Pawel Herzyk, PhD

Address:
The Sir Henry Wellcome Functional Genomics Facility
IBLS, Joseph Black Building,
University of Glasgow, G12 8QQ, UK.

e-mail: p.herzyk@bio.gla.ac.uk
phone: +44 (0)141 3303180

Hi, I am Head of Bioinformatics in The Sir Henry Wellcome Functional Genomics Facility (SHWFGF) in the Institute of Biomedical and Life Sciences (IBLS) as well as a investigator in the Bioinformatics Research Centre (BRC) in Department of Computer Science (DCS) in the University of Glasgow.

In SHWFGF I am responsible for bioinformatics infrastructure necessary for the acquisition, secure storage, analysis and electronic distribution of data generated with the functional genomics high-throughput technologies, as well as providing resource for computational functional genomics. More information on this subject is provided in Bioinformatics in SHWFGF link.

Research interest

My research interests involve:

Developing methods for microarray data analysis, particularly identification of differentially expressed genes and gene functional classes.
Integration of proteomics and gene-expression data
Modelling 3-D structure of proteins, particularly transmembrane domains

Research grants

"Functional Genomics of NutriensTransport in Arabidopsis; Bioinformatics Approach", BBSRC, April 2003 for 2 years

Teaching activity

"Protein Structure" module for the Bioinformatics Strand within the new MSc IT programme in DCS, University of Glasgow
"Protein structure, folding and prediction", "Microarray data analysis" and "Proteomics" sections of the Biological strand of the MRes in Bionformatics in IBLS, UoG.

Publications

Full papers
Wang, J., Kean, L., Yang, J., Allan, A., K., Davies, S., A., Herzyk, P., and Dow, J., A., T., (2004) Function-informed transcriptome analysis of Drosophila renal tubule, Genome Biology 5:R69. [PubMed]

Breitling, R., Armengaud, P., Amtmann, A., and Herzyk, P. (2004) A simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments, FEBS Lett. 573:83-92. [PubMed]

Breitling, R., Amtmann, A., and Herzyk, P. (2004) Graph-based iterative Group Analysis enhances microarray interpretation, BMC Bioinformatics, 5:100. [PubMed]

Breitling, R., Amtmann, A., and Herzyk, P. (2004) Iterative Group Analysis (iGA): A simple tool to enhance sensitivity and facilitate interpretation of microarray experiments, BMC Bioinformatics, 5:34. [PubMed]

Matthuis, F.J.M., Filatov, V., Herzyk, P., Krijger, G.C., Axelsen, K.B., Chen, S., Green, B.J., Madagan, K.L., Sanchez-Fernandez, R., Forde, B.G., Palmgren, M.G., Williams, L.E., Sanders, D., and Amtmann, A. (2003) Transcriptome analysis of root transporters reveals participation of multiple gene families in the response to cation stress, Plant J. 35:675-92. [PubMed]

Tarabykina, S., Scott, D.J., Herzyk, P., Hill, T.J., Tame, J.R.H., Kriajevska, M., Lafitte, D., Derrick, P.J., Dodson, G.G., Maitland, N.J., Lukanidin, E.M. and Bronstein, I.B. (2001) The dimerisation interface of the metastasis associated protein S100A4(Mts1): In vivo and In vitro studies, J. Biol. Chem. 276: 24212-24222. [PubMed]

Herzyk, P. and Hubbard, R. E. (1998) Combined biophysical and biochemical information confirms arrangement of transmembrane helices visible from the three-dimensional map of frog rhodopsin, J. Mol. Biol. 281:741-754. [PubMed]

Herzyk, P. and Hubbard, R. E. (1998) Using experimental information to produce a model of the transmembrane domain of the ion channel phospholamban, Biophysical J. 74:1203-1214. [PubMed]

Prusis, P., Schioth, H. B. , Muceniece, R., Herzyk, P., Afshar, M., Hubbard, R. E. and Wikberg, J. E. S. (1997) Modelling of the three-dimensional structure of the human melanocortin-1 receptor using automated method and docking of rigid cyclic MSH core peptide, J. Mol. Graph. Model., 15:307-317. [PubMed]

Peitsch, M.C., Herzyk, P., Wells, T.N.C., and Hubbard. R.E. (1996) Automated G-protein-coupled receptor modelling by Swiss-Model, Receptors and Channels, 4:161-164. [PubMed]

Herzyk, P. and Hubbard, R.E. (1995) An automated method for modelling seven-helix transmembrane receptors from experimental data, Biophysical J. 69:2419-2442. [PubMed]

Hartshorn, M.J., Herzyk, P., and Hubbard, R.E. (1995) Exploring molecular structure by virtual reality, Trends in Biotechnology 13:83-85. [PubMed]

Herzyk, P. and Hubbard, R.E. (1993) A reduced representation of proteins for use in restraint satisfaction calculations, Proteins: Structure, Function, and Genetics, 17:310-324. [PubMed]

Cooke, R.M., Carter, B.G., Murray-Rust, P., Hartshorn, M.J., Herzyk, P., and Hubbard, R.E. (1992) The solution structure of echistatin: evidence for disulphide bond rearrangement in homologous snake toxins, Protein Eng., 5:473-477. [PubMed]

Herzyk, P., Neidle, S., and Goodfellow, J.M. (1992) Conformation and dynamics of Drug-DNA intercalation, J. Biomol. Struct. Dyn., 10:97-139. [PubMed]

Herzyk, P., Goodfellow, J.M., and Neidle, S. (1991) Molecular dynamics simulations of dinucleoside and dinucleoside?drug crystal hydrates, J. Biomol. Struct. Dyn., 9:363-386. [PubMed]

Orozco, M., Laughton, C.A., Herzyk, P., and Neidle, S. (1990) Molecular?mechanics modelling of drug?DNA structures; the effects of differing dielectric treatment on helix parameters and comparison with a fully solvated structural model, J. Biomol. Struct. Dyn., 8:359-373. [PubMed]

Herzyk, P. and Rabczenko, A. (1989) Simulation of the interconversion path between stable conformations of the furanose ring: methyl b-D-2-deoxyribofuranoside and simpler ribose and
deoxyribose analogues, J.Chem.Soc.Perkin Trans.2, 209-216.

Neidle, S., Pearl, L.H., Herzyk, P., and Berman, H.M. (1988) A molecular model for proflavine-DNA intercalation, Nucleic Acid Res., 16:8999-9016. [PubMed]

Herzyk, P., Beveridge, A., and Neidle, S. (1987) Conformational properties of 3'-azido-3'deoxy-thymidine (AZT), an inhibitor of HIV reverse transcriptase, Biochem. Biophys. Res. Comm., 145:1356-1361. [PubMed]

Herzyk, P. and Rabczenko, A. (1985) A general geometrical model for pseudorotation simulation in five-membered rings, J.Chem.Soc.Perkin Trans.2, 1925-1930.

Herzyk, P. and Rabczenko, A. (1983) A new description of equilateral five?membered rings during pseudorotation, J.Chem.Soc.Perkin Trans.2, 213-217.

Published abstracts

Herzyk, P and Hubbard, R. E. (1998) Using biophysical experimental information to generate 3-D structural models of transmembrane domains of helical, integral membrane proteins,
Biophys. J., 74 (2), A249.

P. Herzyk, M. Afshar, L. S. D. Caves, and R. E. Hubbard. Combined biophysical and biochemical information can determine the architecture of transmembrane domains of helical, integral
membrane proteins. Journal Of Molecular Graphics & Modelling 16 (4-6):288-288, 1998.

Afshar, M., Caves, L.S.D., Herzyk, P. and Hubbard, R.E. (1998) Low resolution modelling of transmembrane proteins - making the most of available information, Biochem. Soc. Trans., 26,
ii.

Herzyk, P. and Hubbard, R. E. (1997) An atomic model of transmembrane domain of bovine rhodopsin from experimentally derived structural restraints, Biophys. J., 72, (2), A114.

Czaplewski, C., Kazmierkiewicz, R., Ciarkowski, J., Herzyk, P., and Hubbard, R.E. (1997) Molecular modeling of the V2 receptor - bioligand interactions, in "Peptides 1996, Proceedings of
the 24th European Peptide Symposium", Ramage,R. & Epton,R., Eds., in press.

Peitsch, M. C. and Herzyk, P. (1996) Molecular modelling of G-protein coupled receptors, in ?G-protein coupled receptors: new opportunities for commercial development?, IBC Biomedical
Library Series.

Herzyk, P. and Hubbard, R. E. (1996) Modelling of aminergic G-protein coupled receptors from experimental data by rule-based automated procedure, Biophys. J., 70, (2), A182.