2024

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, (doi: 10.1007/s12020-024-03701-x) (PMID:38400880) (Early Online Publication)

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

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, (doi: 10.1007/s12020-024-03701-x) (PMID:38400880) (Early Online Publication)

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)