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Prof Andrew Brass - publications

 

List of publications

2011

  • Fabre V, Massart R, Rachalski A, Jennings K, Brass A, Sharp T, Lesch K, Lanfumey L, Hamon M. Differential gene expression in mutant mice overexpressing or deficient in the serotonin transporter: a focus on urocortin 1. European neuropsychopharmacology : the journal of the European College of Neuropsychopharmacology. 2011 January; 21(1): 33-44. eScholarID:112448 | PMID:21075611 | DOI:10.1016/j.euroneuro.2010.10.004
  • Noyes H, Brass A, Obara I, Anderson S, Archibald A, Bradley D, Fisher P, Freeman A, Gibson J, Gicheru M, Hall L, Hanotte O, Hulme H, McKeever D, Murray C, Oh S, Tate C, Smith K, Tapio M, Wambugu J, Williams D, Agaba M, Kemp S. Genetic and expression analysis of cattle identifies candidate genes in pathways responding to Trypanosoma congolense infection. Proceedings of the National Academy of Sciences of the United States of America. 2011 May; 108(22): 9304-9. eScholarID:125832 | PMID:21593421 | DOI:10.1073/pnas.1013486108

2010

  • Alttoa A, Kõiv K, Hinsley T, Brass A, Harro J. Differential gene expression in a rat model of depression based on persistent differences in exploratory activity. European neuropsychopharmacology : the journal of the European College of Neuropsychopharmacology. 2010 May; 20(5): 288-300. eScholarID:112449 | PMID:19854624 | DOI:10.1016/j.euroneuro.2009.09.005
  • Goodhead I, Archibald A, Amwayi P, Brass A, Gibson J, Hall N, Hughes M, Limo M, Iraqi F, Kemp S, Noyes H. A comprehensive genetic analysis of candidate genes regulating response to Trypanosoma congolense infection in mice. PLoS neglected tropical diseases. 2010; 4(11): e880. eScholarID:112452 | PMID:21085469 | DOI:10.1371/journal.pntd.0000880
  • Noyes H, Agaba M, Anderson S, Archibald A, Brass A, Gibson J, Hall L, Hulme H, Oh S, Kemp S. Genotype and expression analysis of two inbred mouse strains and two derived congenic strains suggest that most gene expression is trans regulated and sensitive to genetic background. BMC genomics. 2010; 11: 361. eScholarID:112450 | PMID:20529291 | DOI:10.1186/1471-2164-11-361
  • Thompson P, Tipney H, Brass A, Noyes H, Kemp S, Naessens J, Tassabehji M. Claudin 13, a member of the claudin family regulated in mouse stress induced erythropoiesis. PloS one. 2010; 5(9): eScholarID:112451 | PMID:20844758 | DOI:10.1371/journal.pone.0012667

2009

  • Fisher P, Noyes H, Kemp S, Stevens R, Brass A. A systematic strategy for the discovery of candidate genes responsible for phenotypic variation. Methods in molecular biology (Clifton, N.J.). 2009; 573: 329-45. eScholarID:112456 | PMID:19763936 | DOI:10.1007/978-1-60761-247-6_18
  • Li W, Gracey A, Mello L, Brass A, Cossins A. ExprAlign--the identification of ESTs in non-model species by alignment of cDNA microarray expression profiles. BMC genomics. 2009; 10: 560. eScholarID:112457 | PMID:19939286 | DOI:10.1186/1471-2164-10-560
  • Morris D, Waters S, McCarthy S, Patton J, Earley B, Fitzpatrick R, Murphy J, Diskin M, Kenny D, Brass A, Wathes D. Pleiotropic effects of negative energy balance in the postpartum dairy cow on splenic gene expression: repercussions for innate and adaptive immunity. Physiological genomics. 2009 September; 39(1): 28-37. eScholarID:112455 | PMID:19567785 | DOI:10.1152/physiolgenomics.90394.2008
  • Noyes H, Alimohammadian M, Agaba M, Brass A, Fuchs H, Gailus-Durner V, Hulme H, Iraqi F, Kemp S, Rathkolb B, Wolf E, de Angelis M, Roshandel D, Naessens J. Mechanisms controlling anaemia in Trypanosoma congolense infected mice. PloS one. 2009; 4(4): e5170. eScholarID:112454 | PMID:19365556 | DOI:10.1371/journal.pone.0005170

2008

  • Alttoa, A, T A Hinsley, K Koiv, A Brass, and J Harro. Differential gene expression in rats with persistently high and low exploratory activity. 26th Collegium Internationale Neuro-Psychopharmacologicum Congress (CINP). Cambridge Univ Press: 2008: 119-119. eScholarID:2f90
  • Kemp S, Hanotte O, Agaba M, Noyes H, Gibson J, Archibald A, Rennie C, Hulme H, Brass A. Genomics approaches to study the biology underlying resistance to trypanosomiasis--some unexpected lessons. Developments in biologicals. 2008; 132: 89-91. eScholarID:112460 | PMID:18817289 | DOI:10.1159/000317147
  • Rennie C, Hulme H, Fisher P, Halp L, Agaba M, Noyes H, Kemp S, Brass A. A systematic, data-driven approach to the combined analysis of microarray and QTL data. Developments in biologicals. 2008; 132: 293-9. eScholarID:112461 | PMID:18817316 | DOI:10.1159/000317174
  • Rennie C, Noyes H, Kemp S, Hulme H, Brass A, Hoyle D. Strong position-dependent effects of sequence mismatches on signal ratios measured using long oligonucleotide microarrays. Bmc Genomics. 2008 July; 9: 11. eScholarID:1f129 | DOI:10.1186/1471-2164-9-317

2007

  • Fisher P, Hedeler C, Wolstencroft K, Hulme H, Noyes H, Kemp S, Stevens R, Brass A. A systematic strategy for large-scale analysis of genotype phenotype correlations: identification of candidate genes involved in African trypanosomiasis. Nucleic acids research. 2007; 35(16): 5625-33. eScholarID:1c7427 | PMID:17709344 | DOI:10.1093/nar/gkm623
  • Missier P, Embury S, Hedeler C, Greenwood M, Pennock JL, Brass AA. Accelerating disease gene identification through integrated SNP data analysis. 2007; LNBI 4544: 215-230. eScholarID:1d15967
  • Dark PM, Buchan IE, Warhurst G, New JP, Gibson JM, Baker PP.G, Steve Kemp, Brass AA. Early and sustained acute falls in total serum cholesterol are associated with critical illness mortality in the setting of tight glycaemic control. Inflammation Research. 2007; 53: eScholarID:17d950
  • Fisher P, Hedeler C, Wolstencroft K, Hulme H, Noyes H, Kemp S, Stevens R, Brass A. A systematic strategy for large-scale analysis of genotype-phenotype correlations: identification of candidate genes involved in African trypanosomiasis. Nucleic Acids Research. 2007 August; 35(16): 5625-5633. eScholarID:1f699 | DOI:10.1093/nar/gkm623
  • Fisher, P, C Hedeler, K Wolstencroft, H Hulme, H Noyes, S Kemp, R Stevens, and A Brass. A systematic strategy for the discovery of candidate genes responsible for phenotypic variation. 3rd International-Society-for-Computational-Biology-Student-Council Symposium held at the 15th Annual International Conference on Intelligent Systems for Molecular Biology. Biomed Central Ltd: 2007: eScholarID:2f162 | DOI:10.1186/1471-2105-8-s8-p7
  • Rennie, C, H Hulme, P Fisher, L Hall, M Agaba, H A Noyes, S J Kemp, and A Brass. A Systematic, Data-driven Approach to the Combined Analysis of Microarray and QTL Data. International Symposium on Animal Genomics for Animal Health. Karger: 2007: 293-299. eScholarID:2f117

2006

  • Morrison N, Wood AJ, Hancock D, Shah S, Hakes L, Gray T, Tiwari B, Kille P, Cossins A, Hegarty M, Allen MJ, Wilson WH, Olive P, Last K, Kramer C, Bailhache T, Reeves J, Pallett D, Warne J, Nashar K, Parkinson H, Sansone SA, Rocca-Serra P, Stevens R, Snape J, Brass A, Field D. Annotation of environmental OMICS data: application to the transcriptomics domain. Omics : a journal of integrative biology. 2006; 10(2): 172-8. eScholarID:1c7429 | PMID:16901223 | DOI:10.1089/omi.2006.10.172
  • Kierstein S, Noyes H, Naessens J, Nakamura Y, Pritchard C, Gibson J, Kemp S, Brass A. Gene expression profiling in a mouse model for African trypanosomiasis. Genes and immunity. 2006 December; 7(8): 667-79. eScholarID:1c7428 | PMID:17066074 | DOI:10.1038/sj.gene.6364345
  • Fraser J, de Mello LV, Ward D, Rees HH, Williams DR, Fang Y, Fang Y, Brass A, Gracey AY, Cossins AR. Hypoxia-inducible myoglobin expression in nonmuscle tissues. Proceedings of the National Academy of Sciences of the United States of America. 2006 February; 103(8): 2977-81. eScholarID:1c7430 | PMID:16469844 | DOI:10.1073/pnas.0508270103
  • Wolstencroft K, Lord P, Tabernero L, Brass A, Stevens R. Protein classification using ontology classification. Bioinformatics (Oxford, England). 2006 July; 22(14): e530-8. eScholarID:1c5565 | PMID:16873517 | DOI:10.1093/bioinformatics/btl208

2005

  • Bishop R, Shah T, Pelle R, Hoyle D, Pearson T, Haines L, Brass A, Hulme H, Graham SP, Taracha ELN, Kanga S, Lu C, Hass B, Wortman J, White O, Gardner MJ, Nene V, de Villiers EP. Analysis of the transcriptome of the protozoan Theileria parva using MPSS reveals that the majority of genes are transcriptionally active in the schizont stage. Nucleic Acids Research. 2005; 33: 5503-5511. eScholarID:1c8292
  • Wolstencroft K, Mc Entire R, Stevens R, Tabernero L, and Brass A. Constructing Ontology-Driven Generic Protein Family Databases. Bioinformatics (Oxford, England). 2005; 21(8): 1685-92. eScholarID:1c3464 | DOI:10.1093/bioinformatics/bti158
  • Datta R, deSchoolmeester ML, Hedeler C, Paton NW, Brass AM, Else KJ. Identification of novel genes in intestinal tissue that are regulated after infection with an intestinal nematode parasite. Infection and immunity. 2005; 73(7): 4025-33. eScholarID:1c3782 | PMID:15972490 | DOI:10.1128/IAI.73.7.4025-4033.2005
  • Wolstencroft KJ, Stevens R, Tabernero L, Brass A. PhosphaBase: an ontology-driven database resource for protein phosphatases. Proteins. 2005; 58(2): 290-4. eScholarID:1c4257
  • Hancock D, Wilson M, Velarde G, Morrison N, Hayes A, Hulme H, Wood AJ, Nashar K, Kell DB, Brass A. maxdLoad2 and maxdBrowse: standards-compliant tools for microarray experimental annotation, data management and dissemination. BMC Bioinformatics. 2005; 6: 264. eScholarID:1c4814 | PMID:16269077

2004

  • HinsleyTA, Thompson PD, Tipney HJ, Brass AA, Tassabehji M. Comparison of TFII-I gene family members deleted in Williams-Beuren syndrome. Protein Sci. 2004; 13(10): 2588-99. eScholarID:1d9693
  • Brass A, Cunliffe P, Hinsley TA, Tassabehji M, Tipney HJ. Comparison of TFII-I gene family members deleted in Williams-Beuren syndrome. Protein science : a publication of the Protein Society. 2004; 13(10): 2588-99. eScholarID:1c2703 | PMID:15388857
  • Gracey AY, Fraser EJ, Li W, Fang Y, Taylor RR, Rogers J, Brass a and Cossins A. Coping with cold: an integrative, multi-tissue analysis of the transcriptome of a poikilothermic vertebrate. Proceedings of the National Academy of Sciences of the United States of America. 2004; 101: 16970-16975. eScholarID:1a3491
  • Stevens R, Tipney HJ, Wroe C, Oinn T, Senger M, Lord P, Goble C, Brass AA, Tassabehji M. Exploring Williams-Beuren Syndrome Using myGrid. Bioinformatics. 2004; Aug 4;20 Suppl 1: I303-I310. eScholarID:1d9696
  • Brass A, Goble CA, Oinn TM, Lord PW, Stevens RD, Senger M, Tassabehji M, Tipney HJ, Wroe CJ. Exploring Williams-Beuren syndrome using myGrid. Bioinformatics (Oxford, England). 2004; 20 Suppl 1: I303-I310. eScholarID:1c2705 | PMID:15262813
  • Tipney HJ, Hinsley TA, Brass AA, Metcalfe K, Donnai D, Tassabehji M. Isolation and characterisation of GTF2IRD2, a novel fusion gene and member of the TFII-I family of transcription factors, deleted in Williams-Beuren Syndrome. Eur. J. Hum.Genet.. 2004; 12 (7): 551-60. eScholarID:1d9698 | DOI:10.1038/sj.ejhg.5201174
  • Brass A, Donnai D, Hinsley TA, Metcalfe K, Tassabehji M, Tipney HJ. Isolation and characterisation of GTF2IRD2, a novel fusion gene and member of the TFII-I family of transcription factors, deleted in Williams-Beuren syndrome. European journal of human genetics : EJHG. 2004; 12(7): 551-60. eScholarID:1c2706 | PMID:15100712
  • Gaskell SJ, Paton NW, Brown AJ, Brass A, Hubbard SJ, Taylor CF, Lilley KS, Oliver SG, Yin Z, Whetton AD, Morrison N, Carroll K, Chater K, Evans C, Garwood C, Garwood K, Ghazal P, Hansson L, Hart S, Hesketh A, Howard J, Joens S, McLaughlin T, Mewissen M, Stead D. PEDRo: a database for storing, searching and disseminating experimental proteomics data. BMC Genomics. 2004; 5(1): 68. eScholarID:1c2704 | PMID:15377392
  • Garwood KL, Paton NW, Brass A, Taylor CF, Oliver SG, Runte KJ. Pedro: a configurable data entry tool for XML. Bioinformatics (Oxford, England). 2004; 20(15): 2463-5. eScholarID:1c2707 | PMID:15073025 | DOI:10.1093/bioinformatics/bth251

2003

  • Fang Y, Brass A, Hoyle DC, Hayes A, Bashein A, Oliver SG, Waddington D, Rattray M. A model-based analysis of microarray experimental error and normalisation. Nucleic acids research. 2003; 31(16): e96. eScholarID:1c1423 | PMID:12907748 | DOI:10.1093/nar/gng097
  • Taylor CF, Paton NW, Garwood KL, Kirby PD, Stead DA, Yin Z, Deutsch EW, Selway L, Walker J, Riba-Garcia I, Mohammed S, Deery MJ, Howard JA, Dunkley T, Aebersold R, Kell DB, Lilley KS, Roepstorff P, Yates JR, Brass A, Brown AJ, Cash P, Gaskell SJ, Hubbard SJ, Oliver SG. A systematic approach to modeling, capturing, and disseminating proteomics experimental data. Nature biotechnology. 2003; 21(3): 247-54. eScholarID:1c973 | PMID:12610571 | DOI:10.1038/nbt0303-247
  • Lord PW, Stevens RD, Brass A, Goble CA. Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation. Bioinformatics (Oxford, England). 2003; 19(10): 1275-83. eScholarID:1c1424 | PMID:12835272 | DOI:10.1093/bioinformatics/btg153
  • Lord PW, Stevens RD, Brass A, Goble CA. Semantic similarity measures as tools for exploring the gene ontology. 2003: eScholarID:2c13 | PMID:12603061

2002

  • Hoyle DC, Rattray M, Jupp R, Brass A. Making sense of mRNA Abundance Distributions from Microarray Experiments. Bioinformatics. 2002; 18: 576-584. eScholarID:1a2228
  • Hoyle DC, Rattray M, Jupp R, Brass A. Making sense of microarray data distributions. Bioinformatics (Oxford, England). 2002; 18(4): 576-84. eScholarID:1c1425 | PMID:12016055 | DOI:10.1093/bioinformatics/18.4.576

2001

  • R.D. Stevens, C.A. Goble, P. Baker, and A. Brass. A Classification of Tasks in Bioinformatics. Bioinformatics. 2001; 17: 180-188. eScholarID:1a3493
  • Stevens R, Goble C, Baker P, Brass A. A classification of tasks in bioinformatics. Bioinformatics (Oxford, England). 2001; 17(2): 180-8. eScholarID:1c1426 | PMID:11238075 | DOI:10.1093/bioinformatics/17.2.180
  • Brutsche MH, Brutsche IC, Wood P, Brass A, Morrison N, Rattay M, Mogulkoc N, Simler N, Craven M, Custovic A, Egan JJ, Woodcock A. Apoptosis signals in atopy and asthma measured with cDNA arrays. Clinical and experimental immunology. 2001; 123(2): 181-7. eScholarID:1c1427 | PMID:11207646

2000

  • Paton NW, Khan SA, Hayes A, Moussouni F, Brass A, Eilbeck K, Goble CA, Hubbard SJ, Oliver SG. Conceptual modelling of genomic information. Bioinformatics (Oxford, England). 2000; 16(6): 548-57. eScholarID:1c981 | PMID:10980152 | DOI:10.1093/bioinformatics/16.6.548
  • Stevens R, Baker P, Bechhofer S, Ng G, Jacoby A, Paton NW, Goble CA, Brass A. TAMBIS: transparent access to multiple bioinformatics information sources. Bioinformatics (Oxford, England). 2000; 16(2): 184-5. eScholarID:1c1428 | PMID:0010842744 | DOI:10.1093/bioinformatics/16.2.184

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