---

---

Bitton DA, Smith DL, Connolly Y, Scutt PJ, Miller CJ. An Integrated Mass-Spectrometry Pipeline Identifies Novel Protein Coding-Regions in the Human Genome. PLoS ONE 5(1): e8949. doi:10.1371/journal.pone.0008949. pubmed.

Buffa FM, Harris AL, West CM, Miller CJ. Large meta-analysis of multiple cancers reveals a common, compact and highly prognostic hypoxia metagene. Br J Cancer. 2010 Jan 19;102(2):428-35. pubmed.

---

Moller-Levet CS, Betts GN, Harris AL, Homer JJ, West CM, Miller CJ. Exon Array Analysis of Head and Neck Cancers Identifies a Hypoxia Related Splice Variant of LAMA3 Associated with a Poor Prognosis. PLoS Comput Biol. 2009 Nov;5(11):e1000571. Epub 2009 Nov 20.pubmed

Linton K, Hey Y, Dibben S, Miller C, Freemont A, Radford J, Pepper S. Methods comparison for high-resolution transcriptional analysis of archival material on Affymetrix Plus 2.0 and Exon 1.0 microarrays.Biotechniques.2009 Jul;47(1):587-96. pubmed

Chan CW, Wong NA, Liu Y, Bicknell D, Turley H, Hollins L, Miller CJ, Wilding JL, Bodmer WF. Gastrointestinal differentiation marker Cytokeratin 20 is regulated by homeobox gene CDX1. Proc Natl Acad Sci U S A. 2009 Feb 10;106(6):1936-41. Epub 2009 Feb 2. pubmed

Barenco M, Papouli E, Shah S, Brewer D, Miller CJ, Hubank M. rHVDM: an R package to predict the activity and targets of a transcription factor. Bioinformatics 2009 Feb 1;25(3):419-20. Epub 2008 Dec 15.pubmed

---

Sims AH, Smethurst GJ, Hey Y, Okoniewski MJ, Pepper SD, Howell A, Miller CJ, Clarke RB. The removal of multiplicative, systematic bias allows integration of breast cancer gene expression datasets - improving meta-analysis and prediction of prognosis. BMC Med Genomics. 2008 Sep 21;1(1):42. pubmed

Linton KM, Hey Y, Saunders E, Jeziorska M, Denton J, Wilson CL, Swindell R, Dibben S, Miller CJ, Pepper SD, Radford JA, Freemont AJ. Acquisition of biologically relevant gene expression data by Affymetrix microarray analysis of archival formalin-fixed paraffin-embedded tumours. Br J Cancer. 2008 Apr 1 [Epub ahead of print]. pubmed

Okoniewski MJ, Miller CJ. Comprehensive Analysis of Affymetrix Exon Arrays Using BioConductor. PLoS Computational Biology 2008, 4(2): e6 doi:10.1371/journal.pcbi.0040006. journal

Bitton DA, Okoniewksi MJ, Connolly Y, Miller CJ. Exon level integration of proteomics and microarray data. BMC Bioinformatics 2008, 9:118. pubmed

Yates T, Okoniewski MJ, Miller CJ. X:Map: annotation and visualization of genome structure for Affymetrix exon array analysis. Nucleic Acids Res. 2008 Jan;36(Database issue):D780-6. Epub 2007 Oct 11. pubmed

---

Williamson AJ, Smith DL, Blinco D, Unwin RD, Pearson S, Wilson C, Miller C, Lancashire L, Lacaud G, Kouskoff V, Whetton AD. Quantitative proteomic analysis demonstrates post-transcriptional regulation of embryonic stem cell differentiation to hematopoiesis. Mol Cell Proteomics. 2007 Nov 27; [Epub ahead of print] pubmed

Pierce A, Unwin RD, Evans CA, Griffiths S, Carney L, Zhang L, Jaworska E, Lee CF, Blinco D, Okoniewski MJ, Miller CJ, Bitton DA, Spooncer E, Whetton AD. Eight-channel iTRAQ enables comparison of the activity of 6 leukaemogenic tyrosine kinases. Mol Cell Proteomics. 2007 Oct 21; [Epub ahead of print] pubmed

Möller-Levet CS, West CM, Miller CJ. Exploiting sample variability to enhance multivariate analysis of microarray data. Bioinformatics. 2007 Oct 15;23(20):2733-40. Epub 2007 Sep 7. pubmed

Pepper SD, Saunders EK, Edwards LE, Wilson CL, Miller CJ. The utility of MAS5 expression summary and detection call algorithms. BMC Bioinformatics. 2007 Jul 30;8:273. pubmed

Okoniewski MJ, Yates T, Dibben S, Miller CJ. An annotation infrastructure for the analysis and interpretation of Affymetrix exon array data. Genome Biol. 2007;8(5):R79. pubmed

Winter SC, Buffa FM, Silva P, Miller C, Valentine HR, Turley H, Shah KA, Cox GJ, Corbridge RJ, Homer JJ, Musgrove B, Slevin N, Sloan P, Price P, West CM, Harris AL. Relation of a hypoxia metagene derived from head and neck cancer to prognosis of multiple cancers. Cancer Res. 2007 Apr 1;67(7):3441-9. pubmed

Sims AH, Finnon P, Miller CJ, Bouffler SD, Howell A, Scott D, Clarke RB. TPD52 and NFKB1 gene expression levels correlate with G2 chromosomal radiosensitivity in lymphocytes of women with and at risk of hereditary breast cancer. Int J Radiat Biol. 2007 Jun;83(6):409-20. pubmed

Barenco M, Shah S, Brewer D, Callard R, Stark J, Miller C, Hubank M rHVDM - a fasta and user-friendly R package to predict transcription factor targets from microarray time series data. BMC Systems Biology 2007, 1(Suppl 1):S1 (8 May 2007).

Okoniewski MJ, Hey Y, Pepper SD, Miller CJ. High correspondence between Affymetrix exon and standard expression arrays. Biotechniques. 2007 Feb;42(2):181-5. pubmed

Sakhinia E, Glennie C, Hoyland JA, Menasce LP, Brady G, Miller C, Radford JA, Byers RJ. Clinical quantitation of diagnostic and predictive gene expression levels in follicular and diffuse large B-cell lymphoma by RT-PCR gene expression profiling. Blood. 2007 May 1;109(9):3922-8. Epub 2007 Jan 25. pubmed

Meyer S, Fergusson WD, Whetton AD, Moreira-Leite F, Pepper SD, Miller C, Saunders EK, White DJ, Will AM, Eden T, Ikeda H, Ullmann R, Tuerkmen S, Gerlach A, Klopocki E, Tönnies H. Amplification and translocation of 3q26 with overexpression of EVI1 in Fanconi anemia-derived childhood acute myeloid leukemia with biallelic FANCD1/BRCA2 disruption. Genes Chromosomes Cancer. 2007 Apr;46(4):359-72. pubmed

---

Okoniewski MJ, Miller CJ. Hybridization interactions between probesets in short oligo microarrays lead to spurious correlations. BMC Bioinformatics. 2006 Jun 2;7:276. pubmed

Wilson CL, Sims AH, Howell A, Miller CJ, Clarke RB. Effects of oestrogen on gene expression in epithelium and stroma of normal human breast tissue. Endocr Relat Cancer. 2006 Jun;13(2):617-28. pubmed

Unwin RD, Smith DL, Blinco D, Wilson CL, Miller CJ, Evans CA, Jaworska E, Baldwin SA, Barnes K, Pierce A, Spooncer E, Whetton AD. Quantitative proteomics reveals posttranslational control as a regulatory factor in primary hematopoietic stem cells. Blood. 2006 Jun 15;107(12):4687-94. Epub 2006 Feb 28. pubmed

---

Wilson CL, Miller CJ. Simpleaffy: a BioConductor package for Affymetrix Quality Control and data analysis. Bioinformatics. 2005 Sep 15;21(18):3683-5. Epub 2005 Aug 2. pubmed

Leong HS, Yates T, Wilson C, Miller CJ. ADAPT: a database of Affymetrix probesets and transcripts. Bioinformatics. 2005 May 15;21(10):2552-3. Epub 2005 Mar 3. pubmed

---

Wilson CL, Pepper SD, Hey Y, Miller CJ. Amplification protocols introduce systematic but reproducible errors into gene expression studies. Biotechniques. 2004 Mar;36(3):498-506. pubmed

Erler JT, Cawthorne CJ, Williams KJ, Koritzinsky M, Wouters BG, Wilson C, Miller C, Demonacos C, Stratford IJ, Dive C. Hypoxia-mediated down-regulation of Bid and Bax in tumors occurs via hypoxia-inducible factor 1-dependent and -independent mechanisms and contributes to drug resistance. Mol Cell Biol. 2004 Apr;24(7):2875-89. pubmed

Mabey JE, Anderson MJ, Giles PF, Miller CJ, Attwood TK, Paton NW, Bornberg-Bauer E, Robson GD, Oliver SG, Denning DW. CADRE: the Central Aspergillus Data REpository. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D401-5. pubmed

Miller CJ, Kassem HS, Pepper SD, Hey Y, Ward TH, Margison GP. Mycoplasma infection significantly alters microarray gene expression profiles. Biotechniques. 2003 Oct;35(4):812-4. pubmed

Miller CJ, Attwood TK. Bioinformatics goes back to the future. Nat Rev Mol Cell Biol. 2003 Feb;4(2):157-62. pubmed

Attwood TK, Miller CJ Progress in bioinformatics and the importance of being earnest Biotechnology Annual Review 2002 8, 1-55.

Attwood TK, Miller CJ Which craft is best in bioinformatics? Computers and Chemistry 2001 25(4), 329-339

Miller CJ, Attwood TK 2001 PSST...The probabilistic sequence search tool. IEEE International Symposium on Bioinformatics and Bioengineering. Washington DC, November 2001. IEEE press, ISBN 0-7695-1423-5.

Cornell M, Paton NW, Wu S, Goble CA, Miller CJ, Kirby P, Eilbeck K, Brass A, Hayes A, Oliver SG,GIMS - A Data Warehouse for Storage and Analysis of Genome Sequence and Functional Data, IEEE International Symposium on Bioinformatics and Bioengineering.Washington DC, November 2001. IEEE press, ISBN 0-7695-1423-5

Miller C, Gurd J, Brass A A RAPID algorithm for sequence database comparisons: application to the identification of vector contamination in the EMBL databases. Bioinformatics 2000 Feb 15(2), 111-21.