Reviews & research articles
2012
Fischer, B., Wasbrough, E., Meadows, L.A., Randlet, O., Dorus, S., Karr, T.L., Russell, S. (2012) Conserved properties of Drosophila and human spermatozoal mRNA repertoires. Proc. R. Soc. Lon. B. DOI 10.1098/rspb.2012.0153 (PubMed)
Adryan, B. and Russell, S. (2012) Genome mapping and genomics in Drosophila. In "Genome Mapping and Genomics in Laboratory Animals" Eds P Denny and C. Kole. Springer (In Press)
Roote, J. and Russell, S. (2012) Towards a complete Drosophila deficiency kit. Genome Biol. 13: 149. (PubMed)
2011
Choo, S.W., Russell, S. (2011) Genomic approaches to understanding Hox gene function. In Advances in Genetics. Eds. T Friedman, JC Dunlap and SF Goodwin. 76: p55-91
Baker, D.A., Russell, S. (2011) The role of testis-specific versus somatic gene expression in the sex chromosome evolution of Anopheles gambiae. Genetics 189: 1117-1120 (PubMed)
Baker DA, Nolan T, Fischer B, Pinder A, Crisanti A, Russell S. (2011) A comprehensive atlas of tissue-specific expression in the malaria vector, Anopheles gambiae, reveals genes evolved for specialized feeding and mating behaviours. BMC Genomics 12: 296 (PubMed) Accompanying commentary article
Rees, J.S., Lowe, N., Armean, I.M., Roote, J., Johnson, G., Drummond, E., Spriggs, H., Ryder, E., Russell, S., St Johnston, D., Lilley K.S. (2011). In vivo analysis of proteomes and interactomes using parallel affinity capture (iPAC) coupled to mass spectrometry. Mol Cell Proteomics (PubMed)
Chan, Y.S., Naujoks, D.A., Huen, D.S., Russell, S. (2011). Insect Population Control by Homing Endonuclease-based Gene Drive: An Evaluation in Drosophila melanogaster. Genetics 2011 Mar 2. [Epub ahead of print] (PubMed)
Choo, S.W., White, R., Russell, S. (2011). Genome-Wide Analysis of the Binding of the Hox Protein Ultrabithorax and the Hox Cofactor Homothorax in Drosophila. PLoS ONE 6(4) (Article)
Sykacek, P., Kreil, D.P., Meadows, L.A., Auburn, R.P., Fischer, B., Russell, S., Micklem, G. (2011). The impact of quantitative optimization of hybridization conditions on gene expression analysis. BMC Bioinformatics. 2011 12:73 (Abstract | Article)
Hutchence, K.J., Fischer, B., Paterson, S., Hurst, G.D. (2011). How do insects react to novel inherited symbionts? A microarray analysis of Drosophila melanogaster response to the presence of natural and introduced Spiroplasma. Mol Ecol.(5):950-8 (PubMed)
Nègre, N., Brown, C.D., Ma, L., Bristow, C.A., Miller, S.W., Wagner, U., Kheradpour, P., Eaton, M.L., Loriaux, P., Sealfon, R., Li., Z., Ishii, H., Spokony, R.F., Chen, J., Hwang, L., Cheng, C., Auburn, R.P., Davis, M.B., Domanus, M., Shah, P.K., Morrison, C.A., Zieba, J., Suchy, S., Senderowicz, L., Victorsen, A., Bild, N.A., Grundstad, A.J., Hanley, D., MacAlpine, D.M., Mannervik, M., Venken, K., Bellen, H., White, R., Russell, S., Grossman, R.L., Ren, B., Gerstein, M., Posakony, J.W., Kellis, M., White, K.P. (2011). A cis-regulatory map of the Drosophila genome. Nature. 471(7339):527-31. (PubMed)
2010
The modENCODE Consortium, Roy, S., Ernst, J., Kharchenko, P.V., Kheradpour, P., Nègre, N., Eaton, M.L., Landolin, J.M., Bristow, C.A., Ma, L., Fin, M.L., Washietl, S., Arshinoff, B.I., Ay, F., Meyer, P.E., Robine, N., Washington, N.L., Stefano, L.D., Berezikov, E., Brown, C.D., Candeias, R., Carlson, J.W., Carr, A., Jungreis, I., Marbach, D., Sealfon, R., Tolstorukov, M.Y., Will, S., Alekseyenko, A.A., Artieri, C., Booth, B.W., Brooks, A.N., Dai, Q., Davis, C.A., Duff, M.O., Feng, X., Gorchakov, A., Gu, T., Henikoff, J.G., Kapranov, P., Li, R., Macalpine, H.K., Malone, J., Minoda, A., Nordman, J., Okamura, K., Perry, M., Pwell, S., Riddle, N.C., Sakai, A., Samsonova, A., Sandler, J.E., Schwartz, Y.B., Sher, N., Spokony, R., Sturgill, D., van Baren, M., Wan, K.H., Yang, L., Yu, C., Feingold, E., Good, P., Guyer, M., Lowden, R., Ahmad, K., Andrews, J., Berger, B., Brenner, S.E., Brent, M.R., Cherbas, L., Elgin, S.C.R., Gingeras, T.R., Grossman, R., Hoskins, R.A., Kaufman, T.C., Kent, W., Kuroa, M.I., Orr-Weaver, T., Perrimon, N., Pirrota, V., Posakony, J.W., Ren, B., Russell, S., Cherbas, P., Graveley, B.R., Lewis, S., Micklem, G., Oliver, B., Park, P.J., Celniker, S.E., Henikoff, S., Karpen, G.H., Lai, E.C., MacAlpine, D.M., Stein, L.D., White, K.P., Kelis, M. (2010). Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science. 330(6012):1787-97. (Pubmed | Editorial | Perspective | Supplement)
Meadows, L.A., Chan, Y.S., Roote, J., Russell, S. (2010). Neighbourhood continuity is not required for correct testis gene expression in Drosophila. PLoS Biology. 8(11):e1000552. (Article | Commentary)
Huen, D. and Russell, S. (2010). On the use of resampling tests for evaluating statistical significance of binding site co-occurance. BMC Bioinformatics. 11(1):359. (PubMed)
Lone, M., Kungl, T., Koper, A., Bottenberg, W., Kammerer, R., Klein, M.S., Sweeney, S.T., Auburn, R.P., O’Kane, C., Prokop , A. (2010). The nuclear protein Waharan is required for endosomal-lysosomal trafficking in Drosophila J. Cell Sci. 123(14):2369-74 (PubMed)
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)
Kosik, O., Auburn, R.P., Russell, S., Hrmova, M., Stratilova, E., Garajova, S., Farkas, V. (2010). Polysaccharide microarrays for high-throughput screening of transglycosylase activities in plant extracts. Glycoconj. J. 27(1):79-87. (PubMed)
2009
Fu, A.Q., Adryan, B. (2009). Scoring overlapping and adjacent signals from genome-wide ChIP and DamID assays. Mol. Biosyst. 5(12):1429-1438. (PubMed)
Aleksic, J., Russell, S. (2009). ChIPing away at the genome: the new frontier travel guide. Mol. BioSyst. 5(12):1421-1428. (PubMed)
Phochanukul, N., Russell, S. (2009). No backbone but lots of SOX: the invertebrate SOX family. Int. J. Biochem Cell Biol. 42(3):453-464 (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)
