• Publications

edikt2 Publications

SBIRC BrainImageAnalysisActivity

Refereed Journal Articles

• P.A. Armitage, A.J. Farrall, T.K. Carpenter, F. Doubal, J.M. Wardlaw. Use of dynamic contrast enhanced MRI to measure subtle blood-brain barrier abnormalities. Magnetic Resonance Imaging 2011;29(3): 305 - 314..

• B. Karaszewski, R.G.R. Thomas, F.M. Chappell, P.A. Armitage, T.K. Carpenter, G.K.S. Lymer, M.S. Dennis, I. Marshall, J.M. Wardlaw. Brain choline concentration: early quantitative marker of ischemia and infarct expansion? Neurology 2010;75(10):850 - 856.

• P.A. Armitage, C. Schwindack, M.E. Bastin, I.R. Whittle. Pre-treatment tumoural perfusion correlates with response to dexamethasone in patients with glioblastom multiforme. Journal of Neurology, Neurosurgery, and Psychiatry 81(4), 446-448 (2010).

• V. Cvoro, I. Marshall, P.A. Armitage, M. Bastin, T. Carpenter, C. Rivers, M. Dennis, J. Wardlaw. MR diffusion and perfusion parameters: relationship to metabolites in acute ischaemic stroke. Journal of Neurology, Neurosurgery, and Psychiatry 81(2), 185-191 (2010).

• I. Kane, P.J. Hand, C. Rivers, P. Armitage, M.E. Bastin, R. Lindley, M. Dennis, J. Wardlaw. A practical assessment of magnetic resonance diffusion-perfusion mismatch in acute stroke: observer variation and outcome. J. Neurol 256(11), 1832-1838 (2009).

• B. Karaszewski, J.M. Wardlaw, I. Marshall, V. Cvoro, K. Wartolowska, K. Haga, P.A. Armitage, M.E. Bastin, M.S. Dennis. Early brain temperature elevation and anaerobic metabolism in human acute ischaemic stroke. Brain 132, 955-964 (2009).

• J.M. Wardlaw, F. Doubal, P. Armitage, F. Chappell, T. Carpenter, S. Munoz Maniega, A. Farrall, C. Sudlow, M. Dennis, B. Dhillon. Lacunar stroke is associated with diffuse blood-brain barrier dysfunction. Ann Neurol 2009;65(2):194-202.

• J.M. Starr, A.J. Farrall, P. Armitage, B. McGurn, J. Wardlaw. Blood-brain barrier permeability in Alzheimer’s disease: a case-control MRI study. Psychiatry Research 171(3), 232-241 (2009).

• V. Cvoro, J.M. Wardlaw, I. Marshall, P.A. Armitage, C.S. Rivers, M.E. Bastin, T.K. Carpenter, K. Wartolowska, A. J. Farrall, M.S. Dennis. Associations between diffusion and perfusion parameters, N-acetyl aspartate and lactate in acute ischemic stroke. Stroke 40(3), 767-772 (2009).

• C. Farrell, F. Chappell, P.A. Armitage, P. Keston, A. MacLullich, S. Shenkin, J.M. Wardlaw. Development and initial testing of normal reference MR images for the brain at ages 65-70 and 75-80 years. European Radiology 19(1), 177-183 (2009).

• S. Muñoz Maniega, V. Cvoro, F.M. Chappell, P.A. Armitage, I. Marshall, M.E. Bastin, J.M. Wardlaw. Changes in NAA and lactate following ischemic stroke: A serial MR spectroscopic imaging study. Neurology 71(24), 1993-1999 (2008).

• S. Muñoz Maniega, V. Cvoro, P.A. Armitage, I. Marshall, M.E. Bastin, J.M. Wardlaw. Choline and creatine are not reliable denominators for calculating metabolite ratios in acute ischaemic stroke. Stroke 39(9), 2467-2469 (2008).

• J.M. Wardlaw, A. Farrall, P.A. Armitage, F. Doubal, D. Chowdhury, V. Cvoro, T. Carpenter, M.S. Dennis. Changes in background blood-brain barrier integrity between lacunar and cortical ischemic stroke subtypes. Stroke 39(4), 1327- 1332 (2008).

• S. Muñoz Maniega, M.E. Bastin, P.A. Armitage. Effects of random subject rotation on optimised diffusion gradient sampling schemes in diffusion tensor MRI. Magnetic Resonance Imaging 26(4), 451-460 (2008).

• I. Kane, T. Carpenter, F. Chappell, C. Rivers, P. Armitage, P. Sandercock, J. Wardlaw. Comparison of 10 different magnetic resonance perfusion imaging processing methods in acute ischemic stroke: effect on lesion size, proportion of patients with diffusion/perfusion mismatch, clinical scores, and radiologic outcomes. Stroke 38(12), 3158-3164 (2007).

• C.S. Rivers, J.M. Wardlaw, P.A. Armitage, M.E. Bastin, P.J. Hand. Acute ischaemic stroke lesion measurement on diffusion-weighted imaging – important considerations in designing acute stroke trials with MR imaging. Journal of Stroke and Cerebrovascular Diseases 16(2), 64-70 (2007).

International conference presentations/papers

• B. Karaszewski, R. Thomas, I. Marshall, P.A. Armitage, T. Carpenter, K. Lymer, W. Whiteley, M. Dennis, J.M. Wardlaw. The association between brain temperature, body temperature and tissue salvage in early human ischaemic stroke. In: Proceedings of the nineteenth European Stroke Conference, (2010).

• B. Karaszewski, R. Thomas, I. Marshall, P.A. Armitage, T. Carpenter, K. Lymer, W. Whiteley, M. Dennis, J.M. Wardlaw. The association between uncoupling protein 2 (UCP2) promoter region -866G/A polymorphism, rise in “penumbral” brain temperature and functional outcome in acute ischaemic stroke. In: Proceedings of the nineteenth European Stroke Conference, (2010).

• R. Thomas, B. Karaszewski, P.A. Armitage, T. Carpenter, K. Lymer, J.M. Wardlaw. Apparent diffusion coefficient thresholds do not identify accurately diffusion lesion volume in acute stroke patients. In: Proceedings of the nineteenth European Stroke Conference, (2010).

• R. Thomas, B. Karaszewski, P.A. Armitage, T. Carpenter, K. Lymer, I. Marshall, W. Whiteley, M.S. Dennis, J.M. Wardlaw. Brain and body temperature in acute ischaemic stroke. A magnetic resonance spectroscopy study. In: Proceedings of the nineteenth European Stroke Conference, (2010).

• S. Muñoz Maniega, J.D. Bridson, J. Ang, P.A. Armitage, C. Murray, A.J. Gow, M.E. Bastin, I.J. Deary, J.M. Wardlaw. Quantitative comparison of automatic and manual tract segmentation methods. In : Book of abstracts: Eighteenth Annual Meeting of the International Society for Magnetic Resonance in Medicine, Berkeley, CA: ISMRM, (2010).

• M.E. Bastin, M. Valdés Hernandez, S. Muñoz Maniega, C. Murray, A.J. Gow, P.A. Armitage, J.M. Wardlaw, I.J. Deary. Magnetization Transfer and Spin-Lattice Relaxation Time Measurements of White Matter Lesions in Normal Aging. In : Book of abstracts: Eighteenth Annual Meeting of the International Society for Magnetic Resonance in Medicine, Berkeley, CA: ISMRM, (2010).

• R.G.R. Thomas, B. Karaszewski, F. Chappell, P.A. Armitage, T.K. Carpenter, I. Marshall, K. Lymer, M. Dennis, J.M. Wardlaw. Is there an association between brain temperature, body temperature and outcome in acute ischaemic stroke? A magnetic resonance spectroscopy study. UK Stroke Forum, (2009).

• M. C. Valdes Hernandez, P.A. Armitage, J.M. Wardlaw. Automatic assessment of iron deposits in MR brain images. Medical Image Understanding and Analysis (2009).

• B. Karaszewski, R. Thomas, I. Marshall, P.A. Armitage, T. Carpenter, K. Lymer, M. Dennis, J.M. Wardlaw. MR Spectroscopy choline and lactate brain concentration measurements for early determination of prognosis and direction of infarct expansion in acute stroke patients. In: Proceedings of the eighteenth European Stroke Conference, (2009).

• P.A. Armitage, S. Muñoz Maniega, M.E. Bastin. A global approach to diffusion tensor neighbourhood tractography. In : Book of abstracts: Seventeenth Annual Meeting of the International Society for Magnetic Resonance in Medicine, Berkeley, CA: ISMRM, (2009).

• P.A. Armitage, C. Schwindack, M.E. Bastin, I.R. Whittle. MR measurements of pre-treatment tumour perfusion appear to correlate with response to dexamethasone in patients with glioblastoma multiforme. In : Book of abstracts: Sixteenth Annual Meeting of the International Society for Magnetic Resonance in Medicine, Berkeley, CA: ISMRM, 2198 (2008).

• P. Armitage, N. Woodhouse, D. Kiely, P. Griffiths, J.M. Wild. Comparison of two gadolinium contrast agents for lung perfusion MRI in patients with pulmonary hypertension. In : Book of abstracts: Sixteenth Annual Meeting of the International Society for Magnetic Resonance in Medicine, Berkeley, CA: ISMRM, 2635 (2008).

Books, newsletters, circulars, etc

National Media Coverage (online links)

• http://news.bbc.co.uk/1/hi/scotland/edinburgh_and_east/7940040.stm

• http://www.menshealth.co.uk/Down-time/News-13th-March-2009/v3

• http://www.channel4.com/news/articles/society/health/leaky+vessels+theory+over+strokes/3027662

• http://www.dailymail.co.uk/health/article-1161503/Leaky-blood-vessels-brain-trigger-fifth-strokes.html

• http://news.scotsman.com/health/Blood-leak-clue-to-strokes.5068852.jp

• http://www.nursingtimes.net/news/breakingnews/2009/03/leaky_blood_vessels_in_brain_cause_strokes.html

• http://www.boehringer-ingelheim.co.uk/news/news_archive-Weak-blood-vessels-linked-to-stroke.html.html

• http://living.aol.co.uk/health/health-fitness-news/leaky-vessels-theory-over-strokes/article/20090312100334932538505?rsp=Living%20Health%20News%5D

Cell Biology

Refereed Journal Articles

• Mark G. Beckett, Christopher R. Allton, Christine T.H. Davies, Ilan Davis, Jonathan M. Flynn, Eilidh J. Grant, Russell Hamilton, Alan C. Irving, Richard D. Kenway, Radoslaw H. Ostrowski, James T. Perry, Jason R. Swedlow, Arthur S. Trew. 2009. Building a scientific data grid with DiGS, Phil. Trans. R. Soc. A p367.

• Vendra, G.; Hamilton, R.S. & Davis, I. Dynactin suppresses the retrograde movement of apically localized mRNA in Drosophila blastoderm embryos. RNA 2007 Nov;13(11):1860-7. Epub 2007 Sep 27.

• Hillenmeyer ME, Fung E, Wildenhain J, Pierce SE, Hoon S, Lee W, Proctor M, St. Onge B, Tyers M, Koller D, Altman RB, Davis RW, Nislow C and Giaever G. Large-scale chemical genomic profiling reveals gene and drug relationships in yeast. Science, 320 362-365 (2008).

• Ericson E, Gebbia M, Heisler LE, Wildenhain J, Tyers M, Giaever G and Nislow C. Off-target effects of psychoactive drugs revealed by genome-wide assays in yeast. PLoS Genetics 4(8): e1000151. doi:10.1371/journal.pgen.1000151 (2008)

• Kolas NK, Chapman JR, Nakada S, Ylanko J, Chahwan R, Sweeney FD, Panier S, Mendez M, Wildenhain J, Thomson TM, Pelletier L, Jackson SP, Durocher D. Orchestration of the DNA-damage response by the RNF8 ubiquitin ligase. Science 318,1637-1640. (2007)

• Stewart GS, Panier S, Townsend K, Al-Hakim AK, Kolas NK, Miller ES, Nakada S, Ylanko J, Olivarius S, Mendez M, Oldreive C, Wildenhain J, Tagliaferro A, Pelletier L, Taubenheim N, Durandy A, Byrd PJ, Stankovic T, Taylor AM, Durocher D. The RIDDLE syndrome protein mediates a ubiquitin-dependent signalling cascade at sites of DNA damage. Cell 2009 Feb 6;136(3):420-34. (2009)

• Burns AR, Wallace IM, Wildenhain J, Tyers M, Giaever G, Bader GD, Nislow C, Cutler SR, Roy PJ. A predictive model for drug bioaccumulation and bioactivity in Caenorhabditis elegans. Nature Chemical Biology Jul;6(7):549-57. Epub 2010 May 30 (2010)

• Lara O’Donnell, Stephanie Panier, Jan Wildenhain, Johnny M. Tkach, Abdallah Al-Hakim, Marella Canny, Rachel K. Szilard, Jordan T.F. Young, Nadine K. Kolas, JarkkoYlanko, Meagan Munro, Megan Mendez, Michael Mullin, Bianca Habermann, Alessandro Datti, Anne-Claude Gingras, Michael D. Tyers, Grant W. Brown and Daniel Durocher. The MMS22L-TONSL complex mediates recovery from replication stress and homologous recombination. Molecular Cell doi:10.1016/j.molcel.2010.10.024 (volume 40 issue 4 pp.619 - 631) (2010)

• Hironori Ishizaki, Michaela Spitzer, Jan Wildenhain, Corina Anastasaki, Zhiqiang Zeng, Sonam Dolma, Michael Shaw, Erik Madsen, Jonathan Gitlin, Richard Marais, Mike Tyers, and E. Elizabeth Patton. Combined zebrafish-yeast chemical-genetic screens reveal gene–copper-nutrition interactions that modulate melanocyte pigmentation. Dis. Model. Mech. 2010, doi:10.1242/dmm.005769 (2010)

• Orlicky S, Tang X, Neduva V, Elowe N, Brown ED, Sicheri F, Tyers M. An allosteric inhibitor of substrate recognition by the SCF(Cdc4) ubiquitin ligase Nature Biotechnology Jul;28(7):733-7. Epub 2010 Jun 27 (2010)

• Breitkreutz A, Choi H, Sharom JR, Boucher L, Neduva V, Larsen B, Lin ZY, Breitkreutz BJ, Stark C, Liu G, Ahn J, Dewar-Darch D, Reguly T, Tang X, Almeida R, Qin ZS, Pawson T, Gingras AC, Nesvizhskii AI,Tyers M. A global protein kinase and phosphatase interaction network in yeast Science 21 May 2010: Vol. 328 no. 5981 pp. 1043-1046 DOI: 10.1126/science.1176495

• Winter AG, Wildenhain J, Tyers M. BioGRID REST Service, BiogridPlugin2 and BioGRID WebGraph: new tools for access to interaction data at BioGRID. Bioinformatics 2011 first published online February 7, 2011 doi:10.1093/bioinformatics/btr062.

• Linda Ejim, Maya A. Farha, Shannon B. Falconer, Jan Wildenhain, Brian,K. Coombes, Mike Tyers, Eric D. Brown, and Gerard D. Wright. Combinations of antibiotics and non-antibiotic drugs overcome resistance and enhance efficacy. Nature Chemical Biology 7, 348–350 (2011) doi:10.1038/nchembio.559

• Stark C, Breitkreutz BJ, Chatr-Aryamontri A, Boucher L, Oughtred R, Livstone MS, Nixon J, Van Auken K, Wang X, Shi X, Reguly T, Rust JM, Winter A, Dolinski K, Tyers M. The BioGRID Interaction Database: 2011 update. Nucleic Acids Res. 2011 January; 39(Database issue): D698–D704.

• Orlicky S, Tang X, Neduva V, Elowe N, Brown ED, Sicheri F, Tyers M. An allosteric inhibitor of substrate recognition by the SCF(Cdc4) ubiquitin ligase. Nature Biotechnology. 2010 Jul;28(7):733-7. Epub 2010 Jun 27.

International conference presentations/papers

• M. G. Beckett, Building a scientific data grid with DIGs, UK e-Science All Hands Meeting 2008, 8th-11th September 2008, Edinburgh, UK.

• M. G. Beckett, DiGS: Image Data Sharing for Distributed Collaborations, Mini-symposium on Overcoming Challenges of Managing and Curating Image Datasets, 14th November 2008, University of Oxford, UK.

• M. Tyers, Computational deconvolution of signaling networks, Gordon Research Conference on Cancer Models and Mechanisms 2008 (Keynote),Bryant University RI

• M. Tyers, Interrogation of the Mode of Action of Small Molecule Synergies in Yeast British Yeast Group Meeting, Oxford UK 2010

• M. Tyers, Genome-wide fitness profiles reveal a requirement for autophagy during yeast fermentation, Yeast Genetics & Molecular Biology Meeting, Vancouver 2010.

Books, newsletters, circulars, etc

• G. Beckett, R. Hamilton, DiGs, a Data Grid for Cell Biology, edikt2 Technical Report, available from http://www.edikt.org.uk/edikt2/DataGridForCellBiology, February 2007.

• G. Beckett, Taming the Terabytes, distributed data management for HPC, EPCC News Issue 61, p.9 (2007) .

• Jan Wildenhain, RNAi and HTS microscopy - a guide to discovery and manoeuvre around potential pitfalls,CSBE November 2009

School of Chemistry - ComputationalChemistryActivity

Refereed Journal Articles

• L.M.S. Shepherd and C. A. Morrison. Simulating proton transport through a simplified model of a trans-membrane protein. J. Phys. Chem. B. 2010, 114, 7047.

• C. A. Morrison and A. M. Reilly. Investigating anharmonicity using molecular dynamics calculations: the TM hydride series (PH3)3MH4, (M = Os, Ru and Fe). Dalton Trans. 2010, 39, 5527.

• D. S. Middlemiss, D. Portinari, C. P. Grey, C. A. Morrison and C. C. Wilson. Spin crossover in the CsFeII[CrIII(CN)6] Prussian blue analogue: Phonons and thermodynamics from hybrid functionals. Phys. Rev. B. 2010, 81, 1884410.

• A. M. Reilly, S. Habershon, C. A. Morrison and D. W. H. Rankin, Simulating thermal motion in crystalline phase-I ammonia. J. Chem. Phys. 2010, 132, 134511.

• Keri L. McCall, James R. Jennings, Hongxia Wang, Ana Morandeira, Laurence M. Peter, James R. Durrant, Lesley J. Yellowlees, Neil Robertson. Binuclear Ru-Cu Complexes: Electronic Characterisation and Application to Dye-sensitized Solar Cells, Eur, J. Inorg. Chem., in press

• Keri L. McCall, Ana Morandeira, James Durrant Lesley J. Yellowlees, Neil Robertson. Characterisation of a Ruthenium Bipyridyl Dye Showing a Long-lived Charge-separated State on TiO2 in the Presence of I-/I3-. Dalton Trans, 2010, 39, 4138

• Simon Dalgleish, Neil Robertson. Electropolymerisable Dithiolene Complexes, Coord. Chem. Rev., 2010, 254, 1549

• Nuha Wazzan, Patricia R. Richardson, A. C. Jones. Cis-Trans Isomerisation of Azobenzenes Studied by Laser-Coupled NMR Spectroscopy and DFT Calculations. Photochem. Photobiol. Sci. 2010 (9) 7, 968-974.

• Russell D. L. Johnstone, Maria Ieva, Alistair R. Lennie, Hamish McNab, Elna Pidcock, John E. Warren and Simon Parsons. Pressure as a tool in crystal engineering: inducing a phase transition in a high-Z structure CrystEngComm, 2010, DOI: 10.1039/b917290d

• M. H Palmer and I. C Walker,The electronic states of buta-1,3-diene studied by ab initio configuration interaction and DFT methods, and electron energy loss spectroscopy, Chem. Phys. CEMPH 7913 , DOI: 10.1016/j.chemphys.2010.04.016

• Nicholas P. Funnell, Alice Dawson, Duncan Francis, Alistair R. Lennie, William G. Marshall, Stephen A. Moggach, John E. Warren, Simon Parsons. The effect of pressure on the crystal structure of L-alanine CrystEngComm, 2010, (Advance Article) DOI: 10.1039/c001296c

• Johnstone, Russell D. L.; Lennie, Alistair R.; Parker, Stewart F.; Parsons, Simon; Pidcock, Elna; Richardson, Patricia R.; Warren, John E.; Wood, Peter A. High-pressure polymorphism in salicylamide. CrystEngComm (2010), 12(4), 1065-1078.

• Johnstone, Russell D. L.; Lennie, Alistair R.; Parsons, Simon; Pidcock, Elna; Warren, John E. Comparison of the effects of pressure on three layered hydrates: a partially successful attempt to predict a high-pressure phase transition. Acta Crystallographica, Section B: Structural Science (2009), B65(6), 731-748.

• Crawford, Stephen; Kirchner, Michael T.; Blaeser, Dieter; Boese, Roland; David, William I. F.; Dawson, Alice; Gehrke, Annette; Ibberson, Richard M.; Marshall, William G.; Parsons, Simon; Yamamuro, Osamu. Isotopic polymorphism in pyridine. Angewandte Chemie, International Edition (2009), 48(4), 755-757.

• D. M. S. Martins, C. K. Spanswick, D. S. Middlemiss, N. Abbas, C. R. Pulham and C. A. Morrison,A new polymorph of N,N'–dimethylurea characterized by X–ray diffraction and first principles lattice dynamics calculations. J. Phys. Chem. A, 2009, 113, 5998.

• Charlotte L. Linfoot, Patricia Richardson Tracy E. Hewat, Omar Moudam, Michael M. Forde, Anna Collins, Fraser White and Neil Robertson. Substituted [Cu(I)(POP)(bipridyl)] and related complexes: Synthesis, structure, properties and applications to dye-sensitised solar-cells. Dalton Trans. Accepted for publication 2010.

• R. Noble-Eddy, S. L. Masters (née Hinchley), D. W. H. Rankin, H. E. Robertson and J.-C. Guillemin,Molecular structures of vinylarsine, vinyldichloroarsine and arsine studied by gas-phase electron diffraction and quantum chemical calculations. J. Mol. Struct. 2009.

• A. M. Reilly, S. Habershon, C. A. Morrison and D. W. H. Rankin, Determination of the experimental equilibrium structure of solid nitromethane using path-integral molecular dynamics simulations. J. Chem. Phys., 2010, 132, 094502.

• A. M. Reilly, S. Habershon, C. A. Morrison and D. W. H. Rankin,Simulating thermal motion in crystalline Phase-I ammonia. J. Chem. Phys., 2010, 132, 134511.

• S. I. Wharton, J. B. Henry, H. McNab and A. R. Mount, The production and characterisation of novel conducting luminescent oligomeric thin films from electrooxidised indolo[3,2,1-jk]carbazole. Chem. Eur. J., 2009, 15, 5482-5490

• L. Hill, S. H. Imam, H. McNab and W. J. O’Neill, Regioselective synthesis of quinolin-4-ones by pyrolysis of anilinomethylene derivatives of Meldrum’s acid. Synlett, 2009, 1847-1851.

• L. Hill, G. A. Hunter, S. H. Imam, H. McNab and W. J. O’Neill, Gas-phase synthesis of N-unsubstituted 3-hydroxypyrroles and 1H-pyrrol-3-(2H)-ones. Synthesis, 2009, 2531-2534.

• K. A. Johnston and H. McNab, Synthesis and properties of 5,6-dihydrodipyrrolo[1,2-d;1?,2?-g][1,4]diazepin-11-one. New. J. Chem., 2009, 33, 1703-1708.

• A. P. Gaywood, L. Hill, S. H. Imam, H. McNab, G. Neumajer, W. J. O’Neill and Péter Mátyus, Generation and cyclisation reactions of some pyridazinylimidoylketenes and related intermediates. New J. Chem., 2010, 34, 236-242.

• L. A. Crawford, M. Ieva, H. McNab and S. Parsons, Structural studies of some push-pull N-arylbenzazoles. Dalton Trans., in press (DOI:10.1039/C0DT00029A.)

• Guoxiong Hua, John B. Henry, Yang Li, Andrew R. Mount, Alexandra M. Z. Slawin, J. Derek Woollins,Synthesis of novel 2,5-diarylselenophenes from selenation of 1,4-diarylbutane-1,4-diones or methanol/arylacetylenes. Org. Biomol. Chem. 2010, 8, 1655-1660.

• M. Bühl, G. Schreckenbach, N. Sieffert, G. Wipff,Effect of Counterions on the Structure and Stability of Aqueous Uranyl(VI) Complexes. A First-Principles Molecular Dynamics Study. Inorg. Chem., in press (DOI: 10.1021/ic901298q).

• D. M. S. Martins, D. S. Middlemiss, C. R. Pulham, C. C. Wilson, M. T. Weller, P. F. Henry, N. Shankland, K. Shankland, W. G. Marshall, R. M. Ibberson, S. Moggach, M. Brunelli and C. A. Morrison, Temperature and Pressure-induced Proton Transfer in the 1:1 Adduct formed between Squaric Acid and 4,4'-Bipyridine. J. Am. Chem. Soc., 2009, 131, 3884

• D. M. S. Martins, C. K. Spanswick, D. S. Middlemiss, N. Abbas, C. R. Pulham and C. A. Morrison, A new polymorph of N,N'-dimethylurea characterized by X-ray diffraction and first principles lattice dynamics calculations. J. Phys. Chem. A, 2009, 113, 5998.

• A. Bill, Z. Latajka and C. A. Morrison,C70 oxides and ozonides and the mechanism of ozonolysis on the fullerene surface. A theoretical study, J. Phys. Chem. A, in press.

• K. L. McCall, J. R. Jennings, H. Wang, A. Morandeira, L. M. Peter, J. R. Durrant, L. J. Yellowlees, J. D. Woollins, N. Robertson, Novel Ruthenium Bipyridyl Dyes with S-donor Ligands and their Application in Dye Sensitised Solar Cells, J. Photochem, Photobiol. A, 2009, 202, 196-204

• Simon Dalgleish, Carole A. Morrison, Derek S. Middlemiss, Andrew R. Mount, Anna Collins, Luca Pilia, Angela Serpe, M. Laura Mercuri, Susan J. Roberts-Bleming, Adam Charlton, Paola Deplano, Patrick J. Murphy, Neil Robertson,Structure and Spectroscopic Properties of a New Class of Polymerisable Nickel Dithiolenes, Synthesis, J. Mater. Chem., 2009, 19, 6194

• Simon Dalgleish, Neil Robertson,A Stable Near IR Switchable Electrochromic Polymer Based on an Indole-Substituted Nickel Dithiolene, Chem. Commun., 2009, 5826

• Lucy P. Moorcraft , Lorna A. Jack, James R. Jennings, Laurence M. Peter, Lesley J. Yellowlees, Neil Robertson, Synthesis and Properties of [Pt(4-CO2CH3-py)2(dmit)] and [Pt(4-NO2-py)2(mnt)]: Exploring Tunable Pt Dyes, Polyhedron, 2009, in press

• M. H. Palmer, The electronic states of 1,2,5-oxadiazole studied by VUV spectroscopy and CI, CCSD(T) and DFT methods, Chem. Phys. 2009, 150-161.

• P. L. Arnold, S. Zlatogorsky, N. A. Jones, C. D. Carmichael, S. T. Liddle, A. J. Blake and C. Wilson,Comparisons between yttrium and titanium N-heterocyclic carbene complexes in the search for early transition metal NHC backbonding interactions Inorg. Chem., 2008, 47, 9042-9049.

• D. A. Wann, A. M. Reilly, F. Rataboul, P. D. Lickiss and D. W. H. Rankin, Z. The gas-phase structure of the hexasilsesquioxane Si6O9(OSiMe3)6. Naturforsch. B, 2009, 64, 1269-1275.

• D. A. Wann, A. V. Zakharov, A. M. Reilly, P. D. McCaffrey and D. W. H. Rankin,Experimental equilibrium structures: application of molecular dynamics simulations to vibrational corrections for gas electron diffraction. J. Phys. Chem. A, 2009, 113, 9511-9520.

• John B. Henry and Andrew R. Mount, Calculation of the Redox Properties of Aromatics and Prediction of Their Coupling Mechanism and Oligomer Redox Properties. J. Phys. Chem. A, 2009, 113, 13023.

• Dario Marrocchelli, Paul A Madden, Stefan Norberg and Stephen Hull, Cation composition effects on oxide conductivity in the Zr2Y2O7-Y3NbO7 system. J. Phys.: Condes. Matter 21 405403 (2009)

• R. Noble-Eddy, S. L. Masters (née Hinchley), D. W. H. Rankin, D. A. Wann, H. E. Robertson, B. Khater and J.-C. Guillemin, Primary phosphines studied by gas-phase electron diffraction and quantum chemical calculations. Are they different from amines? Inorg. Chem., 2009, 48 (17), 8603.

• N. Sieffert, M. Bühl,Non-Bonded Interactions in a Transition-Metal Triphenylphosphine Complex: a Density Functional Case Study. Inorg. Chem. 2009, 48, 4622-4624.

• Z. Su, M. Bühl, W. Zhou,Dissociation of Water During Formation of Anodic Aluminium Oxide. J. Am. Chem. Soc., 2009, 131, 8697-8702.

• M. Bühl, D. Peters, R. Herges, Substituent effects on ^61 Ni NMR Chemical Shifts. Dalton Trans., 2009, 6037-6044.

• Simon Dalgleish, Carole A. Morrison, Derek S. Middlemiss, Andrew R. Mount, Anna Collins, Luca Pilia, Angela Serpe, M. Laura Mercuri, Susan J. Roberts-Bleming, Adam Charlton, Paola Deplano,* Patrick J. Murphy, Neil Robertson, Synthesis, Structure and Spectroscopic Properties of a New Class of Polymerisable Nickel , Journal of Materials Chemistry, in press

• M.J. Wójcik, L. Boda and M. Boczar, Theoretical Study of Proton Tunneling in the Excited State of Tropolone JOURNAL OF CHEMICAL PHYSICS, 130, 164306 (2009).

• R. Noble-Eddy, S. L. Masters (née Hinchley), D. W. H. Rankin, D. A. Wann, B. Khater and J.-C. Guillemin,More user-friendly phosphines? Molecular structure of methylphosphine and its adduct with borane, studied by gas-phase electron diffraction and quantum chemical calculations. Dalton Trans., 2008, 5041.

• M.H. Palmer, A. D. Nelson, The electronic states of chlorine oxide (Cl2O) studied by ab initio configuration interaction methods and spectroscopy. Chemical Physics 354 (2008), 94-105

• D. A. Wann, I. Gronde, T. Foerster, S. A. Hayes, S. L. Masters, H. E. Robertson, N. W. Mitzel and D. W. H. Rankin,Highly asymmetric coordination of trimethylsilyl groups to tetrazole and triazole rings: an experimental and computational study in gaseous and crystalline phases. Dalton Trans., 2008, 3817.

• Stefan T Norberg, Istaq Ahmed, Stephen Hull, Dario Marrocchelli and Paul A Madden,Local Structure and Ionic Conductivity in the Zr2Y2O7 - Y3NbO7 system, J. Phys.: Condes. Matter 21 215401 (2009).

• Dario Marrocchelli, Mathieu Salanne, Paul A Madden, C Simon and Pierre Turq,The construction of a reliable potential for GeO2 from first principles, Molecular Physics 107 443-452 (2009)

• Stuart I. Wharton, John B. Henry, Hamish McNab, Andrew R. Mount, The Production and Characterisation of Novel Conducting Redox-Active Oligomeric Thin Films From Electrooxidised Indolo[3,2,1-jk]carbazole Chem. Eur. J., 15, 5482-5490 (2009).

• Asier Unciti-Broceta, M. Rahimi Yusop, Patricia R. Richardson, Jeffrey Walton, Mark Bradley, A fluorescein-derived anthrocyanine-inspired pH sensor Tetrahedron Letters, in press.

• V. I. Danilov, T. van Mourik, N. Kurita, H. Wakabayashi, T. Tsukamoto and D. M. Hovorun,On the mechanism of the mutagenic action of 5-bromouracil: A DFT study of uracil and 5-bromouracil in a water cluster. J. Phys. Chem. A (Letter), in press.

• R. Fandos, B. Gallego, M. I. López-Solera, A. Otero, A. Rodríguez, M. J. Ruiz, P. Terreros, and T. van Mourik, Piano and non-piano stool titanium alkoxide complexes: A combined experimental and theoretical study. Organometallics, in press.

• P. J. Byrne, J. E. Warren, R. E. Morris and S. E. Ashbrook, Structure and NMR Assignment in AlPO-15: a Combined Study by Diffraction, MAS NMR and First-Principles Calculations, Solid State Sciences (in press)

• C J. Pickard and R. J. Needs, Dense low-coordination phases of lithium. Physical Review Letters, in press.

• Chris J. Pickard and R. J. Needs,High-pressure phases of nitrogen, Physical Review Letters, in press.

• J-N Dumez and Chris J. Pickard, Calculation of NMR chemical shifts in organic solids: Accounting for motional effects, Journal of Chemical Physics, in press.

• J. M. Griffin, S. Wimperis, A. J. Berry, C. J. Pickard, S. E. Ashbrook, Solid-State 17O Spectroscopy of Hydrous Magnesium Silicates: Evidence for Proton Dynamics. J. Phys. Chem. C, 113, 465-471 (2009).

• I. Hung, A.-C. Uldry, J. Becker-Paldus, A.L. Webber, A. Wong, M.E.Smith, S.A. Joyce, J.R. Yates, C.J. Pickard, R. Dupree and S.P. Brown, Probing Heteronuclear 15N-17O and 13C-17O Connectivities and Proximities by Solid-State NMR Spectroscopy, Journal of the American Chemical Society, 131, 1820-1834 (2009).

• S. Aldridge, A. J. Downs, C. Y. Tang, S. Parsons, M. C. Clarke, R. D. L. Johnstone, H. E. Robertson, D. W. H. Rankin and D. A. Wann,Structures and aggregation of the methylamine-borane molecules, MenH3-nN.BH3 (n = 1-3), studied by X-ray diffraction, gas-phase electron diffraction, and quantum chemical calculations. J. Am. Chem. Soc., 131, 2231-2243 (2009).

• H. A. Früchtl, T. van Mourik, C. J. Pickard and J. D. Woollins, The structure of (SCN)x. A study using molecular and solid state density functional theory calculations. Chem. Eur. J., 15, 2687-2692 (2009).

• T. van Mourik, Comment on "To stack or not to stack: Performance of a new density functional for the uracil and thymine dimers" [Chem. Phys. Lett. 459 (2008) 164-166]. Chem. Phys. Lett., in press.

• A. M. Jones, S. Patterson, Al. M. Z. Slawin, T. Lebl, T. van Mourik, H.A. Früchtl, G. Vanier and N. J. Westwood, Parallel synthesis and spectroscopic analysis of a collection of heterocycles based on the diazabenz[e]aceanthrylene core structure. Tetrahedron 65, 563-578 (2009).

• Derek A. Wann, Heather E. Robertson, George Bramham, Andrew E. A. Bull, Nicholas C. Norman, Christopher A. Russell and David W. H. Rankin, Unusual chalcogen-boron ring compounds: the gas-phase structures of 1,4-B4S2(NMe2)4 and related molecules. Dalton Transaction, 2009, 1446-1449.

• Anthony M. Reilly, Derek A. Wann and David W. H. Rankin, What makes the huge 31P-31P coupling constants in S(PF2)2 and Se(PF2)2 vary so much with temperature? Journal of Physical Chemistry A, 2009, 113, 938-942.

• M. Bühl, C. Reimann, D. A. Pantazis, T. Bredow, F. Neese, Geometries of Third-Row Transition-Metal Complexes from Density-Functional Theory. J. Chem. Theory Comput. 2008, 4, 1449-1459.

• V. I. Danilov and T. van Mourik, A PM6 quantum chemical study of the H-bonded and stacked associates of the adenine and thymine DNA bases: The nature of base stacking. Mol. Phys. 106, 1487 - 1494 (2008)

• D. S. Middlemiss, L. M. Lawton, C. A. Morrison and C. C. Wilson. First principles study of the magnetism and electronic structure of the [Cu(HF)2(pyz)2]BF4 coordination polymer. Chem. Phys. Lett., 2008, 459, 119.

• P. André, C. Ge, A. Ruseckas, T. van Mourik, H.A. Früchtl, J. A. Crayston, R. E. Morris, D. Cole-Hamilton and I. D. W. Samuel, Hybrid dendritic molecules with confined chromophore architecture to tune fluorescence efficiency. J. Phys. Chem. B 112, 16382--16392 (2008)

• Geary Elaine A M; McCall Keri L; Turner Andrew; Murray Paul R; McInnes Eric J L; Jack Lorna A; Yellowlees Lesley J; Robertson Neil, Spectroscopic, electrochemical and computational study of Pt-diimine-dithiolene complexes: rationalising the properties of solar cell dyes. Dalton transactions 2008;(28):3701-8.

• T. van Mourik,Basis set superposition error effects cause the apparent non-existence of the ethene/benzenium ion complex on the MP2 potential energy surface. J. Phys. Chem. A (Letter) 112,11017--11020 (2008).

• T. van Mourik, Assessment of density functionals for intramolecular dispersion-rich interactions. J. Chem. Theor. Comp 4, 1610-1619 (2008).

• J. Cuny, S. Messaoudi, V. Alonzo, E. Furet, J. F. Halet, E. Le Fur, S. E. Ashbrook, C. J. Pickard, R. Gautier and L. Le Polles, DFT Calculations of Quadrupolar Solid-State NMR Properties: Some Examples in Solid-State Inorganic Chemistry, J. Comp. Chem. 13, 2279-2287 (2008).

• S. E. Ashbrook, M. Cutajar, C. J. Pickard, R. I. Walton and S. Wimperis,Structure and NMR Assignment in Calcined and As-Synthesized Forms of AlPO-14: a Combined Study by First-Principles Calculations and High-Resolution 27Al-31P MAS NMR Correlation, Phys. Chem. Chem. Phys. 10, 5754-5764 (2008).

• A. Uldry, J.M. Griffin, J.R. Yates, M. Perez-Torralba, M.D. Santa Maria, A.L. Webber, M.L.L. Beaumont, A. Samoson, R.M. Claramunt, C.J. Pickard, S.P. Brown, Quantifying Weak Hydrogen Bonding in Uracil and 4-Cyano-4'-ethynylbiphenyl: A Combined Computational and Experimental Investigation of NMR Chemical Shifts in the Solid State. Journal of the American Chemical Society, Vol 130, Issue 3, Page 945-954.

• Thomas Foerster, Derek A. Wann and David W. H. Rankin, Extremely narrow SiON angles in siloxy-substituted nitrogen-containing rings: a computational investigation. Dalton Transactions, 2008, 5999-6004.

• Robert Noble-Eddy, Sarah L. Masters, David W. H. Rankin, Derek A. Wann, Brahim Khater and Jean-Claude Guillemin, More user-friendly phosphines? Molecular structure of methyl phosphine and its adduct with borane, studied by gas-phase electron diffraction and quantum chemical calculations. Dalton Transactions, 2008, 5041-5047.

• Derek A. Wann, Robert J. Less, Franck Rataboul, Philip D. McCaffrey, Anthony M. Reilly, Heather E. Robertson, Paul D. Lickiss and David W. H. Rankin,Accurate gas-phase experimental structures of octasilsesquioxanes (Si8O12X8; X = H, Me). Organometallics, 2008, 27, 4183-4187.

• Derek A. Wann, Ingo Gronde, Thomas Foerster, Stuart A. Hayes, Sarah L. Masters, Heather E. Robertson, Norbert W. Mitzel and David W. H. Rankin,Highly asymmetric coordination of trimethylsilyl groups to tetrazole and triazole rings: an experimental and computational study in gaseous and crystalline phases. Dalton Transactions, 2008, 3817-3823.

• Andrea Keys, Paul T. Brain, Carole A. Morrison, Rhonda L. Callender, Bruce A. Smart, Derek A. Wann, Heather E. Robertson, David W. H. Rankin and Andrew R. Barron, Molecular structures of M(But)3 (M = Al, Ga, In) using gas-phase electron diffraction and ab initio calculations: experimental and computational evidence for charge-transfer processes leading to photodissociation. Dalton Transactions, 2008, 404-410.

• Anthony M. Reilly, Derek S. Middlemiss, M. Murshed Siddick, Derek A. Wann, Graeme J. Ackland, Chick C. Wilson, David W. H. Rankin, and Carole A. Morrison,The phonon spectrum of phase I ammonia: reassignment of lattice mode symmetries from combined molecular- and lattice-dynamics calculations. Journal of Physical Chemistry A, 2008, 112, 1322-1329.

• Ewan M. Brown, Philip D. McCaffrey, Derek A. Wann and David W. H. Rankin,Accurate structures from combined gas electron diffraction and liquid crystal NMR data; the importance of anisotropy of indirect couplings for 1,4-difluorobenzene Physical Chemistry Chemical Physics, 2008, 10, 738-742.

• G. Deniau, A. M. Z. Slawin, J. P. Issberner, T. van Mourik, K. T. Sillar, J. J. Lambert and D. O'Hagan,Synthesis, conformation and biological evaluation of the enantiomers of 3-fluoro-¿-aminobutyric acid ((R)- and (S)- 3F-GABA). An analogue of the neurotransmitter, GABA. ChemBioChem 8, 2265-2274 (2007).

• C.J. Pickard, R.J. Needs, When is H2O not water? Journal of Chemical Physics, Vol 127, Article No. 244503.

• A. E. Shields and T. van Mourik,Comparison of ab initio and DFT electronic structure methods for peptides containing an aromatic ring: The effect of dispersion and BSSE. J. Phys. Chem. A 111, 13272 - 13277 (2007).

• T. van Mourik and A. J. Dingley, Characterizing the cooperativity in H-bonded amino structures. J. Phys. Chem. A 111, 11350-11358 (2007).

• Anthony M. Reilly, Derek. A. Wann, Carole A. Morrison and David W. H. Rankin, Experimental equilibrium crystal structures: Molecular dynamics as a probe for atomic probability density functions, Chemical Physics Letters, 2007, 448, 61.

• María E. Tuttolomondo, Amparo Navarro, Tomás Peña Ruiz, Eduardo L. Varetti, Stuart A. Hayes, Derek A. Wann, Heather E. Robertson, David W. H. Rankin and Aida Ben Altabef. Gas-phase structure, rotational barrier and vibrational properties of methyl methanethiosulfonate, CH3SO2SCH3: an experimental and ;computational study. Journal of Physical Chemistry A, 2007, 111, 9952-9960.

• Tanja van Mourik, Victor I. Danilov, Eduardo Gonzalez, Alexandra Deriabina and Valery I. Poltev,Indication of water droplet formation in hydrated clusters of cytosine and adenine. An electronic structure study using B3LYP, LMP2 and PM6, Chemical Physics Letters, (2007), 445, 305-308

• Leo F. Holroyd and T. van Mourik,Insufficient description of dispersion in B3LYP and large basis set superposition errors in MP2 calculations can hide peptide conformers, Chemical Physics Letters, (2007), 442, 42-46

• Pickard, CJ; Needs, RJ, Structure of phase III of hydrogen. Nature Physics, (2007), 3(7), 473-476

• Pickard, CJ; Salager, E; Pintacuda, G; Elena, B; Emsley, E. Resolving Structures from Powders by NMR Crystallography Using Combined Proton Spin Diffusion and Plane Wave DFT Calculations. Journal of the American Chemical Society, (2007), 129(29), 8932-8933

• Ashbrook, SE; Le Polles, L; Pickard, CJ; Berry, AJ; Wimperis, S; Farnan, I. First-principles calculations of solid-state O-17 and Si-29 NMR spectra of Mg2SiO4 polymorphs. Physical Chemistry Chemical Physics, (2007), 9(13), 1587-1598

• A. O. Ivanov, S. S. Kantorovich, E. N. Reznikov, C. Holm, A. F. Pshenichnikov, A. V. Lebedev, A. Chremos, and P. J. Camp, Magnetic properties of polydisperse ferrofluids: A critical comparison between experiment, theory, and computer simulation. Physical Review E, (2007), 75, 061405

• Csanyi, G; Pickard, CJ; Simons, BD; Needs, RJ, Graphite intercalation compounds under pressure: A first-principles density functional theory study. Physical Review B, (2007), 75(8), 85432

• Philip D. McCaffrey, Richard J. Mawhorter, Andrew R. Turner, Paul T. Brain, David W. H. Rankin,Accurate equilibrium structures obtained from gas-phase electron diffraction data: sodium chloride. Journal of Physical Chemistry A, 2007, 111, 6103-6114.

• Sarah L. Masters, Duncan A. Grassie, Heather E. Robertson, Margit Hölbling and Karl Hassler, Supersilyl radicals from the dissociation of superdisilane observed by gas electron diffraction. Chemical Communications, 2007, 2618-2620.

• G. Ganzenmüller and P. J. Camp,Applications of Wang-Landau sampling to determine phase equilibria in complex fluids. Journal of Chemical Physics, 2007, 127, 154504.

• Y. Wang, A. D. Stretton, M. C. McConnell, J. B. Henry, A. R. Mount, P. A. Wood, S. Parsons, T. H. Galow, Synthesis of 1,4,5,8,9,12-Hexamethyltriphenylene. A molecule with a Flipping Twist?, Journal of the American Chemical Society, (2007), 129, 43, 13193-13200.

• 17O and 29Si NMR Parameters of MgSiO3 Phases from High-Resolution Solid-State NMR Spectroscopy and First-Principles Calculations , S. E. Ashbrook, A. J. Berry, D. J. Frost, A. Gregorovic, C. J. Pickard, J. E. Readman and S. Wimperis, Journal of the American Chemical Society, (2007), 129 13213-13224.

• Z. Han, A. L. Picone, A. M.Z. Slawin, V. R. Seymour, S. E. Ashbrook, W. Zhou, S. P. Thompson, J. E. Parker, and P. A. Wright, A novel large pore aluminophosphate molecular sieve STA-15 prepared using the tetrapropylammonium cation as a structure directing agent, Chem. Mater. (Accepted)

• A. Šarić, V.Vrček, M. Bühl,Density Functional Study of Protonated Formylmetallocenes, Organometallics 2008, 27, 394-401.

• M Bühl, N. Sieffert, V. Golubnychiy, G. Wipff,Density Functional Theory Study of Uranium(VI) Aquo Chloro Complexes inAqueous Solution, J. Phys. Chem. A 2008, 112, 2428-2436.

• M.Bühl, V. Golubnychiy, Density-Functional Computation of 99Tc NMR Chemical Shifts, Magn. Reson. Chem. 2008, 46, S36-S44.

• Bühl, N. Sieffert, G. Wipff, Density Functional Study of Aqueous Uranyl(VI) Fluoride Complexes, Chem. Phys. Lett. 2009, 467, 287-293.

• R. S. Stoll, M. V. Peters, A. Kuhn, S. Heiles, R. Goddard, M. Bühl, C. M. Thiele, S. Hecht, Photoswitchable Catalysts: Correlating Structure and Conformational Dynamics with Reactivity by a Combined Experimental and Computational Approach, J. Am. Chem. Soc. 2009, 131, 357-367. 51

• K. R. Geethalakshmi, M. P. Waller, W. Thiel, M.Bühl, V NMR chemical shifts calculated from QM/MM models of Peroxo-forms of Vanadium Haloperoxidases, J. Phys. Chem. B 2009, 113, 4456-4465.

• M. Bühl,Structure and Stability of Aquotetrafluorouranyl(VI) in the Solid State. Density-Functional Study of [UO2F4(H2O)][NMe4]2.2H2O, Can. J. Chem.2009, 87, 818-823.

• J. M. Griffin, A. J. Miller, A. J. Berry, S. Wimperis and S. E. Ashbrook, Dynamics on the Microsecond Timescale in Hydroxyl-Clinohumite Studied by Solid-State 2H NMR Spectroscopy, Phys. Chem. Chem. Phys. (in press)

• S. W. Reader, M. R. Mitchell, K. E. Johnston, C. J. Pickard, K. R. Whittle and S. E. Ashbrook, Cation Disorder in Pyrochlore Ceramics: 89Y MAS NMR and First-Principles Calculations, J. Phys. Chem. C. 113 18874-18883 (2009).

• D. Carnevale, P. Wormald, B. Ameduri, R. Tayouo and S. E. Ashbrook, Multinuclear Magnetic Resonance and DFT Studies of the Poly(chlorotrifluoroethylene-alt-ethyl vinyl ether) Copolymers, Macromolecules42, 5652-5659 (2009).

• S. E. Ashbrook, M. Cutajar, J. M. Griffin, Z. A. D. Lethbridge, R. I. Walton and S. Wimperis, Transformation of AlPO-53 to JDF-2: Reversible Dehydration of a Templated Aluminphosphate Studied by MAS NMR and Diffraction, J. Phys. Chem. C 113, 10780-10789 (2009).

• D. Modeshia, R. J. Darton, S. E. Ashbrook and R. I. Walton, Control of Polymorphism in NaNbO3 by Hydrothermal Synthesis: Selective Preparation of Ilmenite over Perovskite Structure, Chem. Commun. 68-70 (2009).

• Sean Jensen, Herbert Früchtl and Christopher J. Baddeley, Coupling of Triamines with Diisocyanates on Au(111) Leads to the Formation of Polyurea Networks, J. Am. Chem. Soc., 2009, 131 (46), pp 16706–16713.

• V.I. Poltev, V.M. Anisimov, V.I. Danilov, T. van Mourik, A. Deriabina, E. González, M. Padua, D. Garcia, F. Rivas and N. Polteva, DFT study of polymorphism of the DNA double helix at the level of dinucleoside monophosphates, Int. J. Quant. Chem., in press.

• David Y. Buissonneaud, Tanja van Mourik and David O'Hagan, A DFT study on the fluorine gauche effect in substituted fluoroethanes, Tetrahedron 66, 2196- 2202 (2010).

• Dimitrios Toroz and Tanja van Mourik, The structure of the neutral gas-phase glycine tripeptide, Phys. Chem. Chem. Phys 12, 3463-3473 (2010).

• Cao Jie and Tanja van Mourik, Performance of the M06-L density functional for a folded Tyr-Gly conformer, Chem. Phys. Lett. 485, 40-44 (2010).

• T. van Mourik, V. I. Danilov, V. V. Dailidonis, N. Kurita, H. Wakabayashi and T. Tsukamoto,A DFT study of uracil and 5-bromouracil in nanodroplets, Theor. Chem. Acc. 125, 233-244 (2010).

• A. Dora, J. Tennyson, L. Bryjko and T. van Mourik, R-matrix calculation of low-energy electron collisions with uracil, J. Chem. Phys. 130, 164307 (8 pages) (2009). Also published in: Virtual Journal of Biological Physics 17, issue 9 (2009).

• F. A. M. Rudolph, A. L. Fuller, A. M . Z. Slawin, M. Bühl, R. A. Aitken and J. D. Woollins, The X-Ray Structures of Sulfones, J. Chem. Cryst. 2010, 40, 253-265 (DOI: 10.1007/s10870-009-9643-8).

• M. Bühl, G. Schreckenbach, Oxygen Exchange in Uranyl Hydroxide via Two "Non-Classical" Ions, Inorg. Chem. 2010, 49, 3821-3827 (DOI: 10.1021/ic902508z).

• A. L. Fuller, L. A. S. Scott-Hayward, Y. Li, M. Bühl, A. M. Z. Slawin, J. D. Woollins, Automated Chemical Crystallography, J. Am. Chem. Soc. 2010, 132, 5799-5802 (DOI: 10.1021/ja100247y).

• R. Bjornsson, M. Bühl, Electric field gradients of transition metal complexes from density functional theory: assessment of functionals, geometries and basis sets, Dalton Trans. 2010, 39, 5319-5324 (DOI: 10.1039/c001017k).

• N. Sieffert, M. Bühl, Hydrogen Generation from Alcohols Catalyzed by Ruthenium- Triphenylphosphine Complexes: Multiple Reaction Pathways, J. Am. Chem. Soc. 2010, 132, 8058-8070 (DOI: 10.1021/ja101044c).

• F. R. Knight, A. L. Fuller, M. Bühl, A. M. Z. Slawin, J. D. Woollins, Synthetic and Structural Studies of 1,8-Chalcogen Naphthalene Derivatives, Chem. Eur. J. 2010, 16, 7503 - 7516 (DOI: 10.1002/chem.200903523).

• F. R. Knight, A. L. Fuller, M. Bühl, A. M. Z. Slawin, J. D. Woollins, Synthetic and Structural Studies of 1-Halo-8-(alkylchalcogeno)naphthalene Derivatives, Chem. Eur. J. 2010, 16, 7605 -7616 (DOI: 10.1002/chem.201000435).

• F. R. Knight, A. L. Fuller, M. Bühl, A. M. Z. Slawin, J. D. Woollins, Sterically Crowded peri-Substituted Naphthalene Phosphines and their PV Derivatives. Chem. Eur. J. 2010, 16, 7617 - 7634 (DOI: 10.1002/chem.201000454).

• P. G. Waddell, A. M. Z. Slawin, N. Sieffert, M. Bühl, J. D. Woollins, The Preparation and Structure of Pt(S2N2){P(OR)nR′3-n}2 and Pt(SeSN2){P(OMe)nPh3-n}2 (n = 0-3), Eur. J. Inorg. Chem. 2010, 3185 -3194. (DOI:10.1002/ejic.201000329)

• M. Bühl, B. Wrackmeyer, Density Functional Computations of 93Nb Chemical Shifts, Magn. Reson. Chem., in press (DOI: 10.1002/mrc.2624).

International conferences presentations/papers

• PA Madden, D Marrocchelli, ST Norberg and S Hull,Conduction and Disorder in Y3NbO7 - Zr2Y2O7 in Solid-State Ionics 2008, edited by E. Traversa, T. Armstrong, K. Eguchi, M.R. Palacin (Mater. Res. Soc. Symp. Proc. Volume 1126, Warrendale, PA, 2009), 1126-S06-07-PP05-07

• A. R. Turner and H. Fruchtl. 2007. Computational Chemistry for All. Invited Speakers, ScotCHEM Computational Chemistry Symposium, St. Andrews.

• Sharon E. Ashbrook. Probing Structure and Dynamics in Silicates using Solid-State NMR. British Radiofrequency Spectroscopy Group Christmas Meeting, London UK 2006.
• Sharon E. Ashbrook. Exploiting First-Principles Calculations and High-Resolution NMR for Structural Studies of High-Pressure Silicates. 5th Alpine NMR Conference n Solid-State NMR Chamonix, France 2007.
• T. van Mourik,.Methodological aspects in electronic structure calculations – examples from studies on biological molecules. ScotCHEM computational chemistry symposium, St Andrews, April 2007.
• Sharon E. Ashbrook. Exploiting First-Principles Calculations and High-Resolution NMR for Structural Studies of High-Pressure Silicates. Frontiers in Mineral Sciences, Cambridge, UK 2007
• S. L. Masters (née Hinchley). Stressed disilanes: the emergence of exciting structures from strained systems. Talk presented at Xth Conference on Gas Electron Diffraction, Blaubeuren, Germany, June 2007
• T. van Mourik. DFT vs. MP2: which method gives the correct tyrosine-glycine structure. Methods and Applications of Computational Chemistry, Kiev, Ukraine, July 2007.

Books, newsletters, circulars, etc

• A. R. Turner and H. Fruchtl. 2007. Computational Chemistry for All. Poster. ScotCHEM Computational Chemistry Symposium, St. Andrews.

• EaStCHEM Research Computing Facility: HPC for All, A. R. Turner, EPCC News, Issue 61, Autumn 2007.
• S. L. Hinchley and J.-C. Guillemin, Determination of structures of unstable phosphines, Poster presented at Royal Society of Edinburgh Awards Evening, September 2006
• High-Resolution NMR Studies of Boroxophenanthrene, Diego Carnevale, Douglas Philp, Sharon E. Ashbrook, 5th Alpine NMR Conference on Solid-State NMR Chamonix, France 2007
• Structure and NMR Assignment in Microporous Aluminophosphates: A Combined Study by High-Resolution 27Al/31P MAS NMR Correlation and First- Principles Calculations, Marica Cutajar, Sharon E. Ashbrook, Richard I. Walton, Stephen Wimperis, 5th Alpine NMR Conference on Solid-State NMR Chamonix, France 2007
• An Investigation of Scandium Coordination using 45Sc NMR, Karen Johnston, Philip Lightfoot, Sharon E. Ashbrook, 5th Alpine NMR Conference on Solid-State NMR Chamonix, France 2007
• Study of High-Pressure Minerals using High-Resolution NMR and First-Principles Calculations, Sharon E. Ashbrook, Andrew J. Berry, Chris J. Pickard, Alan Gregorovic and Stephen Wimperis, ScotCHEM Computational Chemistry Symposium, University of St Andrews, April 2007
• Stressed disilanes: the emergence of exciting structures from strained systems, S. L. Masters (née Hinchley), ScotCHEM Computational Chemistry Symposium, University of St Andrews, April 2007
• Towards Stabilization of Reactive Phosphines, R. Noble-Eddy and S. L. Masters (née Hinchley), ScotCHEM Computational Chemistry Symposium, University of St Andrews, April 2007
• Structures from GED and LCNMR: determining the anisotropy of indirect couplings, D. A. Wann, Xth Conference on Gas Electron Diffraction, Blaubeuren, Germany, June 2007
• The structure of (SCN)x. Clues from NMR parameters determined with Density Functional Theory, T. van Mourik, Methods and Applications of Computational Chemistry, Kiev,Ukraine, July 2007 36
• Fluid Phase Equilibria from Wang-Landau Monte Carlo Simulations, G. Ganzenmuller, Conference on Computational Physics, Brussels, September 2007
• Stressed disilanes: the emergence of exciting structures from strained systems, S.L. Masters (née Hinchley), Poster presented at Royal Society of Edinburgh Awards Evening, September 2007

Division of Pathway Medicine - MiareActivity

Refereed Journal Articles

• Chris F Taylor, Dawn Field, Susanna-Assunta Sansone, Rolf Apweiler, Michael Ashburner, Catherine A Ball, Pierre-Alain Binz, Alvis Brazma, Ryan Brinkman, Eric W Deutsch, Oliver Fiehn, Jennifer Fostel, Peter Ghazal, Graeme Grimes, Nigel W Hardy, Henning Hermjakob, Randall K Julian, Jr., Matthew Kane, Eugene Kolker, Martin Kuiper, Nicholas Le Novère, Jim Leebens-Mack, Suzanna E Lewis, Ruth McNally, Alexander Mehrle, Norman Morrison, John Quackenbush, Donald G Robertson, Philippe Rocca-Serra, Barry Smith, Jason Snape, Peter Sterk, Stefan Wiemann. 2007 Promoting Coherent Minimum Reporting Requirements for Biological and Biomedical Investigations: The MIBBI Project. Nature Biotechnology, 2008 8:889-96.

• Buck AH, Santoyo-Lopez J, Robertson KA, Kumar DS, Reczko M, Ghazal P. Discrete clusters of virus-encoded micrornas are associated with complementary strands of the genome and the 7.2-kilobase stable intron in murine cytomegalovirus. J Virol. 2007 81:13761-70.

• Jones AR, Lister AL, Hermida L, Wilkinson P, Eisenacher M, Belhajjame K, Gibson F, Lord P, Pocock M, Rosenfelder H, Santoyo-Lopez J, Wipat A, Paton NW. Modeling and managing experimental data using FuGE. OMICS. 2009 13:239-51.

• Birmingham A, Selfors LM, Forster T, Wrobel D, Kennedy CJ, Shanks E, Santoyo-Lopez J, Dunican DJ, Long A, Kelleher D, Smith Q, Beijersbergen RL, Ghazal P and Shamu CE. Statistical Methods for Analysis of High-Throughput RNA Interference Screens. Nat Methods. 2009 6:569-75.

• Kettner C, Field D, Sansone SA, Taylor C, Aerts J, Binns N, Blake A, Britten CM, de Marco A, Fostel J, Gaudet P, González-Beltrán A, Hardy N, Hellemans J, Hermjakob H, Juty N, Leebens-Mack J, Maguire E, Neumann S, Orchard S, Parkinson H, Piel W, Ranganathan S, Rocca-Serra P, Santarsiero A, Shotton D, Sterk P, Untergasser A, Whetzel PL. Meeting Report from the Second "Minimum Information for Biological and Biomedical Investigations" (MIBBI) workshop. Stand Genomic Sci. 2010 3:259-66.

International conferences presentations/papers

• Moodie S. MIARE proposal Publication Draft and Panel Discussion. April 2006. 2nd Genome-Wide RNAi Global Initiative Meeting. Washington DC, USA.

• G. Grimes. Minimum Information about an RNAi Experiment: MIARE. April 2006 HUPO Proteomics Standards Initiative meeting, San Francisco, USA.

• G. Grimes. MIARE: Standards for RNAi Experiments. April 2006. NCBI, Bethesda Maryland, USA.

• G. Grimes. Informatics Workgroup Updates and Next Workgroup Activities: MIARE. September 2006. 3rd Genome-Wide RNAi Global Initiative Meeting. Amsterdam. Netherlands.

• G. Grimes. MIARE and Informatics Workgroup Update. 4th Genome-Wide RNAi Global Initiative Meeting. April 2007. Colorado. USA.

• J. Santoyo-Lopez. RNAi experiment object model: RiE-OM. IV Genome-Wide RNAi Global Initiative Meeting. Colorado. USA. April 2007.

• J. Santoyo-Lopez. Data Standards for High-Throughput experiments: MIARE. 5th Genome-Wide RNAi Global Initiative Meeting. September 2007. Barcelona, Spain.

• N. Binns. Informatics Working Group. 9th Genome-Wide RNAi Global Initiative Meeting. September 2009. Edinburgh, UK.

• N. Binns. PubChem-MIARE RNAi Deposition Gateway. 11th Genome-Wide RNAi Global Initiative Meeting. October 2010. London, UK.

• N. Binns. MIARE: MIBBI Portal Project Update. 2nd MIBBI Workshop. December 2010. Rüdesheim am Rhein, near Frankfurt, Germany.

NeSCResearch

Refereed Journals

• A. Barker, J. Weissman, and J. van Hemert. The circulate architecture: Avoiding workflow bottlenecks caused by centralised orchestration. Cluster Computing, 12(2):221–235, 2009.

• J. Hemert and J. Koetsier. Giving computational science a friendly face. Zero-In, 1(3):12–13, 2009.

• D. Rodrìguez González, T. Carpenter, J.I. van Hemert, and J. Wardlaw. An open source toolkit for medical imaging de-identification. European Radiology, 20(8):1896–1904, 2010.

• R.R. Kitchen, V.S. Sabine, A.H. Sims, E.J. Macaskill, L. Renshaw, J.S. Thomas, J.I. van Hemert, J.M. Dixon, and J.M.S. Bartlett. Correcting for intra-experiment variation in illumina beadchip data is necessary to generate robust gene-expression profiles. BMC Genomics, 11, 2010.

• Ales Tichopad, Tzachi Bar, Ladislav Pecen, Robert R. Kitchen, Mikael Kubista, and Michael W. Pfaffl. Quality control for quantitative pcr based on amplification compatibility test. Methods, 50:308–312, 2010.

• Robert R. Kitchen, Mikael Kubista, and Ales Tichopad. Statistical aspects of quantitative real-time pcr experiment design. Methods, 50:231–236, 2010.

• Malcolm Atkinson. Guest editorial: Research data: It’s what you do with them. International Journal of Digital Curation, 4, 2009.

• Andrew Grimshaw, Mark Morgan, Duane Merrill, Hiro Kishimoto, Andreas Savva, David Snelling, Chris Smith, and Dave Berry. An open grid services architecture primer. Computer, 42(2):27–34, 2009.

• J. O’Donoghue and J.I. van Hemert. Using the DCC Lifecycle Model to curate a gene expression database: A case study. International Journal of Digital Curation, 2009.

• B. Dobrzelecki, A. Krause, A. Hume, A. Grant, M. Antonioletti, T. Alemu, M. Atkinson, M. Jackson, E. and Theocharopoulos. Integrating Distributed Data Sources with OGSA-DAI DQP and Views. Phil. Trans. R. Soc. A vol. 368 no. 1926 4133-4145, doi: 10.1098/rsta.2010.0166 13 September 2010.

International conferences presentations/papers

• J.I. van Hemert, Mining spatial gene expression data for association rules. Proceedings of the 1st International Conference on BioInformatics Research and Development, pages 66-76.

• Mario Giacobini and Jano van Hemert, editors. European Graduate StudentWorkshop on Evolutionary Computation, 2007.

• Carlos Cotta and Jano van Hemert, editors. Evolutionary Computation in Combinatorial Optimization, 7th European Conference, volume LNCS 4446 of Lecture Notes in Computer Science. Springer, 2007.

• J. Ure, R. Proctor, M. Martone, D. Porteous, S. Lloyd, S. Lawrie, D. Job, R. Baldock, A. Philp, D. Liewald, F. Rakebrand, A. Blaikie, C. McKay, S. Anderson, J. Ainsworth, J. van Hemert, I. Blanquer, R. Sinnott, C. Barillot, F. Bernard Gibaud, A. Williams, M. Hartswood, P. Watson, L. Smith, A. Burger, J. Kennedy, H. Gonzalez-Velez, R. Stevens, O. Coecho, R. Morton, P. Linksted, M. Deschenne, M. McGilchrist, P Johnson, A. Voss, R. Gertz, and J. Wardlaw. Data integration in eHealth: A domain/disease specific roadmap. In N. Jacq, Y. Legré, H. Muller, I. Blanquer, V. Breton, D. Hausser, V. Hernández, T. Solomonides, and M. Hofman-Apitius, editors, Studies in Health Technology and Informatics, volume 126, pages 144-153. IOPress, 2007.

• J.I. van Hemert. Painting with Genes, UK e-Science All Hands Meeting, Nottingham, 10-14 September 2007

• A. Barker and J. van Hemert. Scientific workflow: A survey and research directions. In Parallel Processing and Applied Mathematics, volume 4967 of Lecture Notes in Computer Science, pages 746–753. Springer, 2008.

• A. Barker, J. B. Weissman, and J. van Hemert. Eliminating the Middle Man: Peer-to-Peer Dataflow. In HPDC ’08: Proceedings of the 17th International Symposium on High Performance Distributed Computing, pages 55–64. ACM, June 2008.

• A. Barker, J. B. Weissman, and J. van Hemert. Orchestrating Data-Centric Workflows. In The 8th IEEE International Symposium on Cluster Computing and the Grid (CCGrid), pages 210–217. IEEE Computer Society, May 2008.

• C. Cotta and J. van Hemert. Recent Advances in Evolutionary Computation for Combinatorial Optimization, volume 153 of Studies in Computational Intelligence. Springer, 2008.

• C. Di Chio, M. Giacobini, and J. van Hemert, editors. European Graduate Student Workshopon Evolutionary Computation, 2008.

• I. Juhos and J. van Hemert. Graph colouring heuristics guided by higher order graph properties. In J. van Hemert and C. Cotta, editors, Evolutionary Computation in Combinatorial Optimization, volume 4972 of Lecture Notes in Computer Science, pages 97–108. Springer, 2008.

• J. van Hemert and R. Baldock. Matching spatial regions with combinations of interacting gene expression patterns. In M. Elloumi, J. Küng, M. Linial, R. Murphy, K. Schneider, and C. Toma, editors, Proceedings of the 2nd International Conference on BioInformatics Research and Development, volume 13 of Communications in Computer and Information Science, pages 347–361. Springer Verlag, 2008.

• J. van Hemert and C. Cotta, editors. Evolutionary Computation in Combinatorial Optimization, 8th European Conference, volume LNCS 4972 of Lecture Notes in Computer Science. Springer, 2008.

• A. Barker, J. van Hemert, R. Baldock, and M. Atkinson. An e-infrastructure to support collaborative embryo research. In Cluster Computing and the Grid, pages 520–525. IEEE Computer Society, 2009.

• L. De Ferrari, S. Aitken, J. van Hemert, and I. Goryanin. A model of social collaboration in molecular biology knowledge bases. In Proceedings of the 6th Conference of the European Social Simulation Association (ESSA’09), European Social Simulation Association, ACM, 2009.

• J. Fernández, L. Han, A. Nuñez, J. Carretero, and J. van Hemert. Using architectural simulation models to aid the design of data intensive application. In 3rd Internat. Conf. on Advanced Engineering Computing and Applications in Sciences, IEEE Computer Society, 2009.

• S. Gesing, O. Kohlbacher, and J. van Hemert. Portals for life sciences—a brief introduction. In S. Gesing and J. van Hemert, editors, Proceedings of the IWPLS09 International Workshop on Portals for Life Sciences, CEUR Workshop Proceedings, 2009

• S. Gesing and J. van Hemert, editors. Proceedings of the IWPLS09 International Workshop on Portals for Life Sciences, Edinburgh, UK, 2009. CEUR Workshop Proceedings.

• L. Han, J. van Hemert, R. Baldock, and M. Atkinson. Automating gene expression annotation for mouse embryo. In Advanced Data Mining and Applications, 5th Internation Conference, volume 5678 of LNCS, pages 469–478. Springer, 2009.

• J. Koetsier and J. van Hemert. Rapid development of computational science portals. In S. Gesing and J. van Hemert, editors, Proceedings of the IWPLS09 International Workshop on Portals for Life Sciences, CEUR Workshop Proceedings, Edinburgh, September 2009.

• Gagarine Yaikhom, Chee Sun Liew, Liangxiu Han, Jano van Hemert, Malcolm Atkinson, and Amy Krause. Federated enactment of workflow patterns. In P. D’Ambra, M. Guarracina, and D. Talia., editors, Euro-Par, volume LNCS 6271, pages 317–328. Springer, 2010.

• K. A. Smith-Miles, J.I. van Hemert, and Y. Lim. Understanding tsp dfficulty by learning from evolved instances. In C. Blum, editor, Proceedings of Learning and Intelligent Optimization, Lecture Notes in Computer Science, page In press. Lecture Notes in Computer Science, 2010

• J. Koetsier, A. Turner, P. Richardson, and J.I. van Hemert. Rapid chemistry portals through engaging researchers. In IEEE 5th International Conference on e-Science, 2009.

• Gerhard Wickler, George Beckett, Liangxiu Han, Sung Han Koo, Stephen Potter, Gavin Pringle, and Austin Tate. Using simulation for decision support: Lessons learned from firegrid. In J. Landgren, U. Nulden, and B. Van de Walle, editors, Proceedings of the 6th International Conference on Information Systems for Crisis Response and Management (ISCRAM 2009), Gothenburg, Sweden, 10-13/05/2009 2009.

• Liangxiu Han, Malcolm Atkinson, Ally Hume, Jano van Hemert, Chee Sun Liew, A Distributed Architecture for Data Mining and Integration, Proceedings of the 2nd International Workshop on Data –Aware Distributed Computing, June 9th 2009, Munich, Germany.

• Buil-Aranda C, Corcho O, Krause A, Robust service-based semantic querying to distributed heterogeneous databases, Proceeedings of the 8th International Workshop on Web Semantics, 1st September 2009, Linz, Austria.

• Chee Sun Liew, Liangxiu Han, Jano van Hemert, Malcolm Atkinson. Towards Optimising Data-intensive Workflows using Parallel Streams. The Third International Workshop on Data Intensive Distributed Computing (DIDC2010), Chicago, Illinois - June 22, 2010.

• Malcolm Atkinson, Peter Brezany, Oscar Corcho, Liangxiu Han, Jano van Hemert, Ladislav Hluchý, Ally Hume, Ivan Janciak, Amy Krause, Dave Snelling and Alex Wöhrer. Advanced Data Mining and Integration Research for Europe. The UK e-Science All Hands Meeting, December 2009, Oxford.

Books, newsletters, circulars, etc

• Liangxiu Han. Exploiting P2P and Grid Computing Technologies for Resource Sharing to support High Performance Distributed System, volume 1, chapter 19. IGI Global publishing, 2010.

• C.A. Morrison, N. Robertson, A. Turner, J. van Hemert, and J. Koetsier. Molecular Orbital Calculations of Inorganic Compounds, chapter 3.33, pages 261–267. Wiley-VCH, 3 edition, 2010.

EPCC Collaborations and Core Tools & Techniques

OncologyActivity

Refereed Journal Articles

• Tenesa, A. et al. Genome-wide association scan identifies a colorectal cancer susceptibility locus on 11q23 and replicates risk loci at 8q24 and 18q21. Nat. Genet. 40(5), 631-637, 2008 (doi:10.1038/ng.133). http://www.nature.com/ng/journal/v40/n5/pdf/ng.133.pdf

Books, newsletters, circulars, etc

• K. Kavoussanakis, Bowel cancer research update, EPCC News, Issue 60, Summer 2007.

• F. Reid, Blue Gene tackles cancer genes, EPCC News, Issue 59, October 2006.

ScientificComputingOnFPGAsActivity

Refereed Journal Articles

• Rob Baxter, Stephen Booth, Mark Bull, Geoff Cawood, James Perry, Mark Parsons, Alan Simpson, Arthur Trew, Andrew McCormick, Graham Smart, Ronnie Smart, Allan Cantle, Richard Chamberlain, and Gildas Genest, Maxwell - a 64 FPGA Supercomputer. Engineering Letters, Volume 16 Issue 3, Pages: 426-433

International conference presentations/papers

• Baxter et al, Maxwell - a 64 FPGA Parallel Computer. In: Proceedings of the 2007 Manchester Reconfigurable Supercomputing Conference.

• Baxter et al, Maxwell - a 64 FPGA Supercomputer. In: Proceedings of the 2007 Reconfigurable Systems Summer Institute.

• Baxter et al, High Performance Reconfigurable Computing - the View from Edinburgh, invited keynote. In: Proceedings of the 2007 NASA/ESA Conference on Adaptive Hardware and Systems.

• Baxter et al, The FHPCA Parallel Toolkit, invited talk. In: Proceedings of the 2007 NASA/ESA Conference on Adaptive Hardware and Systems.

• Booth et al, Maxwell - a 64 FPGA Supercomputer, invited talk. In: Proceedings of the 2007 NASA/ESA Conference on Adaptive Hardware and Systems.

Books, newsletters, circulars, etc

• C. Palansuriya, G. Beckett, P. Graham, FPGAs – a new breed of hardware for high performance computing, EPCC News, Issue 59, October 2006.

• G. Beckett, P. Graham, J. Perry, C. Palansuriya, Scientific computing on FPGAs, edikt2 Technical Report, available from http://www.edikt.org.uk/edikt2/ScientificComputingOnFPGAsActivity, August 2006.

GeologicalModellingActivity

Journals

• Hill, J., Tetzlaff, D., Curtis, A. and Wood, R. Modeling shallow marine carbonate depositional systems, Computers & Geosciences, 2009, 35, 1862 - 1874. DOI: 10.1016/j.cageo.2008.12.006.

International conference presentations/papers

• J. Hill, A. Curtis, R. Wood & D. Tetzlaff. Exploring complexity in carbonate sediments. NANIA Meeting 2007, Barony Castle, Eddleston. 26-29th August, 2007.

Other Talks and Publications

• Hill, J., Wood, R., Curtis, A., and Tetzlaff, D. Exploring 5th order cycles in carbonate sediments. BSRG2008, Liverpool, December, 2008.

• Hill, J., Curtis, A., Wood, R., and Tetzlaff, D. Modelling shallow marine carbonate depositional systems. Petroleum Geoscience Research Forum, Aberdeen, November, 2008.

• M. Hambley and J. Hill. The NearCoM model: Applicability to geological forward model verification, edikt2 Technical Report, available from http://www.edikt.org.uk/edikt2/GeologicalModellingActivity, December 2007.

INWAGridAPANDemoActivity

Refereed Journals

• A. Lloyd and T. Sloan, Intercontinental Grids: An Infrastructure for Demand-Driven Innovation, Journal of Grid Computing, Volume 9, Number 2, pp 185-200, DOI http://dx.doi.org/10.1007/s10723-011-9190-3

International conference presentations/papers

• A. D. Lloyd, Intercontinental Grids: an infrastructure for demand-driven innovation, UK e-Science All Hands Meeting 2008, 8th-11th September 2008, Edinburgh, UK.

• A.D.Lloyd, T.M.Sloan and B.Yan. Global Competitiveness and Regional Innovation – using the Grid to “close the gap between Business, Research and Resources. 24th Asia-Pacific Advanced Network Conference, Xi’An, China, 28 August 2007.

• A.D.Lloyd.Grid-enabled fusion of global data and local knowledge - applying the INWA Grid to eResearch links with China. Australian Research Council, Special Research Initiative Workshop on eResearch, Old Parliament House, Canberra, Australia 14-15 February 2007.

Books, newsletters, circulars, etc

• J. Ferguson, INWA, EPCC News Issue 61, Autumn 2007.

Parallel statistics in R - SPRINT

Refereed Journal Articles

• Jon Hill, Matthew Hambley, Thorsten Forster, Muriel Mewissen, Terence M Sloan, Florian Scharinger, Arthur Trew and Peter Ghazal, SPRINT: A new parallel framework for R, BMC Bioinformatics. 2008; 9: 558. Published online 2008 December 29. doi: 10.1186/1471-2105-9-558.

• S. Petrou, T. M. Sloan, M. Mewissen, T. Forster, M. Piotrowski, B. Dobrzelecki, P. Ghazal, A. Trew and J. Hill, “Optimization of a parallel permutation testing function for the SPRINT R package,” Concurrency & Computation: Practice & Experience, Accepted for publication 2011.

International conference presentations/papers

• Petrou, S., Sloan, T.M., Mewissen, M., Forster, T., Piotrowski, M., Dobrzelecki, B., Ghazal, P., Trew, A., Hill, J. Optimization of a parallel permutation testing function for the SPRINT R package. Emerging Computational Methods for the Life Sciences Workshop in conjunction with ACM International Symposium on High Performance and Distributed Computing (HPDC), June 21-25, 2010, Chicago, Illinois, USA.

• M. Mewissen, T. Forster, T. Sloan, S. Petrou, M. Piotrowski, B Dobrelewski, P. Ghazal, A. Trew, J. Hill, SPRINT: a Simple Parallel R INTerface, useR! The RUser Conference 2010, July 20-23, 2010, Gaithersburg, Maryland, USA.

• L. Mitchell, T. M. Sloan, M. Mewissen, P. Ghazal, T. Forster, M. Piotrwowski and A. Trew, A Parallel Random Forest Classifier for R, Emerging Computational Methods for the Life Sciences Workshop, ACM International Symposium on High Performance Distributed Computing, San Jose, USA, 2011.

• M. Piotrowski, T.M. Sloan, M. Mewissen, T. Forster, L. Mitchell, S. Petrou, B. Dobrezelecki, P. Ghazal, A. Trew and J. Hill, Optimisation and Parallelisation of the Partitioning Around Medoids Function in R, International Workshop on High Performance Computing Systems for Biomedical, Bioinformatics and Life Sciences (BILIS 2011), The 2011 International Conference on High Performance Computing & Simulation (HPCS 2011), Istanbul, Turkey, July 2011.

• T. Sloan Using the Simple Parallel R INTerface (SPRINT) in the cloud, Workshop on Grid and Cloud Computing for Computational (Bio-)statistics, 23rd March 2011, Garching, Germany, http://rostlab.org/cms/cloudstat2011/

Books, newsletters, circulars, etc

• B. Dobrzelecki, A. Krause, M. Piotrowski and N. Chue Hong. Managing and analysing Genomic Data using HPC and Clouds, in Grid and Cloud Database Management, 1st ed., Springer, 2011.

• T. Sloan, SPRINT : Data analysis in minutes not days, EPCC News Issue 68, Autumn 2010.

• T. Sloan, Wellcome Trust grants further funding for SPRINT, EPCC News Issue 66, Autumn 2009.

• J. Hill, Parallel statistics with R, EPCC News Issue 62, Spring 2008.

Miscellaneous

Refereed Journal Articles

• P. Boyle, R. Kenway and C. Maynard, UKQCD software for lattice QCD, Phil. Trans. R. Soc. A, vol 367 p2858, 2009.

• Arun Jagatheesan, Michael Wan, Wayne Schroeder, Chris Cribbs, Ray Plante, Jeff Kantor, Tim Axelrod, Chris Smith, Petri Garagorri, Ron Lambert, David Walker, Mark Holliman, Elena Breitmoser, Robert G. Mann, Arthur Trew , Jean-Yves Nief, David Gehrig, Reagan Moore, Arcot Rajasekar, Data-lifecycle Management over a Loosely Coupled Distributed Infrastructure for LSST's HPC Applications, Supercomputing 2008, November15th - 21st, 2008, Austin, Texas, USA.

International conference presentations/papers

• Illingworth, M.,DEISA & DESHL European Projects Showcase, CCGRID 2008 – 8th International Symposium on Cluster Computing and the Grid, May 19th – 22nd 2008, Lyon, France.

• M. Illingworth, Evaluating user-level grid middleware independence, UK e-Science All Hands Meeting 2008, 8th-11th September 2008, Edinburgh, UK.

• Sloan, T., The DEISA Life-Science Portal based on UNICORE 6, UNICORE and Supercomputing Workshop 2009, March 18th 2009 Frankfurt, Germany.

• C. Maynard, UKQCD software for lattice QCD, UK e-Science All Hands Meeting 2008, 8th-11th September 2008, Edinburgh, UK.

• S.J. Lycett, M. Weiland, M.Ward, A. F. Y. Poon, S. L. Kosakovsky Pond, A. J. Leigh-Brown, Detecting VIRAL ADAPTATIONS TO HOST AND EPISTATIC INTERACTIONS USING BAYESIAN GRAPHICAL MODELS, 16th International HIV Dynamics & Evolution held April 4-7, 2009, Oxford, UK.

• Lycett S. J., Weiland M., Raghwani J., Rambaut A., Leigh Brown A. J., Adaptation of H1N1 and H5N1 Influenza viruses to mammalian hosts. Epidemics 2 Athens, Greece 2-4 Dec 2009.

Books, newsletters, circulars, etc

• J. Hill, EPCC on tour with eDIKT2, EPCC News Issue 60, Summer 2007

• J. Hill, Research computing with eDIKT2, EPCC News Issue 59, October 2006

• J. Hill, Exploiting Computers in Research, Invited Seminar. School of Chemistry, The University of Edinburgh, March 1st 2007.

• J. Hill, Exploiting Computers in Research, Invited Seminar. School of Chemistry, The University of Edinburgh, February 27th 2007.

• T. M. Sloan, High Performance Computing in Business, Invited Seminar. The University of Edinburgh Management School, February 13th 2007.

• J. Hill, Exploiting Computers in Research, Invited Seminar. School of Chemistry, The University of Edinburgh, January 26th 2007.

• J. Hill, Exploiting Computers in Research, Invited Seminar. School of Engineering and Electronics, The University of Edinburgh, October 19th 2006.

• J. Hill, Exploiting Computers in Research, Invited Seminar. Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, October 17th 2006.

• J. Hill,Exploiting Computers in Research, Invited Seminar. School of Geosciences, Grant Institute, The University of Edinburgh, October 6th 2006.

• G.Beckett, DiGS - Distributed Grid Storage, A Data Grid for UK QCD and beyond, Research in e-Infrastructure Development Seminar, National e-Science Centre, Edinburgh, March 7th 2007.

• F. Reid, Blue Gene tackles cancer genes, EPCC News, Issue 59, October 2006.

• C. Palansuriya, G. Beckett, P. Graham, FPGAs – a new breed of hardware for high performance computing, EPCC News, Issue 59, October 2006.

• J. Hill, Novel Computing in Science: exploiting High Performance. BITs – Bulletin of IT Services, University of Edinburgh, July 2006.

Edinburgh Compute and Data Facility (ECDF) - ComputationalService

Information on publications resulting from use of the ECDF can be found using the following Google Search

http://scholar.google.co.uk/scholar?hl=en&q=www.ecdf.ed&btnG=Search

Here is small selection of these many publications, of which there are over 100.

Refereed Journal Articles

• Andrea J. Betancourt, John J. Welch, Brian Charlesworth, Reduced Effectiveness of Selection Caused by a Lack of Recombination, 28 April 2009 Current Biology 19(8) pp. 655 - 660.

• Javier Tejedor, Dong Wang, Joe Frankel, Simon King, and José Colás. A comparison of grapheme and phoneme-based units for Spanish spoken term detection, Speech Communication, 50(11-12):980-991, November-December 2008.

• J. Hernández-Sánchez, J.A. Grunchec and S. Knott. A web application to perform linkage disequilibrium and linkage analyses on acomputational grid. Bioinformatics 25(11): 1377-1383 (2009). http://bioinformatics.oxfordjournals.org/cgi/reprint/btp171v1.pdf

International conference presentations/papers

• Abhishek Arun, Chris Dyer, Barry Haddow, Phil Blunsom, Adam Lopez, and Philipp Koehn. Monte Carlo inference and maximization for phrase-based translation Proceedings of CoNLL, June 2009. http://aclweb.org/anthology-new/W/W09/W09-1114.pdf

• Dong Wang, Ivan Himawan, Joe Frankel, Simon King, A Posterior Approach for Microphone Array Based Speech Recognition, Interspeech 08, Brisbane, Australia, September, 2008.

• Zheng Wang and Michael O'Boyle,Partitioning Streaming Parallelism for Multi-cores: A Machine Learning Based Approach, In 19th Intl. Conference on Parallel Architectures and Compilation Techniques (PACT), September, 2010. Best Paper Nominated

Books, newsletters, circulars, etc

Articles on ECDF have appeared in a number of Edinburgh University publications, including the University Bulletin; BITs; the NeSC Newsletter; EPCC News.