Nuno L Barbosa-Morais

Summary

Affiliation: Cancer Research UK
Country: UK

Publications

  1. ncbi A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data
    Nuno L Barbosa-Morais
    Department of Oncology, University of Cambridge, Cambridge CB2 0RE, UK
    Nucleic Acids Res 38:e17. 2010
  2. ncbi A variational Bayesian mixture modelling framework for cluster analysis of gene-expression data
    Andrew E Teschendorff
    Department of Oncology, Cancer Genomics Program, Hutchison MRC Research Centre, University of Cambridge Hills Road, Cambridge CB2 2XZ, UK
    Bioinformatics 21:3025-33. 2005
  3. ncbi High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer
    Suet F Chin
    Breast Cancer Functional Genomics, Cancer Research UK Cambridge Research Institute and Department of Oncology University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
    Genome Biol 8:R215. 2007
  4. ncbi A consensus prognostic gene expression classifier for ER positive breast cancer
    Andrew E Teschendorff
    Cancer Genomics Program, Department of Oncology, University of Cambridge, Hutchison MRC Research Center, Hills Road, Cambridge CB2 2XZ, UK
    Genome Biol 7:R101. 2006
  5. ncbi Expression microarray reproducibility is improved by optimising purification steps in RNA amplification and labelling
    Ali Naderi
    Cancer Genomics Program, Department of Oncology, University of Cambridge, Hutchison MRC Research Centre, Hills Road, Cambridge CB2 2XZ, United Kingdom
    BMC Genomics 5:9. 2004
  6. ncbi Statistical issues in the analysis of Illumina data
    Mark J Dunning
    Department of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
    BMC Bioinformatics 9:85. 2008
  7. ncbi Spike-in validation of an Illumina-specific variance-stabilizing transformation
    Mark J Dunning
    Department of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
    BMC Res Notes 1:18. 2008
  8. ncbi Species-specific transcription in mice carrying human chromosome 21
    Michael D Wilson
    Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
    Science 322:434-8. 2008
  9. ncbi New androgen receptor genomic targets show an interaction with the ETS1 transcription factor
    Charles E Massie
    Uro Oncology Research Group, Department of Oncology, University of Cambridge, Cancer Research UK Cambridge, Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
    EMBO Rep 8:871-8. 2007
  10. ncbi Association of single-nucleotide polymorphisms in the cell cycle genes with breast cancer in the British population
    Kristy E Driver
    Cancer Research UK Department of Oncology, Strangeways Research Laboratory, University of Cambridge, Cambridge CB1 8RN, UK
    Carcinogenesis 29:333-41. 2008

Detail Information

Publications11

  1. ncbi A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data
    Nuno L Barbosa-Morais
    Department of Oncology, University of Cambridge, Cambridge CB2 0RE, UK
    Nucleic Acids Res 38:e17. 2010
    ....
  2. ncbi A variational Bayesian mixture modelling framework for cluster analysis of gene-expression data
    Andrew E Teschendorff
    Department of Oncology, Cancer Genomics Program, Hutchison MRC Research Centre, University of Cambridge Hills Road, Cambridge CB2 2XZ, UK
    Bioinformatics 21:3025-33. 2005
    ..We also compare the two criteria using freely available tumour microarray datasets and show that the variational Bayesian method is more sensitive to capturing biologically relevant structure...
  3. ncbi High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer
    Suet F Chin
    Breast Cancer Functional Genomics, Cancer Research UK Cambridge Research Institute and Department of Oncology University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
    Genome Biol 8:R215. 2007
    ..To date, most genome-wide array comparative genomic hybridization studies have used tumor panels of relatively large tumor size and high Nottingham Prognostic Index (NPI) that are not as representative of breast cancer demographics...
  4. ncbi A consensus prognostic gene expression classifier for ER positive breast cancer
    Andrew E Teschendorff
    Cancer Genomics Program, Department of Oncology, University of Cambridge, Hutchison MRC Research Center, Hills Road, Cambridge CB2 2XZ, UK
    Genome Biol 7:R101. 2006
    ..A consensus prognostic gene expression classifier is still elusive in heterogeneous diseases such as breast cancer...
  5. ncbi Expression microarray reproducibility is improved by optimising purification steps in RNA amplification and labelling
    Ali Naderi
    Cancer Genomics Program, Department of Oncology, University of Cambridge, Hutchison MRC Research Centre, Hills Road, Cambridge CB2 2XZ, United Kingdom
    BMC Genomics 5:9. 2004
    ..Purification steps are critical in RNA amplification and labelling protocols, and there is a lack of sufficient data to validate and optimise the process...
  6. ncbi Statistical issues in the analysis of Illumina data
    Mark J Dunning
    Department of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
    BMC Bioinformatics 9:85. 2008
    ..In this paper, we present our experience of analysing the raw data from an Illumina spike-in experiment and offer guidelines for those wishing to analyse expression data or develop new methodologies for this technology...
  7. ncbi Spike-in validation of an Illumina-specific variance-stabilizing transformation
    Mark J Dunning
    Department of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
    BMC Res Notes 1:18. 2008
    ..We apply VST to the data from a recently published spike-in experiment and compare it both to a regular log2 analysis and a recently recommended analysis that can be applied if all raw data are available...
  8. ncbi Species-specific transcription in mice carrying human chromosome 21
    Michael D Wilson
    Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
    Science 322:434-8. 2008
    ....
  9. ncbi New androgen receptor genomic targets show an interaction with the ETS1 transcription factor
    Charles E Massie
    Uro Oncology Research Group, Department of Oncology, University of Cambridge, Cancer Research UK Cambridge, Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
    EMBO Rep 8:871-8. 2007
    ..Binding sequences for the avian erythroblastosis virus E26 homologue (ETS) transcription factor family were also highly enriched, and we uncovered an interaction between the AR and ETS1 at a subset of AR promoter targets...
  10. ncbi Association of single-nucleotide polymorphisms in the cell cycle genes with breast cancer in the British population
    Kristy E Driver
    Cancer Research UK Department of Oncology, Strangeways Research Laboratory, University of Cambridge, Cambridge CB1 8RN, UK
    Carcinogenesis 29:333-41. 2008
    ..010, P-trend = 0.048). Further large-scale studies are needed to confirm these results...
  11. ncbi MicroRNA expression profiling of human breast cancer identifies new markers of tumor subtype
    Cherie Blenkiron
    Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
    Genome Biol 8:R214. 2007
    ..MicroRNAs (miRNAs), a class of short non-coding RNAs found in many plants and animals, often act post-transcriptionally to inhibit gene expression...