechanical stress in fibroblasts from tendon, cornea and skin. Biochemical Journal, 396(Pt. 2), pp. 307-316.
Bolger, G.B. et al. (2006) Scanning peptide array analysis identify overlapping binding sites for the signaling scaffold proteins, beta-arestin and RACK1 in the cAMP-specific phosphodiesterase, PDE4D5. Biochemical Journal, 398(1), pp. 23-36. (doi: 10.1042/BJ20060423)
Hunter, K. et al. (2006) Divergent routes to oral cancer. Cancer Research, 66, pp. 7405-7413. (doi: 10.1158/0008-5472.CAN-06-0186)
Breitling, R. and Herzyk, P. (2005) Biological master games: Using biologists' reasoning to guide algorithm development for integrated functional genomics. OMICS: A Journal of Integrative Biology, 9, pp. 225-232.
Brown, B. A., Cloix, C., Jiang, G. H., Kaiserli, E. , Herzyk, P., Kliebenstein, D. J. and Jenkins, G. I. (2005) A UV-B-specific signaling component orchestrates plant UV protection. Proceedings of the National Academy of Sciences of the United States of America, 102, pp. 18225-18230. (doi: 10.1073/pnas.0507187102) (PMID:16330762) (PMCID:PMC1312397)
Herzyk, P. (2005) Rank-based statistics as a non-parametric alternative of the t-statistic for the analysis of biological microarray data. Journal of Bioinformatics and Computational Biology, 3(5), pp. 1171-1189. (doi: 10.1142/S0219720005001442)
Breitling, R., Armengaud, P., Amtmann, A. and Herzyk, P. (2004) Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments. FEBS Letters, 573(1-3), pp. 83-92. (doi: 10.1016/j.febslet.2004.07.055)
Amtmann, A. , Armengaud, P., Breitling, R. and Herzyk, P. (2004) Recent advances in using microarray technology to study the role of hormonal control in plant responses to abiotic stress. Acta Physiologiae Plantarum, 26, p. 92.
Breitling, R., Amtmann, A. and Herzyk, P. (2004) Graph-based iterative Group Analysis enhances microarray interpretation. BMC Bioinformatics, 5, (doi: 10.1186/1471-2105-5-100)
Wang, J., Kean, L., Yang, J., Allan, A., Davies, S., Herzyk, P. and Dow, J. (2004) Function-informed transcriptome analysis of Drosophila renal tubule. Genome Biology, 5, (PMID:15345053) (PMCID:PMC522876)
Maathuis, F. et al. (2003) Transcriptome analysis of root transporters reveals participation of multiple gene families in the response to cation stress. Plant Journal, 35, pp. 675-692. (doi: 10.1046/j.1365-313X.2003.01839.x)
Herzyk, P. (2001) The dimerization interface of the metastasis-associated protein S100A4 (Mts1) - In vivo and in vitro studies. Journal of Biological Chemistry, 276(26), pp. 24212-24222. (doi: 10.1074/jbc.M009477200)
Book Sections
MacCallum, A., Herzyk, P., Young, C., Ketley, J. M. and Everest, P. (2005) Campylobacter jejuni interaction with enterocytes - using host gene expressionanalysis to unravel potential disease mechanisms. In: Ketley, J. M. and konkel, M. (eds.) In Campylobacter Cellular and Molecular Biology. Horizon Press, pp. 435-443.
Research Reports or Papers
Ciosi, M. , Cumming, S. A., Alshammari, A. M., Symeonidi, E., Herzyk, P. , Mcguinness, D. , Galbraith, J., Hamilton, G. and Monckton, D. G. (2018) Library preparation and MiSeq sequencing for the genotyping-by-sequencing of the Huntington disease HTT exon one trinucleotide repeat and the quantification of somatic mosaicism [Protocol]. Other. Springer Nature. (doi: 10.21203/rs.2.1581/v2).
Conference Proceedings
Mudaliar, M. , Thomas, F., McLaughlin, M. , Burchmore, R. , Wilson, D., Herzyk, P. , Eckersall, P. and Zadoks, R. (2015) Using label-free quantitative proteomics and untargeted metabolomics to study bovine mastitis. In: Science with Impact – BSAS Annual Conference 2015, University of Chester, UK, 14-15 Apr 2015, p. 70. (doi: 10.1017/S2040470015000023)
Mudaliar, M. , Thomas, F., McLaughlin, M. , Burchmore, R. , Herzyk, P. , Eckersall, P. and Zadoks, R. (2014) Integrative label-free quantitative proteomics study in mastitis. In: Final Showcase Meeting of Farm Animal Proteomics, Milan, Italy, 17-18 Nov 2014, pp. 98-101. ISBN 9789086868100 (doi: 10.3920/978-90-8686-810-0)
Wright, R.H.G., Dornan, E.S., Donaldson, M.M. , MacFarlane, M., Herzyk, P. and Morgan, I.M. (2008) TopBP1 contains transcriptional regulatory domains and regulates gene pathways involved in breast cancer. In: Breast Cancer Research 2008, London, UK, 13 May 2008, P21. (doi: 10.1186/bcr 1905)
Grants
Grants and Awards listed are those received whilst working with the University of Glasgow.
- Hormone transport at the nexus of nutrient deficiency and drought stress in plants
Biotechnology and Biological Sciences Research Council
2023 - 2026
- Predictive Biomarkers of Treatment Response in Kidney Transplant Rejection
National Institutes of Health
2021 - 2022
- Identifying drivers of central nervous system involvement in T-cell acute lymphoblastic leukaemia
Children's Cancer and Leukaemia Group
2021 - 2023
- When are two cells better than one? A comparative approach to insect renal function
Biotechnology and Biological Sciences Research Council
2021 - 2024
- Combining chemical priming and quantitative genetics to increase salt tolerance of soybean
Biotechnology and Biological Sciences Research Council
2018 - 2021
- ISSF Toward universally feasible molecular diagnostics in kidney transplantation through development of novel transcriptomic approaches making use of routine diagnostic tissue
Wellcome Trust
2016 - 2018
- ISSF Catalyst: Integrative polyomics approach to identify metabolomic and genomic signatures of glioma stem cells for therapeutic intervention in glioblastoma
Wellcome Trust
2016 - 2016
- ISSF Catalyst: Unraveling the secret lives of bacteria: RNA-seq for exploring niche-specific gene expression.
Wellcome Trust
2015 - 2016
- ISSF Catalyst: Identification of mechanism(s) of acquired drug resistance in CML using a genome-scale CRISPR-knockout screening approach
Wellcome Trust
2015 - 2016
- Identifying Novel Targets for eradication of acute lymphoblastic leukaemia in the central nervous system
Chief Scientist Office
2015 - 2017
- Identification of stage-specific promoter elements in photosynthetic bacteria (ISSF Catalyst)
Wellcome Trust
2014 - 2015
- Enabling Stratified Medicine in Early Rheumatoid Arthritis - predicting methotrexate (MTX) response and toxicity using an integrated polyomic approach (PROMISERA)
Scottish Funding Council
2014 - 2018
- Joint estimation of epidemiological and genetic processes for Mycobacterium bovis transmission dynamics in cattle and badgers
Biotechnology and Biological Sciences Research Council
2014 - 2017
- The use of polyomic analyses to direct biologic therapy in biologic-naive people with Rheumatoid Arthritis
Chief Scientist Office
2013 - 2015
- The implant microbiome: metagenomics and metabolomics to understand the role of co-infection in orthopaedic surgery and medical implantation
Scottish Government
2013 - 2014
- Development of bioinformatic analysis pipelines to integrate transcriptomic and metabolomic data to map the alpha 7 nicotinic receptor... (ISSF Catalyst)
Wellcome Trust
2013 - 2014
- Exome Sequencing for the Genetic Diagnosis of Rare Diseases: Fostering a New Working Relationship between the NHS, the University of Glasgow and Glasgow Polyomics (ISSF)
Wellcome Trust
2013 - 2015
- Next generation sequencing approaches to genotyping in myotonic dystrophy type 1
Muscular Dystrophy Association
2013 - 2015
- Extraordinary pH - the mechanism of generation of pH 12 in living systems
Biotechnology and Biological Sciences Research Council
2012 - 2014
- Application of a minimally-invasive method for RNA sampling in the detection of recombinant human erythropoietin (r-HuEpo) use by athletes and the role of mRNA
World Anti-Doping Agency
2011 - 2013
- The Role of EPAC1-regulated Protein Kinase C Isoforms in Mediating C/EBPdelta -dependent, Anti-inflammatory Actions of Cyclic AMP in Vascular Endothelial Cells
British Heart Foundation
2010 - 2013
- Centre for Virus Research
Medical Research Council
2010 - 2016
- Centre for Integrated Virology
Medical Research Council
2010 - 2015
- A gene-microarray based approach to the detection of recombinant human erythropoietin doping in athletes
World Anti-Doping Agency
2009 - 2011
- Establishment of an MRC Sequencing Hub at the GenePool, the Scottish next-generation genomics facility
Medical Research Council
2009 - 2012
- Regulation of Pre-B ALL Cell Growth by Adhesion-Independent Signalling via the avb5 Integrin
Leukaemia Research Fund
2008 - 2010
- FlyAtlas: a comprehensive online atlas of gene expression in Drosophilia.
Biotechnology and Biological Sciences Research Council
2008 - 2010
- Identification of TopBP1 target genes in normal and DNA damaged breast cancer cells
Breast Cancer Campaign
2007 - 2008
- Modelling, induction and analysis for biological systems up to the cellular level
Biotechnology and Biological Sciences Research Council
2006 - 2007
- Grid enabled microarray equipment profile search (GEMEPS)
Biotechnology and Biological Sciences Research Council
2005 - 2007
- Functional genomics of nutrient transport in arabidopsis: a bioinformatics approach
Biotechnology and Biological Sciences Research Council
2003 - 2005
Additional information
Grant Advisory Board
- 2012 - present: BBSRC - Core Member Committee C - Genes, development and STEM (Science, Technology, Engineering and Maths) approaches to biology
- 2011: BBSRC - Member, Pool of Experts
Invited International Presentations
- 2005: Glasgow, UK - Invited speaker for the Affymetrix user meeting
- 2005: Poznan, Poland - Session speaker for the Second Conference of the Polish Society of Experimental Biology
- 2004: Glasgow, UK - Member of Local Organising Committee for ISMB/ECCB-2004
- 2004: Leicester, UK - Invited speaker for annual GARNET meeting
- 2004: Warsaw, Poland - Invited speaker at Comparative and Functional Genomics workshop