Gerton Lunter

Summary

Affiliation: University of Oxford
Country: UK

Publications

  1. ncbi request reprint Probabilistic whole-genome alignments reveal high indel rates in the human and mouse genomes
    Gerton Lunter
    MRC Functional Genetics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, United Kingdom
    Bioinformatics 23:i289-96. 2007
  2. pmc Uncertainty in homology inferences: assessing and improving genomic sequence alignment
    Gerton Lunter
    MRC Functional Genetics Unit, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom
    Genome Res 18:298-309. 2008
  3. ncbi request reprint HMMoC--a compiler for hidden Markov models
    Gerton Lunter
    MRC Functional Genetics Unit, Department of Physiology, Anatomy and Genetics, South Parks Road, OX1 3TG, University of Oxford, UK
    Bioinformatics 23:2485-7. 2007
  4. pmc Bayesian coestimation of phylogeny and sequence alignment
    Gerton Lunter
    Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
    BMC Bioinformatics 6:83. 2005
  5. pmc Genome assembly quality: assessment and improvement using the neutral indel model
    Stephen Meader
    Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom
    Genome Res 20:675-84. 2010
  6. pmc Investigating selection on viruses: a statistical alignment approach
    Saskia de Groot
    Department of Statistics, University of Oxford, 1 South Parks Road, OX1 3TG, UK
    BMC Bioinformatics 9:304. 2008
  7. ncbi request reprint A nucleotide substitution model with nearest-neighbour interactions
    Gerton Lunter
    Bioinformatics Group, Department of Statistics, University of Oxford, Oxford, UK
    Bioinformatics 20:i216-23. 2004
  8. pmc Genome-wide identification of human functional DNA using a neutral indel model
    Gerton Lunter
    MRC Functional Genetics Unit, Department of Human Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
    PLoS Comput Biol 2:e5. 2006
  9. pmc GAT: a simulation framework for testing the association of genomic intervals
    Andreas Heger
    MRC CGAT Programme and Functional Genomics Unit, MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
    Bioinformatics 29:2046-8. 2013
  10. pmc Genomic and transcriptional co-localization of protein-coding and long non-coding RNA pairs in the developing brain
    Jasmina Ponjavic
    MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
    PLoS Genet 5:e1000617. 2009

Detail Information

Publications18

  1. ncbi request reprint Probabilistic whole-genome alignments reveal high indel rates in the human and mouse genomes
    Gerton Lunter
    MRC Functional Genetics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, United Kingdom
    Bioinformatics 23:i289-96. 2007
    ..Here, I describe a novel and accurate method for estimating neutral indel rates between divergent pairs of genomes...
  2. pmc Uncertainty in homology inferences: assessing and improving genomic sequence alignment
    Gerton Lunter
    MRC Functional Genetics Unit, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom
    Genome Res 18:298-309. 2008
    ..Alignment errors are inevitable, and should be considered when drawing conclusions from alignments. Software and alignments to assist researchers in doing this are provided at http://genserv.anat.ox.ac.uk/grape/...
  3. ncbi request reprint HMMoC--a compiler for hidden Markov models
    Gerton Lunter
    MRC Functional Genetics Unit, Department of Physiology, Anatomy and Genetics, South Parks Road, OX1 3TG, University of Oxford, UK
    Bioinformatics 23:2485-7. 2007
    ..The compiler is highly customizable, produces efficient and bug-free code, and includes several optimizations...
  4. pmc Bayesian coestimation of phylogeny and sequence alignment
    Gerton Lunter
    Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
    BMC Bioinformatics 6:83. 2005
    ..Whether the main interest be in sequence alignment or phylogeny, a major goal of computational biology is the co-estimation of both...
  5. pmc Genome assembly quality: assessment and improvement using the neutral indel model
    Stephen Meader
    Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom
    Genome Res 20:675-84. 2010
    ..Our approach contributes a new fine-scale quality metric for assemblies that should facilitate development of improved genome sequencing and assembly strategies...
  6. pmc Investigating selection on viruses: a statistical alignment approach
    Saskia de Groot
    Department of Statistics, University of Oxford, 1 South Parks Road, OX1 3TG, UK
    BMC Bioinformatics 9:304. 2008
    ..We show that in this way we obtain un-biased selection parameters for different genomic regions of interest, and can improve in accuracy compared to using a fixed alignment...
  7. ncbi request reprint A nucleotide substitution model with nearest-neighbour interactions
    Gerton Lunter
    Bioinformatics Group, Department of Statistics, University of Oxford, Oxford, UK
    Bioinformatics 20:i216-23. 2004
    ..The model is irreversible, giving an arrow to time, and allowing the position of the root between a pair of sequences to be inferred without using out-groups...
  8. pmc Genome-wide identification of human functional DNA using a neutral indel model
    Gerton Lunter
    MRC Functional Genetics Unit, Department of Human Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
    PLoS Comput Biol 2:e5. 2006
    ..The ability to identify elements under heterogeneous selection enables, for the first time, the genome-wide investigation of positive selection on functional elements other than protein-coding genes...
  9. pmc GAT: a simulation framework for testing the association of genomic intervals
    Andreas Heger
    MRC CGAT Programme and Functional Genomics Unit, MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
    Bioinformatics 29:2046-8. 2013
    ..This question arises, for example, when interpreting ChIP-Seq or RNA-Seq data in functional terms. Because genome organization is complex, answering this question is non-trivial...
  10. pmc Genomic and transcriptional co-localization of protein-coding and long non-coding RNA pairs in the developing brain
    Jasmina Ponjavic
    MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
    PLoS Genet 5:e1000617. 2009
    ....
  11. pmc Massive turnover of functional sequence in human and other mammalian genomes
    Stephen Meader
    MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom
    Genome Res 20:1335-43. 2010
    ..This suggests that, rather than genome size or protein-coding gene complement, it is the number of functional bases that might best mirror our naïve preconceptions of organismal complexity...
  12. ncbi request reprint Signatures of adaptive evolution within human non-coding sequence
    Chris P Ponting
    MRC Functional Genetics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
    Hum Mol Genet 15:R170-5. 2006
    ..Illuminating the functions of this adaptive dark matter will lead to a better understanding of the sequence changes that have shaped the innovative biology of our species...
  13. pmc Accelerated evolution of the Prdm9 speciation gene across diverse metazoan taxa
    Peter L Oliver
    Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
    PLoS Genet 5:e1000753. 2009
    ..We suggest that Prdm9 should be investigated as a candidate gene in other instances of hybrid sterility in metazoans...
  14. pmc 8.2% of the Human genome is constrained: variation in rates of turnover across functional element classes in the human lineage
    Chris M Rands
    MRC Functional Genomics Unit, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford, United Kingdom
    PLoS Genet 10:e1004525. 2014
    ..These results reveal that the evolutionary history of the human genome has been highly dynamic, particularly for its noncoding yet biologically functional fraction. ..
  15. pmc Novel type IV secretion system involved in propagation of genomic islands
    Mario Juhas
    Clinical Microbiology and Infectious Diseases, Nuffield Department of Clinical Laboratory Sciences, University of Oxford, Headington, OX3 9DU Oxford, United Kingdom
    J Bacteriol 189:761-71. 2007
    ..Moreover, the expression of this T4SS was found to be positively regulated by one of its components, the tfc24 gene. We concluded that this gene cluster represents a novel family of T4SSs involved in propagation of genomic islands...
  16. pmc Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs
    Jasmina Ponjavic
    MRC Functional Genetics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom
    Genome Res 17:556-65. 2007
    ..2%). These macroRNAs, taken together, thus possess the imprint of purifying selection, thereby indicating their functionality. Our findings should now provide an incentive for the experimental investigation of these macroRNAs' functions...
  17. ncbi request reprint Evolutionary biology: human brain gene wins genome race
    Chris P Ponting
    Nature 443:149-50. 2006
  18. pmc Dog as an outgroup to human and mouse
    Gerton Lunter
    PLoS Comput Biol 3:e74. 2007