Publications

Danish Memon, Keren Dawson, Christopher SF Smowton, Wei Xing, Caroline Dive and Crispin J Miller. Hypoxia-driven splicing into noncoding isoforms regulates the DNA damage response (2016) npj Genomic Medicine 1, 16020; doi:10.1038/npjgenmed.2016.20

Morrow, C.J., Trapani, F., Metcalf, R.L., Bertolini, G., Hodgkinson, C.L., Khandelwal, G., Kelly, P., Galvin, M., Carter, L., Simpson, K.L., Williamson, S., Wirth, C., Simms, N., Frankliln, L., Frese, K.K., Rothwell, D.G., Nonaka, D., Miller, C.J., Brady, G., F.H.Blackhall, Dive, C. Tumourigenic non-small-cell lung cancer mesenchymal circulating tumour cells: A clinical case study (2016) Annals of Oncology, 27 (6), art. no. mdw122, pp. 1155-1160.

Tape, C.J., Ling, S., Dimitriadi, M., McMahon, K.M., Worboys, J.D., Leong, H.S., Norrie, I.C., Miller, C.J., Poulogiannis, G., Lauffenburger, D.A., Jørgensen, C. Oncogenic KRAS Regulates Tumor Cell Signaling via Stromal Reciprocation (2016) Cell, 165 (4), pp. 910-920.

Rothwell, D.G., Smith, N., Morris, D., Leong, H.S., Li, Y., Hollebecque, A., Ayub, M., Carter, L., Antonello, J., Franklin, L., Miller, C., Blackhall, F., Dive, C., Brady, G. Genetic profiling of tumours using both circulating free DNA and circulating tumour cells isolated from the same preserved whole blood sample (2016) Molecular Oncology, 10 (4), pp. 566-574.

Xing, W., Jie, W., Miller, C. SCAN: A smart application platform for empowering parallelizations of big genomic data analysis in clouds (2015) Proceedings of the International Conference on Parallel Processing, 2015-December, art. no. 7349584, pp. 290-299.

Smowton, C., Copil, G., Truong, H.-L., Miller, C., Xing, W. Genome analysis in a dynamically scaled hybrid cloud (2015) Proceedings - 11th IEEE International Conference on eScience, eScience 2015, art. no. 7304322, pp. 391-400. 

Smowton, C., Miller, C., Xing, W., Balla, A., Antoniades, D., Pallis, G., Dikaiakos, M.D. Analysing cancer genomics in the elastic cloud (2015) Proceedings - 2015 IEEE/ACM 15th International Symposium on Cluster, Cloud, and Grid Computing, CCGrid 2015, art. no. 7152567, pp. 835-844.

Draper JE, Sroczynska P, Tsoulaki O, Leong HS, Fadlullah MZ, Miller C, Kouskoff V, Lacaud G. RUNX1B Expression Is Highly Heterogeneous and Distinguishes Megakaryocytic and Erythroid Lineage Fate in Adult Mouse Hematopoiesis. PLoS Genet. 2016 Jan 25;12(1):e1005814. doi: 10.1371/journal.pgen.1005814.

Rothwell DG, Smith N, Morris D, Leong HS, Li Y, Hollebecque A, Ayub M, Carter L, Antonello J, Franklin L, Miller C, Blackhall F, Dive C, Brady G. Genetic profiling of tumours using both circulating free DNA and circulating tumour cells isolated from the same preserved whole blood sample. Mol Oncol. 2015 Nov 19. pii: S1574-7891(15)00205-7. doi: 10.1016/j.molonc.2015.11.006. 26639657.

Marusiak AA, Stephenson NL, Baik H, Trotter EW, Li Y, Blyth K, Mason S, Chapman P, Puto LA, Read JA, Brassington C, Pollard HK, Phillips C, Green I, Overman R, Collier M, Testoni E, Miller CJ, Hunter T, Sansom OJ, Brognard J. Recurrent MLK4 Loss-of-Function Mutations Suppress JNK Signaling to Promote Colon Tumorigenesis. Cancer Res. 2015 Dec 4.

Thambyrajah R, Mazan M, Patel R, Moignard V, Stefanska M, Marinopoulou E, Li Y, Lancrin C, Clapes T, Möröy T, Robin C, Miller C, Cowley S, Göttgens B, Kouskoff V, Lacaud G. GFI1 proteins orchestrate the emergence of haematopoietic stem cells through recruitment of LSD1. Nat Cell Biol. 2015 Nov 30. doi: 10.1038/ncb3276. 26619147.

Smowton, C., Miller, C., Xing, W., Balla, A., Antoniades, D., Pallis, G., Dikaiakos, M.D. Analysing cancer genomics in the elastic cloud (2015) Proceedings - 2015 IEEE/ACM 15th International Symposium on Cluster, Cloud, and Grid Computing, CCGrid 2015, art. no. 7152567, pp. 835-844.

Hudson AM, Wirth C, Stephenson NL, Fawdar S, Brognard J, Miller CJ. Using large-scale genomics data to identify driver mutations in lung cancer: methods and challenges. Pharmacogenomics. 2015 Jul 31:1-12.

Antal CE, Hudson AM, Kang E, Zanca C, Wirth C, Stephenson NL, Trotter EW, Gallegos LL, Miller CJ, Furnari FB, Hunter T, Brognard J, Newton AC. Cancer-Associated Protein Kinase C Mutations Reveal Kinase's Role as Tumor Suppressor. Cell. 2015 Jan 29;160(3):489-502.

Dominic G Rothwell, Yaoyong Li, Mahmood Ayub, Catriona Tate, Gillian Newton, Yvonne Hey, Louise Carter, Suzanne Faulkner, Massimo Moro, Stuart Pepper, Crispin Miller, Fiona Blackhall, Giulia Bertolini, Luca Roz, Caroline Dive and Ged Brady. Evaluation and validation of a robust single cell RNA-amplification protocol through transcriptional profiling of enriched lung cancer initiating cells. BMC Genomics 2014, 15:1129. doi:10.1186/1471-2164-15-1129

Hudson AM, Yates T, Li Y, Trotter EW, Fawdar S, Chapman P, Lorigan P, Biankin AV, Miller C, Brognard J. Discrepancies in Cancer Genomic Sequencing Highlight Opportunities for Driver Mutation Discovery. Cancer Res; 2014 Sep 25. pii: canres.1020.2014. [Epub ahead of print]

Björner S, Fitzpatrick PA, Li Y, Allred C, Howell A, Ringberg A, Olsson H, Miller CJ, Axelson H, Landberg G. Epithelial and Stromal MicroRNA Signatures of Columnar Cell Hyperplasia Linking Let-7c to Precancerous and Cancerous Breast Cancer Cell Proliferation. PLoS One. 2014 Aug 14;9(8):e105099. doi: 10.1371/journal.pone.0105099. eCollection 2014. PubMed PMID: 25122196; PubMed Central PMCID: PMC4133372.

Lie-A-Ling M, Marinopoulou E, Li Y, Patel R, Stefanska M, Bonifer C, Miller C, Kouskoff V, Lacaud G. RUNX1 positively regulates a cell adhesion and migration program in murine hemogenic endothelium prior to blood emergence. Blood. 2014 Sep 11;124(11):e11-20. doi: 10.1182/blood-2014-04-572958. Epub 2014 Jul 31. PubMed PMID: 25082880.

Hodgkinson CL, Morrow CJ, Li Y, Metcalf RL, Rothwell DG, Trapani F, Polanski R, Burt DJ, Simpson KL, Morris K, Pepper SD, Nonaka D, Greystoke A, Kelly P, Bola B, Krebs MG, Antonello J, Ayub M, Faulkner S, Priest L, Carter L, Tate C, Miller CJ, Blackhall F, Brady G, Dive C. Tumorigenicity and genetic profiling of circulating tumor cells in small-cell lung cancer. Nat Med. 2014 Jun 1. doi: 10.1038/nm.3600. [Epub ahead of print]

Leong HS, Dawson K, Wirth C, Li Y, Connolly Y, Smith DL, Wilkinson CR, Miller CJ. A global non-coding RNA system modulates fission yeast protein levels in response to stress. Nat Commun. 2014 May 23;5:3947. doi: 10.1038/ncomms4947.

Hall JS, Iype R, Senra J, Taylor J, Armenoult L, Oguejiofor K, Li Y, Stratford I, Stern PL, O'Connor MJ, Miller CJ, West CM. Investigation of radiosensitivity gene signatures in cancer cell lines. PLoS One. 2014 Jan 22;9(1):e86329.

Dhani DK, Goult BT, George GM, Rogerson DT, Bitton DA, Miller CJ, Schwabe JW, Tanaka K. (2013) Mzt1/Tam4, a fission yeast MOZART1 homologue, is an essential component of the γ-tubulin complex and directly interacts with GCP3Alp6. Mol Biol Cell. 2013 Nov;24(21):3337-49.

Fawdar S, Trotter EW, Li Y, Stephenson NL, Hanke F, Marusiak AA, Edwards ZC, Ientile S, Waszkowycz B, Miller CJ, Brognard J. Targeted genetic dependency screen facilitates identification of actionable mutations in FGFR4, MAP3K9, and PAK5 in lung cancer. Proc Natl Acad Sci U S A. 2013 Jul 23;110(30):12426-31.

Eustace A, Mani N, Span PN, Irlam JJ, Taylor J, Betts GN, Denley H, Miller CJ, Homer JJ, Rojas AM, Hoskin PJ, Buffa FM, Harris AL, Kaanders JH, West CM. A 26-Gene Hypoxia Signature Predicts Benefit from Hypoxia-Modifying Therapy in Laryngeal Cancer but Not Bladder Cancer. Clin Cancer Res. 2013 Aug 6. [Epub ahead of print]

Ramachandran A, Betts G, Bhana S, Helme G, Blick C, Moller-Levet C, Saunders E, Valentine H, Pepper S, Miller CJ, Buffa F, Harris AL, West CM. An in vivo hypoxia metagene identifies the novel hypoxia inducible factor target gene SLCO1B3.
Eur J Cancer. 2013 May;49(7):1741-51.

Hall JS, Iype R, Armenoult LS, Taylor J, Miller CJ, Davidson S, de Sanjose S, Bosch X, Stern PL, West CM. Poor prognosis associated with human papillomavirus α7 genotypes in cervical carcinoma cannot be explained by intrinsic radiosensitivity. Int J Radiat Oncol Biol Phys. 2013 Apr 1;85(5):e223-9.

Betts GN, Eustace A, Patiar S, Valentine HR, Irlam J, Ramachandran A, Merve A, Homer JJ, Möller-Levet C, Buffa FM, Hall G, Miller CJ, Harris AL, West CM. Prospective technical validation and assessment of intra-tumour heterogeneity of a low density array hypoxia gene profile in head and neck squamous cell carcinoma. Eur J Cancer. 2012 Aug 27. pubmed.

Hall JS, Taylor J, Valentine HR, Irlam JJ, Eustace A, Hoskin PJ, Miller CJ, West CM. Enhanced stability of microRNA expression facilitates classification of FFPE tumour samples exhibiting near total mRNA degradation. Br J Cancer. 2012 Aug 7;107(4):684-94. pubmed

Harris WJ, Huang X, Lynch JT, Spencer GJ, Hitchin JR, Li Y, Ciceri F, Blaser JG, Greystoke BF, Jordan AM, Miller CJ, Ogilvie DJ, Somervaille TC. The histone demethylase KDM1A sustains the oncogenic potential of MLL-AF9 leukemia stem cells. Cancer Cell. 2012 Apr 17;21(4):473-87. pubmed

Bitton DA, Grallert A, Scutt PJ, Yates T, Li Y, Bradford JR, Hey Y, Pepper SD, Hagan IM, Miller CJ. Programmed fluctuations in sense/antisense transcript ratios drive sexual differentiation in S. pombe. Mol Syst Biol. 2011 Dec 20;7:559. doi: 10.1038/msb.2011.90.

Bitton DA, Wood V, Scutt PJ, Grallert A, Yates T, Smith DL, Hagan IM, Miller CJ. Augmented Annotation of the Schizosaccharomyces pombe Genome Reveals Additional Genes Required for Growth and Viability. Genetics. 2011 doi: 10.1534/genetics.110.123497

Bradford JR, Hey Y, Yates T, Li Y, Pepper SD, Miller CJ. A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling. BMC Genomics 2010 May 5: 11:282
doi:10.1186/1471-2164-11-282.

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 2010 5(1): e8949. doi:10.1371/journal.pone.0008949.

Buffa FM, Harris AL, West CM, Miller CJ. (2010) 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.

Moller-Levet CS, Betts GN, Harris AL, Homer JJ, West CM, Miller CJ. (2010) 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.

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

Danny A Bitton, Michal J Okoniewski, Yvonne Connolly and Crispin J Miller Exon level integration of proteomics and microarray data BMC Bioinformatics (2008), 9:118

Tim Yates, Michal J. Okoniewski, and Crispin J. Miller X:Map: annotation and visualization of genome structure for Affymetrix exon array analysis Nucleic Acids Research, Database Issue, Advance Access published on October 11, 2007. 
doi:10.1093/nar/gkm779 Full Text 

Carla S Moller-Levet; Catharine M West; Crispin J Miller. Exploiting sample variability to enhance multivariate analysis of microarray data Bioinformatics 2007; doi: 10.1093/bioinformatics/btm441 

Stuart D Pepper, Emma K Saunders, Laura E Edwards, Claire L Wilson, Crispin J Miller (2007) The utility of MAS5 expression summary and detection call algorithms. BMC Bioinformatics 8:273.

Michal J Okoniewski, Tim Yates, Sian Dibben and Crispin J Miller (2007) An annotation infrastructure for the analysis and interpretation of Affymetrix exon array data. Genome Biology 8:R79 

Ebrahim Sakhinia, Caroline Glennie, Judith A. Hoyland, Lia P. Menasce, Gerard Brady, Crispin Miller, John A. Radford, and Richard J. Byers (2007) Clinical quantitation of diagnostic and predictive gene expression levels in follicular and diffuse large B-cell lymphoma by RT-PCR gene expression profiling. Blood, Vol. 109, No. 9, pp. 3922-3928.

Martino Barenco, Sonia Shah, Daniel Brewer, Robin Callard, Jaroslav Stark, Crispin Miller, Michael Hubank (2007) 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)

A. H. Sims;  P. Finnon;  C. J. Miller;  S. D. Bouffler;  A. Howell;  D. Scott; R. B. Clarke (2007) TPD52 and NFKB1 gene expression levels correlate with G2 chromosomal radiosensitivity in lymphocytes of women with and at risk of hereditary breast cancer. International Journal of Radiation Biology, 1 - 12.

Stuart C. Winter, Francesca M. Buffa, Priyamal Silva, Crispin Miller, Helen R. Valentine, Helen Turley, Ketan A. Shah, Graham J. Cox, Rogan J. Corbridge, Jarrod J. Homer, Brian Musgrove, Nick Slevin, Philip Sloan, Pat Price, Catharine M.L. West and Adrian L. Harris (2007) Relation of a Hypoxia Metagene Derived from Head and Neck Cancer to Prognosis of Multiple Cancers. Cancer Research 67(7):3441:3449.

Okoniewski MJ, Hey Y, Pepper SD, Miller C (2007) "High correspondence between Affymetrix exon and standard expression arrays." Biotechniques, in press.

SD Pepper, H Yvonne, G Newton, M Okoniewski, CJ Miller (2006) A core lab case study: Exon Array Challenges and Opportunities. The Affymetrix Core Lab Communication Bulletin 1:1-4.

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 (2006). "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 in press.

Wilson, C.L., A.H. Sims, A. Howell, C.J. Miller, and R.B. Clarke. (2006). "Effects of oestrogen on gene expression in epithelium and stroma of normal human breast tissue" Endocr Relat Cancer, 13,617-28; abstract.

Michal J Okoniewski and Crispin J Miller (2006) "Hybridization interactions between probesets in short oligo microarrays lead to spurious correlations" BMC Bioinformatics 2006, 7:276; abstract.

Richard D Unwin, Duncan L Smith, David Blinco, Claire L Wilson, Crispin J Miller, Caroline A Evans, Ewa Jaworska, Stephen A Baldwin, Kay Barnes, Andrew Pierce, Elaine Spooncer, and Anthony D Whetton (2006) "Quantitative proteomics reveals post-translational control as a regulatory factor in primary hematopoietic stem cells" Blood First Edition Paper, prepublished online February 28, 2006; DOI 10.1182blood-2005-12-4995.

Claire L Wilson and Crispin J Miller (2005) "Simpleaffy: a BioConductor package for Affymetrix Quality Control and data analysis" Bioinformatics, 21(18), 3683-5.

Hui Sun Leong, Tim Yates, Claire Wilson and Crispin J. Miller (2005) "ADAPT: A Database of Affymetrix Probesets and Transcripts" Bioinformatics, Advance Access, published online on March 3, 2005 pubmed

Claire L. Wilson, Paul E. Boardman, Andrew J. Doig and Simon J. Hubbard (2004) "Improved prediction for N-termini of a-helices using empirical information" Proteins: Structure, Function and Bioinformatics, 1;57(2), 322-30 pubmed

Claire L. Wilson, Stuart D. Pepper, Yvonne Hey, and Crispin J. Miller (2004) "Amplification protocols introduce systematic but reproducible errors into gene expression studies" BioTechniques, 36, 498-506. pubmed

Janine T. Erler, Christopher J. Cawthorne, Kaye J. Williams, Marianne Koritzinsky, Bradley G. Wouters, Clare Wilson, Crispin Miller, Costas Demonacos, Ian J. Stratford, and Caroline Dive (2004) "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" Molecular and Cellular Biology, 24, 2875-2889. pubmed

Mabey J.E., Anderson, M.J., Giles P.F., Miller C.J., Attwood T.K., Paton N.W., Bornberg-Bauer E., Robson G.D., Oliver S.G. and Denning D.W. (2004) "CADRE: the Central Aspergillus Data Repository" Nucleic Acids Res, 32(1), D401-5. pubmed

Crispin J. Miller, Heba S. Kassem, Stuart D. Pepper, Yvonne Hey, Timothy H. Ward, and Geoffrey P. Margison (2003) "Mycoplasma Significantly alters microarray gene expression profiles" BioTechniques, 35, 812-814. pubmed

Miller, C.J. and Attwood, T.K. (2003) "Bioinformatics goes back to the future" Nature Reviews Molecular Cell Biology, 4, 157-162.pubmedPDFjournal.

Attwood, T.K. and Miller, C.J. (2002) "Progress in bioinformatics and the importance of being earnest" Biotechnology Annual Review, 8, 1-55.  amazon

Attwood, T.K. and Miller, C.J. (2001) "Which craft is best in bioinformatics?" Computers and Chemistry, 25(4), 329-339.  pubmed

Miller, C.J. and Attwood, T.K. (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.  IEEE Digital library

Cornell, M., Paton, N.W., Wu, S., Goble, C.A., Miller, C.J., Kirby, P., Eilbeck, K., Brass, A., Hayes, A. and Oliver, S.G., (2001) "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.  PDF

Publications Pre 2000

Miller C, Gurd J, and Brass A. (1999) "A RAPID algorithm for sequence database comparisons: application to the identification of vector contamination in the EMBL databases." Bioinformatics Feb;15(2), 111-21.  pubmed