Publications
Reviews & research articles
2010
Nègre, N., Brown, C.D., Shah, P.K., Kheradpour, P., Morrison, C.A., Henikoff, J.G., Feng, X., Ahmad, K., Russell, S., White, R.A., Stein, L., Henikoff, S., Kellis, M., White, K.P. (2010). A comprehensive map of insulator elements for the Drosophila genome. PLoS Genet. 6(1):e1000814 (PubMed)
2009
Kosik, O., Auburn, R.P., Russell, S., Hrmova, M., Stratilova, E., Garajova, S., Farkas, V. (2009). Polysaccharide microarrays for high-throughput screening of transglycosylase activities in plant extracts. Glycoconj. J. In Press. (PubMed)
Aleksic, J., Russell, S. (2009). ChIPing away at the genome: the new frontier travel guide. Mol. BioSyst. DOI: 10.1039/b906179g (PubMed)
Phochanukul, N., Russell, S. (2009). No backbone but lots of SOX: the invertebrate SOX family. Int. J. Biochem Cell Biol. DOI:10.1016/j.biocel.2009.06.013 (PubMed)
Celniker, S.E., Dillon, L.A., Gerstein, M.B., Gunsalus, K.C., Henikoff, S., Karpen, G.H., Kellis, M., Lai, E.C., Lieb, J.D., MacAlpine, D.M., Micklem, G., Piano, F., Snyder, M., Stein, L., White, K.P., Waterston, R.H.; modENCODE Consortium. (2009). Unlocking the secrets of the genome. Nature. 459(7249):927-40 (PubMed) (modENCODE)
Baker, D.A., Russell, S. (2009). Gene expression during Drosophila melanogaster egg development. BMC Genomics. 10(1):242 (PubMed)
Aleksic, J., Lazic, R., Müller, I., Russell, S., Adryan, B. (2009). Biases in Drosophila melanogaster protein trap screens. BMC Genomics. 10(1):249 (PubMed)
Ryder, E., Spriggs, H., Drummond, E., St. Johnston, D., Russell, S. (2009). The Flannotator - a gene and protein expression annotation tool for Drosophila melanogaster. Bioinformatics. 25(4):548-9 (PubMed) (Flannotator)
Nanda, S., Defalco, T.J., Hui Yong Loh, S., Phochanukul, N., Camara, N., Van Doren, M., Russell, S. (2009). Sox100B, a Drosophila group E Sox-domain gene, is required for somatic testis differentiation. Sex Dev. 3(1):26-37 (PubMed)
2008
Russell, S., Meadows, L.M., Russell, R.R. (2008). Microarray Technology in Practice. Academic Press, San Diego.
Kwong, C., Adryan, B., Bell, I., Meadows, L., Russell, S., Manak, J.R., White, R. (2008). Stability and dynamics of Polycomb target sites in Drosophila development. PLoS Genet. 4(9):e1000178. (PubMed)
Russell, S. (2008). SNPing and chipping away at the fly genome. Nat Methods. 5(4):295-6. (PubMed)
2007
Sykacek, P., Clarkson, R., Print, C., Furlong, R., Micklem, G. (2007). Bayesian modelling of shared gene function. Bioinformatics 23(15):1936-44.(PubMed)
Baker, D.A., Meadows, L.A., Wang, J., Dow, J.A.T., Russell, S. (2007). Variable sexually dimorphic gene-expression in laboratory strains of Drosophila melanogaster. BMC Genomics 8:454 (PubMed)
Adryan, B., Woerfel, G., Birch-Machin, I., Gao, S., Quick, M., Meadows, L., Russell, S., White, R. (2007). Genomic mapping of Suppressor of Hair-wing binding sites in Drosophila. Genome Biol. 8(8):R167. (PubMed)
Holohan, E.E., Kwong, C., Bartkuhn, M., Herold, M., Renkawitz, R., Russell, S., White. R. (2007). CTCF genomic binding sites in Drosophila and the organisation of the Bithorax Complex. PLoS Genet. 3(7):e112. (PubMed)
Samsonova, A.A., Niranjan, M., Russell, S., Brazma. A. (2007). Prediction of gene expression in embryonic structures of Drosophila melanogaster. PLoS Comput Biol. 3(7):e144. (PubMed)
Lyne, R., Smith, R., Rutherford, K., Wakeling, M., Varley, A., Gullier, F., Janssens, H., Wenyan, J., McLaren, P., North, P., Rana, D., Riley, T., Sullivan, J., Watkins, X., Woodbridge, M., Lilley, K., Russell, S., Ashburner, M., Mizguchi, K., Micklem, G. (2007). FlyMine: an integrated database for Drosophila and Anopheles genomics. Genome Biol. 8(7):R129 (PubMed) (FlyMine)
2006
Le Brigand, K., Russell, R., Moreilhon, C., Rouillard, J.M., Jost, B., Amiot, F., Magnone, V., Bole-Feysot, C., Rostagno, P., Virolle, V., Defamie, V., Dessen, P., Williams, G., Lyons, P., Rios, G., Mari, B., Gulari, E., Kastner, P., Gidrol, X., Freeman, T.C., Barbry, P. (2006). An open-access long oligonucleotide microarray resource for analysis of the human and mouse transcriptomes. Nucleic Acids Res. 34(12):e87. (PubMed)
Russell, S. (2006). Learning to fly - getting the best out of microarrays. Mol. Biosyst. 2(9):402-5. (PubMed)
Choksi, S.P., Southall, T.D., Bossing, T., Edoff, K., de Wit, E., Fischer, B.E., van Steensel, B., Micklem, G., Brand, A.H. (2006). Prospero acts as a binary switch between self-renewal and differentiation in Drosophila neural stem cells. Dev Cell. 11(6):775-89. (PubMed)
Kreil, D.P., Russell, R.R., Russell, S. (2006). Microarray oligonucleotide-probes. Methods Enzymol. 410:73-98. (PubMed) (Supplement)
Auburn, R.P., Russell, R., Fischer, B., Meadows, L.A., Sevillano Matilla, S., Russell, S. (2006). SimArray: a user-friendly and user-configurable microarray design tool. BMC Bioinformatics. 7:102. (PubMed) (SimArray)
Ryder, E., Jackson, R., Ferguson-Smith, A., Russell, S. (2006). MAMMOT - a set of tools for the design, management and visualisation of genomic tiling arrays. Bioinformatics. 22(7):883-884. (PubMed) (MAMMOT)
2005
Page, A.R., Kovacs, A., Deak, P., Torok, T., Kiss, I., Dario, P., Bastos, C., Batista, P., Gomes, R., Ohkura, H., Russell, S.,Glover D.M. (2005). Spotted-dick, a zinc-finger protein of Drosophila required for expression of Orc4 and S phase. EMBO J. 24(24):4304-4315. (PubMed)
External RNA Controls Consortium (2005). Proposed methods for testing and selecting the ERCC external RNA controls. BMC Genomics 6:150. (PubMed)
McKimmie, C., Woerfel, G., Russell S. (2005). Conserved genomic organization of group B Sox genes in insects. BMC Genetics. 6(1):26. (PubMed)
Sykacek, P., Furlong, R.A., Micklem, G. (2005). A friendly statistics package for microarray analysis. Bioinformatics. 21(21):4069-4070. (PubMed) (FSPMA)
Doney A.S., Fischer B., Lee S., Morris A.D., Leese G.P., Palmer C.N. (2005). Association of common variation in the PPARA gene with incident myocardial infarction in individuals with type 2 diabetes: A Go-DARTS study. Nucl Recept. 3(1):4 (PubMed)
Cecil J.E., Fischer B., Doney A.S., Hetherington M., Watt P., Wrieden W., Bolton-Smith C., Palmer C.N. (2005). The Pro12Ala and C-681G variants of the PPARG locus are associated with opposing growth phenotypes in young schoolchildren. Diabetologia. 48(8):1496-1502. (PubMed)
Birch-Machin, I., Gao, S., Huen, D., McGirr, R., White, R.A.H., Russell, S. (2005). Genomic analysis of heat-shock factor targets in Drosophila. Genome Biology 6:R63. (PubMed)
Auburn, R.P., Kreil, D. P., Meadows, L. A., Fischer, B., Sevillano Matilla, S., Russell, S. (2005). Robotic spotting of cDNA and oligonucleotide microarrays. Trends Biotechnol. 23(7):374-379. (PubMed)
Woolfson, A., Stebbing, J., Tom, B., Stoner, K., Gilks, W., Kreil, D.P., Mulligan, S., Belov, L., Chrisp, J., Errington, W., Wildfire, A., Erber, W., Bower, M., Gazzard, B., Christopherson, R., Scott, M. (2005). Conservation of unique cell surface CD antigen mosaics in HIV-1 infected individuals. Blood. 106(3):1003-1007.(PubMed)
Kreil, D.P., Russell, R.R.(2005). There is no silver bullet--a guide to low-level data transforms and normalisation methods for microarray data. Brief Bioinform.6(1):86-97. (PubMed)
2004
Kanno, T., Mette, M.F., Kreil, D.P., Aufsatz, W., Matzke, M., Matzke, A.J. (2004). Involvement of putative SNF2 chromatin remodeling protein DRD1 in RNA-directed DNA methylation. Curr Biol. 14(9):801-805. (PubMed)
Doney, A.S., Fischer, B., Leese, G., Morris, A.D., Palmer, C.N. (2004). Cardiovascular risk in type 2 diabetes is associated with variation at the PPARG locus: a Go-DARTS study. Arterioscler Thromb Vasc Biol. 24(12):2403-2407. (PubMed)
Saidi, S.A., Holland, C.M., Kreil, D.P., MacKay, D.J., Charnock-Jones, D.S., Print, C.G., Smith, S.K. (2004). Independent component analysis of microarray data in the study of endometrial cancer. Oncogene. 23(39):6677-6683. (PubMed)
Ryder, E., Blows, F., Ashburner, M., Bautista-Llacer, R., Coulson, D., Drummond, J., Webster, J., Gubb, D., Gunton, N., Johnson, G., O'Kane, C.J., Huen, D., Sharma, P., Asztalos, Z., Baisch, H., Schulze, J., Kube, M., Kittlaus, K., Reuter, G., Maroy, P., Szidonya, J., Rasmuson-Lestander, A., Ekstrom, K., Dickson, B., Hugentobler, C., Stocker, H., Hafen, E., Lepesant, J.A., Pflugfelder, G., Heisenberg, M., Mechler, B., Serras, F., Corominas, M., Schneuwly, S., Preat, T., Roote, J., Russell, S. (2004). The DrosDel collection: a set of P-element insertions for generating custom chromosomal aberrations in Drosophila melanogaster. Genetics. 167(2):797-813. (PubMed)
Doney, A.S., Fischer, B., Cecil, J.E., Boylan, K., McGuigan, F.E., Ralston, S.H., Morris, A.D., Palmer, C.N. (2004). Association of the Pro12Ala and C1431T variants of PPARG and their haplotypes with susceptibility to Type 2 diabetes. Diabetologia. 47(3):555-558. (PubMed)
Karp, N.A., Kreil, D.P., Lilley, K.S. (2004). Determining a significant change in protein expression with DeCyder during a pair-wise comparison using two-dimensional difference gel electrophoresis. Proteomics. 4(5):1421-1432. (PubMed)
Ying, L., White, S.S., Bruckbauer, A., Meadows, L., Korchev, Y.E., Klenerman, D. (2004). Frequency and voltage dependence of the dielectrophoretic trapping of short lengths of DNA and dCTP in a nanopipette. Biophys. J. 86(2): 1018-1027. (PubMed)
Doney, A.S., Fischer, B., Cecil, J.E., Cohen, P.T., Boyle, D.I., Leese, G., Morris, A.D., Palmer, C.N. (2004). Male preponderance in early diagnosed type 2 diabetes is associated with the ARE insertion/deletion polymorphism in the PPP1R3A locus. BMC Genet. 4(1):11.(PubMed)
Kreil, D.P., Karp, N.A., Lilley, K.S.. (2004). DNA microarray normalization methods can remove bias from differential protein expression analysis of 2D difference gel electrophoresis results. Bioinformatics. 20(13):2026-2034. (PubMed)
2003
Russell, R. (2003). Designing microarray oligonucleotide probes. Brief Bioinform. 4(4):361-367. (PubMed)
Ryder, E., Russell, S. (2003). Transposable elements as tools for genomics and genetics in Drosophila. Brief Funct Genomic Proteomic. 2(1):57-71. (PubMed)
Kreil, D.P., Ouzounis, C.A. (2003).Comparison of sequence masking algorithms and the detection of biased protein sequence regions. Bioinformatics. 19(13):1672-1681. (PubMed)
2002
Overton, P.M., Meadows, L.A., Urban, J., Russell, S. (2002). Evidence for differential and redundant function of the Sox genes Dichaete and SoxN during CNS development in Drosophila. Development 129(18):4219-4228. (PubMed)
Doney A., Fischer B., Frew D., Cumming A., Flavell D.M., World M., Montgomery H.E., Boyle D., Morris A., Palmer C.N. (2002). Haplotype analysis of the PPARgamma Pro12Ala and C1431T variants reveals opposing associations with body weight. BMC Genet. 13:3:21. (PubMed)
Conference abstracts & proceedings
2009
Phochanukul, N., Meadows, L., Russell, S. (2009). Genomic analysis of Sox100B during embryogenesis and testis development. 21st European Drosophila Research Conference (EDRC). 18th to 21st November 2009, Nice, France. (EDRC 2009)
Meadows, L., Chan, Y.S., Roote, J., Russell, S. (2009). Neighbourhood continuity is not necessary for correct gene expression in Drosophila testis. 21st European Drosophila Research Conference (EDRC). 18th to 21st November 2009, Nice, France. (EDRC 2009)
2007
Tüchler. T., Sykacek, P., Auburn, R.P., Meadows, L.A., Fischer, B., Micklem, G., Russell, S., Kreil, D.P. (2007). Tenfold improved performance of spatial normalization of microarrays. 17th Annual International Conference on Critical Assessment of Microarray Data Analysis (CAMDA07). 13th to 14th December 2007, Valencia, Spain. (CAMDA07)
Tüchler. T., Sykacek, P., Auburn, R.P., Meadows, L.A., Fischer, B., Micklem, G., Russell, S., Kreil, D.P. (2007). Tenfold improved performance of spatial normalization of microarrays. 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB). 21st to 25th July 2007, Vienna, Austria. (ISMB'07/ECCB / Proceedings)
2006
Lone, G.M., Asztalos, Z., Auburn, R., Bottenberg, W., Kammerer, R., O'Kane, C.J., Rocha, J., Sweeney, S.T., Yang, M., Prokop, A. (2006). Discovery and characterisation of genes involved in de novo formation of Drosophila NMJs. A. Dros. Res. Conf. 47:24. (FlyBase)
Lone, G.M., Asztalos, Z., Auburn, R., Bottenberg, W., Kammerer, R., O'Kane, C.J., Rocha, J., Sweeney, S.T., Yang, M., Prokop, A (2006). Waharan, a novel Drosophila protein involved in Uibiquitin-mediated regulation of NMJ size. 11th Annual European Meeting on the Neurogenetics of Drosophila. 2nd to 6th September 2006, Leuven, Belgium.
Jackson, R.A., Ryder, E., Janes, M., Fischer, B., Auburn, R.P., Russell, S., Fallows, G., Ferguson-Smith, A. (2006). Long-range analysis of chromatin encompassing a 1.7Mb imprinted domain. The European Science Foundation. Signalling to chromatin: epigenetics. 6th to 9th June, Wellcome Trust Genome Campus, Hinxton, UK.
Russell, S. (2006). From expression to regulation: microarray resources for Drosophila. The consortium for post-genome science: genomes to systems. 22nd to 24th March, Manchester, UK. (Consortium).
Crowther, D., Page, R., Ryder, E., Lomas, D. (2006). Genetic screens yield novel therapeutic targets in a Drosophila model of Alzheimer's disease. EMBO-FEBS workshop on Amyloid formation Structure, mechanism of formation and cellular effects of amyloid aggregates. 25th to 28th March, Florence, Italy.
2005
Wang, J., Lynch, M.D., Russell, S., Dow, J.A.T. (2005). GeneChip Affymetrix UK Drosophila Service. A. Dros. Res. Conf. 46:878B. (FlyBase)
Lyne, R., Smith, R., Rutherford, K., Wakeling, M., Riley, T., Ji, W., Guillier, F., Lilley, K., Mizuguchi, K., Russell, S., Ashburner, M., Micklem, G. (2005). The FlyMine project. Europ. Dros. Res. Conf. 19:RE4. (FlyBase) (FlyMine)
Ryder, E., Jackson, R., Russell, S., Ferguson-Smith, A. (2005). MAMMOT - a set of tools for the design, annotation and visualisation of genomic tiling arrays for epigenetic studies. Second Alan Wolffe EMBO Conference on Chromatin and Epigenetics, 19th to 22nd May. Heidelberg, Germany. (EMBO)
2004
Ryder, E., Jackson, R., Ferguson-Smith, A., Russell, S. (2004). MAMMOT - a set of tools for the design and visualisation of genomic tiling arrays. Genome Informatics. 22nd to 26th September. Wellcome Trust Genome Campus, Hinxton, UK.
Russell, S. (2004). Genomics and post-genomics in Drosophila. Neurofly 04. 4th to 8th September, Neuchatel, Switzerland. (Neurofly'04)
Meadows, L., Auburn, R., Fischer, B., Kreil, D., Sevillano-Matilla, S., Micklem, G., Russell, S. (2004). Spatial microarray calibration by abundant spike controls. The Consortium for post-genome science: genomes to systems. 1st to 3rd September, Manchester, UK. (Consortium)
White, R.A.H., Birch-Machin, I., Gao, S., McGirr, R., Russell, S.(2004). A genome-wide analysis of the Heat Shock response in Drosophila by chromatin immunopurification and DNA microarray analysis. A. Dros. Res. Conf. 45:910A. (FlyBase)
Shen, S., Shan, G., Birch-Machin, I., White, R., Russell, S. (2004). The molecular function of Dichaete during Drosophila embryonic development. A. Dros. Res. Conf. 45:692B (FlyBase)
Ryder, E.J., DrosDel Consortium. (2004). DrosDel - A second generation deficiency kit for Drosophila melanogaster. A. Dros. Res. Conf. 45:907A. (FlyBase)
Lyne, R., Varley, A., Guillier, F., Rana, D., Smith, R., Wakeling, A., Woodbridge, M., Lilley, K., Mizuguchi, K., Russell, S., Ashburner, M., Micklem, G. (2004). The FlyMine Project. A. Dros. Res. Conf. 45:904A. (FlyBase) (FlyMine)
Russell, S., Kreil, D. P. (2004). Microarray data analysis - understanding and application of modern methods. Society for Computational Biology conference on Intelligent Systems for Molecular Biology (ISMB), 31st July to 4th August, Glasgow, Scotland. (ISMB'04)
2003
Lone, M., Asztalos, Z., Auburn, R., O'Kane, C., Prokop, A., Rocha, J., Sweeney, S.T., Yang, M. (2003). Discovery and Characterisation of Genes involved in the Structural Organisation of Drosophila Synapses. Europ. Dros. Res. Conf. 18:O07. (FlyBase)
Ryder, E.J., DrosDel Consortium. (2003). DrosDel - A second generation deficiency kit for Drosophila melanogaster. Europ. Dros. Res. Conf. 18:B02. (FlyBase)
Kreil, D.P., Auburn, R.P., Meadows, L.A., Fischer, B., Russell, S., Micklem, G. (2003). Quantitative microarray spot profile optimization: a systematic evaluation of buffer/slide combinations. In German Conference in Bioinformatics, GCB 2003, (Mewes, H-W, Frishman, D., Heun, V. and Kramer, S. eds.) v.I, 77-81. (GCB'03) (Reprint)
Kreil, D.P., Auburn, R.P., Meadows, L.A., Russell, A., Micklem G. (2003). Quantitative microarray spot profile optimization: a systematic evaluation of buffer/slide combinations. International Society for Computational Biology conference on Intelligent Systems for Molecular Biology (ISMB), June 29 to July 3, Brisbane, Australia. (ISMB'03)
Ryder, E.J., DrosDel Consortium. (2003). DrosDel - A second generation deficiency kit for Drosophila melanogaster. A. Dros. Res. Conf. 44:1012A. (FlyBase)
2002
Meadows, L.A., Ashburner, M., Auburn, R., Brookman, J., Glover, D., McWilliam, L., Micklem, G., O'Kane, C., Russell, S., Skelton, J. (2002). The UK Drosophila Microarray Facility. A. Dros. Res. Conf. 43:945C. (FlyBase)
Overton, P.M., Meadows, L.A., Urban, J., Russell, S.R.H.(2002). The Drosophila Group B Sox genes Dichaete and SoxNeuro function redundantly during the development of the embryonic CNS. A. Dros. Res. Conf. 43:747C. (FlyBase)
Russell, R. (2002). Meeting Review: 2nd Bioinformatics Industrialization Workshop: Bioinformatics and Medicine. Comp Funct Genom 3(3): 270-276. (Abstract)
Ryder, E., Blows, F., Ashburner, M., Asztalos, Z., Coulson, D., Drummond, J., Glover, D., Gubb, D., Johnson, G., O'Kane, C., Pal, M., Panchal, P., Roote, J., Wang, S., Webster, J., Russell, S. (2002). High-throughput sequencing and analysis of Drosophila melanogaster P elements. A. Dros. Res. Conf. 43:997A. (FlyBase)
2001
Meadows, L., Ashburner, M., Auburn, R., Blows, F., Brookman, J., Coulson, D., Drummond, J., Glover, D., McWilliam, L., Micklem, D., Micklem, G., O'Kane, C., Russell, S., Ryder, E., Skelton, J., Wang, S., Webster, J. (2001). The UK Drosophila Microarray Facility. Europ. Dros. Res. Conf. 17:I16. (FlyBase)
Overton, P.M., Meadows, L.A., McKimmie, C., Urban, J., Russell, S.R.H.(2001) The role of Group B SOX genes Dichaete and SoxNeuro in the development of the Drosophila embryonic CNS. Europ. Dros. Res. Conf. 17:N14. (FlyBase)
