Publications
Publications
Journal Papers
(2012) Bourn, RL., Pinto, RM., Sandi, C., Al-Mahdawi, S., Pook, M. and Bidichandani, S., Pms2 suppresses large expansions of the (GAA·TTC)n sequence in neuronal tissues, PLoS One 7 (10) : e47085 Download publication
(2012) Xia, H., Cao, Y., Dai, X., Marelja, Z., Zhou, D., Mo, R., Al-Mahdawi, S., Pook, MA., Leimkühler, S., Rouault, TA. and Li, K., Novel frataxin isoforms may contribute to the pathological mechanism of friedreich ataxia, PLoS ONE 7 (10) : e47847
(2012) Ezzatizadeh, V., Mouro Pinto, R., Sandi, C., Sandi, M., Al-Mahdawi, S., te Riele, H. and Pook, MA., The mismatch repair system protects against intergenerational GAA repeat instability in a Friedreich ataxia mouse model, Neurobiology of Disease 46 (1) : 165- 171 Download publication
(2012) Tomassini, B., Arcuri, G., Fortuni, S., Sandi, C., Ezzatizadeh, V., Casali, C., Condò, I., Malisan, F., Al-Mahdawi, S., Pook, M. and Testi, R., Interferon gamma upregulates frataxin and corrects the functional deficits in a Friedreich ataxia model., Hum Mol Genet 21 (13) : 2855- 2861 Download publication
(2012) Tucker, A. and Duplisea, D., Bioinformatics tools in predictive ecology: Applications to fisheries, Philosophical Transactions of the Royal Society: Part B 367 (1586) : 279- 290 Download publication
(2012) Paterson, A., Ashtari, M., Ribe, D., Stenbeck, G. and Tucker, A., Intelligent data analysis to model and understand live cell time-lapse sequences, Methods of Information in Medicine 51 279- 367
(2012) Soldatova, L., Gao, Q. and Gilbert, D., Towards an ontology of biomodelling, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 7605 LNBI 390- 393
(2012) Gao, Q., Gilbert, D., Heiner, M., Liu, F., Maccagnola, D. and Tree, D., Multiscale Modelling and Analysis of Planar Cell Polarity in the Drosophila Wing., IEEE/ACM Trans Comput Biol Bioinform Download publication
(2011) Sandi, C., Pinto, RM., Al-Mahdawi, S., Ezzatizadeh, V., Barnes, G., Jones, S., Rusche, JR., Gottesfeld, JM. and Pook, MA., Prolonged treatment with pimelic o-aminobenzamide HDAC inhibitors ameliorates the disease phenotype of a Friedreich ataxia mouse model, Neurobiology of Disease 42 (3) : 496- 505
(2011) Pey, J., Prada, J., Beasley, JE. and Planes, FJ., Path finding methods accounting for stoichiometry in metabolic networks, Genome Biology 12 (5) : R49-
(2011) Anvar, SY., Tucker, A., Vinciotti, V., Venema, A., van Ommen, GB., van der Maarel, SM., Raz, V. and 't Hoen, PAC., Interspecies translation of disease networks increases robustness and predictive accuracy, PLoS Computational Biology 7 (11) : e1002258
(2011) Whalley, HJ., Sargeant, AW., Steele, JF., Lacoere, T., Lamb, R., Saunders, NJ., Knight, H. and Knight, MR., Transcriptomic analysis reveals calcium regulation of specific promoter motifs in Arabidopsis, Plant Cell 23 (11) : 4079- 4095
(2011) Porter, SL., Wilkinson, DA., Byles, ED., Wadhams, GH., Taylor, S., Saunders, NJ. and Armitage, JP., Genome sequence of Rhodobacter sphaeroides strain WS8N, Journal of Bacteriology 193 (15) : 4027- 4028 Download publication
(2011) Vijayakrishnan, S., Callow, P., Nutley, MA., McGow, DP., Gilbert, D., Kropholler, P., Cooper, A., Byron, O. and Lindsay, JG., Variation in the organization and subunit composition of the mammalian pyruvate dehydrogenase complex E2/E3BP core assembly, Biochemical Journal 437 (3) : 565- 574
(2011) van Kester, MS., Ballabio, E., Benner, MF., Chen, XH., Saunders, NJ., van der Fits, L., van Doorn, R., Vermeer, MH., Willemze, R., Tensen, CP. and Lawrie, CH., miRNA expression profiling of mycosis fungoides, Molecular Oncology 5 (3) : 273- 280
(2011) Chi, JX., Ballabio, E., Chen, XH., Kusec, R., Taylor, S., Hay, D., Tramonti, D., Saunders, NJ., Littlewood, T., Pezzella, F., Boultwood, J., Wainscoat, JS., Hatton, CSR. and Lawrie, CH., MicroRNA expression in multiple myeloma is associated with genetic subtype, isotype and survival, Biology Direct 623 Download publication
(2011) Saunders, NJ., Trivedi, UH., Thomson, ML., Doig, C., Laurenson, IF. and Blaxter, ML., Deep resequencing of serial sputum isolates of Mycobacterium tuberculosis during therapeutic failure due to poor compliance reveals stepwise mutation of key resistance genes on an otherwise stable genetic background, Journal of Infection 62 (3) : 212- 217
(2010) Tucker, A. and Garway-Heath, D., The pseudotemporal bootstrap for predicting glaucoma from cross-sectional visual field data., IEEE Trans Inf Technol Biomed 14 (1) : 79- 85 Download publication
(2010) Anvar, SY., 't Hoen, PA. and Tucker, A., The identification of informative genes from multiple datasets with increasing complexity, BMC Bioinformatics 11 32- Download publication
(2010) Sturm, OE., Orton, R., Grindlay, J., Birtwistle, M., Vyshemirsky, V., Gilbert, D., Calder, M., Pitt, A., Kholodenko, B. and Kolch, W., The mammalian MAPK/ERK pathway exhibits properties of a negative feedback amplifier., Science Signaling 3 (153) : ra90-
(2010) Gu, X., Trybilo, M., Ramsey, S., Jensen, M., Fulton, R., Rosser, S. and Gilbert, D., Engineering a novel self-powering electrochemical biosensor, Systems and Synthetic Biology 4 (3) : 203- 214 Download publication
(2010) Gilbert, D., Heiner, M., Breitling, R. and Orton, R., Computational modelling of kinase signalling cascades, Methods in Molecular Biology 661 369- 384
(2010) Veeramalai, M., Gilbert, D. and Valiente, G., An optimized TOPS plus comparison method for enhanced TOPS models, BMC Bioinformatics 11138 Download publication
(2010) Gilbert, D., Jaramillo, A., Krasnogor, N. and de Lorenzo, V., Editorial: Synthetic biology gains momentum in Europe, Systems and Synthetic Biology 4 (3) : 145- 147
(2010) Ballabio, E., Mitchell, T., van Kester, MS., Taylor, S., Dunlop, HM., Chi, JX., Tosi, I., Vermeer, MH., Tramonti, D., Saunders, NJ., Boultwood, J., Wainscoat, JS., Pezzella, F., Whittaker, SJ., Tensen, CP., Hatton, CSR. and Lawrie, CH., MicroRNA expression in Sezary syndrome: identification, function, and diagnostic potential, Blood 116 (7) : 1105- 1113
(2010) Grzmil, M., Rzymski, T., Milani, M., Harris, AL., Capper, RG., Saunders, NJ., Salhan, A., Ragoussis, J. and Norbury, CJ., An oncogenic role of eIF3e/INT6 in human breast cancer, Oncogene 29 (28) : 4080- 4089
(2010) Farquhar, CA., Paterson, AM., Cobbold, SP., Rueda, HG., Fairchild, PJ., Yates, SF., Adams, E., Saunders, NJ., Waldmann, H. and Nolan, KF., Tolerogenicity is not an absolute property of a dendritic cell, European Journal of Immunology 40 (6) : 1728- 1737
(2010) Sainsbury, S., Ren, J., Nettleship, JE., Saunders, NJ., Stuart, DI. and Owens, RJ., The structure of a reduced form of OxyR from Neisseria meningitidis, BMC Structural Biology 1010 Download publication
(2010) Ren, J., Sainsbury, S., Nettleship, JE., Saunders, NJ. and Owens, RJ., The crystal structure of NGO0477 from Neisseria gonorrhoeae reveals a novel protein fold incorporating a helix-turn-helix motif, Proteins: Structure, Function, and Bioinformatics 78 (7) : 1798- 1802
(2010) Malhas, A., Saunders, NJ. and Vaux, DJ., The nuclear envelope can control gene expression and cell cycle progression via miRNA regulation, Cell Cycle 9 (3) : 531- 539
(2010) Ren, J., Samshury, S., Nettleship, JE., Saunders, NJ. and Owens, RJ., The crytal structure of NGOO47 from Neisseria gonorrhoeae reveals a novel protein fold incorporating a helix-turn-helix motif, Proteins: Structure, Function and Bioinformatics 78 (7) : 1798- 1802
(2009) Planes, FJ. and Beasley, JE., Path finding approaches and metabolic pathways, Discrete Applied Mathematics 157 (10) : 2244- 2256
(2009) Planes, FJ. and Beasley, JE., An optimization model for metabolic pathways, BIOINFORMATICS 25 (20) : 2723- 2729
(2009) de Figueiredo, LF., Podhorski, A., Rubio, A., Kaleta, C., Beasley, JE., Schuster, S. and Planes, FJ., Computing the shortest elementary flux modes in genome-scale metabolic networks, BIOINFORMATICS 25 (23) : 3158- 3165
(2009) Steele, E., Tucker, A., 't Hoen, PAC. and Schuemie, MJ., Literature-based priors for gene regulatory networks, Bioinformatics 25 (14) : 1768- 1774 Download publication
(2009) Park, SH., Reyes, JA., Gilbert, DR., Kim, JW. and Kim, S., Prediction of protein-protein interaction types using association rule based classification, BMC Bioinformatics 1036 Download publication
(2009) von Kriegsheim, A., Baiocchi, D., Birtwistle, M., Sumpton, D., Bienvenut, W., Morrice, N., Yamada, K., Lamond, A., Kalna, G., Orton, R., Gilbert, D. and Kolch, W., Cell fate decisions are specified by the dynamic ERK interactome, Nature Cell Biology 11 (12) : 1458- 1464
(2009) Torrance, GM., Leader, DP., Gilbert, DR. and Milner-White, EJ., A novel main chain motif in proteins bridged by cationic groups: the niche, Journal of Molecular Biology 385 (4) : 1076- 1086
(2009) Orton, RJ., Adriaens, ME., Gormand, A., Sturm, OE., Kolch, W. and Gilbert, DR., Computational modelling of cancerous mutations in the EGFR/ERK signalling pathway, BMC Systems Biology 3 100- Download publication
(2009) Howie, D., Nolan, KF., Daley, S., Butterfield, E., Adams, E., Garcia-Rueda, H., Thompson, C., Saunders, NJ., Cobbold, SP., Tone, Y., Tone, M. and Waldmann, H., MS4A4B is a GITR-associated membrane adapter, expressed by regulatory T cells, which modulates T cell activation, Journal of Immunology 183 (7) : 4197- 4204
(2009) Sainsbury, S., Lane, LA., Ren, J., Gilbert, RJ., Saunders, NJ., Robinson, CV., Stuart, DI. and Owens, RJ., The structure of CrgA from Neisseria meningitidis reveals a new octameric assembly state for LysR transcriptional regulators, Nucleic Acids Research 37 (14) : 4545- 4558 Download publication
(2009) Yao, Y., Zhao, Y., Smith, LP., Lawrie, CH., Saunders, NJ., Watson, M. and Nair, V., Differential expression of microRNAs in Marek's disease virus-transformed T-lymphoma cell lines, Journal of General Virology 90 (Pt 7) : 1551- 1559
(2009) Lawrie, CH., Chi, J., Taylor, S., Tramonti, D., Ballabio, E., Palazzo, S., Saunders, NJ., Pezzella, F., Boultwood, J., Wainscoat, JS. and Hatton, CSR., Expression of microRNAs in diffuse large B cell lymphoma is associated with immunophenotype, survival and transformation from follicular lymphoma, Journal of Cellular and Molecular Medicine 13 (7) : 1248- 1260
(2009) Gamba, P., Veening, JW., Saunders, NJ., Hamoen, LW. and Daniel, RA., Two-step assembly dynamics of the Bacillus subtilis divisome, Journal of Bacteriology 191 (13) : 4186- 4194
(2009) Okamoto, H., Göbel, C., Capper, RG., Saunders, N., Feussner, I. and Knight, MR., The α-subunit of the heterotrimeric G-protein affects jasmonate responses in Arabidopsis thaliana, Journal of Experimental Botany 60 (7) : 1991- 2003
(2009) Jordan, PW. and Saunders, NJ., Host iron binding proteins acting as niche indicators for Neisseria meningitidis, PLoS One 4 (4) : e5198 Download publication
(2009) Waters, MT., Wang, P., Korkaric, M., Capper, RG., Saunders, NJ. and Langdale, JA., GLK transcription factors coordinate expression of the photosynthetic apparatus in Arabidopsis, The Plant Cell 21 (4) : 1109- 1128 Download publication
(2009) Nichols, CE., Sainsbury, S., Ren, J., Walter, TS., Verma, A., Stammers, DK., Saunders, NJ. and Owens, RJ., The structure of NMB1585, a MarR-family regulator from Neisseria meningitidis, Acta Crystallographica Section F: Structural Biology and Crystallization Communications 65 (Pt 3) : 204- 209 Download publication
(2008) Planes, FJ. and Beasley, JE., A critical examination of stoichiometric and path-finding approaches to metabolic pathways, Briefings in Bioinformatics 9 (5) : 422- 436
(2008) Steele, E. and Tucker, A., Consensus and meta-analysis regulatory networks for combining multiple microarray gene expression datasets, Journal of Biomedical Informatics 41 (6) : 914- 926 Download publication
(2008) Breitling, R., Gilbert, D., Heiner, M. and Orton, R., A structured approach for the engineering of biochemical network models, illustrated for signalling pathways, Briefings in Bioinformatics 9 (5) : 404- 421 Download publication
(2008) Veeramalai, M. and Gilbert, D., A novel method for comparing topological models of protein structures enhanced with ligand information, Bioinformatics 24 (23) : 2698- 2705
(2008) Sainsbury, S., Ren, J., Saunders, NJ., Stuart, DI. and Owens, RJ., Crystallization and preliminary X-ray analysis of CrgA, a LysR-type transcriptional regulator from pathogenic Neisseria meningitidis MC58, Acta Crystallographica Section F: Structural Biology and Crystallization Communications 64 (Pt 9) : 797- 801 Download publication
(2008) Grosan, C., Abraham, A. and Tigan, S., Multicriteria programming in medical diagnosis and treatments, Applied Soft Computing 8 (4) : 1407- 1417
(2008) Ren, J., Nettleship, JE., Sainsbury, S., Saunders, NJ. and Owens, RJ., Structure of the cold-shock domain protein from Neisseria meningitidis reveals a strand-exchanged dimer, Acta Crystallographica Section F: Structural Biology and Crystallization Communications 64 (Pt 4) : 247- 251 Download publication
(2008) Lawrie, CH., Saunders, NJ., Soneji, S., Palazzo, S., Dunlop, HM., Cooper, CDO., Brown, PJ., Troussard, X., Mossafa, H., Enver, T., Pezzella, F., Boultwood, J., Wainscoat, JS. and Hatton, CSR., MicroRNA expression in lymphocyte development and malignancy, Leukemia 22 1440- 1446
(2008) Harper, KN., Ocampo, PS., Steiner, BM., George, RW., Silverman, MS., Bolotin, S., Pillay, A., Saunders, NJ. and Armelagos, GJ., On the origin of trepanomatoses: A phylogenetic approach, PLoS Neglected Tropical Diseases 2 (1) : e148 Download publication
(2007) Beasley, JE. and Planes, FJ., Recovering metabolic pathways via optimization, Bioinformatics 23 (1) : 92- 98
(2007) Snyder, LAS., McGowan, S., Rogers, M., Duro, E., O'Farrell, E. and Saunders, NJ., The repertoire of minimal mobile elements in the Neisseria species and evidence that these are involved in horizontal gene transfer in other bacteria, Molecular Biology and Evolution 24 (12) : 2802- 2815
(2007) Bennett, JS., Jolley, KA., Sparling, PF., Saunders, NJ., Hart, CA., Feavers, IM. and Maiden, MCJ., Species status of Neisseria gonorrhoeae: Evolutionary and epidemiological inferences from multilocus sequence typing, BMC Biology 535 Download publication
(2007) Tett, A., Spiers, AJ., Crossman, LC., Ager, D., Ciric, L., Dow, JM., Fry, JC., Harris, D., Lilley, A., Oliver, A., Parkhill, J., Quail, MA., Rainey, PB., Saunders, NJ., Seeger, K., Snyder, LAS., Squares, R., Thomas, CM., Turner, SL., Zhang, XX., Field, D. and Bailey, MJ., Sequence-based analysis of pQBR103; a representative of a unique, transfer-proficient mega plasmid resident in the microbial community of sugar beet, ISME Journal 1 (4) : 331- 340
(2007) Yates, SF., Paterson, AM., Nolan, KF., Cobbold, SP., Saunders, NJ., Waldmann, H. and Fairchild, PJ., Induction of regulatory T cells and dominant tolerance by dendritic cells incapable of full activation, Journal of Immunology 179 (2) : 967- 976
(2007) Ren, J., Sainsbury, S., Combs, SE., Capper, RG., Jordan, PW., Berrow, NS., Stammers, DK., Saunders, NJ. and Owens, RJ., The structure and transcriptional analysis of a global regulator from Neisseria meningitidis, Journal of Biological Chemistry 282 (19) : 14655- 14664
(2007) Malhas, A., Lee, CF., Sanders, R., Saunders, NJ. and Vaux, DJ., Defects in lamin B1 expression or processing affect interphase chromosome position and gene expression, The Journal of Cell Biology 176 (5) : 593- 603 Download publication
(2007) Bentley, SD., Vernikos, GS., Snyder, LAS., Churcher, C., Arrowsmith, C., Chillingworth, T., Cronin, A., Davis, PH., Holroyd, NE., Jagels, K., Maddison, M., Moule, S., Rabbinowitsch, E., Sharp, S., Unwin, L., Whitehead, S., Quail, MA., Achtman, M., Barrell, B., Saunders, NJ. and Parkhill, J., Meningococcal genetic variation mechanisms viewed through comparative analysis of Serogroup C strain FAM18, PLoS Genetics 3 (2) : e23 Download publication
(2007) Whitehead, RN., Overton, TW., Snyder, LAS., McGowan, SJ., Smith, H., Cole, JA. and Saunders, NJ., The small FNR regulon of Neisseria gonorrhoeae: Comparison with the larger E. coli FNR regulon and interaction with the NarQ-NarP regulon, BMC Genomics 835 Download publication
(2006) Vinciotti, V., Tucker, A., Kellam, P. and Liu, X., The robust selection of predictive genes via a simple classifier, Applied Bioinformatics 5 (1) : 1- 11 Download publication
(2006) Tucker, A., 't Hoen, PAC., Vinciotti, V. and Liu, X., Temporal Bayesian classifiers for modelling muscular dystrophy expression data, Intelligent Data Analysis 10 (5) : 441- 455 Download publication
(2006) Morrison, JL., Breitling, R., Higham, DJ. and Gilbert, DR., A lock-and-key model for protein-protein interactions., Bioinformatics 22 2012- 2019
(2006) Overton, TW., Whitehead, R., Li, Y., Snyder, LAS., Saunders, NJ., Smith, H. and Cole, JA., Coordinated regulation of the Neisseria gonorrhoeae-truncated denitrification pathway by the Nitric Oxide-sensitive repressor, NsrR, and Nitrite-insensitive NarQ-NarP, Journal of Biological Chemistry 281 (44) : 33115- 33126
(2006) Salaün, L. and Saunders, NJ., Population-associated differences between the phase variable LPS biosynthetic genes of Helicobacter pylori, BMC Microbiology 679 Download publication
(2006) Gunesekere, IC., Kahler, CM., Powell, DR., Snyder, LAS., Saunders, NJ., Rood, JI. and Davies, JK., Comparison of the RpoH-dependent regulon and general stress response in Neisseria gonorrhoeae, Journal of Bacteriology 188 (13) : 4769- 4776
(2006) Nichols, CE., Sainsbury, S., Berrow, NS., Alderton, D., Saunders, NJ., Stammers, DK. and Owens, RJ., Structure of the PII signal transduction protein of Neisseria meningitidis at 1.85 Ȃ resolution, Acta Crystallographica Section F: Structural Biology and Crystallization Communications 62 (Pt 6) : 494- 497 Download publication
(2006) Snyder, LAS. and Saunders, N., The majority of genes in the pathogenic Neisseria species are present in non-pathogenic Neisseria lactamica, including those designated as 'virulence genes', BMC Genomics 7128 Download publication
(2006) Gunesekere, IC., Kahler, CM., Ryan, CS., Snyder, LAS., Saunders, NJ., Rood, JI. and Davies, JK., Ecf, an alternative sigma factor from Neisseria gonorrhoeae, controls expression of msrAB, which encodes methionine sulfoxide reductase, Journal of Bacteriology 188 (10) : 3463- 3469
(2005) Torrance, GM., Gilbert, DR., Michalopoulos, I. and Westhead, DR., Protein structure topological comparison, discovery and matching service., Bioinformatics 21 2537- 2538
(2005) Snyder, LAS., Jarvis, SA. and Saunders, NJ., Complete and variant forms of the ‘gonococcal genetic island’ in Neisseria meningitidis, Microbiology 151 (12) : 4005- 4013
(2005) Saunders, NJ., Boonmee, P., Peden, JF. and Jarvis, SA., Inter-species horizontal transfer resulting in core-genome and niche-adaptive variation within Helicobacter pylori, BMC Genomics 69 Download publication
(2005) Snyder, LAS., Davies, JK., Ryan, CS. and Saunders, NJ., Comparative overview of the genomic and genetic differences between the pathogenic Neisseria strains and species, Plasmid 54 (3) : 191- 218
(2005) Ren, JS., Sainsbury, S., Berrow, NS., Alderton, D., Nettleship, JE., Stammers, DK., Saunders, NJ. and Owens, RJ., Crystal structure of nitrogen regulatory protein IIA(Ntr) from Neisseria meningitidis, BMC Structural Biology 513 Download publication
(2005) Herbert, MA., Beveridge, CJE., McCormick, D., Aten, E., Jones, N., Snyder, LAS. and Saunders, NJ., Genetic islands of Streptococcus agalactiae strains NEM316 and 2603VR and their presence in other Group B Streptococcal strains, BMC Microbiology 531 Download publication
(2005) Jordan, PW., Snyder, LAS. and Saunders, NJ., Strain-specific differences in Neisseria gonorrhoeae associated with the phase variable gene repertoire, BMC Microbiology 521 Download publication
(2005) Letarte, M., Voulgaraki, D., Hatherley, D., Foster-Cuevas, M., Saunders, NJ. and Barclay, AN., Analysis of leukocyte membrane protein interactions using protein microarrays, BMC Biochemistry 62 Download publication
(2005) Salaün, L., Ayraud, S. and Saunders, NJ., Phase variation mediated niche adaptation during prolonged experimental murine infection with Helicobacter pylori, Microbiology 151 (3) : 917- 923
(2004) Swift, S., Tucker, A., Vinciotti, V., Martin, N., Orengo, C., Liu, X. and Kellam, P., Consensus clustering and functional interpretation of gene-expression data, Genome Biology 5 (11) : R94- R94 Download publication
(2004) Michalopoulos, I., Torrance, GM., Gilbert, DR. and Westhead, DR., TOPS: an enhanced database of protein structural topology., Nucleic Acids Research 32 251- 254
(2004) Gravenor, MB. and Saunders, NJ., Estimation of mutation rates, Biometrics 60 (4) : 1053- 1054
(2004) Herbert, MA., Beveridge, CJE. and Saunders, NJ., Bacterial virulence factors in neonatal sepsis: Group B streptococcus, Current Opinion in Infectious Diseases 17 (3) : 225- 229
(2004) Snyder, LAS., Davies, JK. and Saunders, NJ., Microarray genomotyping of key experimental strains of Neisseria gonorrhoeae reveals gene complement diversity and five new neisserial genes associated with minimal mobile elements, BMC Genomics 523 Download publication
(2004) Salaün, L., Linz, B., Suerbaum, S. and Saunders, NJ., The diversity within an expanded and redefined repertoire of phase-variable genes in Helicobacter pylori, Microbiology 150 (4) : 817- 830
(2003) Jordan, P., Snyder, LAS. and Saunders, NJ., Diversity in coding tandem repeats in related Neisseria spp, BMC Microbiology 323 Download publication
(2003) Saunders, NJ., Richard Moxon, E. and Gravenor, MB., Mutation rates: Estimating phase variation rates when fitness differences are present and their impact on population structure, Microbiology 149 (2) : 485- 495
(2003) Maloy, KJ., Salaun, L., Cahill, R., Dougan, G., Saunders, NJ. and Powrie, F., CD4+CD25+ TR cells suppress innate immune pathology through cytokine-dependent mechanisms, Journal of Experimental Medicine 197 (1) : 111- 119 Download publication
(2003) Salaün, L., Snyder, LAS. and Saunders, NJ., Adaptation by phase variation in pathogenic bacteria, Advances in Applied Microbiology 52 263- 301
(2003) Snyder, LAS., Shafer, WM. and Saunders, NJ., Divergence and transcriptional analysis of the division cell wall (dcw) gene cluster in Neisseria spp., Molecular Microbiology 47 (2) : 431- 442
(2002) Saunders, NJ. and Snyder, LAS., The minimal mobile element, Microbiology 148 (12) : 3756- 3760
(2002) Liu, SV., Saunders, NJ., Jeffries, A. and Rest, RF., Genome analysis and strain comparison of Correia repeats and Correia repeat-enclosed elements in pathogenic Neisseria, Journal of Bacteriology 184 (22) : 6163- 6173
(2002) Moxon, ER., Hood, DW., Saunders, NJ., Schweda, EKH. and Richards, JC., Functional genomics of pathogenic bacteria, Philosophical Transactions of the Royal Society of London: Biological Sciences 357 (1417) : 109- 116
(2001) Snyder, LAS., Butcher, SA. and Saunders, NJ., Comparative whole genome analyses reveal over 100 putative phase variable genes in the pathogenic Neisseria spp, Microbiology 147 (8) : 2321- 2332
(2001) Snyder, LAS., Saunders, NJ. and Shafer, WM., A putatively phase variable gene (dca) required for natural competence in Neisseria gonorrhoeae but not Neisseria meningitidis is located within the division cell wall (dcw) gene cluster, Journal of Bacteriology 183 (4) : 1233- 1241
(2000) Gilbert, DR., Schroeder, M. and Van Helden, J., Interactive visualization and exploration of relationships between biological objects, Trends in Biotechnology 18 (12) : 487- 494
(2000) Saunders, NJ., Jeffries, AC., Peden, JF., Hood, DW., Tettelin, H., Rappuoli, R. and Richard Moxon, E., Repeat-associated phase variable genes in the complete genome sequence of Neisseria meningitidis strain MC58, Molecular Microbiology 37 (1) : 207- 215
(2000) Saunders, NJ. and Jeffries, AC., The growing utility of microbial genome sequences (Meeting Report), Genome Biology 1 (1) : 410 Download publication
(2000) Saunders, NJ., Peden, JF. and Richard Moxon, E., DNA uptake sequences in Helicobacter pylori - Authors’ reply, Microbiology 146 (6) : 1255- 1256
(2000) Saunders, NJ., Jeffries, AC., Hood, DW. and Richard Moxon, E., High rates of phase variation in Campylobacter jejuni, Molecular Microbiology 36 (6) : 1504- 1505
(2000) Saunders, NJ., Working from the particular to the general: The development of comparative genomics - A meeting report from the 4th Annual Conference on Microbial Genomes, Molecular Microbiology 36 (5) : 1034- 1036
(2000) Tettelin, H., Saunders, NJ., Heidelberg, J., Jeffries, AC., Nelson, KE., Eisen, JA., Ketchum, KA., Hood, DW., Peden, JF., Dodson, RJ., Nelson, WC., Gwinn, ML., DeBoy, R., Peterson, JD., Hickey, EK., Haft, DH., Salzberg, SL., White, O., Fleischmann, RD., Dougherty, BA., Mason, T., Ciecko, A., Parksey, DS., Blair, E., Cittone, H., Clark, EB., Cotton, MD., Utterback, TR., Khouri, H., Qin, H., Vamathevan, J., Gill, J., Scarlato, V., Masignani, V., Pizza, M., Grandi, G., Sun, L., Smith, HO., Fraser, CM., Richard Moxon, E., Rappuoli, R. and Craig Venter, J., Complete genome sequence of Neisseria meningitidis Serogroup B Strain MC58, Science 287 (5459) : 1809- 1815
(2000) Pizza, M., Scarlato, V., Masignani, V., Giuliani, MM., Aricò, B., Comanducci, M., Jennings, GT., Baldi, L., Bartolini, E., Capecchi, B., Galeotti, CL., Luzzi, E., Manetti, R., Marchetti, E., Mora, M., Nuti, S., Ratti, G., Santini, L., Savino, S., Scarselli, M., Storni, E., Zuo, P., Broeker, M., Hundt, E., Knapp, B., Blair, E., Mason, T., Tettelin, H., Hood, DW., Jeffries, AC., Saunders, NJ., Granoff, DM., Venter, JC., Moxon, ER., Grandi, G. and Rappuoli, R., Identification of vaccine candidates against Serogroup B Meningococcus by whole-genome sequencing, Science 287 (5459) : 1816- 1820
(2000) De Bolle, X., Bayliss, CD., Field, D., Van De Ven, T., Saunders, NJ., Hood, DW. and Richard Moxon, E., The length of a tetranucleotide repeat tract in Haemophilus influenzae determines the phase variation rate of a gene with homology to type III DNA methyltransferases, Molecular Microbiology (35) : 211- 222
(1999) Saunders, NJ., Peden, JF. and Richard Moxon, E., Absence in Helicobacter pylori of an uptake sequence for enhancing uptake of homospecific DNA during transformation, Microbiology 145 (12) : 3523- 3528
(1999) Saunders, NJ., Hood, DW. and Richard Moxon, E., Bacterial evolution: Bacteria play pass the gene, Current Biology 9 (5) : R180- R183
(1998) Saunders, NJ. and Richard Moxon, E., Implications of sequencing bacterial genomes for pathogenesis and vaccine development, Current Opinion in Biotechnology 9 (6) : 618- 623
(1998) Hosking, SL., Deadman, ME., Richard Moxon, E., Peden, JF., Saunders, NJ. and High, NJ., An in silico evaluation of Tn916 as a tool for generalized mutagenesis in Haemophilus influenzae Rd, Microbiology 144 (9) : 2525- 2530
(1998) Saunders, NJ., Peden, JF., Hood, DW. and Richard Moxon, E., Simple sequence repeats in the Helicobacter pylori genome, Molecular Microbiology 27 (6) : 1091- 1098
(1998) Shackley, F., Roberts, P., Heath, P., Bowler, I. and Saunders, NJ., Trough-only monitoring of serum vancomycin concentrations in neonates, Journal of Antimicrobial Chemotherapy 41 (1) : 141- 142
(1995) Saunders, NJ., Adams, DJ. and Lynn, WA., A prospective laboratory-based audit of gentamicin use and therapeutic monitoring, Journal of Antimicrobial Chemotherapy 36 (4) : 729- 736
(1995) Saunders, NJ., Want, SV. and Adams, DJ., Assay of vancomycin by fluorescence polarisation immunoassay and EMIT in patients with renal failure, Journal of Antimicrobial Chemotherapy 36 (2) : 411- 415
(1995) Saunders, NJ., Vancomycin administration and monitoring reappraisal, Journal of Antimicrobial Chemotherapy 36 (2) : 279- 282
(1995) Saunders, NJ. and Cohen, J., A study of the interaction between recombinant bactericidal permeability increasing protein (rBPI23) and gentamicin, International Journal of Antimicrobial Agents 5 (4) : 259- 263
(1995) MacGowan, A., Lovering, A., White, L., Reeves, D., Collyns, TA., Oppenheim, BA., Wysocki, M., Thomas, F., Wolff, M., de Hoog, M., Mouton, JW., van den Anker, JN., Duffull, SB., Begg, EJ. and Saunders, NJ., Why monitor peak vancomycin concentrations? - Letters to the Editor, Lancet 345 (8950) : 645- 647
(1995) Esfahani, RF., Saunders, N., Ward, KN. and Hodgson, HJF., The spectrum of hepatitis C antibody positive disease in a teaching hospital, Journal of Infection 30 (2) : 115- 119
(1994) Saunders, NJ., Why monitor peak vancomycin concentrations?, Lancet 344 (8989-8940) : 1748- 1750
Conference Papers
(2012) Pook, M., Ezzatizadeh, V., Sandi, C. and Al-Mahdawi, S., MLH1 PROMOTES SOMATIC GAA REPEAT EXPANSIONS IN A FRIEDREICH ATAXIA MOUSE MODEL, 7th International Conference on Unstable Microsatellites and Human Disease
(2011) Gao, Q., Liu, F., Gilbert, D., Heiner, M. and Tree, D., A multiscale approach to modelling planar cell polarity in Drosophila wing using hierarchically coloured petri nets, 9th International Conference on Computational Methods in Systems Biology (CMSB 2011), ACM digital library 209- 218
(2011) Gao, Q., Liu, F., Tree, D. and Gilbert, D., Multi-cell modelling using coloured petri nets applied to planar cell polarity, 2nd International Workshop on Biological Processes & Petri Nets (BioPPN 2011), CEUR Workshop Proceedings (http://ceur-ws.org) 135- 150
(2011) Gilbert, D. and Heiner, M., How might petri nets enhance your systems biology toolkit, Applications and Theory of Petri Nets 32nd International Conference (PETRI NETS 2011), Lecture Notes in Computer Science (6709) : 17- 37
(2010) Wu, Z., Gao, Q. and Gilbert, D., Target driven biochemical network reconstruction based on petri nets and simulated annealing, 8th Conference on Computational Methods in Systems Biology (CMSB 2010)
(2009) Wang, J., Liu, X., Mustafee, N., Gao, Q., Taylor, SJE. and Gilbert, D., Grid-enabled SIMAP utility: motivation, integration technology and performance results, UK e-Science All Hands Meeting (AHM 2009) Download publication
(2007) Park, SH., Gilbert, D. and Ryu, KH., Fast structural similarity search based on topology string matching, 5th Asia-Pacific Bioinformatics Conference (APBC2007)
(2010) Kolch, W., Birtwistle, M., Kholodenko, B., Grindlay, J., Sturm, O., Orton, R., Gilbert, D. and von Kriegsheim, A., From benchside to byteside: what we can learn from computational modelling, 21st Meeting of the European-Association-for-Cancer-Research, EJC SUPPLEMENTS (8) : 3- 3
(1999) Helden, JV., Gilbert, D., Wernisch, L., Mancuso, R., Eldridge, M., Degtyarenko, K. and Wodak, SJ., Logical Tools for Quering and Assisting Annotation of a Biochemical Pathway Database., , German Conference on Bioinformatics 227- 229
(2007) Al-Shahib, A., Gilbert, D. and Breitling, R., Discriminating Microbial Species Using Protein Sequence Properties and Machine Learning., , IDEAL (4881) : 890- 897
Book Chapters
(2012) Pook, M., DNA methylation and trinucleotide repeat expansion diseases. In: Tatarinova, T. and Kerton, O. eds. DNA Methylation - From Genomics to Technology. on-line : InTech 193- 208
(2011) Lodhi, H. and Gilbert, D., Bootstrapping parameter estimation in dynamic systems. In: Elomaa, T., Hollmen, J. and Mannila, H. eds. Discovery Science: Proceedings of the 14th International Conference, DS 2011, Espoo, Finland, October 5-7, 2011. Springer (6926) : 194- 208
(2011) Saunders, NJ. and Davies, JK., The use of the pan-Neisseria microarray and experimental design for transcriptomics studies of Neisseria. In: Chrisodoulides, M. ed. Neisseria Meningitidis: Advanced Methods and Protocols. Springer (799) : 295- 317
(2010) Breitling, R., Donaldson, RA., Gilbert, DR. and Heiner, M., Biomodel engineering – from structure to behavior. In: Priami, C., Donaldson, RA., Gilbert, DR. and Heiner, M. eds. Transactions on Computational Systems Biology XII. Berlin/Heidelberg : Springer (5945/2010) : 1- 12
(2009) Heiner, M., Lehrack, S., Gilbert, D. and Marwan, W., Extended stochastic petri nets for model-based design of wetlab experiments. In: Transactions on Computational Systems Biology XI. Berlin/Heidelberg : Springer (5750/2009) : 138- 163
(2009) Gilbert, D., Breitling, R., Heiner, M. and Donaldson, R., An introduction to BioModel Engineering, illustrated for signal transduction pathways. In: Corne, DW., Frisco, P., Paun, G., Rozenberg, G. and Salomaa, A. eds. Membrane Computing. (5391/2009) : 13- 28 Download publication
(2008) Liu, X., Jiang, J., Ajayi, O., Gu, X., Gilbert, D. and Sinnott, R., BioNessieG - a grid enabled biochemical networks simulation environment. In: Solomonides, T., Silverstein, JC., Saltz, J., Legré, Y., Kratz, M., Foster, I., Breton, V. and Beck, JR. eds. Studies in Health Technology and Informatics. (138) : 147- 157 Download publication
(2008) Donaldson, R. and Gilbert, D., A model checking approach to the parameter estimation of biochemical pathways. In: Heiner, M. and Uhrmacher, AM. eds. Computational Methods in Systems Biology. (5307/2008) : 269- 287 Download publication
(2008) Gilbert, D., Heiner, M., Rosser, S., Fulton, R., Gu, X. and Trybilo, M., A case study in model-driven synthetic biology. In: Hinchey, M., Pagnoni, A., Rammig, FJ. and Schmeck, H. eds. Biologically-Inspired Collaborative Computing. (268/2008) : 163- 175 Download publication
(2007) Snyder, LAS., Jordan, PW. and Saunders, NJ., Neisseria: A post-genomic view. In: Pallen, MJ., Nelson, KE. and Preston, GM. eds. Bacterial pathogenomics. Washington, DC : American Society for Microbiology 90- 119
(2007) Snyder, LAS., Snudden, G., Haan, N. and Saunders, NJ., Comparative genomics: The nature of GCH analysis and data interpretation. In: Falciani, F. ed. Microarray technology through applications. Abingdon : Taylor & Francis 269- 284
(2007) Saunders, N., Protein microarrays. In: Falciani, F. ed. Microarray technology through applications. Abingdon : Taylor & Francis 211- 226
(2005) Saunders, NJ. and Snyder, LAS., The neisserial genomes: What they reveal about the diversity and behavior of these species. In: Dunn, MJ., Jorde, LB., Little, PFR. and Subramaniam, S. eds. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. Wiley
(2003) Saunders, NJ. and Butcher, S., The use of complete genome sequences in vaccine design. In: Vaccine Protocols. New Jersey : Humana Press (87) : 301- 312
(2003) Saunders, NJ., Evasion of antibody responses: Bacterial phase variation. In: Henderson, B. and Oyston, PCF. eds. Bacterial evasion of host immune responses. Cambridge : Cambridge University Press 103- 124
(2001) Jeffries, AC., Saunders, NJ. and Hood, DW., Genome sequencing and annotation. In: Pollard, AJ. and Maiden, MCJ. eds. Meningococcal disease. Humana Press Inc 215- 231
Books
(2010) Priami, C., Breitling, R., Gilbert, D., Heiner, M. and Uhrmacher, AM., Transactions on computational systems biology XII. Springer
(2009) Saunders, NJ., Flu And You: Your Questions Answered, And What You Need To Know. Twin Serpents Ltd
