A

Alber, F. and Forster, F. and Korkin, D. and Topf, Maya and Sali, A. (2008) Integrating diverse data for structure determination of macromolecular assemblies. Annual Review of Biochemistry 77 , pp. 443-477. ISSN 0066-4154.

B

Bagneris, Claire and Ageichik, A.V. and Cronin, Nora and Wallace, Bonnie A. and Collins, M. and Boshoff, C. and Waksman, Gabriel and Barrett, Tracey E. (2008) Crystal structure of a vFlip-IKK gamma complex: Insights into viral activation of the IKK signalosome. Molecular Cell 30 (5), pp. 620-631. ISSN 1097-2765.

Bagneris, Claire and Ageichik, A.V. and Cronin, Nora and Wallace, Bonnie A. and Collins, M. and Boshoff, C. and Waksman, Gabriel and Barrett, Tracey E. (2008) Crystal structure of a vFlip-IKKγ Complex: insights into viral activation of the IKK Signalosome. Molecular Cell 30 (5), pp. 620-631. ISSN 1097-2765.

Bashton, M. and Nobeli, Irene and Thornton, Janet M. (2008) Procognate: a cognate ligand domain mapping for enzymes. Nucleic Acids Research 36 , D618-D622. ISSN 0305-1048.

Booth, C.R. and Meyer, A.S. and Cong, Y. and Topf, Maya and Sali, A. and Ludtke, Steven J. and Chiu, W. and Frydman, J. (2008) Mechanism of lid closure in the eukaryotic chaperonin TRiC/CCT. Nature Structural and Molecular Biology 15 (7), pp. 746-753. ISSN 1545-9993.

Bulheller, B.M. and Miles, Andrew J. and Wallace, Bonnie A. and Hirst, J.D. (2008) Charge-transfer transitions in the vacuum-ultraviolet of protein circular dichroism spectra. Journal of Physical Chemistry B 112 (6), pp. 1866-1874. ISSN 1520-6106.

C

Chandramouli, P. and Topf, Maya and Menetret, J.F. and Eswar, N. and Cannone, J.J. and Gutell, R.R. and Sali, A. and Akey, C.W. (2008) Structure of the mammalian 80S ribosome at 87 angstrom resolution. Structure 16 (4), pp. 535-548. ISSN 0969-2126.

Clegg, A.B. and Shepherd, Adrian J. (2008) Text Mining. Methods in Molecular Biology 453 (4), pp. 471-491. ISSN 1064-3745.

Cong, Y. and Topf, Maya and Sali, A. and Matsudaira, P. and Dougherty, M. and Chiu, W. and Schmid, M.F. (2008) Crystallographic conformers of Actin in a biologically active bundle of filaments. Journal of Molecular Biology 375 (2), pp. 331-336. ISSN 0022-2836.

Connell, S.R. and Topf, Maya and Qin, Y. and Wilson, D.N. and Mielke, T. and Fucini, P. and Nierhaus, K.H. and Spahn, C.M.T. (2008) A new tRNA intermediate revealed on the ribosome during EF4-mediated back-translocation. Nature Structural & Molecular Biology 15 , pp. 910-915. ISSN 1545-9985.

Cowieson, N.P. and Miles, Andrew J. and Robin, G. and Forwood, J.K. and Kobe, B. and Martin, J.L. and Wallace, Bonnie A. (2008) Evaluating protein : protein complex formation using synchrotron radiation circular dichroism spectroscopy. Proteins-Structure, Function and Bioinformatics 70 (2), pp. 1142-1146. ISSN 0887-3585.

D

Davies, T.G.E. and O’Reilly, Andrias O. and Field, L.M. and Wallace, Bonnie A. and Williamson, M.S. (2008) Knockdown resistance to DDT and pyrethroids: from target-site mutations to molecular modelling. Pest Management Science 64 (11), pp. 1126-1130. ISSN 1526-498X.

de Freitas, Sara and Harrison, I. and Magoulas, George D. and Papamarkos, G. and Poulovassilis, Alexandra and van Labeke, N. and Mee, A. and Oliver, M. (2008) L4All: a web-service based system for lifelong learners. In: Salerno, S. and Gaeta, M. and Ritrovato, P. and Capuano, N. and Orciuoli, F. and Miranda, S. and Pierri, A. (eds.) The Learning Grid Handbook: Concepts, Technologies and Applications: The Future of Learning. Amsterdam, The Netherlands: IOS Press, pp. 143-155. ISBN 9781586038298.

E

Evans, P. and Slingsby, Christine and Wallace, Bonnie A. (2008) Association of partially folded lens beta B2-crystallins with the alpha-crystallin molecular chaperone. Biochemical Journal 409 , pp. 691-699. ISSN 0264-6021.

F

Favia, A.D. and Nobeli, Irene and Glaser, F. and Thornton, Janet M. (2008) Molecular docking for substrate identification: the short-chain dehydrogenases/reductases. Journal of Molecular Biology 375 (3), pp. 855-874. ISSN 0022-2836.

H

Halling-Brown, Mark D. and Moss, David S. and Shepherd, Adrian J. (2008) Towards a lightweight generic computational grid framework for biological research. BMC Bioninformatics 9 , ISSN 1471-2105.

Halling-Brown, Mark D. and Shepherd, Adrian J. (2008) Constructing computational pipelines. Methods in Molecular Biology 453 (4), pp. 451-470. ISSN 1064-3745.

Harvey, R.J. and Topf, Maya and Harvey, K. and Rees, M.I. (2008) The genetics of hyperekplexia: more than startle! Trends in Genetics 24 (9), pp. 439-447. ISSN 0168-9525.

Hurtado, C.A. and Poulovassilis, Alexandra and Wood, Peter T. (2008) Query relaxation in RDF. In: Spaccapietra, Spaccapietra (ed.) Journal on Data Semantics X. Lecture Notes in Computer Science 4900 4900. Berlin, Germany: Springer, pp. 31-61. ISBN 9783540776871.

K

Keenoy, K. and Christophides, V. and Papamarkos, G. and Poulovassilis, Alexandra and Kotzinos, D. and Rigaux, P. and Spyratos, N. and Wood, Peter T. (2008) Personalisation services for self e-learning networks. In: Salerno, S. and Gaeta, M. and Ritrovato, P. and Capuano, N. and Orciuoli, F. and Miranda, S. and Pierri, A. (eds.) The Learning Grid Handbook: Concepts, Technologies and Applications: The Future of Learning. Amsterdam, The Netherlands: IOS Press, pp. 157-172. ISBN 9781586038298.

L

Labeke, N. and Poulovassilis, Alexandra and Magoulas, George D. (2008) Using similarity metrics for matching lifelong learners. In: Woolf, B. and Aimeur, E. and Nkambou, R. and Lajoie, S. (eds.) Intelligent Tutoring Systems. Lecture Notes in Computer Science 5091. Berlin, Germany: Springer Verlag, pp. 142-151. ISBN 9783540691327.

Lampert, A. and O’Reilly, Andrias O. and Dib-Hajj, S.D. and Tyrrell, L. and Wallace, Bonnie A. and Waxman, S.G. (2008) A pore-blocking hydrophobic motif at the cytoplasmic aperture of the closed-state Na(v)17 channel is disrupted by the erythromelalgia-associated F1449V mutation. Journal of Biological Chemistry 283 , pp. 24118-24127. ISSN 0021-9258.

M

Miles, Andrew J. and Drechsler, A. and Kristan, K. and Anderluh, G. and Norton, R.S. and Wallace, Bonnie A. and Separovic, F. (2008) The effects of lipids on the structure of the eukaryotic cytolysin equinatoxin II: a synchrotron radiation circular dichroism spectroscopic study. Biochimica et Biophysica Acta (BBA) - Biomembranes 1778 (10), pp. 2091-2096. ISSN 0006-3002.

Miles, Andrew J. and Hoffmann, S.V. and Tao, Y. and Janes, R.W. and Wallace, Bonnie A. (2008) Synchrotron radiation circular dichroism (SRCD) spectroscopy: new beamlines and new applications in biology. Spectroscopy 21 (5-6), pp. 245-255. ISSN 0712-4813.

Miles, Andrew J. and Janes, R.W. and Brown, A. and Clarke, D.T. and Sutherland, J.C. and Tao, Y. and Wallace, Bonnie A. and Hoffmann, S.V. (2008) Light flux density threshold at which protein denaturation is induced by synchrotron radiation circular dichroism beamlines. Journal of Synchrotron Radiation 15 , pp. 420-422. ISSN 0909-0495.

Miller, P.S. and Topf, Maya and Smart, T.G. (2008) Mapping a molecular link between allosteric inhibition and activation of the glycine receptor. Nature Structural & Molecular Biology 15 , pp. 1084-1093. ISSN 1545-9985.

N

Nurani, G. and Radford, M. and O’Reilly, Andrias O. and Cronin, Nora and Haque, S. and Wallace, Bonnie A. (2008) Tetrameric bacterial sodium channels: characterization of structure, stability, and drug binding. Biochemistry 47 (31), pp. 8114-8121. ISSN 0006-2960.

O

Olsson, T.S.G. and Williams, Mark A. and Pitt, W.R. and Ladbury, J.E. (2008) The thermodynamics of protein–ligand interaction and solvation: insights for ligand design. Journal of Molecular Biology 384 (4), pp. 1002-1017. ISSN 0022-2836.

O’Reilly, Andrias O. and Nurani, G. and Powl, Andrew M. and Charalambous, Kalypso and Wallace, Bonnie A. (2008) G219S mutagenesis as a means of stabilizing conformational flexibility in the bacterial sodium channel NaChBac. Molecular Membrane Biology 25 (8), pp. 670-676. ISSN 0968-7688.

P

Pappalardo, F. and Zhang, P. and Halling-Brown, Mark D. and Basford, K.E. and Scalia, A. and Shepherd, Adrian J. and Moss, David S. and Motta, S. and Brusic, V. (2008) Computational simulations of the immune system for personalized medicine: state of the art and challenges. Current Pharmacogenomics and Personalized Medicine 6 (4), pp. 260-271. ISSN 1875-6921.

Poulovassilis, Alexandra and Kargas, G. and Kerkides, P. (2008) Comments on the paper "Application of the "Proportionate partitioning" method suggested by Poulovassilis and Kargas (2000) for determination of the domain distribution function" by Mualem and Beriozkin (2008). Transport in Porous Media 75 (2), pp. 223-226. ISSN 0169-3913.

Poulovassilis, Alexandra and Zamboulis, Lucas and Wang, J. (2008) Ontology-assisted data transformation and integration. In: 4th International VLDB Workshop on Ontology-based Techniques for DataBases in Information Systems and Knowledge Systems, August 24-30, 2008, Auckland, New Zealand. (Unpublished)

S

Serysheva, I.I. and Baker, M.L. and Cong, Y. and Topf, Maya and Eramian, D. and Sali, A. and Hamilton, S.L. and Chiu, W. (2008) Subnanometer-resolution electron cryomicroscopy-based domain models for the cytoplasmic region of skeletal muscle RyR channel. Proceedings of the National Academy of Sciences of the United States of America 105 (28), pp. 9610-9615. ISSN 0027-8424.

Shepherd, Adrian J. and Clegg, A.B. (2008) Syntactic pattern matching with GraphSpider and MPL. In: Proceedings of the Third Symposium on Semantic Mining in Biomedicine, September 1-3 2008, Turku, Finland.

Shepherd, Adrian J. and Kabiljo, R. (2008) Protein name tagging in the immunological domain. In: Proceedings of the Third Symposium on Semantic Mining in Biomedicine, September 1-3 2008, Turku, Finland.

Siepen, J.A. and Belhajjame, K. and Selley, J.N. and Embury, S.M. and Paton, N.W. and Goble, C.A. and Oliver, S.G. and Stevens, R. and Zamboulis, Lucas and Martin, Nigel and Poulovassilis, Alexandra and Jones, P. and Côté, R. and Hermjakob, H. and Pentony, M.M. and Jones, D.T. and Orengo, C.A. and Hubbard, S.J. (2008) ISPIDER Central: an integrated database web-server for proteomics. Nucleic Acids Research 36 (2), W485-W490. ISSN 0305-1048.

T

Taylor, J.D. and Ababou, A. and Fawaz, R.R. and Hobbs, C.J. and Williams, Mark A. and Ladbury, J.E. (2008) Structure, dynamics, and binding thermodynamics of the v-Src SH2 domain: implications for drug design. Proteins: Structure, Function, and Bioinformatics 73 (4), pp. 929-940. ISSN 0887-3585.

Thornton, Janet M. and Favia, A.D. and Nobeli, Irene and Furnham, N. (2008) The evolution of specificity in large protein families. In: 33rd FEBS Congress & 11th IUBMB Conference: Biochemistry of Cell Regulation, June 28-July 3 2008, Athens, Greece.

Topf, Maya and Lasker, K. and Webb, B. and Wolfson, H.J. and Chiu, W. and Sali, A. (2008) Protein structure fitting and refinement guided by cryo-EM density. Structure 16 (2), pp. 295-307. ISSN 0969-2126.

W

Whitmore, Lee and Wallace, Bonnie A. (2008) Protein secondary structure analyses from circular dichroism spectroscopy: Methods and reference databases. Biopolymers 89 (5), pp. 392-400. ISSN 0006-3525.

Williams, D. and Poulovassilis, Alexandra (2008) Combining data integration and IE techniques to support partially structured data. In: Kapetanios, E. and Sugumaran, V. and Spiliopoulou, M. (eds.) Natural Language and Information Systems. Lecture Notes in Computer Science 5039. Berlin, Germany: Springer Verlag, pp. 175-186. ISBN 9783540698586.

Z

Zamboulis, Lucas and Poulovassilis, Alexandra and Roussos, George (2008) Flexible data integration and ontology-based data access to medical records. In: UNSPECIFIED (ed.) IEEE International Conference on BioInformatics and BioEngineering. Institute of Electrical and Electronics Engineers. ISBN 9781424428441.