John C Marioni

Summary

Affiliation: University of Cambridge
Country: UK

Publications

  1. ncbi Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization
    John C Marioni
    Computational Biology Group, Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Centre for Mathematical Sciences, Wilberforce Road, Cambridge CB3 0WA, UK
    Genome Biol 8:R228. 2007
  2. ncbi RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays
    John C Marioni
    Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
    Genome Res 18:1509-17. 2008
  3. ncbi BioHMM: a heterogeneous hidden Markov model for segmenting array CGH data
    J C Marioni
    Hutchison MRC Research Centre, Department of Oncology, Computational Biology Group, University of Cambridge Hills Road, Cambridge
    Bioinformatics 22:1144-6. 2006
  4. ncbi Hidden copy number variation in the HapMap population
    John C Marioni
    Department of Oncology, Computational Biology Group, University of Cambridge, Cancer Research UK Cambridge Research Institute, Robinson Way, Cambridge, United Kingdom
    Proc Natl Acad Sci U S A 105:10067-72. 2008
  5. 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
  6. ncbi A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis
    Thomas A Down
    Wellcome Trust Cancer Research UK Gurdon Institute, and Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
    Nat Biotechnol 26:779-85. 2008
  7. ncbi The pitfalls of platform comparison: DNA copy number array technologies assessed
    Christina Curtis
    Department of Oncology, University of Cambridge, Addenbrooke s Hopsital, Hills Road, Cambridge CB20XZ, UK
    BMC Genomics 10:588. 2009
  8. ncbi ESR1 gene amplification in breast cancer: a common phenomenon?
    Lindsay A Brown
    Nat Genet 40:806-7; author reply 810-2. 2008
  9. ncbi An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)
    Vardhman K Rakyan
    Institute of Cell and Molecular Science, Barts and The London, London E1 2AT, United Kingdom
    Genome Res 18:1518-29. 2008
  10. ncbi Numbers of copy-number variations and false-negative rates will be underestimated if we do not account for the dependence between repeated experiments
    Andy G Lynch
    Am J Hum Genet 81:418-20; author reply 420-1. 2007

Detail Information

Publications10

  1. ncbi Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization
    John C Marioni
    Computational Biology Group, Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Centre for Mathematical Sciences, Wilberforce Road, Cambridge CB3 0WA, UK
    Genome Biol 8:R228. 2007
    ..However, methods for analyzing the complex data produced and identifying regions of CNV are still being refined...
  2. ncbi RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays
    John C Marioni
    Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA
    Genome Res 18:1509-17. 2008
    ..Based on our observations, we propose an empirical protocol and a statistical framework for the analysis of gene expression using ultra-high-throughput sequencing technology...
  3. ncbi BioHMM: a heterogeneous hidden Markov model for segmenting array CGH data
    J C Marioni
    Hutchison MRC Research Centre, Department of Oncology, Computational Biology Group, University of Cambridge Hills Road, Cambridge
    Bioinformatics 22:1144-6. 2006
    ..By utilizing a heterogeneous hidden Markov model, BioHMM incorporates relevant biological factors (e.g. the distance between adjacent clones) in the segmentation process...
  4. ncbi Hidden copy number variation in the HapMap population
    John C Marioni
    Department of Oncology, Computational Biology Group, University of Cambridge, Cancer Research UK Cambridge Research Institute, Robinson Way, Cambridge, United Kingdom
    Proc Natl Acad Sci U S A 105:10067-72. 2008
    ..Finally, we discuss how this methodology might be applied to future studies to obtain better estimates of the extent of CNV across the genome...
  5. 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...
  6. ncbi A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis
    Thomas A Down
    Wellcome Trust Cancer Research UK Gurdon Institute, and Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
    Nat Biotechnol 26:779-85. 2008
    ....
  7. ncbi The pitfalls of platform comparison: DNA copy number array technologies assessed
    Christina Curtis
    Department of Oncology, University of Cambridge, Addenbrooke s Hopsital, Hills Road, Cambridge CB20XZ, UK
    BMC Genomics 10:588. 2009
    ..By careful consideration and avoidance of potential sources of bias, we aim to provide a fair assessment of platform performance...
  8. ncbi ESR1 gene amplification in breast cancer: a common phenomenon?
    Lindsay A Brown
    Nat Genet 40:806-7; author reply 810-2. 2008
  9. ncbi An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)
    Vardhman K Rakyan
    Institute of Cell and Molecular Science, Barts and The London, London E1 2AT, United Kingdom
    Genome Res 18:1518-29. 2008
    ....
  10. ncbi Numbers of copy-number variations and false-negative rates will be underestimated if we do not account for the dependence between repeated experiments
    Andy G Lynch
    Am J Hum Genet 81:418-20; author reply 420-1. 2007