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

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

  • Identifying Novel Targets for eradication of acute lymphoblastic leukaemia in the central nervous system
    Scottish Executive Health Department
    2014 - 2016
     
  • Identification of stage-specific promoter elements in photosynthetic bacteria (ISSF Catalyst)
    Wellcome Trust
    2014 - 2015
     
  • 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
    MRC
    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.
    BBSRC
    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
    BBSRC
    2006 - 2007
     
  • Grid enabled microarray equipment profile search (GEMEPS)
    BBSRC
    2005 - 2007
     
  • Functional genomics of nutrient transport in arabidopsis: a bioinformatics approach
    BBSRC
    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

Publications

List by: Type | Date

Jump to: 2014 | 2013 | 2012 | 2011 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2001
Number of items: 45.

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, 17-18 Nov 2014, Milan, Italy.

Gauson, E. J., Windle, B., Donaldson, M. 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)

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)

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)

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)

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)

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)

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)

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.A., 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)

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.

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)

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). p. 63. (doi:10.1186/1471-2105-13-63)

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)

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)

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)

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)

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)

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 .

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)

This list was generated on Fri Jan 30 15:15:02 2015 GMT.
Number of items: 45.

Articles

Gauson, E. J., Windle, B., Donaldson, M. 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)

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)

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)

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)

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)

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)

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)

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.A., 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)

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.

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)

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). p. 63. (doi:10.1186/1471-2105-13-63)

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)

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)

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)

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.

Conference Proceedings

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, 17-18 Nov 2014, Milan, Italy.

This list was generated on Fri Jan 30 15:15:02 2015 GMT.