e-Protein: Publications

Publication list

Journal Publications

Barker, J.A., and Thornton, J.M. 2003. An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis. Bioinformatics 19: 1644-1649.

Bartlett, G.J., Borkakoti, N., and Thornton, J.M. 2003. Catalysing new reactions during evolution: economy of residues and mechanism. J Mol Biol 331: 829-860.

Bartlett, G.J., Porter, C.T., Borkakoti, N., and Thornton, J.M. 2002. Analysis of catalytic residues in enzyme active sites. J Mol Biol 324: 105-121.

Bartlett, G.J., Todd, A.E., and Thornton, J.M. 2003. Inferring protein function from structure. Methods Biochem Anal 44: 387-407.

Bateman, A., Birney, E., Cerruti, L., Durbin, R., Etwiller, L., Eddy, S.R., Griffiths-Jones, S., Howe, K.L., Marshall, M., and Sonnhammer, E.L. 2002. The Pfam protein families database. Nucleic Acids Res 30: 276-280.

Birney, E., Clamp, M., and Hubbard, T. 2002. Databases and tools for browsing genomes. Annu Rev Genomics Hum Genet 3: 293-310.

Birney, E., and Clamp, M. 2004. Biological database design and implementation. Brief Bioinform 5: 31-38.

Bray, J.E., Marsden, R.L., Rison, S.C., Savchenko, A., Edwards, A.M., Thornton, J.M., and Orengo, C.A. 2004. A practical and robust sequence search strategy for structural genomics target selection. Bioinformatics 20: 2288-2295.

Bryson, K., McGuffin, L.J., Marsden, R.L., Ward, J.J., Sodhi, J.S., and Jones, D.T. 2005. Protein structure prediction servers at University College London. Nucleic Acids Res 33: W36-38.

Buchan, D.W., Rison, S.C., Bray, J.E., Lee, D., Pearl, F., Thornton, J.M., and Orengo, C.A. 2003. Gene3D: structural assignments for the biologist and bioinformaticist alike. Nucleic Acids Res 31: 469-473.

Buchan, D.W., Shepherd, A.J., Lee, D., Pearl, F.M., Rison, S.C., Thornton, J.M., and Orengo, C.A. 2002. Gene3D: structural assignment for whole genes and genomes using the CATH domain structure database. Genome Res 12: 503-514.

de la Cruz, X., Hutchinson, E.G., Shepherd, A., and Thornton, J.M. 2002. Toward predicting protein topology: an approach to identifying beta hairpins. Proc Natl Acad Sci U S A 99: 11157-11162.

de la Cruz, X., Sillitoe, I., and Orengo, C. 2002. Use of structure comparison methods for the refinement of protein structure predictions. I. Identifying the structural family of a protein from low-resolution models. Proteins 46: 72-84.

Espadaler, J., Fernandez-Fuentes, N., Hermoso, A., Querol, E., Aviles, F.X., Sternberg, M.J., and Oliva, B. 2004. ArchDB: automated protein loop classification as a tool for structural genomics. Nucleic Acids Res 32: D185-188.

Eyre, T.A., Partridge, L., and Thornton, J.M. 2004. Computational analysis of alpha-helical membrane protein structure: implications for the prediction of 3D structural models. Protein Eng Des Sel 17: 613-624.

Fernandez-Fuentes, N., Querol, E., Aviles, F.X., Sternberg, M.J., and Oliva, B. 2005. Prediction of the conformation and geometry of loops in globular proteins: testing ArchDB, a structural classification of loops. Proteins 60: 746-757.

Ferrer-Costa, C., Shanahan, H.P., Jones, S., and Thornton, J.M. 2005. HTHquery: a method for detecting DNA-binding proteins with a helix-turn-helix structural motif. Bioinformatics 21: 3679-3680.

Fleming, K., Kelley, L.A., Islam, S.A., MacCallum, R.M., Muller, A., Pazos, F., and Sternberg, M.J.E. 2006. The proteome: structure, function and evolution. Philos Trans R Soc Lond B Biol Sci 361: 441-451.

Fleming, K., Muller, A., MacCallum, R.M., and Sternberg, M.J.E. 2004. 3D-GENOMICS: a database to compare structural and functional annotations of proteins between sequenced genomes. Nucleic Acids Res 32: D245-250.

Freilich, S., Spriggs, R.V., George, R.A., Al-Lazikani, B., Swindells, M., and Thornton, J.M. 2005. The complement of enzymatic sets in different species. J Mol Biol 349: 745-763.

Gaasterland, T., and Orengo, C.A. 2002. Genomic insights into evolution. Curr Opin Struct Biol 12: 345-347.

George, R.A., Spriggs, R.V., Bartlett, G.J., Gutteridge, A., MacArthur, M.W., Porter, C.T., Al-Lazikani, B., Thornton, J.M., and Swindells, M.B. 2005. Effective function annotation through catalytic residue conservation. Proc Natl Acad Sci U S A 102: 12299-12304.

George, R.A., Spriggs, R.V., Thornton, J.M., Al-Lazikani, B., and Swindells, M.B. 2004. SCOPEC: a database of protein catalytic domains. Bioinformatics 20 Suppl 1: I130-I136.

Gerstein, M., and Thornton, J.M. 2003. Sequences and topology. Curr Opin Struct Biol 13: 341-343.

Glaser, F., Morris, R.J., Najmanovich, R.J., Laskowski, R.A., and Thornton, J.M. 2006. A method for localizing ligand binding pockets in protein structures. Proteins 62: 479-488.

Grant, A., Lee, D., and Orengo, C. 2004. Progress towards mapping the universe of protein folds. Genome Biol 5: 107.

Gutteridge, A., Bartlett, G.J., and Thornton, J.M. 2003. Using a neural network and spatial clustering to predict the location of active sites in enzymes. J Mol Biol 330: 719-734.

Gutteridge, A., and Thornton, J.M. 2005. Understanding nature's catalytic toolkit. Trends Biochem Sci 30: 622-629.

Harrison, A., Pearl, F., Mott, R., Thornton, J., and Orengo, C. 2002. Quantifying the similarities within fold space. J Mol Biol 323: 909-926.

Harrison, A., Pearl, F., Sillitoe, I., Slidel, T., Mott, R., Thornton, J., and Orengo, C. 2003. Recognizing the fold of a protein structure. Bioinformatics 19: 1748-1759.

Holliday, G.L., Bartlett, G.J., Almonacid, D.E., O'Boyle, N.M., Murray-Rust, P., Thornton, J.M., and Mitchell, J.B. 2005. MACiE: a database of enzyme reaction mechanisms. Bioinformatics 21: 4315-4316.

Holzerlandt, R., Orengo, C., Kellam, P., and Alba, M.M. 2002. Identification of new herpesvirus gene homologs in the human genome. Genome Res 12: 1739-1748.

Hurwitz, N., Pellegrini-Calace, M., and Jones, D.T. 2006. Towards genome-scale structure prediction for transmembrane proteins. Philos Trans R Soc Lond B Biol Sci 361: 465-475.

Kasprzyk, A., Keefe, D., Smedley, D., London, D., Spooner, W., Melsopp, C., Hammond, M., Rocca-Serra, P., Cox, T., and Birney, E. 2004. EnsMart: a generic system for fast and flexible access to biological data. Genome Res 14: 160-169.

Kersey, P.J., Duarte, J., Williams, A., Karavidopoulou, Y., Birney, E., and Apweiler, R. 2004. The International Protein Index: an integrated database for proteomics experiments. Proteomics 4: 1985-1988.

Jefferys, B.R., Kelley, L.A., Sergot, M.J., Fox, J., and Sternberg, M.J. 2006. Capturing expert knowledge with argumentation: a case study in bioinformatics. Bioinformatics 22: 924-933.

Jones, D.T. 2000. A practical guide to protein structure prediction. Methods Mol Biol 143: 131-154.

Jones, D.T. 2001. Critically assessing the state-of-the-art in protein structure prediction. Pharmacogenomics J 1: 126-134.

Jones, D.T. 2001. Predicting novel protein folds by using FRAGFOLD. Proteins Suppl 5: 127-132.

Jones, D.T. 2003. Structural biology. Learning to speak the language of proteins. Science 302: 1347-1348.

Jones, D.T., Bryson, K., Coleman, A., McGuffin, L.J., Sadowski, M.I., Sodhi, J.S., and Ward, J.J. 2005. Prediction of novel and analogous folds using fragment assembly and fold recognition. Proteins 61 Suppl 7: 143-151.

Jones, D.T., and McGuffin, L.J. 2003. Assembling novel protein folds from super-secondary structural fragments. Proteins 53 Suppl 6: 480-485.

Jones, D.T., Sternberg, M.J., and Thornton, J.M. 2006. Introduction. Bioinformatics: from molecules to systems. Philos Trans R Soc Lond B Biol Sci 361: 389-391.

Jones, D.T., and Swindells, M.B. 2002. Getting the most from PSI-BLAST. Trends Biochem Sci 27: 161-164.

Jones, D.T., and Ward, J.J. 2003. Prediction of disordered regions in proteins from position specific score matrices. Proteins 53 Suppl 6: 573-578.

Jones, S., Barker, J.A., Nobeli, I., and Thornton, J.M. 2003. Using structural motif templates to identify proteins with DNA binding function. Nucleic Acids Res 31: 2811-2823.

Jones, S., Shanahan, H.P., Berman, H.M., and Thornton, J.M. 2003. Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins. Nucleic Acids Res 31: 7189-7198.

Jones, S., and Thornton, J.M. 2004. Searching for functional sites in protein structures. Curr Opin Chem Biol 8: 3-7.

Laskowski, R.A., Chistyakov, V.V., and Thornton, J.M. 2005. PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids. Nucleic Acids Res 33: D266-268.

Laskowski, R.A., Watson, J.D., and Thornton, J.M. 2003. From protein structure to biochemical function? J Struct Funct Genomics 4: 167-177.

Laskowski, R.A., Watson, J.D., and Thornton, J.M. 2005. ProFunc: a server for predicting protein function from 3D structure. Nucleic Acids Res 33: W89-93.

Laskowski, R.A., Watson, J.D., and Thornton, J.M. 2005. Protein function prediction using local 3D templates. J Mol Biol 351: 614-626.

Lee, D., Grant, A., Buchan, D., and Orengo, C. 2003. A structural perspective on genome evolution. Curr Opin Struct Biol 13: 359-369.

Lee, D., Grant, A., Marsden, R.L., and Orengo, C. 2005. Identification and distribution of protein families in 120 completed genomes using Gene3D. Proteins 59: 603-615.

Lee, D.A., Fefeu, S., Edo-Ukeh, A.A., Orengo, C.A., and Slingsby, C. 2004. EyeSite: a semi-automated database of protein families in the eye. Nucleic Acids Res 32: D148-152.

Lise, S., and Jones, D.T. 2005. Sequence patterns associated with disordered regions in proteins. Proteins 58: 144-150.

Luscombe, N.M., and Thornton, J.M. 2002. Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity. J Mol Biol 320: 991-1009.

Macchiarulo, A., Nobeli, I., and Thornton, J.M. 2004. Ligand selectivity and competition between enzymes in silico. Nat Biotechnol 22: 1039-1045.

Marsden, R.L., McGuffin, L.J., and Jones, D.T. 2002. Rapid protein domain assignment from amino acid sequence using predicted secondary structure. Protein Sci 11: 2814-2824.

Martin, A.C., Facchiano, A.M., Cuff, A.L., Hernandez-Boussard, T., Olivier, M., Hainaut, P., and Thornton, J.M. 2002. Integrating mutation data and structural analysis of the TP53 tumor-suppressor protein. Hum Mutat 19: 149-164.

Mayor, L.R., Fleming, K.P., Muller, A., Balding, D.J., and Sternberg, M.J.E. 2004. Clustering of protein domains in the human genome. J Mol Biol 340: 991-1004.

McGuffin, L.J., and Jones, D.T. 2002. Targeting novel folds for structural genomics. Proteins 48: 44-52.

McGuffin, L.J., and Jones, D.T. 2003. Benchmarking secondary structure prediction for fold recognition. Proteins 52: 166-175.

McGuffin, L.J., and Jones, D.T. 2003. Improvement of the GenTHREADER method for genomic fold recognition. Bioinformatics 19: 874-881.

McGuffin, L.J., Street, S., Sorensen, S.A., and Jones, D.T. 2004. The genomic threading database. Bioinformatics 20: 131-132

McGuffin, L.J., Street, S.A., Bryson, K., Sorensen, S.A., and Jones, D.T. 2004. The Genomic Threading Database: a comprehensive resource for structural annotations of the genomes from key organisms. Nucleic Acids Res 32: D196-199.

Morris, R.J., Najmanovich, R.J., Kahraman, A., and Thornton, J.M. 2005. Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons. Bioinformatics 21: 2347-2355.

Muller, A., MacCallum, R.M., and Sternberg, M.J. 2002. Structural characterization of the human proteome. Genome Res 12: 1625-1641.

Murray, K.B., Gorse, D., and Thornton, J.M. 2002. Wavelet transforms for the characterization and detection of repeating motifs. J Mol Biol 316: 341-363.

Murray, K.B., Taylor, W.R., and Thornton, J.M. 2004. Toward the detection and validation of repeats in protein structure. Proteins 57: 365-380.

Nagano, N., Orengo, C.A., and Thornton, J.M. 2002. One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions. J Mol Biol 321: 741-765.

Najmanovich, R.J., Torrance, J.W., and Thornton, J.M. 2005. Prediction of protein function from structure: insights from methods for the detection of local structural similarities. Biotechniques 38: 847, 849, 851.

Nobeli, I., Ponstingl, H., Krissinel, E.B., and Thornton, J.M. 2003. A structure-based anatomy of the E.coli metabolome. J Mol Biol 334: 697-719.

Nobeli, I., Spriggs, R.V., George, R.A., and Thornton, J.M. 2005. A ligand-centric analysis of the diversity and evolution of protein-ligand relationships in E.coli. J Mol Biol 347: 415-436.

Nooren, I.M., and Thornton, J.M. 2003. Diversity of protein-protein interactions. Embo J 22: 3486-3492.

Nooren, I.M., and Thornton, J.M. 2003. Structural characterisation and functional significance of transient protein-protein interactions. J Mol Biol 325: 991-1018.

O'Malley, K.J., Orengo, C.A., Kunik, M.E., Snow, L., and Molinari, V. 2002. Measuring aggression in older adults: a latent variable modeling approach. Aging Ment Health 6: 231-238.

Orengo, C.A., Bray, J.E., Buchan, D.W., Harrison, A., Lee, D., Pearl, F.M., Sillitoe, I., Todd, A.E., and Thornton, J.M. 2002. The CATH protein family database: a resource for structural and functional annotation of genomes. Proteomics 2: 11-21.

Orengo, C.A., Pearl, F.M., and Thornton, J.M. 2003. The CATH domain structure database. Methods Biochem Anal 44: 249-271.

Orengo, C.A., and Thornton, J.M. 2005. Protein families and their evolution-a structural perspective. Annu Rev Biochem 74: 867-900.

Paszkiewicz, K.H., Sternberg, M.J., and Lappe, M. 2006. Prediction of viable circular permutants using a graph theoretic approach. Bioinformatics.

Pazos, F., Ranea, J.A., Juan, D., and Sternberg, M.J.E. 2005. Assessing protein co-evolution in the context of the tree of life assists in the prediction of the interactome. J Mol Biol 352: 1002-1015.

Pazos, F., and Sternberg, M.J.E 2004. Automated prediction of protein function and detection of functional sites from structure. Proc Natl Acad Sci U S A 101: 14754-14759.

Pearl, F., Todd, A., Sillitoe, I., Dibley, M., Redfern, O., Lewis, T., Bennett, C., Marsden, R., Grant, A., Lee, D., et al. 2005. The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis. Nucleic Acids Res 33: D247-251.

Pearl, F.M., Bennett, C.F., Bray, J.E., Harrison, A.P., Martin, N., Shepherd, A., Sillitoe, I., Thornton, J., and Orengo, C.A. 2003. The CATH database: an extended protein family resource for structural and functional genomics. Nucleic Acids Res 31: 452-455.

Pearl, F.M., Lee, D., Bray, J.E., Buchan, D.W., Shepherd, A.J., and Orengo, C.A. 2002. The CATH extended protein-family database: providing structural annotations for genome sequences. Protein Sci 11: 233-244.

Pellegrini-Calace, M., Carotti, A., and Jones, D.T. 2003. Folding in lipid membranes (FILM): a novel method for the prediction of small membrane protein 3D structures. Proteins 50: 537-545.

Pellegrini-Calace, M., and Thornton, J.M. 2005. Detecting DNA-binding helix-turn-helix structural motifs using sequence and structure information. Nucleic Acids Res 33: 2129-2140.

Pettitt, C.S., McGuffin, L.J., and Jones, D.T. 2005. Improving sequence-based fold recognition by using 3D model quality assessment. Bioinformatics 21: 3509-3515.

Ponstingl, H., Kabir, T., Gorse, D., and Thornton, J.M. 2005. Morphological aspects of oligomeric protein structures. Prog Biophys Mol Biol 89: 9-35.

Porter, C.T., Bartlett, G.J., and Thornton, J.M. 2004. The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data. Nucleic Acids Res 32: D129-133.

Ranea, J.A., Buchan, D.W., Thornton, J.M., and Orengo, C.A. 2004. Evolution of protein superfamilies and bacterial genome size. J Mol Biol 336: 871-887.

Ranea, J.A., Grant, A., Thornton, J.M., and Orengo, C.A. 2005. Microeconomic principles explain an optimal genome size in bacteria. Trends Genet 21: 21-25.

Redfern, O., Grant, A., Maibaum, M., and Orengo, C. 2005. Survey of current protein family databases and their application in comparative, structural and functional genomics. J Chromatogr B Analyt Technol Biomed Life Sci 815: 97-107.

Rison, S.C., Teichmann, S.A., and Thornton, J.M. 2002. Homology, pathway distance and chromosomal localization of the small molecule metabolism enzymes in Escherichia coli. J Mol Biol 318: 911-932.

Rison, S.C., and Thornton, J.M. 2002. Pathway evolution, structurally speaking. Curr Opin Struct Biol 12: 374-382.

Robinson, D.M., Jones, D.T., Kishino, H., Goldman, N., and Thorne, J.L. 2003. Protein evolution with dependence among codons due to tertiary structure. Mol Biol Evol 20: 1692-1704.

Salzberg, S., Birney, E., Eddy, S., and White, O. 2003. Unrestricted free access works and must continue. Nature 422: 801.

Sanishvili, R., Yakunin, A.F., Laskowski, R.A., Skarina, T., Evdokimova, E., Doherty-Kirby, A., Lajoie, G.A., Thornton, J.M., Arrowsmith, C.H., Savchenko, A., et al. 2003. Integrating structure, bioinformatics, and enzymology to discover function: BioH, a new carboxylesterase from Escherichia coli. J Biol Chem 278: 26039-26045.

Shanahan, H.P., Garcia, M.A., Jones, S., and Thornton, J.M. 2004. Identifying DNA-binding proteins using structural motifs and the electrostatic potential. Nucleic Acids Res 32: 4732-4741.

Shanahan, H.P., and Thornton, J.M. 2004. An examination of the conservation of surface patch polarity for proteins. Bioinformatics 20: 2197-2204.

Shanahan, H.P., and Thornton, J.M. 2005. Amino acid architecture and the distribution of polar atoms on the surfaces of proteins. Biopolymers 78: 318-328.

Shepherd, A.J., Gorse, D., and Thornton, J.M. 2003. A novel approach to the recognition of protein architecture from sequence using Fourier analysis and neural networks. Proteins 50: 290-302.

Shepherd, A.J., Martin, N.J., Johnson, R.G., Kellam, P., and Orengo, C.A. 2002. PFDB: a generic protein family database integrating the CATH domain structure database with sequence based protein family resources. Bioinformatics 18: 1666-1672.

Sillitoe, I., Dibley, M., Bray, J., Addou, S., and Orengo, C. 2005. Assessing strategies for improved superfamily recognition. Protein Sci 14: 1800-1810.

Slater, G.S., and Birney, E. 2005. Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 6: 31.

Smith, G.R., Sternberg, M.J., and Bates, P.A. 2005. The relationship between the flexibility of proteins and their conformational states on forming protein-protein complexes with an application to protein-protein docking. J Mol Biol 347: 1077-1101.

Sodhi, J.S., Bryson, K., McGuffin, L.J., Ward, J.J., Wernisch, L., and Jones, D.T. 2004. Predicting metal-binding site residues in low-resolution structural models. J Mol Biol 342: 307-320.

Stajich, J.E., Block, D., Boulez, K., Brenner, S.E., Chervitz, S.A., Dagdigian, C., Fuellen, G., Gilbert, J.G., Korf, I., Lapp, H., et al. 2002. The Bioperl toolkit: Perl modules for the life sciences. Genome Res 12: 1611-1618.

Steward, R.E., MacArthur, M.W., Laskowski, R.A., and Thornton, J.M. 2003. Molecular basis of inherited diseases: a structural perspective. Trends Genet 19: 505-513.

Steward, R.E., and Thornton, J.M. 2002. Prediction of strand pairing in antiparallel and parallel beta-sheets using information theory. Proteins 48: 178-191.

Stockwell, G.R., and Thornton, J.M. 2006. Conformational diversity of ligands bound to proteins. J Mol Biol 356: 928-944.

Swift, S., Tucker, A., Vinciotti, V., Martin, N., Orengo, C., Liu, X., and Kellam, P. 2004. Consensus clustering and functional interpretation of gene-expression data. Genome Biol 5: R94.

Thornton, J.M., Aziz, T., Schlugman, D., and Paterson, D.J. 2002. Electrical stimulation of the midbrain increases heart rate and arterial blood pressure in awake humans. J Physiol 539: 615-621.

Todd, A.E., Marsden, R.L., Thornton, J.M., and Orengo, C.A. 2005. Progress of structural genomics initiatives: an analysis of solved target structures. J Mol Biol 348: 1235-1260.

Todd, A.E., Orengo, C.A., and Thornton, J.M. 2002. Plasticity of enzyme active sites. Trends Biochem Sci 27: 419-426.

Todd, A.E., Orengo, C.A., and Thornton, J.M. 2002. Sequence and structural differences between enzyme and nonenzyme homologs. Structure 10: 1435-1451.

Torrance, J.W., Bartlett, G.J., Porter, C.T., and Thornton, J.M. 2005. Using a library of structural templates to recognise catalytic sites and explore their evolution in homologous families. J Mol Biol 347: 565-581.

Ward, J.J., McGuffin, L.J., Bryson, K., Buxton, B.F., and Jones, D.T. 2004. The DISOPRED server for the prediction of protein disorder. Bioinformatics 20: 2138-2139.

Ward, J.J., McGuffin, L.J., Buxton, B.F., and Jones, D.T. 2003. Secondary structure prediction with support vector machines. Bioinformatics 19: 1650-1655.

Ward, J.J., Sodhi, J.S., McGuffin, L.J., Buxton, B.F., and Jones, D.T. 2004. Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J Mol Biol 337: 635-645.

Watson, J.D., Laskowski, R.A., and Thornton, J.M. 2005. Predicting protein function from sequence and structural data. Curr Opin Struct Biol 15: 275-284.

Watson, J.D., Todd, A.E., Bray, J., Laskowski, R.A., Edwards, A., Joachimiak, A., Orengo, C.A., and Thornton, J.M. 2003. Target selection and determination of function in structural genomics. IUBMB Life 55: 249-255.

Publications in Computer Science Conference Proceedings

Cohen J.H., Furmento N, Kong G, Mayer A, Newhouse S, Darlington J, RealityGrid: an integrated approach to middleware through ICENI, In: Cox SJ, editor, UK e-science all-hands meeting, AHM 2004, Nottingham, UK, September 2004, EPSRC, 2004, Pages: 451 - 456, ISBN: 1-9044-2521-6

Cohen J.H., McGough A. S., Darlington J., Furmento N., Kong G. and Mayer A. J. (2005) RealityGrid: an integrated approach to middleware through ICENI. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences Issue:�Volume 363, Number 1833 / August 15, 2005

Darlington J., Cohen, J. H. & Lee W. H. (2006) An Architecture for a Next-Generation Internet based on Web Services and Utility Computing. Accepted for publication in Emerging Technologies for Next-Generation GRID. Manchester, June 2006.

Das S., McGough A. S., Cohen J. H. and Darlington J. (2005) A Lightweight Solution for Protein Annotation. In UK e-Science All Hands Meeting, p. 396--402, Nottingham, UK, Sept 2005

Furmento N, Hau J, Lee W, Newhouse S, Darlington J, Implementations of a service-oriented architecture on top of Jini, JXTA and OGSI, In: Dikaiakos MD, editor, Grid computing: second European AcrossGrids conference, AxGrids 2004, Nicosia, Cyprus, 28 - 30 January 2004, 2004, Pages: 90 - 99, ISBN: 3-5402-2888-8

Furmento N, Lee W, Mayer A, Newhouse S, Darlington J. ICENI: an open grid service architecture implemented with Jini, Supercomputing '02: proceedings of the 2002 ACM/IEEE conference on supercomputing, Baltimore, Maryland, IEEE Computer Society Press, 2002, Pages: 1 - 10

Furmento N, Mayer A, McGough S, Newhouse S, Field T, Darlington J, ICENI: optimisation of component applications within a Grid environment, Parallel Computing, 2002, Vol: 28, Pages: 1753 - 1772, ISSN: 0167-8191

Gulamali M.Y., McGough AS, Marsh RJ, Edwards NR, Lenton TM, Valdes PJ, Cox SJ, Newhouse SJ, Darlington J, Performance guided scheduling in GENIE through ICENI, In: Cox SJ, editor, UK e-science all-hands meeting, AHM 2004, Nottingham, UK, September 2004, EPSRC, 2004, Pages: 792 - 799, ISBN: 1-9044-2521-6

Lee W.H., McGough A. S. and Darlington J. (2005). Performance Evaluation of the GridSAM Job Submission and Monitoring System. In UK e-Science All Hands Meeting, Nottingham, UK, Sept 2005

Lee W, McGough S, Newhouse S, Darlington J. A standard based approach to job submission through web services, In: Cox SJ, editor, UK e-science all-hands meeting, AHM 2004, Nottingham, UK, September 2004, EPSRC, 2004, Pages: 901 - 905, ISBN: 1-9044-2521-6

Mayer A, McGough S, Gulamali M, Young L, Stanton J, Newhouse S, Darlington J, Meaning and behaviour in Grid oriented components, In: Parashar M, editor, 3rd international workshop on grid computing, Baltimore, Maryland, 2002, Berlin, Springer-Verlag, 2002, Pages: 100 - 111, ISBN: 3-5400-0133-6

McGough A. S., Afzal A., Darlington J., Furmento N., Mayer A. H. and Young L. (2005) Making the Grid Predictable through Reservations and Performance Modelling. The Computer Journal, 48(3):358--368, 2005

McGough S, Young L, Afzal A, Newhouse S, Darlington J, Workflow enactment in ICENI, In: Cox SJ, editor, UK e-science all-hands meeting, AHM 2004, Nottingham, UK, September 2004, EPSRC, 2004, Pages: 894 - 900, ISBN: 1-9044-2521-6

McGough S, Young L, Afzal A, Newhouse S, Darlington J, Performance architecture within ICENI, In: Cox SJ, editor, UK e-science all-hands meeting, AHM 2004, Nottingham, UK, September 2004, EPSRC, 2004, Pages: 906 - 911, ISBN: 1-9044-2521-6

O'Brien A, Newhouse S, Darlington J, Mapping of scientific workflow within the e-Protein project to distributed resources, In: Cox SJ, editor, UK e-science all-hands meeting, AHM 2004, Nottingham, UK, September 2004, EPSRC, 2004, Pages: 404 - 409, ISBN: 1-9044-2521-6

Saleem A, Krznaric M, Cohen J, Newhouse S, Darlington J, Using the VOM portal to manage policy within globus toolkit, community authorisation service & ICENI resources, In: Cox SJ, editor, UK e-science all-hands meeting, AHM 2004, Nottingham, UK, September 2004, EPSRC, 2004, Pages: 418 - 423, ISBN: 1-9044-2521-6

Stanton J, Newhouse S, Darlington J, Implementing a scientific visualisation capability within a grid enabled component framework, In: Monien B, Feldmann R, editor, 8th international Euro-Par conference on parallel processing, Paderborn, Germany, 2002, Berlin, Springer-Verlag, 2002, Pages: 885 - 888, ISBN: 3-5404-4049-6