Crispin Miller

Crispin Miller

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Crispin Miller

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Publisher Correction: In silico prediction of housekeeping long intergenic non-coding RNAs reveals HKlincR1 as an essential player in lung cancer cell survival.

Sci Rep 2019 Dec 24;9(1):20211. Epub 2019 Dec 24.

RNA Biology Group, CRUK Manchester Institute, The University of Manchester, Alderley Park, Manchester, SK10 4TG, UK.

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http://dx.doi.org/10.1038/s41598-019-55753-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6930325PMC
December 2019

In silico prediction of housekeeping long intergenic non-coding RNAs reveals HKlincR1 as an essential player in lung cancer cell survival.

Sci Rep 2019 May 14;9(1):7372. Epub 2019 May 14.

RNA Biology Group, CRUK Manchester Institute, The University of Manchester, Alderley Park, Manchester, SK10 4TG, UK.

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http://dx.doi.org/10.1038/s41598-019-43758-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6517443PMC
May 2019

Genomic Evaluation of Multiparametric Magnetic Resonance Imaging-visible and -nonvisible Lesions in Clinically Localised Prostate Cancer.

Eur Urol Oncol 2019 Feb 5;2(1):1-11. Epub 2018 Sep 5.

Belfast-Manchester Movember Centre of Excellence, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, UK; Prostate Oncobiology, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, UK. Electronic address:

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http://dx.doi.org/10.1016/j.euo.2018.08.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6472613PMC
February 2019

Improved PDX and CDX Data Processing-Response.

Mol Cancer Res 2018 11;16(11):1814

RNABiology Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, United Kingdom.

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http://dx.doi.org/10.1158/1541-7786.MCR-18-0535DOI Listing
November 2018

Mutation pattern analysis reveals polygenic mini-drivers associated with relapse after surgery in lung adenocarcinoma.

Sci Rep 2018 10 4;8(1):14830. Epub 2018 Oct 4.

RNA Biology Group, CRUK Manchester Institute, The University of Manchester, Alderley Park, Manchester, SK10 4TG, UK.

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http://www.nature.com/articles/s41598-018-33276-3
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http://dx.doi.org/10.1038/s41598-018-33276-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6172282PMC
October 2018

Truncation- and motif-based pan-cancer analysis reveals tumor-suppressing kinases.

Sci Signal 2018 04 17;11(526). Epub 2018 Apr 17.

Signalling Networks in Cancer Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester M20 4BX, UK.

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http://dx.doi.org/10.1126/scisignal.aan6776DOI Listing
April 2018

twoddpcr: an R/Bioconductor package and Shiny app for Droplet Digital PCR analysis.

Bioinformatics 2017 Sep;33(17):2743-2745

RNA Biology Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester M20?4BX, UK.

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http://dx.doi.org/10.1093/bioinformatics/btx308DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860069PMC
September 2017

Next-Generation Sequencing Analysis and Algorithms for PDX and CDX Models.

Mol Cancer Res 2017 08 25;15(8):1012-1016. Epub 2017 Apr 25.

RNA Biology Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, United Kingdom.

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http://dx.doi.org/10.1158/1541-7786.MCR-16-0431DOI Listing
August 2017

Mouse RUNX1C regulates premegakaryocytic/erythroid output and maintains survival of megakaryocyte progenitors.

Blood 2017 07 10;130(3):271-284. Epub 2017 May 10.

Cancer Research UK Stem Cell Biology Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, United Kingdom.

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http://dx.doi.org/10.1182/blood-2016-06-723635DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5833261PMC
July 2017

Hypoxia-driven splicing into noncoding isoforms regulates the DNA damage response.

NPJ Genom Med 2016 20;1:16020. Epub 2016 Jul 20.

RNA Biology Group, CRUK Manchester Institute, The University of Manchester, Manchester, UK.

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http://dx.doi.org/10.1038/npjgenmed.2016.20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5417364PMC
July 2016

Using large-scale genomics data to identify driver mutations in lung cancer: methods and challenges.

Pharmacogenomics 2015 31;16(10):1149-60. Epub 2015 Jul 31.

RNA Biology Group & Computational Biology Support Team, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, UK.

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http://dx.doi.org/10.2217/pgs.15.60DOI Listing
June 2016

Oncogenic KRAS Regulates Tumor Cell Signaling via Stromal Reciprocation.

Cell 2016 May 14;165(4):910-20. Epub 2016 Apr 14.

The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK; Cancer Research UK Manchester Institute, University of Manchester, Wilmslow Road, Manchester M20 4BX, UK. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2016.03.029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4868820PMC
May 2016

Epithelial and stromal microRNA signatures of columnar cell hyperplasia linking Let-7c to precancerous and cancerous breast cancer cell proliferation.

PLoS One 2014 14;9(8):e105099. Epub 2014 Aug 14.

Center for Molecular Pathology, Skåne University Hospital, Department of Laboratory Medicine Malmö, Lund University, Malmö, Sweden; Breakthrough Breast Cancer Research Unit, Institute of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Paterson Institute for Cancer Research, The Christie National Health Service Foundation Trust, Manchester, United Kingdom; Sahlgrenska Cancer Center, Department of Biomedicine, University of Gothenburg, Gothenburg, Sweden.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0105099PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4133372PMC
March 2016

GFI1 proteins orchestrate the emergence of haematopoietic stem cells through recruitment of LSD1.

Nat Cell Biol 2016 Jan 30;18(1):21-32. Epub 2015 Nov 30.

CRUK Stem Cell Biology Group, Cancer Research UK Manchester Institute, The University of Manchester, Wilmslow Road, Manchester M20 4BX, UK.

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http://dx.doi.org/10.1038/ncb3276DOI Listing
January 2016

RUNX1B Expression Is Highly Heterogeneous and Distinguishes Megakaryocytic and Erythroid Lineage Fate in Adult Mouse Hematopoiesis.

PLoS Genet 2016 Jan 25;12(1):e1005814. Epub 2016 Jan 25.

Cancer Research UK Stem Cell Biology Group, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, United Kingdom.

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http://dx.doi.org/10.1371/journal.pgen.1005814DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4726605PMC
January 2016

Onco-STS: a web-based laboratory information management system for sample and analysis tracking in oncogenomic experiments.

Source Code Biol Med 2014 5;9(1):25. Epub 2014 Dec 5.

Molecular Oncology Group, University of Manchester, Wilmslow Road, Manchester, M20 4BX UK.

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http://dx.doi.org/10.1186/s13029-014-0025-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4288629PMC
January 2015

A global non-coding RNA system modulates fission yeast protein levels in response to stress.

Nat Commun 2014 May 23;5:3947. Epub 2014 May 23.

Applied Computational Biology and Bioinformatics Group, Cancer Research UK Manchester Institute, University of Manchester, Wilmslow Road, Manchester M20 4BX, UK.

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http://dx.doi.org/10.1038/ncomms4947DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4050258PMC
May 2014

Mzt1/Tam4, a fission yeast MOZART1 homologue, is an essential component of the γ-tubulin complex and directly interacts with GCP3(Alp6).

Mol Biol Cell 2013 Nov 4;24(21):3337-49. Epub 2013 Sep 4.

Department of Biochemistry, University of Leicester, Leicester LE1 9HN, United Kingdom Paterson Institute for Cancer Research, University of Manchester, Manchester M20 4BX, United Kingdom.

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http://dx.doi.org/10.1091/mbc.E13-05-0253DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3814152PMC
November 2013

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 8;110(30):12426-31. Epub 2013 Jul 8.

Signalling Networks in Cancer Group, Cancer Research UK, Paterson Institute for Cancer Research, University of Manchester, Manchester M20 4BX, United Kingdom.

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http://dx.doi.org/10.1073/pnas.1305207110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3725071PMC
July 2013

An in vivo hypoxia metagene identifies the novel hypoxia inducible factor target gene SLCO1B3.

Eur J Cancer 2013 May 23;49(7):1741-51. Epub 2013 Jan 23.

Cancer Research UK Molecular Oncology Laboratories, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK.

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http://dx.doi.org/10.1016/j.ejca.2012.12.003DOI Listing
May 2013

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 17;85(5):e223-9. Epub 2013 Jan 17.

Translational Radiobiology Group, Institute of Cancer Sciences, Manchester Academic Health Science Centre, University of Manchester, Manchester, United Kingdom.

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http://dx.doi.org/10.1016/j.ijrobp.2012.11.030DOI Listing
April 2013

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 2013 Jan 27;49(1):156-65. Epub 2012 Aug 27.

Translational Radiobiology Group, Institute of Cancer Sciences, Manchester Academic Health Science Centre, Christie Hospital, Wilmslow Road, Manchester M20 4BX, United Kingdom.

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http://dx.doi.org/10.1016/j.ejca.2012.07.028DOI Listing
January 2013

The histone demethylase KDM1A sustains the oncogenic potential of MLL-AF9 leukemia stem cells.

Cancer Cell 2012 Apr 29;21(4):473-87. Epub 2012 Mar 29.

Cancer Research UK Leukaemia Biology Laboratory, Paterson Institute for Cancer Research, University of Manchester, Manchester, United Kingdom.

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http://dx.doi.org/10.1016/j.ccr.2012.03.014DOI Listing
April 2012

Programmed fluctuations in sense/antisense transcript ratios drive sexual differentiation in S. pombe.

Mol Syst Biol 2011 Dec 20;7:559. Epub 2011 Dec 20.

CRUK Applied Computational Biology and Bioinformatics Group, Cancer Research UK, Paterson Institute for Cancer Research, The University of Manchester, Manchester, UK.

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http://dx.doi.org/10.1038/msb.2011.90DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3738847PMC
December 2011

RAC2, AEP, and ICAM1 expression are associated with CNS disease in a mouse model of pre-B childhood acute lymphoblastic leukemia.

Blood 2011 Jul 23;118(3):638-49. Epub 2011 May 23.

Cancer Research UK Children's Cancer Group, Manchester Academic Health Science Centre, School of Cancer & Enabling Sciences, University of Manchester, Manchester, United Kingdom.

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http://dx.doi.org/10.1182/blood-2010-09-307330DOI Listing
July 2011

Augmented annotation of the Schizosaccharomyces pombe genome reveals additional genes required for growth and viability.

Genetics 2011 Apr 26;187(4):1207-17. Epub 2011 Jan 26.

Cancer Research UK Applied Computational Biology and Bioinformatics Group, University of Manchester, Christie Hospital Site, Manchester M20 4BX, United Kingdom.

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http://dx.doi.org/10.1534/genetics.110.123497DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070528PMC
April 2011

A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling.

BMC Genomics 2010 May 5;11:282. Epub 2010 May 5.

Applied Computational Biology and Bioinformatics, Cancer Research UK, Paterson Institute for Cancer Research, The University of Manchester, Wilmslow Road, Manchester M20 4BX UK.

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http://dx.doi.org/10.1186/1471-2164-11-282DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877694PMC
May 2010

An integrated mass-spectrometry pipeline identifies novel protein coding-regions in the human genome.

PLoS One 2010 Jan 28;5(1):e8949. Epub 2010 Jan 28.

Applied Computational Biology and Bioinformatics Group, Cancer Research UK, Paterson Institute for Cancer Research, The University of Manchester, Manchester, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0008949PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812506PMC
January 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 20;5(11):e1000571. Epub 2009 Nov 20.

Applied Computational Biology and Bioinformatics Group, Cancer Research UK Paterson Institute for Cancer Research, The University of Manchester, Christie Hospital, Manchester, United Kingdom.

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http://dx.doi.org/10.1371/journal.pcbi.1000571DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2773424PMC
November 2009

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

Cancer Research UK Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, UK.

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http://dx.doi.org/10.2144/000113169DOI Listing
July 2009

Gastrointestinal differentiation marker Cytokeratin 20 is regulated by homeobox gene CDX1.

Proc Natl Acad Sci U S A 2009 Feb 2;106(6):1936-41. Epub 2009 Feb 2.

Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, OX3 9DS, United Kingdom.

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http://dx.doi.org/10.1073/pnas.0812904106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2644142PMC
February 2009

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;1:42. Epub 2008 Sep 21.

Applied Bioinformatics of Cancer Research Group, Breakthrough Research Unit, Edinburgh Cancer Research Centre, Western General Hospital, Crewe Road South, Edinburgh, EH4 2XR, UK.

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http://dx.doi.org/10.1186/1755-8794-1-42DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2563019PMC
September 2008

Eight-channel iTRAQ enables comparison of the activity of six leukemogenic tyrosine kinases.

Mol Cell Proteomics 2008 May 21;7(5):853-63. Epub 2007 Oct 21.

Stem Cell and Leukaemia Proteomics Laboratory, University of Manchester, Christie Hospital, Kinnaird House, Kinnaird Road, Manchester M204QL, United Kingdom.

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http://dx.doi.org/10.1074/mcp.M700251-MCP200DOI Listing
May 2008

Quantitative proteomics analysis demonstrates post-transcriptional regulation of embryonic stem cell differentiation to hematopoiesis.

Mol Cell Proteomics 2008 Mar 27;7(3):459-72. Epub 2007 Nov 27.

Stem Cell and Leukemia Proteomics Laboratory, Faculty of Medical and Human Sciences, University of Manchester, Kinnaird House, Kinnaird Road, Manchester M20 4QL, United Kingdom.

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http://dx.doi.org/10.1074/mcp.M700370-MCP200DOI Listing
March 2008

Exon level integration of proteomics and microarray data.

BMC Bioinformatics 2008 Feb 25;9:118. Epub 2008 Feb 25.

Cancer Research UK, Applied Computational Biology and Bioinformatics Group, Paterson Institute for Cancer Research, The University of Manchester, Christie Hospital Site, Wilmslow Road, Manchester, M20 4BX, UK.

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http://dx.doi.org/10.1186/1471-2105-9-118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2267708PMC
February 2008

Comprehensive analysis of affymetrix exon arrays using BioConductor.

PLoS Comput Biol 2008 Feb;4(2):e6

Applied Computational Biology and Bioinformatics Group, Cancer Research UK.

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http://dx.doi.org/10.1371/journal.pcbi.0040006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2323405PMC
February 2008

X:Map: annotation and visualization of genome structure for Affymetrix exon array analysis.

Nucleic Acids Res 2008 Jan 11;36(Database issue):D780-6. Epub 2007 Oct 11.

Cancer Research UK, Bioinformatics Group, Paterson Institute for Cancer Research, The University of Manchester, Christie Hospital Site, Wilmslow Road, Withington, Manchester, M20 4BX, UK.

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http://dx.doi.org/10.1093/nar/gkm779DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238884PMC
January 2008

Exploiting sample variability to enhance multivariate analysis of microarray data.

Bioinformatics 2007 Oct 7;23(20):2733-40. Epub 2007 Sep 7.

Paterson Institute for Cancer Research, Cancer Research UK, Manchester, M20 4BX, UK.

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http://dx.doi.org/10.1093/bioinformatics/btm441DOI Listing
October 2007

An annotation infrastructure for the analysis and interpretation of Affymetrix exon array data.

Genome Biol 2007 ;8(5):R79

Bioinformatics Group, Cancer Research UK, Paterson Institute for Cancer Research, The University of Manchester, Christie Hospital Site, Wilmslow Road, Manchester M20 4BX, UK.

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http://dx.doi.org/10.1186/gb-2007-8-5-r79DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1929135PMC
September 2007

The utility of MAS5 expression summary and detection call algorithms.

BMC Bioinformatics 2007 Jul 30;8:273. Epub 2007 Jul 30.

Cancer Research UK, Paterson Institute for Cancer Research, The University of Manchester, Christie Hospital Site, Withington, Manchester, UK.

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http://dx.doi.org/10.1186/1471-2105-8-273DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1950098PMC
July 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 2007 May 25;109(9):3922-8. Epub 2007 Jan 25.

Division of Regenerative Medicine, School of Medicine, Faculty of Medical and Human Sciences, The University of Manchester, Oxford Road, Manchester, UK.

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http://www.bloodjournal.org/cgi/doi/10.1182/blood-2006-09-04
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http://dx.doi.org/10.1182/blood-2006-09-046391DOI Listing
May 2007

High correspondence between Affymetrix exon and standard expression arrays.

Biotechniques 2007 Feb;42(2):181-5

The Paterson Institute for Cancer Research, The University of Manchester, Christie Hospital Site, Manchester, UK.

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http://dx.doi.org/10.2144/000112315DOI Listing
February 2007

Quantitative proteomics reveals posttranslational control as a regulatory factor in primary hematopoietic stem cells.

Blood 2006 Jun 28;107(12):4687-94. Epub 2006 Feb 28.

Stem Cell and Leukaemia Proteomics Laboratory, Faculty of Medical and Human Sciences, University of Manchester, Manchester M20 4QL, UK.

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http://dx.doi.org/10.1182/blood-2005-12-4995DOI Listing
June 2006

Hybridization interactions between probesets in short oligo microarrays lead to spurious correlations.

BMC Bioinformatics 2006 Jun 2;7:276. Epub 2006 Jun 2.

Paterson Institute For Cancer Research, Christie Hospital site, University of Manchester, Wilmslow Road, Manchester, M20 4BX, UK.

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http://dx.doi.org/10.1186/1471-2105-7-276DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1513401PMC
June 2006

Simpleaffy: a BioConductor package for Affymetrix Quality Control and data analysis.

Bioinformatics 2005 Sep 2;21(18):3683-5. Epub 2005 Aug 2.

Paterson Institute for Cancer Research, Manchester M20 4BX, UK.

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http://dx.doi.org/10.1093/bioinformatics/bti605DOI Listing
September 2005

ADAPT: a database of affymetrix probesets and transcripts.

Bioinformatics 2005 May 3;21(10):2552-3. Epub 2005 Mar 3.

Paterson Institute for Cancer Research, Wilmslow Road, Manchester M20 4BX, UK.

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http://dx.doi.org/10.1093/bioinformatics/bti359DOI Listing
May 2005

Amplification protocols introduce systematic but reproducible errors into gene expression studies.

Biotechniques 2004 Mar;36(3):498-506

Paterson Institute for Cancer Research, Withington, Manchester, UK.

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http://dx.doi.org/10.2144/04363RN05DOI Listing
March 2004

Mycoplasma infection significantly alters microarray gene expression profiles.

Biotechniques 2003 Oct;35(4):812-4

Bioinformatics Group, Paterson Institute for Cancer Research, Christie Hospital Trust, Manchester, M20, 4BX, UK.

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http://www.biotechniques.com/multimedia/archive/00009/03354m
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http://dx.doi.org/10.2144/03354mt02DOI Listing
October 2003

Bioinformatics goes back to the future.

Nat Rev Mol Cell Biol 2003 02;4(2):157-62

Paterson Institute for Cancer Research, Christie Hospital, Wilmslow Road, Withington, Manchester M20 4BX, UK.

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http://dx.doi.org/10.1038/nrm1013DOI Listing
February 2003