Tim Massingham

Summary

Affiliation: Wellcome Trust Genome Campus
Country: UK

Publications

  1. pmc Error-correcting properties of the SOLiD Exact Call Chemistry
    Tim Massingham
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
    BMC Bioinformatics 13:145. 2012
  2. doi request reprint All Your Base: a fast and accurate probabilistic approach to base calling
    Tim Massingham
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1RQ, UK
    Genome Biol 13:R13. 2012
  3. ncbi request reprint Statistics of the log-det estimator
    T Massingham
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
    Mol Biol Evol 24:2277-85. 2007
  4. pmc Genomic DNA k-mer spectra: models and modalities
    Benny Chor
    School of Computer Science, Tel Aviv University, Klausner St, Ramat Aviv, Tel Aviv 39040, Israel
    Genome Biol 10:R108. 2009
  5. pmc PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment
    Botond Sipos
    EMBL European Bioinformatics Institute, Hinxton, UK
    BMC Bioinformatics 12:104. 2011
  6. pmc Relating tissue specialization to the differentiation of expression of singleton and duplicate mouse proteins
    Shiri Freilich
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
    Genome Biol 7:R89. 2006
  7. pmc An improved protocol for sequencing of repetitive genomic regions and structural variations using mutagenesis and next generation sequencing
    Botond Sipos
    European Bioinformatics Institute, EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    PLoS ONE 7:e43359. 2012
  8. doi request reprint Detecting the presence and location of selection in proteins
    Tim Massingham
    European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
    Methods Mol Biol 452:311-29. 2008
  9. pmc Ensembl's 10th year
    Paul Flicek
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 38:D557-62. 2010
  10. pmc Detecting amino acid sites under positive selection and purifying selection
    Tim Massingham
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
    Genetics 169:1753-62. 2005

Detail Information

Publications11

  1. pmc Error-correcting properties of the SOLiD Exact Call Chemistry
    Tim Massingham
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
    BMC Bioinformatics 13:145. 2012
    ..Additionally, the Exact Call Chemistry allows reads produced by the platform to be decoded directly into nucleotide sequence rather than its two-base 'color' encoding...
  2. doi request reprint All Your Base: a fast and accurate probabilistic approach to base calling
    Tim Massingham
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1RQ, UK
    Genome Biol 13:R13. 2012
    ..AYB is available at http://www.ebi.ac.uk/goldman-srv/AYB/...
  3. ncbi request reprint Statistics of the log-det estimator
    T Massingham
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
    Mol Biol Evol 24:2277-85. 2007
    ..The log-det estimator is found to have good statistical properties under such general models...
  4. pmc Genomic DNA k-mer spectra: models and modalities
    Benny Chor
    School of Computer Science, Tel Aviv University, Klausner St, Ramat Aviv, Tel Aviv 39040, Israel
    Genome Biol 10:R108. 2009
    ....
  5. pmc PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment
    Botond Sipos
    EMBL European Bioinformatics Institute, Hinxton, UK
    BMC Bioinformatics 12:104. 2011
    ..This calls for an extensible simulation framework written in a high-level functional language, offering new functionality and making it easy to incorporate further complexity...
  6. pmc Relating tissue specialization to the differentiation of expression of singleton and duplicate mouse proteins
    Shiri Freilich
    EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
    Genome Biol 7:R89. 2006
    ..We explored the relationship between duplication events, the time at which they took place, and both the expression breadth of the duplicated genes and the cumulative expression breadth of the gene family to which they belong...
  7. pmc An improved protocol for sequencing of repetitive genomic regions and structural variations using mutagenesis and next generation sequencing
    Botond Sipos
    European Bioinformatics Institute, EMBL EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    PLoS ONE 7:e43359. 2012
    ..Moreover, our simulations suggest that NG-SAM is capable of reconstructing robustly a wide range of potential target sequences of varying lengths and repetitive structures...
  8. doi request reprint Detecting the presence and location of selection in proteins
    Tim Massingham
    European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
    Methods Mol Biol 452:311-29. 2008
    ..Both data quality issues and statistical assessment of the results are considered...
  9. pmc Ensembl's 10th year
    Paul Flicek
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Nucleic Acids Res 38:D557-62. 2010
    ....
  10. pmc Detecting amino acid sites under positive selection and purifying selection
    Tim Massingham
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
    Genetics 169:1753-62. 2005
    ..We also show that the SLR method performs well even under circumstances where the results from some previous methods can be misleading...
  11. pmc Relationship between the tissue-specificity of mouse gene expression and the evolutionary origin and function of the proteins
    Shiri Freilich
    EMBL EBI, Wellcome Trust Genome Campus, Cambridge, CB10 1SB, UK
    Genome Biol 6:R56. 2005
    ..In this study, mouse proteins were assigned into functional and phyletic groups and the gene expression patterns of the different protein groupings were examined by microarray analysis in various mouse tissues...