Dr Pawel Herzyk

  • Senior Lecturer (Institute of Molecular Cell and Systems Biology)
  • Affiliate (Polyomics Facility)

telephone: 01413303180
email: Pawel.Herzyk@glasgow.ac.uk

Research interests

'Analysis of data generated by -omics technologies, structural bioinformatics, molecular modelling of transmembrane proteins'


Grants and Awards listed are those received whilst working with the University of Glasgow.

  • ISSF Toward universally feasible molecular diagnostics in kidney transplantation through development of novel transcriptomic approaches making use of routine diagnostic tissue
    Wellcome Trust
    2016 - 2016
  • 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
    Scottish Executive Health Department
    2015 - 2016
  • 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 - 2016
  • 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
    Scottish Executive Health Department
    2013 - 2015
  • The implant microbiome: metagenomics and metabolomics to understand the role of co-infection in orthopaedic surgery and medical implantation
    Scottish Government Health Directorates
    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 - 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
    2010 - 2012
  • 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 Integrated Virology
    2010 - 2015
  • A gene-microarray based approach to the detection of recombinant human erythropoietin doping in athletes
    World Anti Doping Agency
    2009 - 2011
  • Regulation of Pre-B ALL Cell Growth by Adhesion-Independent Signalling via the avb5 Integrin
    Leukaemia Research Fund
    2008 - 2009
  • FlyAtlas: a comprehensive online atlas of gene expression in Drosophilia.
    2008 - 2010
  • Identification of TopBP1 target genes in normal and DNA damaged breast cancer cells
    Breast Cancer Campaign
    2007 - 2007
  • Modelling, induction and analysis for biological systems up to the cellular level
    2006 - 2007
  • Grid enabled microarray equipment profile search (GEMEPS)
    2005 - 2007
  • Functional genomics of nutrient transport in arabidopsis: a bioinformatics approach
    2003 - 2005

Additional information

Grant Advisory Board

  • 2012 - ongoing: BBSRC - Core Member Committee C - Genes, development and STEM (Science, Technology, Engineering and Maths) approaches to biology
  • 2011 - 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


List by: Type | Date

Jump to: 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2001
Number of items: 51.


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, (doi:10.1039/C6MB00290K) (PMID:27412694) (Early Online Publication)

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, (doi:10.1039/C6MB00289G) (PMID:27412568) (Early Online Publication)

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)

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, (doi:10.1007/s11103-016-0522-3) (Early Online Publication)


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)


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)

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)


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)

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)

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)

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.


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,


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)

This list was generated on Sun Sep 25 16:53:01 2016 BST.